biology/seqan: update 1.3.1 -> 2.1.1

biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage

PR:		204127
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org>

13 files changed, 3717 insertions, 1915 deletions

diff --git a/UPDATING b/UPDATING
index a2e63abd91de..4d717a4fbc67 100644
--- a/UPDATING
+++ b/UPDATING
@@ -5,6 +5,17 @@ they are unavoidable.
 You should get into the habit of checking this file for changes each time
 you update your ports collection, before attempting any port upgrades.
 
+20160510:
+  AFFECTS: Users of biology/seqan
+  AUTHOR: junovitch@FreeBSD.org
+
+  The biology/seqan port has been split into biology/seqan (only the
+  library) and biology/seqan-apps for the programs based on SeqAn. Both
+  ports are based on version 2.1.1 of the SeqAn repository. There is a new
+  biology/seqan1 port with version 1.3 of SeqAn for backwards compatibility,
+  but this port will likely be deprecated in the next year so please update
+  your software to SeqAn2.
+
 20160505:
   AFFECTS: Users of www/node
   AUTHOR: bradleythughes@fastmail.fm
diff --git a/biology/Makefile b/biology/Makefile
index 4a21bff385f4..68aaba32ad79 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -91,6 +91,7 @@
     SUBDIR += seaview
     SUBDIR += seqan
     SUBDIR += seqan-apps
+    SUBDIR += seqan1
     SUBDIR += seqio
     SUBDIR += seqtools
     SUBDIR += sim4
diff --git a/biology/seqan/Makefile b/biology/seqan/Makefile
index 2abf70d857b0..60663f571dd3 100644
--- a/biology/seqan/Makefile
+++ b/biology/seqan/Makefile
@@ -2,33 +2,31 @@
 # $FreeBSD$
 
 PORTNAME=	seqan
-PORTVERSION=	1.3.1
-PORTREVISION=	3
+PORTVERSION=	2.1.1
 CATEGORIES=	biology
-MASTER_SITES=	http://ftp.seqan.de/releases/
+MASTER_SITES=	http://packages.seqan.de/seqan-library/
+DISTNAME=	${PORTNAME}-library-${PORTVERSION}
 
 MAINTAINER=	h2+fbsdports@fsfe.org
-COMMENT=	C++ Sequence Analysis Library
+COMMENT=	C++ Sequence Analysis Template Library
 
-LICENSE=	BSD3CLAUSE GPLv3
-LICENSE_COMB=	multi
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE=	${WRKSRC}/share/doc/seqan/LICENSE
 
-LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE
-LICENSE_FILE_GPLv3=${WRKSRC}/apps/LICENSE
+USES=		tar:xz
+NO_BUILD=	yes
 
-USES=		cmake:outsource python:build zip
-CMAKE_SOURCE_PATH=${WRKSRC}/cmake
-MAKE_JOB_SAFE=	yes
+CONFLICTS=	seqan1-[0-9]*
 
-SUB_FILES=	pkg-message
-PKG_MESSAGE=	${WRKDIR}/pkg-message
+OPTIONS_DEFINE=	DOCS
+DOCS_DESC=	Install official API documentation (html)
 
-USE_GCC=	4.8
+do-install:
+	${MKDIR} ${STAGEDIR}/${PREFIX}/include/${PORTNAME}
+	cd ${WRKSRC}/include/ && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include
 
-# unsafe workaround because FreeBSD lacks logl and expl
-# see "BUGS" in `man 3 math`
-post-patch:
-	@${REINPLACE_CMD} -e 's|expl|exp|g' ${WRKSRC}/apps/snp_store/snp_store.h
-	@${REINPLACE_CMD} -e 's|logl|log|g' ${WRKSRC}/apps/snp_store/snp_store.h
+post-install:
+	${MKDIR} ${STAGEDIR}${DOCSDIR}
+	cd ${WRKSRC}/share/doc/ && ${COPYTREE_SHARE} ./seqan/ ${STAGEDIR}${DOCSDIR}/../
 
 .include <bsd.port.mk>
diff --git a/biology/seqan/distinfo b/biology/seqan/distinfo
index 3e7a0a49d7b4..ab08fbcf3252 100644
--- a/biology/seqan/distinfo
+++ b/biology/seqan/distinfo
@@ -1,2 +1,2 @@
-SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb
-SIZE (seqan-1.3.1.zip) = 8787521
+SHA256 (seqan-library-2.1.1.tar.xz) = 8926f91fec5ce57e8efc70ac16cbf041bde0e0be463685b86e0d2e1e6a8169d7
+SIZE (seqan-library-2.1.1.tar.xz) = 5238884
diff --git a/biology/seqan/files/patch-cmake-CMakeLists.txt b/biology/seqan/files/patch-cmake-CMakeLists.txt
deleted file mode 100644
index 8f39eebd62f6..000000000000
--- a/biology/seqan/files/patch-cmake-CMakeLists.txt
+++ /dev/null
@@ -1,13 +0,0 @@
---- cmake/CMakeLists.txt.orig	2012-05-04 12:56:23.000000000 +0800
-+++ cmake/CMakeLists.txt	2012-05-04 13:00:03.000000000 +0800
-@@ -146,6 +146,10 @@
-             COMPONENT headers)
-     #message("install(FILES ${HEADER} RENAME seqan${NEW_PATH} DESTINATION include COMPONENT headers)")
- endforeach()
-+#seqan.h
-+install(FILES ${CMAKE_CURRENT_SOURCE_DIR}/../seqan.h
-+	DESTINATION include
-+	COMPONENT headers)
- 
- ################################################################################
- # Set Compiler Flags
diff --git a/biology/seqan/files/patch-cmake-apps-CMakeLists.txt b/biology/seqan/files/patch-cmake-apps-CMakeLists.txt
deleted file mode 100644
index 21f5acf7b97f..000000000000
--- a/biology/seqan/files/patch-cmake-apps-CMakeLists.txt
+++ /dev/null
@@ -1,8 +0,0 @@
---- cmake/apps/CMakeLists.txt.orig	2012-05-04 11:12:35.000000000 +0800
-+++ cmake/apps/CMakeLists.txt	2012-05-04 11:23:26.000000000 +0800
-@@ -108,4 +108,4 @@
- 
- # Install RazerS gapped parameters.
- install(DIRECTORY ${SEQAN_LIBRARY}/apps/razers2/gapped_params
--        DESTINATION bin)
-+        DESTINATION share/seqan)
diff --git a/biology/seqan/files/pkg-message.in b/biology/seqan/files/pkg-message.in
deleted file mode 100644
index 71fbb10d6371..000000000000
--- a/biology/seqan/files/pkg-message.in
+++ /dev/null
@@ -1,6 +0,0 @@
-gapped_params for Razers2 have been installed to 
-      %%PREFIX%%/share/seqan/gapped_params
-      
-If you require these, make sure to set the correct 
-path with --param-dir as Razers2 will not pick them 
-up automatically.
diff --git a/biology/seqan/pkg-descr b/biology/seqan/pkg-descr
index 298ab519446f..705046885848 100644
--- a/biology/seqan/pkg-descr
+++ b/biology/seqan/pkg-descr
@@ -3,4 +3,7 @@ and data structures for the analysis of sequences with the
 focus on biological data. The library is licensed under the
 3-clause BSD license except the applications which are GPL.
 
+This port now only contains the header library and API
+documentation. The apps are separate.
+
 WWW: http://www.seqan.de/
diff --git a/biology/seqan/pkg-plist b/biology/seqan/pkg-plist
index 4e5828318deb..4592c53d4e0c 100644
--- a/biology/seqan/pkg-plist
+++ b/biology/seqan/pkg-plist
@@ -1,169 +1,227 @@
-bin/dfi
-bin/insegt
-bin/mason
-bin/micro_razers
-bin/pair_align
-bin/param_chooser
-bin/rabema
-bin/razers
-bin/razers2
-bin/rep_sep
-bin/sak
-bin/seqan_tcoffee
-bin/seqcons
-bin/snp_store
-bin/splazers
-bin/stellar
-bin/tree_recon
-include/seqan.h
 include/seqan/align.h
-include/seqan/align/align_algorithms.h
 include/seqan/align/align_base.h
-include/seqan/align/align_cols_base.h
-include/seqan/align/align_dynprog.h
-include/seqan/align/align_generated_forwards.h
-include/seqan/align/align_hirschberg.h
+include/seqan/align/align_cols.h
+include/seqan/align/align_config.h
 include/seqan/align/align_iterator_base.h
-include/seqan/align/align_local_dynprog.h
-include/seqan/align/align_local_dynprog_banded.h
-include/seqan/align/align_myers.h
-include/seqan/align/align_trace.h
+include/seqan/align/align_metafunctions.h
+include/seqan/align/align_traceback.h
+include/seqan/align/alignment_algorithm_tags.h
+include/seqan/align/alignment_operations.h
+include/seqan/align/dp_algorithm_impl.h
+include/seqan/align/dp_band.h
+include/seqan/align/dp_cell.h
+include/seqan/align/dp_cell_affine.h
+include/seqan/align/dp_cell_dynamic.h
+include/seqan/align/dp_cell_linear.h
+include/seqan/align/dp_context.h
+include/seqan/align/dp_formula.h
+include/seqan/align/dp_formula_affine.h
+include/seqan/align/dp_formula_dynamic.h
+include/seqan/align/dp_formula_linear.h
+include/seqan/align/dp_matrix.h
+include/seqan/align/dp_matrix_navigator.h
+include/seqan/align/dp_matrix_navigator_score_matrix.h
+include/seqan/align/dp_matrix_navigator_score_matrix_sparse.h
+include/seqan/align/dp_matrix_navigator_trace_matrix.h
+include/seqan/align/dp_matrix_sparse.h
+include/seqan/align/dp_meta_info.h
+include/seqan/align/dp_profile.h
+include/seqan/align/dp_scout.h
+include/seqan/align/dp_setup.h
+include/seqan/align/dp_trace_segment.h
+include/seqan/align/dp_traceback_adaptor.h
+include/seqan/align/dp_traceback_impl.h
+include/seqan/align/evaluate_alignment.h
+include/seqan/align/fragment.h
+include/seqan/align/gap_anchor.h
+include/seqan/align/gapped_value_type.h
+include/seqan/align/gaps_anchor.h
 include/seqan/align/gaps_array.h
 include/seqan/align/gaps_base.h
+include/seqan/align/gaps_iterator_anchor.h
+include/seqan/align/gaps_iterator_array.h
 include/seqan/align/gaps_iterator_base.h
-include/seqan/align/gaps_sumlist.h
-include/seqan/align/hirschberg_set.h
+include/seqan/align/global_alignment_banded.h
+include/seqan/align/global_alignment_hirschberg_impl.h
+include/seqan/align/global_alignment_myers_hirschberg_impl.h
+include/seqan/align/global_alignment_myers_impl.h
+include/seqan/align/global_alignment_specialized.h
+include/seqan/align/global_alignment_unbanded.h
+include/seqan/align/local_alignment_banded.h
+include/seqan/align/local_alignment_banded_waterman_eggert_impl.h
+include/seqan/align/local_alignment_enumeration.h
+include/seqan/align/local_alignment_enumeration_banded.h
+include/seqan/align/local_alignment_enumeration_unbanded.h
+include/seqan/align/local_alignment_unbanded.h
+include/seqan/align/local_alignment_waterman_eggert_impl.h
 include/seqan/align/matrix_base.h
+include/seqan/align_extend.h
+include/seqan/align_extend/align_extend.h
+include/seqan/align_extend/align_extend_base.h
+include/seqan/align_extend/dp_scout_xdrop.h
+include/seqan/align_profile.h
+include/seqan/align_profile/add_to_profile.h
+include/seqan/align_profile/score_profile_seq.h
+include/seqan/align_split.h
+include/seqan/align_split/align_split_interface.h
+include/seqan/align_split/dp_scout_split.h
+include/seqan/alignment_free.h
+include/seqan/alignment_free/af_d2.h
+include/seqan/alignment_free/af_d2star.h
+include/seqan/alignment_free/af_d2z.h
+include/seqan/alignment_free/af_n2.h
+include/seqan/alignment_free/alignment_free_base.h
+include/seqan/alignment_free/alignment_free_comparison.h
+include/seqan/alignment_free/kmer_functions.h
+include/seqan/arg_parse.h
+include/seqan/arg_parse/arg_parse_argument.h
+include/seqan/arg_parse/arg_parse_ctd_support.h
+include/seqan/arg_parse/arg_parse_doc.h
+include/seqan/arg_parse/arg_parse_exceptions.h
+include/seqan/arg_parse/arg_parse_option.h
+include/seqan/arg_parse/arg_parse_parse.h
+include/seqan/arg_parse/arg_parse_type_support.h
+include/seqan/arg_parse/argument_parser.h
+include/seqan/arg_parse/tool_doc.h
+include/seqan/arg_parse/xml_support.h
+include/seqan/bam_io.h
+include/seqan/bam_io/bam_alignment_record.h
+include/seqan/bam_io/bam_alignment_record_util.h
+include/seqan/bam_io/bam_file.h
+include/seqan/bam_io/bam_header_record.h
+include/seqan/bam_io/bam_index_bai.h
+include/seqan/bam_io/bam_io_context.h
+include/seqan/bam_io/bam_sam_conversion.h
+include/seqan/bam_io/bam_scanner_cache.h
+include/seqan/bam_io/bam_tags_dict.h
+include/seqan/bam_io/cigar.h
+include/seqan/bam_io/read_bam.h
+include/seqan/bam_io/read_sam.h
+include/seqan/bam_io/write_bam.h
+include/seqan/bam_io/write_sam.h
 include/seqan/basic.h
-include/seqan/basic/basic_aggregates.h
-include/seqan/basic/basic_allocator_chunkpool.h
-include/seqan/basic/basic_allocator_interface.h
-include/seqan/basic/basic_allocator_multipool.h
-include/seqan/basic/basic_allocator_simple.h
-include/seqan/basic/basic_allocator_singlepool.h
-include/seqan/basic/basic_allocator_to_std.h
-include/seqan/basic/basic_alphabet_interface.h
-include/seqan/basic/basic_alphabet_interface2.h
-include/seqan/basic/basic_alphabet_simple.h
-include/seqan/basic/basic_alphabet_simple_tabs.h
-include/seqan/basic/basic_alphabet_trait_basic.h
-include/seqan/basic/basic_compare.h
-include/seqan/basic/basic_converter.h
-include/seqan/basic/basic_counted_ptr.h
+include/seqan/basic/aggregate_concept.h
+include/seqan/basic/allocator_chunkpool.h
+include/seqan/basic/allocator_interface.h
+include/seqan/basic/allocator_multipool.h
+include/seqan/basic/allocator_simple.h
+include/seqan/basic/allocator_singlepool.h
+include/seqan/basic/allocator_to_std.h
+include/seqan/basic/alphabet_adapt_builtins.h
+include/seqan/basic/alphabet_bio.h
+include/seqan/basic/alphabet_concept.h
+include/seqan/basic/alphabet_math.h
+include/seqan/basic/alphabet_profile.h
+include/seqan/basic/alphabet_qualities.h
+include/seqan/basic/alphabet_residue.h
+include/seqan/basic/alphabet_residue_funcs.h
+include/seqan/basic/alphabet_residue_tabs.h
+include/seqan/basic/alphabet_simple_type.h
+include/seqan/basic/alphabet_storage.h
+include/seqan/basic/array_construct_destruct.h
+include/seqan/basic/basic_aggregate.h
+include/seqan/basic/basic_allocator.h
+include/seqan/basic/basic_alphabet.h
+include/seqan/basic/basic_concept.h
+include/seqan/basic/basic_container.h
 include/seqan/basic/basic_debug.h
-include/seqan/basic/basic_definition.h
-include/seqan/basic/basic_forwards.h
-include/seqan/basic/basic_generated_forwards.h
-include/seqan/basic/basic_holder.h
-include/seqan/basic/basic_holder_dynamic.h
-include/seqan/basic/basic_host.h
+include/seqan/basic/basic_device.h
+include/seqan/basic/basic_exception.h
+include/seqan/basic/basic_functors.h
+include/seqan/basic/basic_fundamental.h
 include/seqan/basic/basic_iterator.h
-include/seqan/basic/basic_iterator_adapt_std.h
-include/seqan/basic/basic_iterator_adaptor.h
-include/seqan/basic/basic_iterator_base.h
-include/seqan/basic/basic_iterator_position.h
-include/seqan/basic/basic_iterator_simple.h
-include/seqan/basic/basic_logvalue.h
+include/seqan/basic/basic_math.h
 include/seqan/basic/basic_metaprogramming.h
-include/seqan/basic/basic_operator.h
 include/seqan/basic/basic_parallelism.h
-include/seqan/basic/basic_pointer.h
-include/seqan/basic/basic_profchar.h
-include/seqan/basic/basic_profile.h
 include/seqan/basic/basic_proxy.h
-include/seqan/basic/basic_sse2.h
-include/seqan/basic/basic_tag.h
-include/seqan/basic/basic_testing.h
-include/seqan/basic/basic_transport.h
+include/seqan/basic/basic_simd_vector.h
+include/seqan/basic/basic_smart_pointer.h
+include/seqan/basic/basic_stream.h
+include/seqan/basic/basic_tangle.h
 include/seqan/basic/basic_type.h
-include/seqan/basic/basic_volatile_ptr.h
+include/seqan/basic/basic_view.h
+include/seqan/basic/boost_preprocessor_subset.h
+include/seqan/basic/builtin_functions.h
+include/seqan/basic/concept_checking.h
+include/seqan/basic/container_concept.h
+include/seqan/basic/debug_helper.h
+include/seqan/basic/debug_test_system.h
+include/seqan/basic/fundamental_chunking.h
+include/seqan/basic/fundamental_comparison.h
+include/seqan/basic/fundamental_concepts.h
+include/seqan/basic/fundamental_conversion.h
+include/seqan/basic/fundamental_metafunctions.h
+include/seqan/basic/fundamental_tags.h
+include/seqan/basic/fundamental_transport.h
+include/seqan/basic/holder_base.h
+include/seqan/basic/holder_simple.h
+include/seqan/basic/holder_tristate.h
+include/seqan/basic/hosted_type_interface.h
+include/seqan/basic/iterator_adapt_pointer.h
+include/seqan/basic/iterator_adapt_std.h
+include/seqan/basic/iterator_adaptor.h
+include/seqan/basic/iterator_base.h
+include/seqan/basic/iterator_concept.h
+include/seqan/basic/iterator_counting.h
+include/seqan/basic/iterator_interface.h
+include/seqan/basic/iterator_position.h
+include/seqan/basic/iterator_range.h
+include/seqan/basic/iterator_zip.h
+include/seqan/basic/macro_deprecated.h
+include/seqan/basic/math_functions.h
+include/seqan/basic/math_log_space_value.h
+include/seqan/basic/metaprogramming_control.h
+include/seqan/basic/metaprogramming_enable_if.h
+include/seqan/basic/metaprogramming_logic.h
+include/seqan/basic/metaprogramming_math.h
+include/seqan/basic/metaprogramming_type.h
+include/seqan/basic/metaprogramming_type_algebra.h
+include/seqan/basic/pair_base.h
+include/seqan/basic/pair_bit_compressed.h
+include/seqan/basic/pair_packed.h
+include/seqan/basic/profiling.h
+include/seqan/basic/property_map_concept.h
+include/seqan/basic/proxy_base.h
+include/seqan/basic/proxy_iterator.h
+include/seqan/basic/test_system.h
+include/seqan/basic/triple_base.h
+include/seqan/basic/triple_packed.h
+include/seqan/basic/tuple_base.h
+include/seqan/basic/tuple_bit_compressed.h
+include/seqan/basic/volatile_ptr.h
+include/seqan/bed_io.h
+include/seqan/bed_io/bed_file.h
+include/seqan/bed_io/bed_record.h
+include/seqan/bed_io/read_bed.h
+include/seqan/bed_io/write_bed.h
 include/seqan/blast.h
 include/seqan/blast/blast_base.h
-include/seqan/blast/blast_generated_forwards.h
-include/seqan/blast/blast_hit.h
-include/seqan/blast/blast_hit_iterator.h
-include/seqan/blast/blast_hsp.h
-include/seqan/blast/blast_hsp_iterator.h
-include/seqan/blast/blast_iterator.h
-include/seqan/blast/blast_parsing.h
-include/seqan/blast/blast_report.h
-include/seqan/blast/blast_run.h
-include/seqan/blast/blast_stream_hit.h
-include/seqan/blast/blast_stream_hit_iterator.h
-include/seqan/blast/blast_stream_hsp_iterator.h
-include/seqan/blast/blast_stream_report.h
-include/seqan/chaining.h
-include/seqan/chaining/chain_base.h
-include/seqan/chaining/chain_generic.h
-include/seqan/chaining/chain_meta_fragment.h
-include/seqan/chaining/chain_point.h
-include/seqan/chaining/chain_wrapper_point.h
-include/seqan/chaining/chaining_generated_forwards.h
-include/seqan/chaining/fragment.h
-include/seqan/chaining/geom_distribution.h
-include/seqan/chaining/range_max_tree.h
-include/seqan/chaining/range_tree.h
-include/seqan/chaining/rmt_base.h
-include/seqan/chaining/rmt_common_algos.h
-include/seqan/chaining/rmt_compl_algos.h
-include/seqan/chaining/rmt_def_algos.h
-include/seqan/chaining/rmt_skip_base_element.h
-include/seqan/chaining/rmt_skip_element.h
-include/seqan/chaining/rt_base.h
-include/seqan/chaining/rt_common_algos.h
-include/seqan/chaining/rt_impl.h
-include/seqan/chaining/rt_skip_base_element.h
-include/seqan/chaining/rt_skip_element.h
-include/seqan/chaining/rt_sl_base.h
-include/seqan/chaining/rt_sl_compl_algos.h
-include/seqan/chaining/rt_sl_def_algos.h
-include/seqan/chaining/rt_sl_impl.h
-include/seqan/chaining/score_chain.h
-include/seqan/chaining/score_chain_sop.h
-include/seqan/chaining/score_manhattan.h
-include/seqan/chaining/score_zero.h
-include/seqan/chaining/skip_base_element.h
-include/seqan/chaining/skip_element.h
-include/seqan/chaining/skip_list.h
-include/seqan/chaining/skip_list_base.h
-include/seqan/chaining/skip_list_dynamic.h
-include/seqan/chaining/skip_list_impl.h
-include/seqan/chaining/skip_list_iterator.h
-include/seqan/chaining/skip_list_type.h
-include/seqan/chaining/skip_pool_alloc.h
-include/seqan/chaining/tree_chain.h
-include/seqan/chaining/tree_chain_sop.h
-include/seqan/chaining/tree_chain_utils.h
+include/seqan/blast/blast_io_context.h
+include/seqan/blast/blast_record.h
+include/seqan/blast/blast_report_out.h
+include/seqan/blast/blast_statistics.h
+include/seqan/blast/blast_tabular.h
+include/seqan/blast/blast_tabular_in.h
+include/seqan/blast/blast_tabular_lowlevel.h
+include/seqan/blast/blast_tabular_out.h
 include/seqan/consensus.h
+include/seqan/consensus/consensus_aligner.h
+include/seqan/consensus/consensus_aligner_interface.h
+include/seqan/consensus/consensus_alignment_options.h
 include/seqan/consensus/consensus_base.h
-include/seqan/consensus/consensus_generated_forwards.h
+include/seqan/consensus/consensus_builder.h
 include/seqan/consensus/consensus_library.h
 include/seqan/consensus/consensus_realign.h
 include/seqan/consensus/consensus_score.h
+include/seqan/consensus/overlap_info_computation.h
+include/seqan/consensus/overlapper.h
 include/seqan/file.h
-include/seqan/file/chunk_collector.h
-include/seqan/file/cstream.h
-include/seqan/file/file_array.h
 include/seqan/file/file_base.h
 include/seqan/file/file_cstyle.h
-include/seqan/file/file_filereader.h
-include/seqan/file/file_filereaderiterator.h
-include/seqan/file/file_format.h
-include/seqan/file/file_format_cgviz.h
-include/seqan/file/file_format_embl.h
-include/seqan/file/file_format_fasta.h
-include/seqan/file/file_format_fasta_align.h
-include/seqan/file/file_format_genbank.h
-include/seqan/file/file_format_guess.h
-include/seqan/file/file_format_mmap.h
-include/seqan/file/file_format_raw.h
 include/seqan/file/file_forwards.h
-include/seqan/file/file_generated_forwards.h
+include/seqan/file/file_interface.h
+include/seqan/file/file_mapping.h
 include/seqan/file/file_page.h
-include/seqan/file/file_page_raid0.h
-include/seqan/file/meta.h
-include/seqan/file/stream.h
-include/seqan/file/stream_algorithms.h
 include/seqan/file/string_external.h
 include/seqan/file/string_mmap.h
 include/seqan/find.h
@@ -173,9 +231,9 @@ include/seqan/find/find_base.h
 include/seqan/find/find_begin.h
 include/seqan/find/find_bndm.h
 include/seqan/find/find_bom.h
-include/seqan/find/find_generated_forwards.h
 include/seqan/find/find_hamming_simple.h
 include/seqan/find/find_horspool.h
+include/seqan/find/find_lambda.h
 include/seqan/find/find_multi.h
 include/seqan/find/find_multiple_bfam.h
 include/seqan/find/find_multiple_shiftand.h
@@ -189,50 +247,42 @@ include/seqan/find/find_shiftor.h
 include/seqan/find/find_simple.h
 include/seqan/find/find_wild_shiftand.h
 include/seqan/find/find_wumanber.h
-include/seqan/find2.h
-include/seqan/find2/find2_generated_forwards.h
-include/seqan/find2/find_approx_dpsearch.h
-include/seqan/find2/find_approx_find_begin.h
-include/seqan/find2/find_base.h
-include/seqan/find2/find_exact_shiftand.h
-include/seqan/find2/find_exact_simple.h
-include/seqan/find2/find_finder_default.h
-include/seqan/find2/find_hamming_simple.h
-include/seqan/find2/find_multiple_exact_simple.h
-include/seqan/find2/find_pattern_wild_shiftand.h
-include/seqan/find_motif.h
-include/seqan/find_motif/em_algorithm.h
-include/seqan/find_motif/find_motif_base.h
-include/seqan/find_motif/find_motif_epatternbranching.h
-include/seqan/find_motif/find_motif_generated_forwards.h
-include/seqan/find_motif/find_motif_pms1.h
-include/seqan/find_motif/find_motif_pmsp.h
-include/seqan/find_motif/find_motif_projection.h
-include/seqan/find_motif/frequency_distribution.h
-include/seqan/find_motif/profile.h
-include/seqan/find_motif/pseudocount_base.h
-include/seqan/find_motif/pseudocount_mode_c.h
-include/seqan/find_motif/pseudocount_mode_p.h
-include/seqan/find_motif/sequence_model_types.h
+include/seqan/gff_io.h
+include/seqan/gff_io/gff_file.h
+include/seqan/gff_io/gff_io_base.h
 include/seqan/graph_algorithms.h
-include/seqan/graph_algorithms/graph_algorithm.h
+include/seqan/graph_algorithms/all_pairs_shortest_path.h
+include/seqan/graph_algorithms/bellman_ford.h
+include/seqan/graph_algorithms/bipartite_matching.h
+include/seqan/graph_algorithms/breadth_first_search.h
+include/seqan/graph_algorithms/connected_components.h
+include/seqan/graph_algorithms/depth_first_search.h
+include/seqan/graph_algorithms/dijkstra.h
+include/seqan/graph_algorithms/floyd_warshall.h
+include/seqan/graph_algorithms/ford_fulkerson.h
 include/seqan/graph_algorithms/graph_algorithm_heap_tree.h
 include/seqan/graph_algorithms/graph_algorithm_hmm.h
 include/seqan/graph_algorithms/graph_algorithm_lis_his.h
-include/seqan/graph_algorithms/graph_algorithms_generated_forwards.h
+include/seqan/graph_algorithms/kruskal.h
+include/seqan/graph_algorithms/path_growing.h
+include/seqan/graph_algorithms/prim.h
+include/seqan/graph_algorithms/single_source_shortest_path.h
+include/seqan/graph_algorithms/strongly_connected_compnents.h
+include/seqan/graph_algorithms/topological_sort.h
+include/seqan/graph_algorithms/transitive_closure.h
+include/seqan/graph_algorithms/weakly_connected_components.h
+include/seqan/graph_algorithms/weighted_bipartite_matching.h
 include/seqan/graph_align.h
-include/seqan/graph_align/graph_align_banded_gotoh.h
-include/seqan/graph_align/graph_align_banded_needleman_wunsch.h
-include/seqan/graph_align/graph_align_banded_smith_waterman_clump.h
-include/seqan/graph_align/graph_align_base.h
-include/seqan/graph_align/graph_align_config.h
-include/seqan/graph_align/graph_align_generated_forwards.h
-include/seqan/graph_align/graph_align_gotoh.h
-include/seqan/graph_align/graph_align_hirschberg.h
-include/seqan/graph_align/graph_align_interface.h
-include/seqan/graph_align/graph_align_needleman_wunsch.h
-include/seqan/graph_align/graph_align_smith_waterman.h
-include/seqan/graph_align/graph_align_smith_waterman_clump.h
+include/seqan/graph_align/graph_algorithm_refine_align.h
+include/seqan/graph_align/graph_algorithm_refine_aligngraph.h
+include/seqan/graph_align/graph_algorithm_refine_annotation.h
+include/seqan/graph_align/graph_algorithm_refine_exact.h
+include/seqan/graph_align/graph_algorithm_refine_exact_iterative.h
+include/seqan/graph_align/graph_algorithm_refine_fragment.h
+include/seqan/graph_align/graph_algorithm_refine_inexact.h
+include/seqan/graph_align/graph_algorithm_refine_scoring.h
+include/seqan/graph_align/graph_impl_align.h
+include/seqan/graph_align/graph_impl_align_adapt.h
 include/seqan/graph_msa.h
 include/seqan/graph_msa/graph_align_tcoffee_base.h
 include/seqan/graph_msa/graph_align_tcoffee_distance.h
@@ -243,7 +293,6 @@ include/seqan/graph_msa/graph_align_tcoffee_library.h
 include/seqan/graph_msa/graph_align_tcoffee_msa.h
 include/seqan/graph_msa/graph_align_tcoffee_progressive.h
 include/seqan/graph_msa/graph_align_tcoffee_refinement.h
-include/seqan/graph_msa/graph_msa_generated_forwards.h
 include/seqan/graph_types.h
 include/seqan/graph_types/graph_base.h
 include/seqan/graph_types/graph_drawing.h
@@ -251,7 +300,6 @@ include/seqan/graph_types/graph_edgestump.h
 include/seqan/graph_types/graph_idmanager.h
 include/seqan/graph_types/graph_impl_automaton.h
 include/seqan/graph_types/graph_impl_directed.h
-include/seqan/graph_types/graph_impl_fragment.h
 include/seqan/graph_types/graph_impl_hmm.h
 include/seqan/graph_types/graph_impl_oracle.h
 include/seqan/graph_types/graph_impl_tree.h
@@ -266,44 +314,74 @@ include/seqan/graph_types/graph_iterator_dfs.h
 include/seqan/graph_types/graph_iterator_edge.h
 include/seqan/graph_types/graph_iterator_outedge.h
 include/seqan/graph_types/graph_iterator_vertex.h
-include/seqan/graph_types/graph_property.h
-include/seqan/graph_types/graph_types_generated_forwards.h
 include/seqan/graph_types/graph_utility_parsing.h
+include/seqan/graph_types/property_map_generic.h
+include/seqan/graph_types/property_map_internal.h
+include/seqan/graph_types/property_map_internal_pointer.h
 include/seqan/index.h
+include/seqan/index/find2_backtracking.h
+include/seqan/index/find2_base.h
+include/seqan/index/find2_functors.h
+include/seqan/index/find2_index.h
+include/seqan/index/find2_index_multi.h
+include/seqan/index/find2_vstree_factory.h
+include/seqan/index/find_backtracking.h
 include/seqan/index/find_index.h
 include/seqan/index/find_index_approx.h
+include/seqan/index/find_index_binary.h
 include/seqan/index/find_index_esa.h
+include/seqan/index/find_index_lambda.h
 include/seqan/index/find_index_qgram.h
+include/seqan/index/find_pigeonhole.h
 include/seqan/index/find_quasar.h
 include/seqan/index/find_swift.h
 include/seqan/index/index_base.h
 include/seqan/index/index_bwt.h
 include/seqan/index/index_childtab.h
+include/seqan/index/index_device.h
 include/seqan/index/index_dfi.h
 include/seqan/index/index_esa_algs.h
 include/seqan/index/index_esa_algs_multi.h
 include/seqan/index/index_esa_base.h
 include/seqan/index/index_esa_drawing.h
 include/seqan/index/index_esa_stree.h
-include/seqan/index/index_generated_forwards.h
+include/seqan/index/index_fm.h
+include/seqan/index/index_fm_compressed_sa.h
+include/seqan/index/index_fm_compressed_sa_iterator.h
+include/seqan/index/index_fm_device.h
+include/seqan/index/index_fm_dox.h
+include/seqan/index/index_fm_lf_table.h
+include/seqan/index/index_fm_rank_dictionary_base.h
+include/seqan/index/index_fm_rank_dictionary_levels.h
+include/seqan/index/index_fm_rank_dictionary_naive.h
+include/seqan/index/index_fm_rank_dictionary_wt.h
+include/seqan/index/index_fm_right_array_binary_tree.h
+include/seqan/index/index_fm_right_array_binary_tree_iterator.h
+include/seqan/index/index_fm_sparse_string.h
+include/seqan/index/index_fm_stree.h
+include/seqan/index/index_forwards.h
 include/seqan/index/index_lcp.h
 include/seqan/index/index_lcp_tree.h
-include/seqan/index/index_manual_forwards.h
 include/seqan/index/index_pizzachili.h
 include/seqan/index/index_pizzachili_find.h
 include/seqan/index/index_pizzachili_string.h
 include/seqan/index/index_qgram.h
+include/seqan/index/index_qgram_bucketrefinement.h
 include/seqan/index/index_qgram_openaddressing.h
+include/seqan/index/index_qgram_stree.h
 include/seqan/index/index_sa_btree.h
 include/seqan/index/index_sa_bwtwalk.h
 include/seqan/index/index_sa_lss.h
 include/seqan/index/index_sa_mm.h
 include/seqan/index/index_sa_qsort.h
+include/seqan/index/index_sa_stree.h
+include/seqan/index/index_sa_truncated.h
 include/seqan/index/index_shawarma.h
 include/seqan/index/index_shims.h
 include/seqan/index/index_skew3.h
 include/seqan/index/index_skew7.h
 include/seqan/index/index_skew7_multi.h
+include/seqan/index/index_view.h
 include/seqan/index/index_wotd.h
 include/seqan/index/pipe_merger3.h
 include/seqan/index/pipe_merger7.h
@@ -316,48 +394,99 @@ include/seqan/index/radix.h
 include/seqan/index/repeat_base.h
 include/seqan/index/shape_base.h
 include/seqan/index/shape_gapped.h
+include/seqan/index/shape_minimizer.h
 include/seqan/index/shape_onegapped.h
 include/seqan/index/shape_predefined.h
 include/seqan/index/shape_threshold.h
+include/seqan/journaled_set.h
+include/seqan/journaled_set/journal_alignment_interface.h
+include/seqan/journaled_set/journal_alignment_traceback_adaptor.h
+include/seqan/journaled_set/journaled_set_base.h
+include/seqan/journaled_set/journaled_set_impl.h
+include/seqan/journaled_set/journaled_set_join.h
+include/seqan/journaled_set/journaled_set_join_config.h
+include/seqan/journaled_set/journaled_set_join_global_align_compact.h
+include/seqan/journaled_set/journaled_set_join_global_align_manhatten.h
+include/seqan/journaled_set/journaled_set_journal_trace_descriptor.h
+include/seqan/journaled_set/score_biaffine.h
+include/seqan/journaled_string_tree.h
+include/seqan/journaled_string_tree/delta_map.h
+include/seqan/journaled_string_tree/delta_map_entry.h
+include/seqan/journaled_string_tree/delta_map_iterator.h
+include/seqan/journaled_string_tree/delta_store.h
+include/seqan/journaled_string_tree/journaled_string_tree_base.h
+include/seqan/journaled_string_tree/journaled_string_tree_impl.h
+include/seqan/journaled_string_tree/journaled_string_tree_sequence_buffer.h
+include/seqan/journaled_string_tree/journaled_string_tree_traverser.h
+include/seqan/journaled_string_tree/journaled_string_tree_traverser_node.h
+include/seqan/journaled_string_tree/journaled_string_tree_traverser_util.h
+include/seqan/journaled_string_tree/jst_extension_base.h
+include/seqan/journaled_string_tree/jst_extension_horspool.h
+include/seqan/journaled_string_tree/jst_extension_myers_ukkonen.h
+include/seqan/journaled_string_tree/jst_extension_shiftand.h
+include/seqan/journaled_string_tree/jst_extension_shiftor.h
+include/seqan/journaled_string_tree/observable.h
+include/seqan/journaled_string_tree/stack_observer.h
 include/seqan/map.h
 include/seqan/map/map_adapter_stl.h
 include/seqan/map/map_base.h
 include/seqan/map/map_chooser.h
-include/seqan/map/map_generated_forwards.h
 include/seqan/map/map_skiplist.h
 include/seqan/map/map_vector.h
 include/seqan/map/sumlist.h
 include/seqan/map/sumlist_mini.h
 include/seqan/map/sumlist_skip.h
+include/seqan/math.h
+include/seqan/math/math_common_factor.h
+include/seqan/math/math_operators.h
+include/seqan/math/math_rational.h
+include/seqan/misc/accumulators.h
+include/seqan/misc/base.h
+include/seqan/misc/bit_twiddling.h
+include/seqan/misc/bit_twiddling_functors.h
+include/seqan/misc/cuda.h
+include/seqan/misc/dequeue.h
 include/seqan/misc/edit_environment.h
-include/seqan/misc/misc_base.h
-include/seqan/misc/misc_cmdparser.h
-include/seqan/misc/misc_dequeue.h
-include/seqan/misc/misc_generated_forwards.h
-include/seqan/misc/misc_interval_tree.h
-include/seqan/misc/misc_long_word.h
-include/seqan/misc/misc_map.h
-include/seqan/misc/misc_parsing.h
-include/seqan/misc/misc_random.h
-include/seqan/misc/misc_set.h
-include/seqan/misc/misc_svg.h
+include/seqan/misc/interval_tree.h
+include/seqan/misc/map.h
+include/seqan/misc/memset.h
+include/seqan/misc/name_store_cache.h
 include/seqan/misc/priority_type_base.h
 include/seqan/misc/priority_type_heap.h
+include/seqan/misc/set.h
+include/seqan/misc/svg.h
+include/seqan/misc/terminal.h
+include/seqan/misc/union_find.h
 include/seqan/modifier.h
+include/seqan/modifier/cyclic_shape.h
 include/seqan/modifier/modifier_alphabet.h
 include/seqan/modifier/modifier_alphabet_expansion.h
+include/seqan/modifier/modifier_cyclic_shape.h
 include/seqan/modifier/modifier_functors.h
-include/seqan/modifier/modifier_generated_forwards.h
 include/seqan/modifier/modifier_iterator.h
+include/seqan/modifier/modifier_position.h
 include/seqan/modifier/modifier_reverse.h
 include/seqan/modifier/modifier_shortcuts.h
 include/seqan/modifier/modifier_string.h
 include/seqan/modifier/modifier_view.h
 include/seqan/parallel.h
+include/seqan/parallel/parallel_algorithms.h
 include/seqan/parallel/parallel_atomic_misc.h
 include/seqan/parallel/parallel_atomic_primitives.h
-include/seqan/parallel/parallel_generated_forwards.h
+include/seqan/parallel/parallel_lock.h
 include/seqan/parallel/parallel_macros.h
+include/seqan/parallel/parallel_queue.h
+include/seqan/parallel/parallel_queue_suspendable.h
+include/seqan/parallel/parallel_resource_pool.h
+include/seqan/parallel/parallel_sequence.h
+include/seqan/parallel/parallel_serializer.h
+include/seqan/parallel/parallel_splitting.h
+include/seqan/parallel/parallel_tags.h
+include/seqan/parse_lm.h
+include/seqan/parse_lm/local_match_store.h
+include/seqan/parse_lm/parse_blastn_tabular.h
+include/seqan/parse_lm/parse_lastz_general.h
+include/seqan/parse_lm/parse_stellar_gff.h
 include/seqan/pipe.h
 include/seqan/pipe/pipe_base.h
 include/seqan/pipe/pipe_caster.h
@@ -365,7 +494,6 @@ include/seqan/pipe/pipe_counter.h
 include/seqan/pipe/pipe_echoer.h
 include/seqan/pipe/pipe_edit_environment.h
 include/seqan/pipe/pipe_filter.h
-include/seqan/pipe/pipe_generated_forwards.h
 include/seqan/pipe/pipe_iterator.h
 include/seqan/pipe/pipe_joiner.h
 include/seqan/pipe/pipe_namer.h
@@ -378,118 +506,109 @@ include/seqan/pipe/pool_mapper.h
 include/seqan/pipe/pool_sorter.h
 include/seqan/platform.h
 include/seqan/platform/platform_gcc.h
-include/seqan/platform/platform_generated_forwards.h
-include/seqan/platform/platform_mingw.h
-include/seqan/platform/platform_solaris.h
+include/seqan/platform/platform_icc.h
+include/seqan/platform/platform_nvcc.h
 include/seqan/platform/platform_windows.h
 include/seqan/random.h
-include/seqan/random/ext_MersenneTwister.h
 include/seqan/random/random_base.h
-include/seqan/random/random_generated_forwards.h
-include/seqan/random/random_geometric.h
-include/seqan/random/random_lognormal.h
-include/seqan/random/random_mt19937.h
-include/seqan/random/random_normal.h
-include/seqan/random/random_rng_functor.h
-include/seqan/random/random_shuffle.h
-include/seqan/random/random_uniform.h
-include/seqan/refinement.h
-include/seqan/refinement/graph_algorithm_refine_align.h
-include/seqan/refinement/graph_algorithm_refine_aligngraph.h
-include/seqan/refinement/graph_algorithm_refine_annotation.h
-include/seqan/refinement/graph_algorithm_refine_exact.h
-include/seqan/refinement/graph_algorithm_refine_exact_iterative.h
-include/seqan/refinement/graph_algorithm_refine_fragment.h
-include/seqan/refinement/graph_algorithm_refine_inexact.h
-include/seqan/refinement/graph_algorithm_refine_scoring.h
-include/seqan/refinement/graph_impl_align.h
-include/seqan/refinement/graph_impl_align_adapt.h
-include/seqan/refinement/refinement_generated_forwards.h
+include/seqan/random/random_beta.h
+include/seqan/random/random_util.h
+include/seqan/realign.h
+include/seqan/realign/realign_base.h
+include/seqan/realign/realign_helper_functions.h
+include/seqan/reduced_aminoacid.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_base.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_base_late.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_base.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_20_to_n_b62.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_22_to_n_b62.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_cluster_red_tables_24_to_n_b62.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_base.h
+include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.h
+include/seqan/roi_io.h
+include/seqan/roi_io/read_roi.h
+include/seqan/roi_io/roi_file.h
+include/seqan/roi_io/roi_io_context.h
+include/seqan/roi_io/roi_record.h
+include/seqan/roi_io/write_roi.h
 include/seqan/score.h
 include/seqan/score/score_base.h
 include/seqan/score/score_edit.h
-include/seqan/score/score_generated_forwards.h
 include/seqan/score/score_matrix.h
 include/seqan/score/score_matrix_data.h
+include/seqan/score/score_matrix_io.h
 include/seqan/score/score_simple.h
 include/seqan/seeds.h
-include/seqan/seeds/banded_align.h
-include/seqan/seeds/banded_chain_align.h
-include/seqan/seeds/banded_chain_align_affine.h
-include/seqan/seeds/global_seed_chain.h
-include/seqan/seeds/memoryManager_base.h
-include/seqan/seeds/memoryManager_int.h
-include/seqan/seeds/propertyMap.h
-include/seqan/seeds/seedHandlingTags.h
-include/seqan/seeds/seedSet_base.h
-include/seqan/seeds/seedSet_iterator.h
-include/seqan/seeds/seedSet_score.h
-include/seqan/seeds/seed_base.h
-include/seqan/seeds/seed_multi.h
-include/seqan/seeds/seeds_generated_forwards.h
-include/seqan/seeds2.h
-include/seqan/seeds2/align_chain_banded.h
-include/seqan/seeds2/align_dynprog_affine.h
-include/seqan/seeds2/align_dynprog_banded_affine.h
-include/seqan/seeds2/align_dynprog_banded_linear.h
-include/seqan/seeds2/align_dynprog_linear.h
-include/seqan/seeds2/basic_iter_indirect.h
-include/seqan/seeds2/seeds2_generated_forwards.h
-include/seqan/seeds2/seeds_base.h
-include/seqan/seeds2/seeds_combination.h
-include/seqan/seeds2/seeds_extension.h
-include/seqan/seeds2/seeds_global_chaining.h
-include/seqan/seeds2/seeds_global_chaining_base.h
-include/seqan/seeds2/seeds_global_chaining_gusfield.h
-include/seqan/seeds2/seeds_seed_base.h
-include/seqan/seeds2/seeds_seed_chained.h
-include/seqan/seeds2/seeds_seed_diagonal.h
-include/seqan/seeds2/seeds_seed_set_base.h
-include/seqan/seeds2/seeds_seed_set_non_scored.h
-include/seqan/seeds2/seeds_seed_set_scored.h
-include/seqan/seeds2/seeds_seed_set_unordered.h
-include/seqan/seeds2/seeds_seed_simple.h
+include/seqan/seeds/banded_chain_alignment.h
+include/seqan/seeds/banded_chain_alignment_impl.h
+include/seqan/seeds/banded_chain_alignment_profile.h
+include/seqan/seeds/banded_chain_alignment_scout.h
+include/seqan/seeds/banded_chain_alignment_traceback.h
+include/seqan/seeds/basic_iter_indirect.h
+include/seqan/seeds/seeds_base.h
+include/seqan/seeds/seeds_combination.h
+include/seqan/seeds/seeds_extension.h
+include/seqan/seeds/seeds_global_chaining.h
+include/seqan/seeds/seeds_global_chaining_base.h
+include/seqan/seeds/seeds_global_chaining_gusfield.h
+include/seqan/seeds/seeds_seed_base.h
+include/seqan/seeds/seeds_seed_chained.h
+include/seqan/seeds/seeds_seed_diagonal.h
+include/seqan/seeds/seeds_seed_set_base.h
+include/seqan/seeds/seeds_seed_set_non_scored.h
+include/seqan/seeds/seeds_seed_set_scored.h
+include/seqan/seeds/seeds_seed_set_unordered.h
+include/seqan/seeds/seeds_seed_simple.h
+include/seqan/seq_io.h
+include/seqan/seq_io/fai_index.h
+include/seqan/seq_io/fasta_fastq.h
+include/seqan/seq_io/genomic_region.h
+include/seqan/seq_io/read_embl.h
+include/seqan/seq_io/read_genbank.h
+include/seqan/seq_io/sequence_file.h
 include/seqan/sequence.h
 include/seqan/sequence/adapt_array_pointer.h
-include/seqan/sequence/adapt_std_list.h
-include/seqan/sequence/adapt_std_string.h
-include/seqan/sequence/adapt_std_vector.h
+include/seqan/sequence/adapt_stl_container.h
+include/seqan/sequence/adapt_thrust_vector.h
+include/seqan/sequence/container_view.h
+include/seqan/sequence/container_view_zip.h
 include/seqan/sequence/iter_concat_virtual.h
 include/seqan/sequence/segment_base.h
 include/seqan/sequence/segment_infix.h
 include/seqan/sequence/segment_prefix.h
 include/seqan/sequence/segment_suffix.h
+include/seqan/sequence/segment_utils.h
 include/seqan/sequence/sequence_concatenator.h
 include/seqan/sequence/sequence_forwards.h
-include/seqan/sequence/sequence_generated_forwards.h
 include/seqan/sequence/sequence_interface.h
 include/seqan/sequence/sequence_lexical.h
 include/seqan/sequence/sequence_shortcuts.h
-include/seqan/sequence/sequence_stream.h
 include/seqan/sequence/string_alloc.h
 include/seqan/sequence/string_array.h
 include/seqan/sequence/string_base.h
 include/seqan/sequence/string_block.h
 include/seqan/sequence/string_cstyle.h
 include/seqan/sequence/string_packed.h
+include/seqan/sequence/string_packed_old.h
 include/seqan/sequence/string_set_base.h
 include/seqan/sequence/string_set_concat_direct.h
 include/seqan/sequence/string_set_dependent_generous.h
 include/seqan/sequence/string_set_dependent_tight.h
+include/seqan/sequence/string_set_device.h
 include/seqan/sequence/string_set_owner.h
+include/seqan/sequence/string_set_segment.h
+include/seqan/sequence/string_set_view.h
 include/seqan/sequence_journaled.h
 include/seqan/sequence_journaled/journal_entries_sorted_array.h
-include/seqan/sequence_journaled/journal_entries_unbalanced_tree.h
-include/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h
-include/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h
 include/seqan/sequence_journaled/journal_entry.h
 include/seqan/sequence_journaled/sequence_journaled.h
-include/seqan/sequence_journaled/sequence_journaled_forwards.h
-include/seqan/sequence_journaled/sequence_journaled_generated_forwards.h
 include/seqan/sequence_journaled/sequence_journaled_iterator.h
+include/seqan/sequence_journaled/sequence_journaled_iterator_fast.h
+include/seqan/simple_intervals_io.h
+include/seqan/simple_intervals_io/simple_intervals_file.h
+include/seqan/simple_intervals_io/simple_intervals_io.h
 include/seqan/statistics.h
 include/seqan/statistics/statistics_base.h
-include/seqan/statistics/statistics_generated_forwards.h
 include/seqan/statistics/statistics_markov_model.h
 include/seqan/store.h
 include/seqan/store/store_align.h
@@ -498,1614 +617,1285 @@ include/seqan/store/store_all.h
 include/seqan/store/store_annotation.h
 include/seqan/store/store_base.h
 include/seqan/store/store_contig.h
-include/seqan/store/store_generated_forwards.h
 include/seqan/store/store_intervaltree.h
 include/seqan/store/store_io.h
-include/seqan/store/store_io_bam.h
 include/seqan/store/store_io_gff.h
 include/seqan/store/store_io_sam.h
 include/seqan/store/store_io_ucsc.h
 include/seqan/store/store_library.h
 include/seqan/store/store_matepair.h
 include/seqan/store/store_read.h
+include/seqan/stream.h
+include/seqan/stream/adapt_ios.h
+include/seqan/stream/buffered_stream.h
+include/seqan/stream/file_stream.h
+include/seqan/stream/formatted_file.h
+include/seqan/stream/guess_format.h
+include/seqan/stream/iostream_bgzf.h
+include/seqan/stream/iostream_bzip2.h
+include/seqan/stream/iostream_bzip2_impl.h
+include/seqan/stream/iostream_zip.h
+include/seqan/stream/iostream_zip_impl.h
+include/seqan/stream/iostream_zutil.h
+include/seqan/stream/iter_stream.h
+include/seqan/stream/lexical_cast.h
+include/seqan/stream/stream_base.h
+include/seqan/stream/stream_compressor.h
+include/seqan/stream/tokenization.h
+include/seqan/stream/virtual_stream.h
 include/seqan/system.h
 include/seqan/system/file_async.h
 include/seqan/system/file_directory.h
-include/seqan/system/file_manual_forwards.h
+include/seqan/system/file_forwards.h
 include/seqan/system/file_sync.h
 include/seqan/system/system_base.h
+include/seqan/system/system_condition.h
+include/seqan/system/system_critical_section.h
 include/seqan/system/system_event.h
-include/seqan/system/system_generated_forwards.h
-include/seqan/system/system_manual_forwards.h
+include/seqan/system/system_forwards.h
 include/seqan/system/system_mutex.h
-include/seqan/system/system_sema.h
 include/seqan/system/system_thread.h
+include/seqan/tabix_io.h
+include/seqan/tabix_io/tabix_index_tbi.h
+include/seqan/translation.h
+include/seqan/translation/translation.h
+include/seqan/translation/translation_tables.h
+include/seqan/ucsc_io.h
+include/seqan/ucsc_io/ucsc_file.h
+include/seqan/ucsc_io/ucsc_io.h
+include/seqan/ucsc_io/ucsc_record.h
+include/seqan/vcf_io.h
+include/seqan/vcf_io/read_vcf.h
+include/seqan/vcf_io/vcf_file.h
+include/seqan/vcf_io/vcf_header.h
+include/seqan/vcf_io/vcf_header_record.h
+include/seqan/vcf_io/vcf_io_context.h
+include/seqan/vcf_io/vcf_record.h
+include/seqan/vcf_io/write_vcf.h
 include/seqan/version.h
-%%DATADIR%%/docs/ADAPTION.char+array.html
-%%DATADIR%%/docs/ADAPTION.std_3a_3a_F_I_L_E+_2a.html
-%%DATADIR%%/docs/ADAPTION.std_3a_3abasic__string.html
-%%DATADIR%%/docs/ADAPTION.std_3a_3aiostream.html
-%%DATADIR%%/docs/ADAPTION.std_3a_3alist.html
-%%DATADIR%%/docs/ADAPTION.std_3a_3avector.html
-%%DATADIR%%/docs/CLASS_Align.html
-%%DATADIR%%/docs/CLASS_Align_Cols.html
-%%DATADIR%%/docs/CLASS_Align_Config.html
-%%DATADIR%%/docs/CLASS_Align_Quality_Store_Element.html
-%%DATADIR%%/docs/CLASS_Aligned_Read_Layout.html
-%%DATADIR%%/docs/CLASS_Aligned_Read_Store_Element.html
-%%DATADIR%%/docs/CLASS_Allocator.html
-%%DATADIR%%/docs/CLASS_Async_Request.html
-%%DATADIR%%/docs/CLASS_Auto_Seq_Format.html
-%%DATADIR%%/docs/CLASS_Blast_Hit.html
-%%DATADIR%%/docs/CLASS_Blast_Hsp.html
-%%DATADIR%%/docs/CLASS_Blast_Report.html
-%%DATADIR%%/docs/CLASS_Bundle2.html
-%%DATADIR%%/docs/CLASS_Bundle3.html
-%%DATADIR%%/docs/CLASS_Bundle5.html
-%%DATADIR%%/docs/CLASS_Command_Line_Option.html
-%%DATADIR%%/docs/CLASS_Command_Line_Parser.html
-%%DATADIR%%/docs/CLASS_Concatenator_Many_To_One.html
-%%DATADIR%%/docs/CLASS_Contig_File.html
-%%DATADIR%%/docs/CLASS_Contig_Store_Element.html
-%%DATADIR%%/docs/CLASS_Dequeue.html
-%%DATADIR%%/docs/CLASS_Edge_Stump.html
-%%DATADIR%%/docs/CLASS_External+_Property+_Map.html
-%%DATADIR%%/docs/CLASS_File.html
-%%DATADIR%%/docs/CLASS_File_Format.html
-%%DATADIR%%/docs/CLASS_Finder.html
-%%DATADIR%%/docs/CLASS_Fragment.html
-%%DATADIR%%/docs/CLASS_Fragment_Store.html
-%%DATADIR%%/docs/CLASS_Frequency_Distribution.html
-%%DATADIR%%/docs/CLASS_Functor_Complement.html
-%%DATADIR%%/docs/CLASS_Functor_Convert.html
-%%DATADIR%%/docs/CLASS_Functor_Lowcase.html
-%%DATADIR%%/docs/CLASS_Functor_Upcase.html
-%%DATADIR%%/docs/CLASS_Gap_Anchor.html
-%%DATADIR%%/docs/CLASS_Gaps.html
-%%DATADIR%%/docs/CLASS_Graph.html
-%%DATADIR%%/docs/CLASS_Hardwired_Shape.html
-%%DATADIR%%/docs/CLASS_Holder.html
-%%DATADIR%%/docs/CLASS_Id_Manager.html
-%%DATADIR%%/docs/CLASS_Index.html
-%%DATADIR%%/docs/CLASS_Internal_Map.html
-%%DATADIR%%/docs/CLASS_Internal_Pointer_Map.html
-%%DATADIR%%/docs/CLASS_Internal_Raw_Map.html
-%%DATADIR%%/docs/CLASS_Interval_And_Cargo.html
-%%DATADIR%%/docs/CLASS_Interval_Tree.html
-%%DATADIR%%/docs/CLASS_Interval_Tree_Node.html
-%%DATADIR%%/docs/CLASS_Iter.html
-%%DATADIR%%/docs/CLASS_Lexical.html
-%%DATADIR%%/docs/CLASS_Library_Store_Element.html
-%%DATADIR%%/docs/CLASS_Local_Alignment_Finder.html
-%%DATADIR%%/docs/CLASS_Map.html
-%%DATADIR%%/docs/CLASS_Markov_Model.html
-%%DATADIR%%/docs/CLASS_Mate_Pair_Store_Element.html
-%%DATADIR%%/docs/CLASS_Matrix.html
-%%DATADIR%%/docs/CLASS_Memory_Manager.html
-%%DATADIR%%/docs/CLASS_Modified_Alphabet.html
-%%DATADIR%%/docs/CLASS_Modified_Iterator.html
-%%DATADIR%%/docs/CLASS_Modified_String.html
-%%DATADIR%%/docs/CLASS_Motif_Finder.html
-%%DATADIR%%/docs/CLASS_Name_Store_Cache.html
-%%DATADIR%%/docs/CLASS_Pair.html
-%%DATADIR%%/docs/CLASS_Pattern.html
-%%DATADIR%%/docs/CLASS_Pdf.html
-%%DATADIR%%/docs/CLASS_Pipe.html
-%%DATADIR%%/docs/CLASS_Point_And_Cargo.html
-%%DATADIR%%/docs/CLASS_Pool.html
-%%DATADIR%%/docs/CLASS_Priority_Type.html
-%%DATADIR%%/docs/CLASS_Property_Map.html
-%%DATADIR%%/docs/CLASS_Proxy.html
-%%DATADIR%%/docs/CLASS_Pseudocount.html
-%%DATADIR%%/docs/CLASS_Read_Store_Element.html
-%%DATADIR%%/docs/CLASS_Rng.html
-%%DATADIR%%/docs/CLASS_Score.html
-%%DATADIR%%/docs/CLASS_Seed.html
-%%DATADIR%%/docs/CLASS_Seed_Set.html
-%%DATADIR%%/docs/CLASS_Segment.html
-%%DATADIR%%/docs/CLASS_Shape.html
-%%DATADIR%%/docs/CLASS_Simple_Type.html
-%%DATADIR%%/docs/CLASS_String.html
-%%DATADIR%%/docs/CLASS_String_Set.html
-%%DATADIR%%/docs/CLASS_Tag_Selector.html
-%%DATADIR%%/docs/CLASS_To_Std_Allocator.html
-%%DATADIR%%/docs/CLASS_Triple.html
-%%DATADIR%%/docs/CLASS_Tuple.html
-%%DATADIR%%/docs/CONCEPT_Allocator.html
-%%DATADIR%%/docs/CONCEPT_Container.html
-%%DATADIR%%/docs/CONCEPT_Finder.html
-%%DATADIR%%/docs/CONCEPT_Iterator.html
-%%DATADIR%%/docs/CONCEPT_Pattern.html
-%%DATADIR%%/docs/CONCEPT_Rooted+_Iterator.html
-%%DATADIR%%/docs/CONCEPT_Simple+_Type.html
-%%DATADIR%%/docs/DEMO_All+_Pairs+_Shortest+_Path.html
-%%DATADIR%%/docs/DEMO_Allocators.html
-%%DATADIR%%/docs/DEMO_Alphabets.html
-%%DATADIR%%/docs/DEMO_Approximate+_Searching.html
-%%DATADIR%%/docs/DEMO_Bellman-_Ford+_Algorithm.html
-%%DATADIR%%/docs/DEMO_Blast+_Reports.html
-%%DATADIR%%/docs/DEMO_Breadth-_First+_Search.html
-%%DATADIR%%/docs/DEMO_Constraint+_Iterator.html
-%%DATADIR%%/docs/DEMO_Depth-_First+_Search.html
-%%DATADIR%%/docs/DEMO_Dijkstras+_Algorithm.html
-%%DATADIR%%/docs/DEMO_Exact+_Searching.html
-%%DATADIR%%/docs/DEMO_File+_Format+_I_2f_O.html
-%%DATADIR%%/docs/DEMO_Floyd-_Warshall+_Algorithm.html
-%%DATADIR%%/docs/DEMO_Global+_Alignments.html
-%%DATADIR%%/docs/DEMO_H_M_M+_Silent+_States.html
-%%DATADIR%%/docs/DEMO_H_M_M.html
-%%DATADIR%%/docs/DEMO_Heaviest+_Increasing+_Subsequence.html
-%%DATADIR%%/docs/DEMO_Index+_Finder+_String_Set.html
-%%DATADIR%%/docs/DEMO_Index+_Finder.html
-%%DATADIR%%/docs/DEMO_Iterator+_Basics.html
-%%DATADIR%%/docs/DEMO_Kruskals+_Algorithm.html
-%%DATADIR%%/docs/DEMO_Local+_Alignments.html
-%%DATADIR%%/docs/DEMO_Longest+_Common+_Subsequence.html
-%%DATADIR%%/docs/DEMO_Longest+_Increasing+_Subsequence.html
-%%DATADIR%%/docs/DEMO_Maximal+_Repeats.html
-%%DATADIR%%/docs/DEMO_Maximal+_Unique+_Matches.html
-%%DATADIR%%/docs/DEMO_Maximum+_Flow.html
-%%DATADIR%%/docs/DEMO_Mod_Reverse.html
-%%DATADIR%%/docs/DEMO_Mod_View.html
-%%DATADIR%%/docs/DEMO_Motif+_Finder.html
-%%DATADIR%%/docs/DEMO_Mummy.html
-%%DATADIR%%/docs/DEMO_Nested+_Modifiers.html
-%%DATADIR%%/docs/DEMO_Pizza+_26+_Chili+_Index.html
-%%DATADIR%%/docs/DEMO_Prims+_Algorithm.html
-%%DATADIR%%/docs/DEMO_Rooted+_Iterators.html
-%%DATADIR%%/docs/DEMO_Shortest+_Path+in+_D_A_Gs.html
-%%DATADIR%%/docs/DEMO_String+_Basics.html
-%%DATADIR%%/docs/DEMO_Strongly+_Connected+_Components.html
-%%DATADIR%%/docs/DEMO_Suffix+_Array.html
-%%DATADIR%%/docs/DEMO_Supermaximal+_Repeats.html
-%%DATADIR%%/docs/DEMO_Topological+_Sort.html
-%%DATADIR%%/docs/DEMO_Transitive+_Closure.html
-%%DATADIR%%/docs/DEMO_Wildcard+_Searching.html
-%%DATADIR%%/docs/FUNCTION.abs_Freq_Of_Letters_In_Seq.html
-%%DATADIR%%/docs/FUNCTION.abs_Freq_Of_Letters_In_Set_Of_Seqs.html
-%%DATADIR%%/docs/FUNCTION.add_Argument_Text.html
-%%DATADIR%%/docs/FUNCTION.add_Child.html
-%%DATADIR%%/docs/FUNCTION.add_Edge.html
-%%DATADIR%%/docs/FUNCTION.add_Edges.html
-%%DATADIR%%/docs/FUNCTION.add_Help_Line.html
-%%DATADIR%%/docs/FUNCTION.add_Interval.html
-%%DATADIR%%/docs/FUNCTION.add_Line.html
-%%DATADIR%%/docs/FUNCTION.add_Option.html
-%%DATADIR%%/docs/FUNCTION.add_Section.html
-%%DATADIR%%/docs/FUNCTION.add_Seed.html
-%%DATADIR%%/docs/FUNCTION.add_Seeds.html
-%%DATADIR%%/docs/FUNCTION.add_Title_Line.html
-%%DATADIR%%/docs/FUNCTION.add_Usage_Line.html
-%%DATADIR%%/docs/FUNCTION.add_Value.html
-%%DATADIR%%/docs/FUNCTION.add_Version_Line.html
-%%DATADIR%%/docs/FUNCTION.add_Vertex.html
-%%DATADIR%%/docs/FUNCTION.adjust_Top.html
-%%DATADIR%%/docs/FUNCTION.alignment.html
-%%DATADIR%%/docs/FUNCTION.alignment_Evaluation.html
-%%DATADIR%%/docs/FUNCTION.all_Pairs_Shortest_Path.html
-%%DATADIR%%/docs/FUNCTION.allocate.html
-%%DATADIR%%/docs/FUNCTION.append.html
-%%DATADIR%%/docs/FUNCTION.append_Aligned_Read.html
-%%DATADIR%%/docs/FUNCTION.append_Diag.html
-%%DATADIR%%/docs/FUNCTION.append_Mate_Pair.html
-%%DATADIR%%/docs/FUNCTION.append_Name.html
-%%DATADIR%%/docs/FUNCTION.append_Read.html
-%%DATADIR%%/docs/FUNCTION.append_Seqs.html
-%%DATADIR%%/docs/FUNCTION.append_Value.html
-%%DATADIR%%/docs/FUNCTION.argument_Count.html
-%%DATADIR%%/docs/FUNCTION.argument_Text.html
-%%DATADIR%%/docs/FUNCTION.array_Clear_Space.html
-%%DATADIR%%/docs/FUNCTION.array_Construct.html
-%%DATADIR%%/docs/FUNCTION.array_Construct_Copy.html
-%%DATADIR%%/docs/FUNCTION.array_Construct_Move.html
-%%DATADIR%%/docs/FUNCTION.array_Copy.html
-%%DATADIR%%/docs/FUNCTION.array_Copy_Backward.html
-%%DATADIR%%/docs/FUNCTION.array_Copy_Forward.html
-%%DATADIR%%/docs/FUNCTION.array_Destruct.html
-%%DATADIR%%/docs/FUNCTION.array_Fill.html
-%%DATADIR%%/docs/FUNCTION.array_Move.html
-%%DATADIR%%/docs/FUNCTION.array_Move_Backward.html
-%%DATADIR%%/docs/FUNCTION.array_Move_Forward.html
-%%DATADIR%%/docs/FUNCTION.assign.html
-%%DATADIR%%/docs/FUNCTION.assign_Begin_State.html
-%%DATADIR%%/docs/FUNCTION.assign_Cargo.html
-%%DATADIR%%/docs/FUNCTION.assign_Cropped_Seq_Id.html
-%%DATADIR%%/docs/FUNCTION.assign_Emission_Probability.html
-%%DATADIR%%/docs/FUNCTION.assign_End_State.html
-%%DATADIR%%/docs/FUNCTION.assign_Next_S.html
-%%DATADIR%%/docs/FUNCTION.assign_Next_T.html
-%%DATADIR%%/docs/FUNCTION.assign_Property.html
-%%DATADIR%%/docs/FUNCTION.assign_Qual.html
-%%DATADIR%%/docs/FUNCTION.assign_Qual_Id.html
-%%DATADIR%%/docs/FUNCTION.assign_Qualities.html
-%%DATADIR%%/docs/FUNCTION.assign_Quality_Value.html
-%%DATADIR%%/docs/FUNCTION.assign_Root.html
-%%DATADIR%%/docs/FUNCTION.assign_Seq.html
-%%DATADIR%%/docs/FUNCTION.assign_Seq_Id.html
-%%DATADIR%%/docs/FUNCTION.assign_Silent_Status.html
-%%DATADIR%%/docs/FUNCTION.assign_Source.html
-%%DATADIR%%/docs/FUNCTION.assign_String_Set.html
-%%DATADIR%%/docs/FUNCTION.assign_Target.html
-%%DATADIR%%/docs/FUNCTION.assign_Transition_Probability.html
-%%DATADIR%%/docs/FUNCTION.assign_Value.html
-%%DATADIR%%/docs/FUNCTION.assign_Value_By_Id.html
-%%DATADIR%%/docs/FUNCTION.async_Read_At.html
-%%DATADIR%%/docs/FUNCTION.async_Write_At.html
-%%DATADIR%%/docs/FUNCTION.at_Begin.html
-%%DATADIR%%/docs/FUNCTION.at_End.html
-%%DATADIR%%/docs/FUNCTION.at_End_Of_Sequence.html
-%%DATADIR%%/docs/FUNCTION.at_Nil.html
-%%DATADIR%%/docs/FUNCTION.atomic_Add.html
-%%DATADIR%%/docs/FUNCTION.atomic_Cas.html
-%%DATADIR%%/docs/FUNCTION.atomic_Dec.html
-%%DATADIR%%/docs/FUNCTION.atomic_Inc.html
-%%DATADIR%%/docs/FUNCTION.atomic_Max.html
-%%DATADIR%%/docs/FUNCTION.atomic_Min.html
-%%DATADIR%%/docs/FUNCTION.atomic_Or.html
-%%DATADIR%%/docs/FUNCTION.atomic_Xor.html
-%%DATADIR%%/docs/FUNCTION.back.html
-%%DATADIR%%/docs/FUNCTION.background_Frequency.html
-%%DATADIR%%/docs/FUNCTION.backward_Algorithm.html
-%%DATADIR%%/docs/FUNCTION.banded_Alignment.html
-%%DATADIR%%/docs/FUNCTION.banded_Chain_Alignment.html
-%%DATADIR%%/docs/FUNCTION.begin.html
-%%DATADIR%%/docs/FUNCTION.begin_Position.html
-%%DATADIR%%/docs/FUNCTION.begin_Read.html
-%%DATADIR%%/docs/FUNCTION.begin_State.html
-%%DATADIR%%/docs/FUNCTION.begin_Write.html
-%%DATADIR%%/docs/FUNCTION.bellman_Ford_Algorithm.html
-%%DATADIR%%/docs/FUNCTION.binomial_Coefficient.html
-%%DATADIR%%/docs/FUNCTION.blast_23get_Alignment.html
-%%DATADIR%%/docs/FUNCTION.breadth_First_Search.html
-%%DATADIR%%/docs/FUNCTION.bundle2.html
-%%DATADIR%%/docs/FUNCTION.bundle3.html
-%%DATADIR%%/docs/FUNCTION.bundle5.html
-%%DATADIR%%/docs/FUNCTION.bwt_At.html
-%%DATADIR%%/docs/FUNCTION.calculate_Insert_Sizes.html
-%%DATADIR%%/docs/FUNCTION.calculate_Mate_Indices.html
-%%DATADIR%%/docs/FUNCTION.can_Parse_String.html
-%%DATADIR%%/docs/FUNCTION.cancel.html
-%%DATADIR%%/docs/FUNCTION.capacity.html
-%%DATADIR%%/docs/FUNCTION.cargo.html
-%%DATADIR%%/docs/FUNCTION.child_At.html
-%%DATADIR%%/docs/FUNCTION.child_Vertex.html
-%%DATADIR%%/docs/FUNCTION.children_Are_Leaves.html
-%%DATADIR%%/docs/FUNCTION.clear.html
-%%DATADIR%%/docs/FUNCTION.clear_Edges.html
-%%DATADIR%%/docs/FUNCTION.clear_Gaps.html
-%%DATADIR%%/docs/FUNCTION.clear_Reads.html
-%%DATADIR%%/docs/FUNCTION.clear_Vertices.html
-%%DATADIR%%/docs/FUNCTION.clipped_Begin_Position.html
-%%DATADIR%%/docs/FUNCTION.clipped_End_Position.html
-%%DATADIR%%/docs/FUNCTION.close.html
-%%DATADIR%%/docs/FUNCTION.col.html
-%%DATADIR%%/docs/FUNCTION.collect_Leaves.html
-%%DATADIR%%/docs/FUNCTION.cols.html
-%%DATADIR%%/docs/FUNCTION.compact_Aligned_Reads.html
-%%DATADIR%%/docs/FUNCTION.compact_Pair_Match_Ids.html
-%%DATADIR%%/docs/FUNCTION.compare.html
-%%DATADIR%%/docs/FUNCTION.complement.html
-%%DATADIR%%/docs/FUNCTION.complete_Profile.html
-%%DATADIR%%/docs/FUNCTION.compute_Generous_Capacity.html
-%%DATADIR%%/docs/FUNCTION.concat.html
-%%DATADIR%%/docs/FUNCTION.connected_Components.html
-%%DATADIR%%/docs/FUNCTION.container.html
-%%DATADIR%%/docs/FUNCTION.convert.html
-%%DATADIR%%/docs/FUNCTION.convert_Alignment.html
-%%DATADIR%%/docs/FUNCTION.convert_Impl.html
-%%DATADIR%%/docs/FUNCTION.convert_Matches_To_Global_Alignment.html
-%%DATADIR%%/docs/FUNCTION.convert_Pair_Wise_To_Global_Alignment.html
-%%DATADIR%%/docs/FUNCTION.convert_Pattern_To_Profile.html
-%%DATADIR%%/docs/FUNCTION.convert_Residue_To_Frequency_Dist.html
-%%DATADIR%%/docs/FUNCTION.convert_Set_Of_Patterns_To_Profile.html
-%%DATADIR%%/docs/FUNCTION.count_Characters.html
-%%DATADIR%%/docs/FUNCTION.count_Children.html
-%%DATADIR%%/docs/FUNCTION.count_Gaps.html
-%%DATADIR%%/docs/FUNCTION.count_Occurrences.html
-%%DATADIR%%/docs/FUNCTION.count_Occurrences_Multiple.html
-%%DATADIR%%/docs/FUNCTION.cpu_Time.html
-%%DATADIR%%/docs/FUNCTION.create.html
-%%DATADIR%%/docs/FUNCTION.create_B_W_Table.html
-%%DATADIR%%/docs/FUNCTION.create_Childtab.html
-%%DATADIR%%/docs/FUNCTION.create_Count_Array.html
-%%DATADIR%%/docs/FUNCTION.create_Interval_Tree.html
-%%DATADIR%%/docs/FUNCTION.create_Lcp_Table.html
-%%DATADIR%%/docs/FUNCTION.create_Oracle.html
-%%DATADIR%%/docs/FUNCTION.create_Oracle_On_Reverse.html
-%%DATADIR%%/docs/FUNCTION.create_Q_Gram_Index.html
-%%DATADIR%%/docs/FUNCTION.create_Q_Gram_Index_Dir_Only.html
-%%DATADIR%%/docs/FUNCTION.create_Q_Gram_Index_S_A_Only.html
-%%DATADIR%%/docs/FUNCTION.create_Root.html
-%%DATADIR%%/docs/FUNCTION.create_Source.html
-%%DATADIR%%/docs/FUNCTION.create_Suffix_Array.html
-%%DATADIR%%/docs/FUNCTION.create_Suffix_Trie.html
-%%DATADIR%%/docs/FUNCTION.create_Trie.html
-%%DATADIR%%/docs/FUNCTION.create_Trie_On_Reverse.html
-%%DATADIR%%/docs/FUNCTION.create_Wotd_Index.html
-%%DATADIR%%/docs/FUNCTION.dag_Shortest_Path.html
-%%DATADIR%%/docs/FUNCTION.database_Name.html
-%%DATADIR%%/docs/FUNCTION.database_Orientation_Plus.html
-%%DATADIR%%/docs/FUNCTION.deallocate.html
-%%DATADIR%%/docs/FUNCTION.degree.html
-%%DATADIR%%/docs/FUNCTION.dependent.html
-%%DATADIR%%/docs/FUNCTION.dependent_Source.html
-%%DATADIR%%/docs/FUNCTION.depth_First_Search.html
-%%DATADIR%%/docs/FUNCTION.detach.html
-%%DATADIR%%/docs/FUNCTION.determine_Consensus_Seq.html
-%%DATADIR%%/docs/FUNCTION.difference.html
-%%DATADIR%%/docs/FUNCTION.dijkstra.html
-%%DATADIR%%/docs/FUNCTION.dimension.html
-%%DATADIR%%/docs/FUNCTION.dir_At.html
-%%DATADIR%%/docs/FUNCTION.display.html
-%%DATADIR%%/docs/FUNCTION.display_Result.html
-%%DATADIR%%/docs/FUNCTION.em.html
-%%DATADIR%%/docs/FUNCTION.emission_Probability.html
-%%DATADIR%%/docs/FUNCTION.empty.html
-%%DATADIR%%/docs/FUNCTION.empty_Parent_Edge.html
-%%DATADIR%%/docs/FUNCTION.empty_Source.html
-%%DATADIR%%/docs/FUNCTION.end.html
-%%DATADIR%%/docs/FUNCTION.end_Diagonal.html
-%%DATADIR%%/docs/FUNCTION.end_Position.html
-%%DATADIR%%/docs/FUNCTION.end_Read.html
-%%DATADIR%%/docs/FUNCTION.end_State.html
-%%DATADIR%%/docs/FUNCTION.end_Write.html
-%%DATADIR%%/docs/FUNCTION.erase.html
-%%DATADIR%%/docs/FUNCTION.erase_Back.html
-%%DATADIR%%/docs/FUNCTION.expectation.html
-%%DATADIR%%/docs/FUNCTION.extend_Seed.html
-%%DATADIR%%/docs/FUNCTION.extend_Seed_Score.html
-%%DATADIR%%/docs/FUNCTION.extend_Seeds.html
-%%DATADIR%%/docs/FUNCTION.extend_Seeds_Score.html
-%%DATADIR%%/docs/FUNCTION.factorial.html
-%%DATADIR%%/docs/FUNCTION.find.html
-%%DATADIR%%/docs/FUNCTION.find_Begin.html
-%%DATADIR%%/docs/FUNCTION.find_Edge.html
-%%DATADIR%%/docs/FUNCTION.find_Intervals.html
-%%DATADIR%%/docs/FUNCTION.find_Intervals_Exclude_Touching.html
-%%DATADIR%%/docs/FUNCTION.find_Motif.html
-%%DATADIR%%/docs/FUNCTION.find_Vertex.html
-%%DATADIR%%/docs/FUNCTION.flatten.html
-%%DATADIR%%/docs/FUNCTION.floyd_Warshall_Algorithm.html
-%%DATADIR%%/docs/FUNCTION.flush.html
-%%DATADIR%%/docs/FUNCTION.ford_Fulkerson_Algorithm.html
-%%DATADIR%%/docs/FUNCTION.forward_Algorithm.html
-%%DATADIR%%/docs/FUNCTION.fragment_Begin.html
-%%DATADIR%%/docs/FUNCTION.fragment_Length.html
-%%DATADIR%%/docs/FUNCTION.front.html
-%%DATADIR%%/docs/FUNCTION.gap_Value.html
-%%DATADIR%%/docs/FUNCTION.gap_Value_Impl.html
-%%DATADIR%%/docs/FUNCTION.generate_Sequence.html
-%%DATADIR%%/docs/FUNCTION.get_Adjacency_Matrix.html
-%%DATADIR%%/docs/FUNCTION.get_Alignment.html
-%%DATADIR%%/docs/FUNCTION.get_Argument_Value.html
-%%DATADIR%%/docs/FUNCTION.get_Argument_Values.html
-%%DATADIR%%/docs/FUNCTION.get_Begin_Score.html
-%%DATADIR%%/docs/FUNCTION.get_Begin_State.html
-%%DATADIR%%/docs/FUNCTION.get_Bit_Score.html
-%%DATADIR%%/docs/FUNCTION.get_Cargo.html
-%%DATADIR%%/docs/FUNCTION.get_Database_Begin.html
-%%DATADIR%%/docs/FUNCTION.get_Database_End.html
-%%DATADIR%%/docs/FUNCTION.get_Database_Name.html
-%%DATADIR%%/docs/FUNCTION.get_Distance_Matrix.html
-%%DATADIR%%/docs/FUNCTION.get_E_Value.html
-%%DATADIR%%/docs/FUNCTION.get_E_Value_Cutoff.html
-%%DATADIR%%/docs/FUNCTION.get_Emission_Probability.html
-%%DATADIR%%/docs/FUNCTION.get_End_State.html
-%%DATADIR%%/docs/FUNCTION.get_Fibre.html
-%%DATADIR%%/docs/FUNCTION.get_First_Covered_Position.html
-%%DATADIR%%/docs/FUNCTION.get_Frequency.html
-%%DATADIR%%/docs/FUNCTION.get_Gapped_Kappa.html
-%%DATADIR%%/docs/FUNCTION.get_Gapped_Lambda.html
-%%DATADIR%%/docs/FUNCTION.get_Get_Extension.html
-%%DATADIR%%/docs/FUNCTION.get_Get_Open.html
-%%DATADIR%%/docs/FUNCTION.get_Id_By_Name.html
-%%DATADIR%%/docs/FUNCTION.get_Id_Lower_Bound.html
-%%DATADIR%%/docs/FUNCTION.get_Id_Upper_Bound.html
-%%DATADIR%%/docs/FUNCTION.get_Kappa.html
-%%DATADIR%%/docs/FUNCTION.get_Kmer_Similarity_Matrix.html
-%%DATADIR%%/docs/FUNCTION.get_Lambda.html
-%%DATADIR%%/docs/FUNCTION.get_Last_Covered_Position.html
-%%DATADIR%%/docs/FUNCTION.get_Left_Boundary.html
-%%DATADIR%%/docs/FUNCTION.get_Mate_No.html
-%%DATADIR%%/docs/FUNCTION.get_Motif.html
-%%DATADIR%%/docs/FUNCTION.get_Next.html
-%%DATADIR%%/docs/FUNCTION.get_Next_S.html
-%%DATADIR%%/docs/FUNCTION.get_Next_T.html
-%%DATADIR%%/docs/FUNCTION.get_Nil.html
-%%DATADIR%%/docs/FUNCTION.get_Num_Gaps.html
-%%DATADIR%%/docs/FUNCTION.get_Occurrence.html
-%%DATADIR%%/docs/FUNCTION.get_Occurrences.html
-%%DATADIR%%/docs/FUNCTION.get_Occurrences_Bwt.html
-%%DATADIR%%/docs/FUNCTION.get_Option_Value_Long.html
-%%DATADIR%%/docs/FUNCTION.get_Option_Value_Short.html
-%%DATADIR%%/docs/FUNCTION.get_Option_Values_Long.html
-%%DATADIR%%/docs/FUNCTION.get_Option_Values_Short.html
-%%DATADIR%%/docs/FUNCTION.get_Projected_Position.html
-%%DATADIR%%/docs/FUNCTION.get_Property.html
-%%DATADIR%%/docs/FUNCTION.get_Query_Begin.html
-%%DATADIR%%/docs/FUNCTION.get_Query_End.html
-%%DATADIR%%/docs/FUNCTION.get_Query_Name.html
-%%DATADIR%%/docs/FUNCTION.get_Read.html
-%%DATADIR%%/docs/FUNCTION.get_Right_Boundary.html
-%%DATADIR%%/docs/FUNCTION.get_Root.html
-%%DATADIR%%/docs/FUNCTION.get_Score.html
-%%DATADIR%%/docs/FUNCTION.get_Seq_No.html
-%%DATADIR%%/docs/FUNCTION.get_Seq_Offset.html
-%%DATADIR%%/docs/FUNCTION.get_Source.html
-%%DATADIR%%/docs/FUNCTION.get_Step_Size.html
-%%DATADIR%%/docs/FUNCTION.get_String_Set.html
-%%DATADIR%%/docs/FUNCTION.get_Successor.html
-%%DATADIR%%/docs/FUNCTION.get_Swift_Hits.html
-%%DATADIR%%/docs/FUNCTION.get_Target.html
-%%DATADIR%%/docs/FUNCTION.get_Transition_Probability.html
-%%DATADIR%%/docs/FUNCTION.get_Value.html
-%%DATADIR%%/docs/FUNCTION.get_Value_By_Id.html
-%%DATADIR%%/docs/FUNCTION.global_Alignment.html
-%%DATADIR%%/docs/FUNCTION.global_Chaining.html
-%%DATADIR%%/docs/FUNCTION.global_Msa_Alignment.html
-%%DATADIR%%/docs/FUNCTION.go_Begin.html
-%%DATADIR%%/docs/FUNCTION.go_Down.html
-%%DATADIR%%/docs/FUNCTION.go_End.html
-%%DATADIR%%/docs/FUNCTION.go_Further.html
-%%DATADIR%%/docs/FUNCTION.go_Next.html
-%%DATADIR%%/docs/FUNCTION.go_Nil.html
-%%DATADIR%%/docs/FUNCTION.go_Previous.html
-%%DATADIR%%/docs/FUNCTION.go_Right.html
-%%DATADIR%%/docs/FUNCTION.go_Root.html
-%%DATADIR%%/docs/FUNCTION.go_Up.html
-%%DATADIR%%/docs/FUNCTION.guess_File_Format.html
-%%DATADIR%%/docs/FUNCTION.guess_Format.html
-%%DATADIR%%/docs/FUNCTION.guess_Format_From_Filename.html
-%%DATADIR%%/docs/FUNCTION.hamming_Distance.html
-%%DATADIR%%/docs/FUNCTION.has_Option_Long.html
-%%DATADIR%%/docs/FUNCTION.has_Option_Short.html
-%%DATADIR%%/docs/FUNCTION.has_Prefix.html
-%%DATADIR%%/docs/FUNCTION.hash.html
-%%DATADIR%%/docs/FUNCTION.hash2.html
-%%DATADIR%%/docs/FUNCTION.hash2_Next.html
-%%DATADIR%%/docs/FUNCTION.hash2_Upper.html
-%%DATADIR%%/docs/FUNCTION.hash_Next.html
-%%DATADIR%%/docs/FUNCTION.hash_Upper.html
-%%DATADIR%%/docs/FUNCTION.haystack.html
-%%DATADIR%%/docs/FUNCTION.heaviest_Increasing_Subsequence.html
-%%DATADIR%%/docs/FUNCTION.help.html
-%%DATADIR%%/docs/FUNCTION.help_Text.html
-%%DATADIR%%/docs/FUNCTION.host.html
-%%DATADIR%%/docs/FUNCTION.host_Graph.html
-%%DATADIR%%/docs/FUNCTION.host_Hit.html
-%%DATADIR%%/docs/FUNCTION.host_Report.html
-%%DATADIR%%/docs/FUNCTION.id.html
-%%DATADIR%%/docs/FUNCTION.id_Count.html
-%%DATADIR%%/docs/FUNCTION.id_In_Use.html
-%%DATADIR%%/docs/FUNCTION.id_To_Position.html
-%%DATADIR%%/docs/FUNCTION.in_Degree.html
-%%DATADIR%%/docs/FUNCTION.index_Bucket_Map.html
-%%DATADIR%%/docs/FUNCTION.index_Bwt.html
-%%DATADIR%%/docs/FUNCTION.index_Childtab.html
-%%DATADIR%%/docs/FUNCTION.index_Counts.html
-%%DATADIR%%/docs/FUNCTION.index_Counts_Dir.html
-%%DATADIR%%/docs/FUNCTION.index_Create.html
-%%DATADIR%%/docs/FUNCTION.index_Dir.html
-%%DATADIR%%/docs/FUNCTION.index_Lcp.html
-%%DATADIR%%/docs/FUNCTION.index_Lcpe.html
-%%DATADIR%%/docs/FUNCTION.index_Raw_S_A.html
-%%DATADIR%%/docs/FUNCTION.index_Raw_Text.html
-%%DATADIR%%/docs/FUNCTION.index_Require.html
-%%DATADIR%%/docs/FUNCTION.index_S_A.html
-%%DATADIR%%/docs/FUNCTION.index_Shape.html
-%%DATADIR%%/docs/FUNCTION.index_Supplied.html
-%%DATADIR%%/docs/FUNCTION.index_Text.html
-%%DATADIR%%/docs/FUNCTION.infimum_Value_Impl.html
-%%DATADIR%%/docs/FUNCTION.infix.html
-%%DATADIR%%/docs/FUNCTION.infix_With_Length.html
-%%DATADIR%%/docs/FUNCTION.insert.html
-%%DATADIR%%/docs/FUNCTION.insert_Gap.html
-%%DATADIR%%/docs/FUNCTION.insert_Gaps.html
-%%DATADIR%%/docs/FUNCTION.insert_Value.html
-%%DATADIR%%/docs/FUNCTION.integrate_Align.html
-%%DATADIR%%/docs/FUNCTION.inverse_Hash.html
-%%DATADIR%%/docs/FUNCTION.is_Boolean_Option.html
-%%DATADIR%%/docs/FUNCTION.is_Double_Option.html
-%%DATADIR%%/docs/FUNCTION.is_Equal.html
-%%DATADIR%%/docs/FUNCTION.is_Gap.html
-%%DATADIR%%/docs/FUNCTION.is_Greater.html
-%%DATADIR%%/docs/FUNCTION.is_Greater_Or_Equal.html
-%%DATADIR%%/docs/FUNCTION.is_Hidden_Option.html
-%%DATADIR%%/docs/FUNCTION.is_Int_Option.html
-%%DATADIR%%/docs/FUNCTION.is_Label_Option.html
-%%DATADIR%%/docs/FUNCTION.is_Left_Maximal.html
-%%DATADIR%%/docs/FUNCTION.is_Less.html
-%%DATADIR%%/docs/FUNCTION.is_Less_Or_Equal.html
-%%DATADIR%%/docs/FUNCTION.is_Not_Equal.html
-%%DATADIR%%/docs/FUNCTION.is_Option_List.html
-%%DATADIR%%/docs/FUNCTION.is_Option_Mandatory.html
-%%DATADIR%%/docs/FUNCTION.is_Partially_Left_Extensible.html
-%%DATADIR%%/docs/FUNCTION.is_Prefix.html
-%%DATADIR%%/docs/FUNCTION.is_Reversed.html
-%%DATADIR%%/docs/FUNCTION.is_Right_Terminal.html
-%%DATADIR%%/docs/FUNCTION.is_Root.html
-%%DATADIR%%/docs/FUNCTION.is_Set_Long.html
-%%DATADIR%%/docs/FUNCTION.is_Set_Short.html
-%%DATADIR%%/docs/FUNCTION.is_Silent.html
-%%DATADIR%%/docs/FUNCTION.is_String_Option.html
-%%DATADIR%%/docs/FUNCTION.is_Unique.html
-%%DATADIR%%/docs/FUNCTION.iter.html
-%%DATADIR%%/docs/FUNCTION.key.html
-%%DATADIR%%/docs/FUNCTION.kruskals_Algorithm.html
-%%DATADIR%%/docs/FUNCTION.label.html
-%%DATADIR%%/docs/FUNCTION.layout_Alignment.html
-%%DATADIR%%/docs/FUNCTION.lca.html
-%%DATADIR%%/docs/FUNCTION.lcp.html
-%%DATADIR%%/docs/FUNCTION.lcp_At.html
-%%DATADIR%%/docs/FUNCTION.lcp_Length.html
-%%DATADIR%%/docs/FUNCTION.lcpe_At.html
-%%DATADIR%%/docs/FUNCTION.left_Boundary.html
-%%DATADIR%%/docs/FUNCTION.left_Diagonal.html
-%%DATADIR%%/docs/FUNCTION.left_Dim0.html
-%%DATADIR%%/docs/FUNCTION.left_Dim1.html
-%%DATADIR%%/docs/FUNCTION.left_Position.html
-%%DATADIR%%/docs/FUNCTION.length.html
-%%DATADIR%%/docs/FUNCTION.load_Contig.html
-%%DATADIR%%/docs/FUNCTION.load_Contigs.html
-%%DATADIR%%/docs/FUNCTION.load_Reads.html
-%%DATADIR%%/docs/FUNCTION.load_Score_Matrix.html
-%%DATADIR%%/docs/FUNCTION.local_Alignment.html
-%%DATADIR%%/docs/FUNCTION.lock_Contig.html
-%%DATADIR%%/docs/FUNCTION.lock_Contigs.html
-%%DATADIR%%/docs/FUNCTION.log2.html
-%%DATADIR%%/docs/FUNCTION.logarithmize.html
-%%DATADIR%%/docs/FUNCTION.long_Name.html
-%%DATADIR%%/docs/FUNCTION.longest_Common_Subsequence.html
-%%DATADIR%%/docs/FUNCTION.longest_Increasing_Subsequence.html
-%%DATADIR%%/docs/FUNCTION.lower_Bound_Aligned_Reads.html
-%%DATADIR%%/docs/FUNCTION.map_23add.html
-%%DATADIR%%/docs/FUNCTION.map_23cargo.html
-%%DATADIR%%/docs/FUNCTION.map_23erase.html
-%%DATADIR%%/docs/FUNCTION.map_23erase_All.html
-%%DATADIR%%/docs/FUNCTION.map_23find.html
-%%DATADIR%%/docs/FUNCTION.map_23has_Key.html
-%%DATADIR%%/docs/FUNCTION.map_23insert.html
-%%DATADIR%%/docs/FUNCTION.map_23value.html
-%%DATADIR%%/docs/FUNCTION.map_Value.html
-%%DATADIR%%/docs/FUNCTION.match_Refinement.html
-%%DATADIR%%/docs/FUNCTION.max_Value.html
-%%DATADIR%%/docs/FUNCTION.maximum_Distance.html
-%%DATADIR%%/docs/FUNCTION.min_Value.html
-%%DATADIR%%/docs/FUNCTION.motif_Count.html
-%%DATADIR%%/docs/FUNCTION.move.html
-%%DATADIR%%/docs/FUNCTION.move_Source.html
-%%DATADIR%%/docs/FUNCTION.move_Value.html
-%%DATADIR%%/docs/FUNCTION.mt_Rand.html
-%%DATADIR%%/docs/FUNCTION.mt_Rand_Double.html
-%%DATADIR%%/docs/FUNCTION.mt_Rand_Init.html
-%%DATADIR%%/docs/FUNCTION.multi_Local_Alignment.html
-%%DATADIR%%/docs/FUNCTION.needle.html
-%%DATADIR%%/docs/FUNCTION.next_S.html
-%%DATADIR%%/docs/FUNCTION.next_T.html
-%%DATADIR%%/docs/FUNCTION.node_Depth.html
-%%DATADIR%%/docs/FUNCTION.node_Hull_Predicate.html
-%%DATADIR%%/docs/FUNCTION.node_Predicate.html
-%%DATADIR%%/docs/FUNCTION.node_Up.html
-%%DATADIR%%/docs/FUNCTION.normalize.html
-%%DATADIR%%/docs/FUNCTION.num_Children.html
-%%DATADIR%%/docs/FUNCTION.num_Edges.html
-%%DATADIR%%/docs/FUNCTION.num_Hits.html
-%%DATADIR%%/docs/FUNCTION.num_Hsps.html
-%%DATADIR%%/docs/FUNCTION.num_Tree_Edges.html
-%%DATADIR%%/docs/FUNCTION.num_Vertices.html
-%%DATADIR%%/docs/FUNCTION.obtain_I_D.html
-%%DATADIR%%/docs/FUNCTION.obtain_Id.html
-%%DATADIR%%/docs/FUNCTION.open.html
-%%DATADIR%%/docs/FUNCTION.open_Temp.html
-%%DATADIR%%/docs/FUNCTION.ord_Value.html
-%%DATADIR%%/docs/FUNCTION.order_Occurrences.html
-%%DATADIR%%/docs/FUNCTION.out_Degree.html
-%%DATADIR%%/docs/FUNCTION.parent_Edge_First_Char.html
-%%DATADIR%%/docs/FUNCTION.parent_Edge_Label.html
-%%DATADIR%%/docs/FUNCTION.parent_Edge_Length.html
-%%DATADIR%%/docs/FUNCTION.parent_Rep_Length.html
-%%DATADIR%%/docs/FUNCTION.parent_Vertex.html
-%%DATADIR%%/docs/FUNCTION.parse.html
-%%DATADIR%%/docs/FUNCTION.parse_String.html
-%%DATADIR%%/docs/FUNCTION.pick_Random_Number.html
-%%DATADIR%%/docs/FUNCTION.pop.html
-%%DATADIR%%/docs/FUNCTION.pos_Globalize.html
-%%DATADIR%%/docs/FUNCTION.pos_Local_To_X.html
-%%DATADIR%%/docs/FUNCTION.pos_Localize.html
-%%DATADIR%%/docs/FUNCTION.pos_Of_Max.html
-%%DATADIR%%/docs/FUNCTION.position.html
-%%DATADIR%%/docs/FUNCTION.position_Range.html
-%%DATADIR%%/docs/FUNCTION.position_Range_No_Clip.html
-%%DATADIR%%/docs/FUNCTION.position_To_Id.html
-%%DATADIR%%/docs/FUNCTION.prefix.html
-%%DATADIR%%/docs/FUNCTION.prepend_Value.html
-%%DATADIR%%/docs/FUNCTION.prims_Algorithm.html
-%%DATADIR%%/docs/FUNCTION.print_Alignment.html
-%%DATADIR%%/docs/FUNCTION.print_Debug_Level.html
-%%DATADIR%%/docs/FUNCTION.progressive_Alignment.html
-%%DATADIR%%/docs/FUNCTION.property.html
-%%DATADIR%%/docs/FUNCTION.push.html
-%%DATADIR%%/docs/FUNCTION.quality_Value.html
-%%DATADIR%%/docs/FUNCTION.query_Name.html
-%%DATADIR%%/docs/FUNCTION.query_Orientation_Plus.html
-%%DATADIR%%/docs/FUNCTION.range.html
-%%DATADIR%%/docs/FUNCTION.rawsa_At.html
-%%DATADIR%%/docs/FUNCTION.rawtext_At.html
-%%DATADIR%%/docs/FUNCTION.re_Align.html
-%%DATADIR%%/docs/FUNCTION.read.html
-%%DATADIR%%/docs/FUNCTION.read_At.html
-%%DATADIR%%/docs/FUNCTION.read_Feature.html
-%%DATADIR%%/docs/FUNCTION.read_Line_Type.html
-%%DATADIR%%/docs/FUNCTION.read_Meta.html
-%%DATADIR%%/docs/FUNCTION.refresh.html
-%%DATADIR%%/docs/FUNCTION.release_All.html
-%%DATADIR%%/docs/FUNCTION.release_I_D.html
-%%DATADIR%%/docs/FUNCTION.release_Id.html
-%%DATADIR%%/docs/FUNCTION.remove_All_Children.html
-%%DATADIR%%/docs/FUNCTION.remove_Child.html
-%%DATADIR%%/docs/FUNCTION.remove_Edge.html
-%%DATADIR%%/docs/FUNCTION.remove_Gap.html
-%%DATADIR%%/docs/FUNCTION.remove_Gaps.html
-%%DATADIR%%/docs/FUNCTION.remove_In_Edges.html
-%%DATADIR%%/docs/FUNCTION.remove_Out_Edges.html
-%%DATADIR%%/docs/FUNCTION.remove_Value_By_Id.html
-%%DATADIR%%/docs/FUNCTION.remove_Vertex.html
-%%DATADIR%%/docs/FUNCTION.rep_Length.html
-%%DATADIR%%/docs/FUNCTION.replace.html
-%%DATADIR%%/docs/FUNCTION.representative.html
-%%DATADIR%%/docs/FUNCTION.required_Arguments.html
-%%DATADIR%%/docs/FUNCTION.reserve.html
-%%DATADIR%%/docs/FUNCTION.resize.html
-%%DATADIR%%/docs/FUNCTION.resize_Edge_Map.html
-%%DATADIR%%/docs/FUNCTION.resize_Space.html
-%%DATADIR%%/docs/FUNCTION.resize_Vertex_Map.html
-%%DATADIR%%/docs/FUNCTION.reverse.html
-%%DATADIR%%/docs/FUNCTION.reverse_Complement.html
-%%DATADIR%%/docs/FUNCTION.rewind.html
-%%DATADIR%%/docs/FUNCTION.right_Boundary.html
-%%DATADIR%%/docs/FUNCTION.right_Diagonal.html
-%%DATADIR%%/docs/FUNCTION.right_Dim0.html
-%%DATADIR%%/docs/FUNCTION.right_Dim1.html
-%%DATADIR%%/docs/FUNCTION.right_Position.html
-%%DATADIR%%/docs/FUNCTION.root.html
-%%DATADIR%%/docs/FUNCTION.row.html
-%%DATADIR%%/docs/FUNCTION.rows.html
-%%DATADIR%%/docs/FUNCTION.sa_At.html
-%%DATADIR%%/docs/FUNCTION.score.html
-%%DATADIR%%/docs/FUNCTION.score_Gap.html
-%%DATADIR%%/docs/FUNCTION.score_Gap_Extend.html
-%%DATADIR%%/docs/FUNCTION.score_Gap_Extend_Horizontal.html
-%%DATADIR%%/docs/FUNCTION.score_Gap_Extend_Vertical.html
-%%DATADIR%%/docs/FUNCTION.score_Gap_Horizontal.html
-%%DATADIR%%/docs/FUNCTION.score_Gap_Open.html
-%%DATADIR%%/docs/FUNCTION.score_Gap_Open_Horizontal.html
-%%DATADIR%%/docs/FUNCTION.score_Gap_Open_Vertical.html
-%%DATADIR%%/docs/FUNCTION.score_Gap_Vertical.html
-%%DATADIR%%/docs/FUNCTION.score_Limit.html
-%%DATADIR%%/docs/FUNCTION.score_Match.html
-%%DATADIR%%/docs/FUNCTION.score_Mismatch.html
-%%DATADIR%%/docs/FUNCTION.score_Seed.html
-%%DATADIR%%/docs/FUNCTION.scoring_Scheme.html
-%%DATADIR%%/docs/FUNCTION.seed_Score.html
-%%DATADIR%%/docs/FUNCTION.seek.html
-%%DATADIR%%/docs/FUNCTION.sequence_Id.html
-%%DATADIR%%/docs/FUNCTION.set.html
-%%DATADIR%%/docs/FUNCTION.set_Begin.html
-%%DATADIR%%/docs/FUNCTION.set_Begin_Position.html
-%%DATADIR%%/docs/FUNCTION.set_Default_Score_Matrix.html
-%%DATADIR%%/docs/FUNCTION.set_End.html
-%%DATADIR%%/docs/FUNCTION.set_End_Position.html
-%%DATADIR%%/docs/FUNCTION.set_Eof.html
-%%DATADIR%%/docs/FUNCTION.set_Haystack.html
-%%DATADIR%%/docs/FUNCTION.set_Help_Text.html
-%%DATADIR%%/docs/FUNCTION.set_Host.html
-%%DATADIR%%/docs/FUNCTION.set_Left_Diagonal.html
-%%DATADIR%%/docs/FUNCTION.set_Left_Dim0.html
-%%DATADIR%%/docs/FUNCTION.set_Left_Dim1.html
-%%DATADIR%%/docs/FUNCTION.set_Left_Position.html
-%%DATADIR%%/docs/FUNCTION.set_Long_Name.html
-%%DATADIR%%/docs/FUNCTION.set_Maximum_Distance.html
-%%DATADIR%%/docs/FUNCTION.set_Needle.html
-%%DATADIR%%/docs/FUNCTION.set_Option_Type.html
-%%DATADIR%%/docs/FUNCTION.set_Position.html
-%%DATADIR%%/docs/FUNCTION.set_Quality_Value.html
-%%DATADIR%%/docs/FUNCTION.set_Right_Diagonal.html
-%%DATADIR%%/docs/FUNCTION.set_Right_Dim0.html
-%%DATADIR%%/docs/FUNCTION.set_Right_Dim1.html
-%%DATADIR%%/docs/FUNCTION.set_Right_Position.html
-%%DATADIR%%/docs/FUNCTION.set_Score.html
-%%DATADIR%%/docs/FUNCTION.set_Score_Gap.html
-%%DATADIR%%/docs/FUNCTION.set_Score_Gap_Extend.html
-%%DATADIR%%/docs/FUNCTION.set_Score_Gap_Open.html
-%%DATADIR%%/docs/FUNCTION.set_Score_Limit.html
-%%DATADIR%%/docs/FUNCTION.set_Score_Match.html
-%%DATADIR%%/docs/FUNCTION.set_Score_Mismatch.html
-%%DATADIR%%/docs/FUNCTION.set_Scoring_Scheme.html
-%%DATADIR%%/docs/FUNCTION.set_Short_Name.html
-%%DATADIR%%/docs/FUNCTION.set_Source.html
-%%DATADIR%%/docs/FUNCTION.set_Step_Size.html
-%%DATADIR%%/docs/FUNCTION.set_Strings.html
-%%DATADIR%%/docs/FUNCTION.set_Value.html
-%%DATADIR%%/docs/FUNCTION.shape_To_String.html
-%%DATADIR%%/docs/FUNCTION.share_Resources.html
-%%DATADIR%%/docs/FUNCTION.short_Help.html
-%%DATADIR%%/docs/FUNCTION.short_Name.html
-%%DATADIR%%/docs/FUNCTION.shrink_To_Fit.html
-%%DATADIR%%/docs/FUNCTION.shuffle.html
-%%DATADIR%%/docs/FUNCTION.silent_Status.html
-%%DATADIR%%/docs/FUNCTION.size.html
-%%DATADIR%%/docs/FUNCTION.slow_Nj_Tree.html
-%%DATADIR%%/docs/FUNCTION.sort_Aligned_Reads.html
-%%DATADIR%%/docs/FUNCTION.source.html
-%%DATADIR%%/docs/FUNCTION.source_Begin.html
-%%DATADIR%%/docs/FUNCTION.source_End.html
-%%DATADIR%%/docs/FUNCTION.source_Length.html
-%%DATADIR%%/docs/FUNCTION.source_Segment.html
-%%DATADIR%%/docs/FUNCTION.source_Vertex.html
-%%DATADIR%%/docs/FUNCTION.split.html
-%%DATADIR%%/docs/FUNCTION.start_Diagonal.html
-%%DATADIR%%/docs/FUNCTION.string_Set.html
-%%DATADIR%%/docs/FUNCTION.string_Set_Limits.html
-%%DATADIR%%/docs/FUNCTION.string_To_Shape.html
-%%DATADIR%%/docs/FUNCTION.strongly_Connected_Components.html
-%%DATADIR%%/docs/FUNCTION.suffix.html
-%%DATADIR%%/docs/FUNCTION.sum.html
-%%DATADIR%%/docs/FUNCTION.sum_Of_Pairs_Score.html
-%%DATADIR%%/docs/FUNCTION.supremum_Value_Impl.html
-%%DATADIR%%/docs/FUNCTION.swap.html
-%%DATADIR%%/docs/FUNCTION.sys_Time.html
-%%DATADIR%%/docs/FUNCTION.target.html
-%%DATADIR%%/docs/FUNCTION.target_Vertex.html
-%%DATADIR%%/docs/FUNCTION.tell.html
-%%DATADIR%%/docs/FUNCTION.text_At.html
-%%DATADIR%%/docs/FUNCTION.to_C_String.html
-%%DATADIR%%/docs/FUNCTION.to_Lower.html
-%%DATADIR%%/docs/FUNCTION.to_Source_Position.html
-%%DATADIR%%/docs/FUNCTION.to_Upper.html
-%%DATADIR%%/docs/FUNCTION.to_View_Position.html
-%%DATADIR%%/docs/FUNCTION.topological_Sort.html
-%%DATADIR%%/docs/FUNCTION.transition_Probability.html
-%%DATADIR%%/docs/FUNCTION.transitive_Closure.html
-%%DATADIR%%/docs/FUNCTION.transpose.html
-%%DATADIR%%/docs/FUNCTION.triplet_Library_Extension.html
-%%DATADIR%%/docs/FUNCTION.unlock_And_Free_Contig.html
-%%DATADIR%%/docs/FUNCTION.unlock_And_Free_Contigs.html
-%%DATADIR%%/docs/FUNCTION.unlock_Contig.html
-%%DATADIR%%/docs/FUNCTION.unlock_Contigs.html
-%%DATADIR%%/docs/FUNCTION.upgma_Tree.html
-%%DATADIR%%/docs/FUNCTION.upper_Bound_Aligned_Reads.html
-%%DATADIR%%/docs/FUNCTION.value.html
-%%DATADIR%%/docs/FUNCTION.value_By_Id.html
-%%DATADIR%%/docs/FUNCTION.value_Construct.html
-%%DATADIR%%/docs/FUNCTION.value_Construct_Move.html
-%%DATADIR%%/docs/FUNCTION.value_Destruct.html
-%%DATADIR%%/docs/FUNCTION.variance.html
-%%DATADIR%%/docs/FUNCTION.version.html
-%%DATADIR%%/docs/FUNCTION.viterbi_Algorithm.html
-%%DATADIR%%/docs/FUNCTION.wait_For.html
-%%DATADIR%%/docs/FUNCTION.weight.html
-%%DATADIR%%/docs/FUNCTION.window_Find_Begin.html
-%%DATADIR%%/docs/FUNCTION.window_Find_End.html
-%%DATADIR%%/docs/FUNCTION.window_Find_Next.html
-%%DATADIR%%/docs/FUNCTION.write.html
-%%DATADIR%%/docs/FUNCTION.write_At.html
-%%DATADIR%%/docs/FUNCTION.write_Contigs.html
-%%DATADIR%%/docs/FUNCTION.zscore.html
-%%DATADIR%%/docs/FUNCTION_Allocator_23clear.html
-%%DATADIR%%/docs/FUNCTION_Automaton_23label.html
-%%DATADIR%%/docs/FUNCTION_Blast_23get_Blast_Match_Score.html
-%%DATADIR%%/docs/FUNCTION_Fileformat_23read.html
-%%DATADIR%%/docs/FUNCTION_Fileformat_23write.html
-%%DATADIR%%/docs/FUNCTION_Graph_23assign_Source.html
-%%DATADIR%%/docs/FUNCTION_Graph_23is_Leaf.html
-%%DATADIR%%/docs/FUNCTION_Graph_23is_Root.html
-%%DATADIR%%/docs/FUNCTION_Index_23is_Leaf.html
-%%DATADIR%%/docs/FUNCTION_Pipelining_23front.html
-%%DATADIR%%/docs/FUNCTION_Priority_Type_23pop.html
-%%DATADIR%%/docs/FUNCTION_Priority_Type_23push.html
-%%DATADIR%%/docs/FUNCTION_Priority_Type_23top.html
-%%DATADIR%%/docs/INDEXPAGE_Adaption.html
-%%DATADIR%%/docs/INDEXPAGE_Class.html
-%%DATADIR%%/docs/INDEXPAGE_Concept.html
-%%DATADIR%%/docs/INDEXPAGE_Demo.html
-%%DATADIR%%/docs/INDEXPAGE_Function.html
-%%DATADIR%%/docs/INDEXPAGE_Metafunction.html
-%%DATADIR%%/docs/INDEXPAGE_Shortcut.html
-%%DATADIR%%/docs/INDEXPAGE_Spec.html
-%%DATADIR%%/docs/INDEXPAGE_Tag.html
-%%DATADIR%%/docs/INDEX_Adaption.html
-%%DATADIR%%/docs/INDEX_Class.html
-%%DATADIR%%/docs/INDEX_Class_Aggregates.html
-%%DATADIR%%/docs/INDEX_Class_Alignments.html
-%%DATADIR%%/docs/INDEX_Class_Basic.html
-%%DATADIR%%/docs/INDEX_Class_Blast.html
-%%DATADIR%%/docs/INDEX_Class_Fragment+_Store.html
-%%DATADIR%%/docs/INDEX_Class_Graph.html
-%%DATADIR%%/docs/INDEX_Class_Index.html
-%%DATADIR%%/docs/INDEX_Class_Input_2f_Output.html
-%%DATADIR%%/docs/INDEX_Class_Map.html
-%%DATADIR%%/docs/INDEX_Class_Markov_Model.html
-%%DATADIR%%/docs/INDEX_Class_Miscellaneous.html
-%%DATADIR%%/docs/INDEX_Class_Modifier.html
-%%DATADIR%%/docs/INDEX_Class_Motif+_Search.html
-%%DATADIR%%/docs/INDEX_Class_Pipelining.html
-%%DATADIR%%/docs/INDEX_Class_Random.html
-%%DATADIR%%/docs/INDEX_Class_Searching.html
-%%DATADIR%%/docs/INDEX_Class_Seed+_Handling.html
-%%DATADIR%%/docs/INDEX_Class_Sequences.html
-%%DATADIR%%/docs/INDEX_Concept.html
-%%DATADIR%%/docs/INDEX_Demo.html
-%%DATADIR%%/docs/INDEX_Demo_Basics.html
-%%DATADIR%%/docs/INDEX_Demo_Graph.html
-%%DATADIR%%/docs/INDEX_Demo_Index.html
-%%DATADIR%%/docs/INDEX_Demo_Miscellaneous.html
-%%DATADIR%%/docs/INDEX_Demo_Modifier.html
-%%DATADIR%%/docs/INDEX_Demo_Motif+_Search.html
-%%DATADIR%%/docs/INDEX_Demo_Searching.html
-%%DATADIR%%/docs/INDEX_Demo_System.html
-%%DATADIR%%/docs/INDEX_Function.html
-%%DATADIR%%/docs/INDEX_Function.sequences.html
-%%DATADIR%%/docs/INDEX_Function_Alignments.html
-%%DATADIR%%/docs/INDEX_Function_Alphabets.html
-%%DATADIR%%/docs/INDEX_Function_Array+_Handling.html
-%%DATADIR%%/docs/INDEX_Function_Atomic+_Operations.html
-%%DATADIR%%/docs/INDEX_Function_Blast.html
-%%DATADIR%%/docs/INDEX_Function_Chaining.html
-%%DATADIR%%/docs/INDEX_Function_Class._Align.html
-%%DATADIR%%/docs/INDEX_Function_Class.html
-%%DATADIR%%/docs/INDEX_Function_Comparisons.html
-%%DATADIR%%/docs/INDEX_Function_Containers.html
-%%DATADIR%%/docs/INDEX_Function_Content+_Manipulation.html
-%%DATADIR%%/docs/INDEX_Function_Dependent+_Objects.html
-%%DATADIR%%/docs/INDEX_Function_Fragment+_Store.html
-%%DATADIR%%/docs/INDEX_Function_Graph.html
-%%DATADIR%%/docs/INDEX_Function_Index.html
-%%DATADIR%%/docs/INDEX_Function_Input_2f_Output.html
-%%DATADIR%%/docs/INDEX_Function_Iteration.html
-%%DATADIR%%/docs/INDEX_Function_Map.html
-%%DATADIR%%/docs/INDEX_Function_Memory.html
-%%DATADIR%%/docs/INDEX_Function_Misc.html
-%%DATADIR%%/docs/INDEX_Function_Miscellaneous.html
-%%DATADIR%%/docs/INDEX_Function_Miscellaneous_3a.html
-%%DATADIR%%/docs/INDEX_Function_Modifier.html
-%%DATADIR%%/docs/INDEX_Function_Modifiers.html
-%%DATADIR%%/docs/INDEX_Function_Motif+_Search.html
-%%DATADIR%%/docs/INDEX_Function_Pipelining.html
-%%DATADIR%%/docs/INDEX_Function_Random.html
-%%DATADIR%%/docs/INDEX_Function_Scoring.html
-%%DATADIR%%/docs/INDEX_Function_Searching.html
-%%DATADIR%%/docs/INDEX_Function_Seed+_Handling.html
-%%DATADIR%%/docs/INDEX_Function_Sequences.html
-%%DATADIR%%/docs/INDEX_Metafunction.html
-%%DATADIR%%/docs/INDEX_Metafunction_Basic.html
-%%DATADIR%%/docs/INDEX_Metafunction_Index.html
-%%DATADIR%%/docs/INDEX_Metafunction_Map.html
-%%DATADIR%%/docs/INDEX_Metafunction_Miscellaneous.html
-%%DATADIR%%/docs/INDEX_Metafunction_Searching.html
-%%DATADIR%%/docs/INDEX_Metafunction_Sequences.html
-%%DATADIR%%/docs/INDEX_Page.html
-%%DATADIR%%/docs/INDEX_Shortcut.html
-%%DATADIR%%/docs/INDEX_Shortcut_Input_2f_Output.html
-%%DATADIR%%/docs/INDEX_Shortcut_Iterators.html
-%%DATADIR%%/docs/INDEX_Shortcut_Modifier.html
-%%DATADIR%%/docs/INDEX_Shortcut_Pattern+_Matching.html
-%%DATADIR%%/docs/INDEX_Shortcut_Scoring.html
-%%DATADIR%%/docs/INDEX_Shortcut_Strings.html
-%%DATADIR%%/docs/INDEX_Spec.html
-%%DATADIR%%/docs/INDEX_Spec_Aggregates.html
-%%DATADIR%%/docs/INDEX_Spec_Alignments.html
-%%DATADIR%%/docs/INDEX_Spec_Allocators.html
-%%DATADIR%%/docs/INDEX_Spec_Alphabets.html
-%%DATADIR%%/docs/INDEX_Spec_Blast.html
-%%DATADIR%%/docs/INDEX_Spec_Chaining.html
-%%DATADIR%%/docs/INDEX_Spec_Files.html
-%%DATADIR%%/docs/INDEX_Spec_Graph.html
-%%DATADIR%%/docs/INDEX_Spec_Holders.html
-%%DATADIR%%/docs/INDEX_Spec_Index.html
-%%DATADIR%%/docs/INDEX_Spec_Iterators.html
-%%DATADIR%%/docs/INDEX_Spec_Map.html
-%%DATADIR%%/docs/INDEX_Spec_Miscellaneous.html
-%%DATADIR%%/docs/INDEX_Spec_Modifier.html
-%%DATADIR%%/docs/INDEX_Spec_Motif+_Search.html
-%%DATADIR%%/docs/INDEX_Spec_Pattern+_Matching.html
-%%DATADIR%%/docs/INDEX_Spec_Pipelining.html
-%%DATADIR%%/docs/INDEX_Spec_Proxies.html
-%%DATADIR%%/docs/INDEX_Spec_Random.html
-%%DATADIR%%/docs/INDEX_Spec_Scoring.html
-%%DATADIR%%/docs/INDEX_Spec_Searching.html
-%%DATADIR%%/docs/INDEX_Spec_Seed+_Handling.html
-%%DATADIR%%/docs/INDEX_Spec_Segments.html
-%%DATADIR%%/docs/INDEX_Spec_Sequences.html
-%%DATADIR%%/docs/INDEX_Spec_Strings.html
-%%DATADIR%%/docs/INDEX_Tag.html
-%%DATADIR%%/docs/INDEX_Tag_Fragment+_Store.html
-%%DATADIR%%/docs/INDEX_Tag_Index.html
-%%DATADIR%%/docs/INDEX_Tag_Miscellaneous.html
-%%DATADIR%%/docs/INDEX_Tag_Motif+_Search.html
-%%DATADIR%%/docs/INDEX_Tag_Random.html
-%%DATADIR%%/docs/INDEX_Tag_Scoring.html
-%%DATADIR%%/docs/INDEX_Tag_Searching.html
-%%DATADIR%%/docs/INDEX_Tag_Seed+_Handling.html
-%%DATADIR%%/docs/INDEX_Tag_Strings.html
-%%DATADIR%%/docs/MEMFUNC.~_Holder.html
-%%DATADIR%%/docs/MEMFUNC_Adaptor_Iterator_23_Iter.html
-%%DATADIR%%/docs/MEMFUNC_Align_Quality_Store_Element_23_Align_Quality_Store_Element.html
-%%DATADIR%%/docs/MEMFUNC_Aligned_Read_Store_Element_23_Aligned_Read_Store_Element.html
-%%DATADIR%%/docs/MEMFUNC_Bottom_Up+_Iterator_23_Iterator.html
-%%DATADIR%%/docs/MEMFUNC_Chained_Seed_23_Seed.html
-%%DATADIR%%/docs/MEMFUNC_Command_Line_Option_23_Command_Line_Option.html
-%%DATADIR%%/docs/MEMFUNC_Command_Line_Parser_23_Command_Line_Parser.html
-%%DATADIR%%/docs/MEMFUNC_Concat_Virtual+_Iterator_23_Iter.html
-%%DATADIR%%/docs/MEMFUNC_Concatenator_Many_To_One_23_Concatenator_Many_To_One.html
-%%DATADIR%%/docs/MEMFUNC_Contig_Store_Element_23_Contig_Store_Element.html
-%%DATADIR%%/docs/MEMFUNC_Ext_String_23_String.html
-%%DATADIR%%/docs/MEMFUNC_Filter_23_Pipe.html
-%%DATADIR%%/docs/MEMFUNC_Finder_23_Finder.html
-%%DATADIR%%/docs/MEMFUNC_Fragment_23_Fragment.html
-%%DATADIR%%/docs/MEMFUNC_Gap_Anchor_23_Gap_Anchor.html
-%%DATADIR%%/docs/MEMFUNC_Gaps_23_Gaps.html
-%%DATADIR%%/docs/MEMFUNC_Generic_Shape_23_Shape.html
-%%DATADIR%%/docs/MEMFUNC_Geometric+_Pdf_23_Pdf.html
-%%DATADIR%%/docs/MEMFUNC_Holder.html
-%%DATADIR%%/docs/MEMFUNC_Infix_Segment_23_Segment.html
-%%DATADIR%%/docs/MEMFUNC_Interval_And_Cargo_23_Interval_And_Cargo.html
-%%DATADIR%%/docs/MEMFUNC_Interval_Tree_23_Interval_Tree.html
-%%DATADIR%%/docs/MEMFUNC_Interval_Tree_Node_23_Interval_Tree_Node.html
-%%DATADIR%%/docs/MEMFUNC_Library_Store_Element_23_Library_Store_Element.html
-%%DATADIR%%/docs/MEMFUNC_Local_Alignment_Finder_23_Local_Alignment_Finder.html
-%%DATADIR%%/docs/MEMFUNC_Log-_Normal+_Pdf_23_Pdf.html
-%%DATADIR%%/docs/MEMFUNC_Markov_Model_23_Markov_Model.html
-%%DATADIR%%/docs/MEMFUNC_Markov_Model_23build.html
-%%DATADIR%%/docs/MEMFUNC_Markov_Model_23emitted_Probability.html
-%%DATADIR%%/docs/MEMFUNC_Markov_Model_23read.html
-%%DATADIR%%/docs/MEMFUNC_Markov_Model_23set.html
-%%DATADIR%%/docs/MEMFUNC_Markov_Model_23write.html
-%%DATADIR%%/docs/MEMFUNC_Mate_Pair_Store_Element_23_Mate_Pair_Store_Element.html
-%%DATADIR%%/docs/MEMFUNC_Max_Repeats+_Iterator_23_Iterator.html
-%%DATADIR%%/docs/MEMFUNC_Mersenne+_Twister+_Rng_23_Rng.html
-%%DATADIR%%/docs/MEMFUNC_Multi_Mems+_Iterator_23_Iterator.html
-%%DATADIR%%/docs/MEMFUNC_Mums+_Iterator_23_Iterator.html
-%%DATADIR%%/docs/MEMFUNC_Namer_23_Pipe.html
-%%DATADIR%%/docs/MEMFUNC_Normal+_Pdf_23_Pdf.html
-%%DATADIR%%/docs/MEMFUNC_One_Gapped_Shape_23_Shape.html
-%%DATADIR%%/docs/MEMFUNC_Pair_23_Pair.html
-%%DATADIR%%/docs/MEMFUNC_Pipe_23_Pipe.html
-%%DATADIR%%/docs/MEMFUNC_Point_And_Cargo_23_Point_And_Cargo.html
-%%DATADIR%%/docs/MEMFUNC_Position_Iterator_23_Iter.html
-%%DATADIR%%/docs/MEMFUNC_Prefix_Segment_23_Segment.html
-%%DATADIR%%/docs/MEMFUNC_Read_Store_Element_23_Read_Store_Element.html
-%%DATADIR%%/docs/MEMFUNC_Rng+_Functor_23_Rng.html
-%%DATADIR%%/docs/MEMFUNC_Rng_23operator_28_29.html
-%%DATADIR%%/docs/MEMFUNC_Score+_Matrix_23_Score.html
-%%DATADIR%%/docs/MEMFUNC_Score_23_Score.html
-%%DATADIR%%/docs/MEMFUNC_Seed_Set_23_Seed_Set.html
-%%DATADIR%%/docs/MEMFUNC_Shape_23_Shape.html
-%%DATADIR%%/docs/MEMFUNC_Simple_Seed_23_Seed.html
-%%DATADIR%%/docs/MEMFUNC_Simple_Shape_23_Shape.html
-%%DATADIR%%/docs/MEMFUNC_Suffix_Segment_23_Segment.html
-%%DATADIR%%/docs/MEMFUNC_Super_Max_Repeats+_Iterator_23_Iterator.html
-%%DATADIR%%/docs/MEMFUNC_Super_Max_Repeats_Fast+_Iterator_23_Iterator.html
-%%DATADIR%%/docs/MEMFUNC_To_Std_Allocator.html
-%%DATADIR%%/docs/MEMFUNC_Top_Down+_Iterator_23_Iterator.html
-%%DATADIR%%/docs/MEMFUNC_Top_Down_History+_Iterator_23_Iterator.html
-%%DATADIR%%/docs/MEMFUNC_Triple_23_Triple.html
-%%DATADIR%%/docs/MEMVAR_Align_Quality_Store_Element_23errors.html
-%%DATADIR%%/docs/MEMVAR_Align_Quality_Store_Element_23pair_Score.html
-%%DATADIR%%/docs/MEMVAR_Align_Quality_Store_Element_23score.html
-%%DATADIR%%/docs/MEMVAR_Aligned_Read_Layout_23contig_Rows.html
-%%DATADIR%%/docs/MEMVAR_Aligned_Read_Store_Element_23_I_N_V_A_L_I_D___I_D.html
-%%DATADIR%%/docs/MEMVAR_Aligned_Read_Store_Element_23begin_Pos.html
-%%DATADIR%%/docs/MEMVAR_Aligned_Read_Store_Element_23contig_Id.html
-%%DATADIR%%/docs/MEMVAR_Aligned_Read_Store_Element_23end_Pos.html
-%%DATADIR%%/docs/MEMVAR_Aligned_Read_Store_Element_23gaps.html
-%%DATADIR%%/docs/MEMVAR_Aligned_Read_Store_Element_23id.html
-%%DATADIR%%/docs/MEMVAR_Aligned_Read_Store_Element_23pair_Match_Id.html
-%%DATADIR%%/docs/MEMVAR_Aligned_Read_Store_Element_23read_Id.html
-%%DATADIR%%/docs/MEMVAR_Bundle2_23in1.html
-%%DATADIR%%/docs/MEMVAR_Bundle2_23in2.html
-%%DATADIR%%/docs/MEMVAR_Bundle3_23in1.html
-%%DATADIR%%/docs/MEMVAR_Bundle3_23in2.html
-%%DATADIR%%/docs/MEMVAR_Bundle3_23in3.html
-%%DATADIR%%/docs/MEMVAR_Bundle5_23in1.html
-%%DATADIR%%/docs/MEMVAR_Bundle5_23in2.html
-%%DATADIR%%/docs/MEMVAR_Bundle5_23in3.html
-%%DATADIR%%/docs/MEMVAR_Bundle5_23in4.html
-%%DATADIR%%/docs/MEMVAR_Bundle5_23in5.html
-%%DATADIR%%/docs/MEMVAR_Concat_Direct_23concat.html
-%%DATADIR%%/docs/MEMVAR_Contig_File_23file_Name.html
-%%DATADIR%%/docs/MEMVAR_Contig_File_23first_Contig_Id.html
-%%DATADIR%%/docs/MEMVAR_Contig_File_23format.html
-%%DATADIR%%/docs/MEMVAR_Contig_Store_Element_23_I_N_V_A_L_I_D___I_D.html
-%%DATADIR%%/docs/MEMVAR_Contig_Store_Element_23file_Begin_Pos.html
-%%DATADIR%%/docs/MEMVAR_Contig_Store_Element_23file_End_Pos.html
-%%DATADIR%%/docs/MEMVAR_Contig_Store_Element_23file_Id.html
-%%DATADIR%%/docs/MEMVAR_Contig_Store_Element_23gaps.html
-%%DATADIR%%/docs/MEMVAR_Contig_Store_Element_23seq.html
-%%DATADIR%%/docs/MEMVAR_Contig_Store_Element_23usage.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23align_Quality_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23aligned_Read_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23aligned_Read_Tag_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23annotation_Name_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23annotation_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23contig_File_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23contig_Name_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23contig_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23library_Name_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23library_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23mate_Pair_Name_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23mate_Pair_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23read_Name_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23read_Seq_Store.html
-%%DATADIR%%/docs/MEMVAR_Fragment_Store_23read_Store.html
-%%DATADIR%%/docs/MEMVAR_Gap_Anchor_23gap_Pos.html
-%%DATADIR%%/docs/MEMVAR_Gap_Anchor_23seq_Pos.html
-%%DATADIR%%/docs/MEMVAR_Interval_And_Cargo_23cargo.html
-%%DATADIR%%/docs/MEMVAR_Interval_And_Cargo_23i1.html
-%%DATADIR%%/docs/MEMVAR_Interval_And_Cargo_23i2.html
-%%DATADIR%%/docs/MEMVAR_Interval_Tree_Node_23center.html
-%%DATADIR%%/docs/MEMVAR_Interval_Tree_Node_23list1.html
-%%DATADIR%%/docs/MEMVAR_Interval_Tree_Node_23list2.html
-%%DATADIR%%/docs/MEMVAR_Library_Store_Element_23mean.html
-%%DATADIR%%/docs/MEMVAR_Library_Store_Element_23std.html
-%%DATADIR%%/docs/MEMVAR_Markov_Model_23order.html
-%%DATADIR%%/docs/MEMVAR_Markov_Model_23stationary_Distribution.html
-%%DATADIR%%/docs/MEMVAR_Markov_Model_23transition.html
-%%DATADIR%%/docs/MEMVAR_Mate_Pair_Store_Element_23_I_N_V_A_L_I_D___I_D.html
-%%DATADIR%%/docs/MEMVAR_Mate_Pair_Store_Element_23lib_Id.html
-%%DATADIR%%/docs/MEMVAR_Mate_Pair_Store_Element_23read_Id[2].html
-%%DATADIR%%/docs/MEMVAR_Name_Store_Cache_23_Name_Store_Cache.html
-%%DATADIR%%/docs/MEMVAR_Open_Addressing_23alpha.html
-%%DATADIR%%/docs/MEMVAR_Pair_23i1.html
-%%DATADIR%%/docs/MEMVAR_Pair_23i2.html
-%%DATADIR%%/docs/MEMVAR_Point_And_Cargo_23cargo.html
-%%DATADIR%%/docs/MEMVAR_Point_And_Cargo_23point.html
-%%DATADIR%%/docs/MEMVAR_Read_Store_Element_23_I_N_V_A_L_I_D___I_D.html
-%%DATADIR%%/docs/MEMVAR_Read_Store_Element_23mate_Pair_Id.html
-%%DATADIR%%/docs/MEMVAR_Tag_Selector_23tag_Id.html
-%%DATADIR%%/docs/MEMVAR_Triple_23i1.html
-%%DATADIR%%/docs/MEMVAR_Triple_23i2.html
-%%DATADIR%%/docs/MEMVAR_Triple_23i3.html
-%%DATADIR%%/docs/METAFUNCTION_Allows_Fast_Random_Access.html
-%%DATADIR%%/docs/METAFUNCTION_Alphabet.html
-%%DATADIR%%/docs/METAFUNCTION_Bits_Per_Value.html
-%%DATADIR%%/docs/METAFUNCTION_Bytes_Per_Value.html
-%%DATADIR%%/docs/METAFUNCTION_Cargo.html
-%%DATADIR%%/docs/METAFUNCTION_Col.html
-%%DATADIR%%/docs/METAFUNCTION_Cols.html
-%%DATADIR%%/docs/METAFUNCTION_Comparator.html
-%%DATADIR%%/docs/METAFUNCTION_Compare_Type.html
-%%DATADIR%%/docs/METAFUNCTION_Concatenator.html
-%%DATADIR%%/docs/METAFUNCTION_Container.html
-%%DATADIR%%/docs/METAFUNCTION_Convert.html
-%%DATADIR%%/docs/METAFUNCTION_Deepest_Spec.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Find_Begin_Pattern_Spec.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Finder.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Get_Iterator_Spec.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Index_Creator.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Index_Spec.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Index_String_Spec.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Iterator_Spec.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Overflow_Explicit.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Overflow_Implicit.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Pattern.html
-%%DATADIR%%/docs/METAFUNCTION_Default_Prefix_Order.html
-%%DATADIR%%/docs/METAFUNCTION_Difference.html
-%%DATADIR%%/docs/METAFUNCTION_Edge_Descriptor.html
-%%DATADIR%%/docs/METAFUNCTION_Edge_Id_Handler.html
-%%DATADIR%%/docs/METAFUNCTION_Edge_Type.html
-%%DATADIR%%/docs/METAFUNCTION_Fibre.html
-%%DATADIR%%/docs/METAFUNCTION_Gapped_Value_Type.html
-%%DATADIR%%/docs/METAFUNCTION_Get_Source.html
-%%DATADIR%%/docs/METAFUNCTION_Get_V_S_Tree_Iterator_Traits.html
-%%DATADIR%%/docs/METAFUNCTION_Get_Value.html
-%%DATADIR%%/docs/METAFUNCTION_Haystack.html
-%%DATADIR%%/docs/METAFUNCTION_Hit.html
-%%DATADIR%%/docs/METAFUNCTION_Host.html
-%%DATADIR%%/docs/METAFUNCTION_Hsp.html
-%%DATADIR%%/docs/METAFUNCTION_Id.html
-%%DATADIR%%/docs/METAFUNCTION_Infix.html
-%%DATADIR%%/docs/METAFUNCTION_Insertion_Buffer.html
-%%DATADIR%%/docs/METAFUNCTION_Integral_For_Value.html
-%%DATADIR%%/docs/METAFUNCTION_Is_Contiguous.html
-%%DATADIR%%/docs/METAFUNCTION_Is_Integral.html
-%%DATADIR%%/docs/METAFUNCTION_Is_Sequence.html
-%%DATADIR%%/docs/METAFUNCTION_Is_Simple.html
-%%DATADIR%%/docs/METAFUNCTION_Iter_Complement_Const.html
-%%DATADIR%%/docs/METAFUNCTION_Iter_Make_Const.html
-%%DATADIR%%/docs/METAFUNCTION_Iterator.html
-%%DATADIR%%/docs/METAFUNCTION_Journal_Type.html
-%%DATADIR%%/docs/METAFUNCTION_Key.html
-%%DATADIR%%/docs/METAFUNCTION_L_E_N_G_T_H.html
-%%DATADIR%%/docs/METAFUNCTION_List_Type.html
-%%DATADIR%%/docs/METAFUNCTION_Map_Value.html
-%%DATADIR%%/docs/METAFUNCTION_Max_Value.html
-%%DATADIR%%/docs/METAFUNCTION_Min_Value.html
-%%DATADIR%%/docs/METAFUNCTION_Motif.html
-%%DATADIR%%/docs/METAFUNCTION_Needle.html
-%%DATADIR%%/docs/METAFUNCTION_Pex_Multi_Finder.html
-%%DATADIR%%/docs/METAFUNCTION_Position.html
-%%DATADIR%%/docs/METAFUNCTION_Prefix.html
-%%DATADIR%%/docs/METAFUNCTION_Reference.html
-%%DATADIR%%/docs/METAFUNCTION_Row.html
-%%DATADIR%%/docs/METAFUNCTION_Rows.html
-%%DATADIR%%/docs/METAFUNCTION_S_A_Value.html
-%%DATADIR%%/docs/METAFUNCTION_Scoring_Scheme.html
-%%DATADIR%%/docs/METAFUNCTION_Size.html
-%%DATADIR%%/docs/METAFUNCTION_Source.html
-%%DATADIR%%/docs/METAFUNCTION_Spec.html
-%%DATADIR%%/docs/METAFUNCTION_Std_Container_Iterator.html
-%%DATADIR%%/docs/METAFUNCTION_String_Set_Type.html
-%%DATADIR%%/docs/METAFUNCTION_Suffix.html
-%%DATADIR%%/docs/METAFUNCTION_Value.html
-%%DATADIR%%/docs/METAFUNCTION_Value_Size.html
-%%DATADIR%%/docs/METAFUNCTION_Vertex_Descriptor.html
-%%DATADIR%%/docs/METAFUNCTION_Vertex_Id_Handler.html
-%%DATADIR%%/docs/METAFUNCTION_W_E_I_G_H_T.html
-%%DATADIR%%/docs/METAFUNCTION_Weight.html
-%%DATADIR%%/docs/PAGE.dddoc.html
-%%DATADIR%%/docs/PAGE_Glossary.html
-%%DATADIR%%/docs/SHORTCUT_Blosum30.html
-%%DATADIR%%/docs/SHORTCUT_Blosum45.html
-%%DATADIR%%/docs/SHORTCUT_Blosum62.html
-%%DATADIR%%/docs/SHORTCUT_Blosum80.html
-%%DATADIR%%/docs/SHORTCUT_Char_Iterator.html
-%%DATADIR%%/docs/SHORTCUT_Char_String.html
-%%DATADIR%%/docs/SHORTCUT_Dna5_Iterator.html
-%%DATADIR%%/docs/SHORTCUT_Dna5_String.html
-%%DATADIR%%/docs/SHORTCUT_Dna5_String_Complement.html
-%%DATADIR%%/docs/SHORTCUT_Dna5_String_Reverse.html
-%%DATADIR%%/docs/SHORTCUT_Dna5_String_Reverse_Complement.html
-%%DATADIR%%/docs/SHORTCUT_Dna_Iterator.html
-%%DATADIR%%/docs/SHORTCUT_Dna_String.html
-%%DATADIR%%/docs/SHORTCUT_Dna_String_Complement.html
-%%DATADIR%%/docs/SHORTCUT_Dna_String_Reverse.html
-%%DATADIR%%/docs/SHORTCUT_Dna_String_Reverse_Complement.html
-%%DATADIR%%/docs/SHORTCUT_Edit_Distance_Score.html
-%%DATADIR%%/docs/SHORTCUT_Iupac_Iterator.html
-%%DATADIR%%/docs/SHORTCUT_Iupac_String.html
-%%DATADIR%%/docs/SHORTCUT_Mod_Complement_Dna.html
-%%DATADIR%%/docs/SHORTCUT_Mod_Complement_Dna5.html
-%%DATADIR%%/docs/SHORTCUT_Mod_Complement_Rna.html
-%%DATADIR%%/docs/SHORTCUT_Mod_Complement_Rna5.html
-%%DATADIR%%/docs/SHORTCUT_Multi_Fasta.html
-%%DATADIR%%/docs/SHORTCUT_Multi_Seq_File.html
-%%DATADIR%%/docs/SHORTCUT_Myers_Ukkonen.html
-%%DATADIR%%/docs/SHORTCUT_Myers_Ukkonen_Banded.html
-%%DATADIR%%/docs/SHORTCUT_Myers_Ukkonen_Global.html
-%%DATADIR%%/docs/SHORTCUT_Myers_Ukkonen_Global_Banded.html
-%%DATADIR%%/docs/SHORTCUT_Pam120.html
-%%DATADIR%%/docs/SHORTCUT_Pam200.html
-%%DATADIR%%/docs/SHORTCUT_Pam250.html
-%%DATADIR%%/docs/SHORTCUT_Pam40.html
-%%DATADIR%%/docs/SHORTCUT_Peptide.html
-%%DATADIR%%/docs/SHORTCUT_Peptide_Iterator.html
-%%DATADIR%%/docs/SHORTCUT_Rna5_Iterator.html
-%%DATADIR%%/docs/SHORTCUT_Rna5_String.html
-%%DATADIR%%/docs/SHORTCUT_Rna5_String_Complement.html
-%%DATADIR%%/docs/SHORTCUT_Rna5_String_Reverse.html
-%%DATADIR%%/docs/SHORTCUT_Rna5_String_Reverse_Complement.html
-%%DATADIR%%/docs/SHORTCUT_Rna_Iterator.html
-%%DATADIR%%/docs/SHORTCUT_Rna_String.html
-%%DATADIR%%/docs/SHORTCUT_Rna_String_Complement.html
-%%DATADIR%%/docs/SHORTCUT_Rna_String_Reverse.html
-%%DATADIR%%/docs/SHORTCUT_Rna_String_Reverse_Complement.html
-%%DATADIR%%/docs/SHORTCUT_Simple_Score.html
-%%DATADIR%%/docs/SHORTCUT_Unicode_Iterator.html
-%%DATADIR%%/docs/SHORTCUT_Unicode_String.html
-%%DATADIR%%/docs/SHORTCUT_Vtml200.html
-%%DATADIR%%/docs/SPEC_Abndm_Algo.html
-%%DATADIR%%/docs/SPEC_Adaptor+_Iterator.html
-%%DATADIR%%/docs/SPEC_Adjacency+_Iterator.html
-%%DATADIR%%/docs/SPEC_Aho_Corasick.html
-%%DATADIR%%/docs/SPEC_Align_Col_Iterator.html
-%%DATADIR%%/docs/SPEC_Alignment+_Graph.html
-%%DATADIR%%/docs/SPEC_Alloc+_String.html
-%%DATADIR%%/docs/SPEC_Alphabet+_Expansion.html
-%%DATADIR%%/docs/SPEC_Amino_Acid.html
-%%DATADIR%%/docs/SPEC_Anchor_Gaps.html
-%%DATADIR%%/docs/SPEC_Array+_String.html
-%%DATADIR%%/docs/SPEC_Array_Gaps.html
-%%DATADIR%%/docs/SPEC_Async.html
-%%DATADIR%%/docs/SPEC_Automaton.html
-%%DATADIR%%/docs/SPEC_Basic_Info.html
-%%DATADIR%%/docs/SPEC_Bfam.html
-%%DATADIR%%/docs/SPEC_Bfam_3c_Oracle_3e.html
-%%DATADIR%%/docs/SPEC_Bfam_3c_Trie_3e.html
-%%DATADIR%%/docs/SPEC_Bfs+_Iterator.html
-%%DATADIR%%/docs/SPEC_Bit+_Compressed+_Pair.html
-%%DATADIR%%/docs/SPEC_Bit+_Packed+_Tuple.html
-%%DATADIR%%/docs/SPEC_Blast_N.html
-%%DATADIR%%/docs/SPEC_Blast_P.html
-%%DATADIR%%/docs/SPEC_Block+_String.html
-%%DATADIR%%/docs/SPEC_Bndm_Algo.html
-%%DATADIR%%/docs/SPEC_Bottom_Up+_Iterator.html
-%%DATADIR%%/docs/SPEC_C_Mode.html
-%%DATADIR%%/docs/SPEC_C_Style+_String.html
-%%DATADIR%%/docs/SPEC_Caster.html
-%%DATADIR%%/docs/SPEC_Chained.html
-%%DATADIR%%/docs/SPEC_Chained_Seed.html
-%%DATADIR%%/docs/SPEC_Chunk+_Pool+_Allocator.html
-%%DATADIR%%/docs/SPEC_Concat_Direct.html
-%%DATADIR%%/docs/SPEC_Concat_Virtual+_Iterator.html
-%%DATADIR%%/docs/SPEC_Counter.html
-%%DATADIR%%/docs/SPEC_Counting+_Id_Manager.html
-%%DATADIR%%/docs/SPEC_D_P_Search.html
-%%DATADIR%%/docs/SPEC_Dependent.html
-%%DATADIR%%/docs/SPEC_Dfs+_Preorder+_Iterator.html
-%%DATADIR%%/docs/SPEC_Directed+_Graph.html
-%%DATADIR%%/docs/SPEC_Dna.html
-%%DATADIR%%/docs/SPEC_Dna5.html
-%%DATADIR%%/docs/SPEC_Dna5_Q.html
-%%DATADIR%%/docs/SPEC_Dna_Q.html
-%%DATADIR%%/docs/SPEC_E_Pattern_Branching.html
-%%DATADIR%%/docs/SPEC_Echoer.html
-%%DATADIR%%/docs/SPEC_Edge+_Iterator.html
-%%DATADIR%%/docs/SPEC_Edit_Distance.html
-%%DATADIR%%/docs/SPEC_Edit_Environment.html
-%%DATADIR%%/docs/SPEC_Exact_Fragment.html
-%%DATADIR%%/docs/SPEC_Exact_Reversable_Fragment.html
-%%DATADIR%%/docs/SPEC_External+_String.html
-%%DATADIR%%/docs/SPEC_File+_Reader+_String.html
-%%DATADIR%%/docs/SPEC_Filter.html
-%%DATADIR%%/docs/SPEC_Finite.html
-%%DATADIR%%/docs/SPEC_Full_Info.html
-%%DATADIR%%/docs/SPEC_Gapped_Shape.html
-%%DATADIR%%/docs/SPEC_Generic_Shape.html
-%%DATADIR%%/docs/SPEC_Geometric+_Pdf.html
-%%DATADIR%%/docs/SPEC_Hamming_Simple_Finder.html
-%%DATADIR%%/docs/SPEC_Hierarchical.html
-%%DATADIR%%/docs/SPEC_Hit_Iterator.html
-%%DATADIR%%/docs/SPEC_Hmm.html
-%%DATADIR%%/docs/SPEC_Horspool.html
-%%DATADIR%%/docs/SPEC_Hsp_Iterator.html
-%%DATADIR%%/docs/SPEC_Index_Dfi.html
-%%DATADIR%%/docs/SPEC_Index_Esa.html
-%%DATADIR%%/docs/SPEC_Index_Q_Gram.html
-%%DATADIR%%/docs/SPEC_Index_Wotd.html
-%%DATADIR%%/docs/SPEC_Infix_Segment.html
-%%DATADIR%%/docs/SPEC_Interval+_Tree+_Node.html
-%%DATADIR%%/docs/SPEC_Iterator+_Proxy.html
-%%DATADIR%%/docs/SPEC_Iupac.html
-%%DATADIR%%/docs/SPEC_Joiner.html
-%%DATADIR%%/docs/SPEC_Journaled+_String.html
-%%DATADIR%%/docs/SPEC_Log-_Normal+_Pdf.html
-%%DATADIR%%/docs/SPEC_M_Map+_String.html
-%%DATADIR%%/docs/SPEC_Mapper_Config.html
-%%DATADIR%%/docs/SPEC_Mapper_Config_Size.html
-%%DATADIR%%/docs/SPEC_Mapper_Spec.html
-%%DATADIR%%/docs/SPEC_Max_Repeats+_Iterator.html
-%%DATADIR%%/docs/SPEC_Memory_Manager_Index.html
-%%DATADIR%%/docs/SPEC_Memory_Manager_Pointer.html
-%%DATADIR%%/docs/SPEC_Mersenne+_Twister+_Rng.html
-%%DATADIR%%/docs/SPEC_Mod_Reverse.html
-%%DATADIR%%/docs/SPEC_Mod_View.html
-%%DATADIR%%/docs/SPEC_Multi+_Pool+_Allocator.html
-%%DATADIR%%/docs/SPEC_Multi_Bfam.html
-%%DATADIR%%/docs/SPEC_Multi_Bfam_3c_Oracle_3e.html
-%%DATADIR%%/docs/SPEC_Multi_Mems+_Iterator.html
-%%DATADIR%%/docs/SPEC_Multi_Seed.html
-%%DATADIR%%/docs/SPEC_Multiple_Shift_And.html
-%%DATADIR%%/docs/SPEC_Mums+_Iterator.html
-%%DATADIR%%/docs/SPEC_Myers.html
-%%DATADIR%%/docs/SPEC_Namer.html
-%%DATADIR%%/docs/SPEC_Non_Hierarchical.html
-%%DATADIR%%/docs/SPEC_Non_Scored+_Seed_Set.html
-%%DATADIR%%/docs/SPEC_Normal+_Pdf.html
-%%DATADIR%%/docs/SPEC_One_Gapped_Shape.html
-%%DATADIR%%/docs/SPEC_Open_Addressing.html
-%%DATADIR%%/docs/SPEC_Oracle.html
-%%DATADIR%%/docs/SPEC_Out-_Edge+_Iterator.html
-%%DATADIR%%/docs/SPEC_Owner.html
-%%DATADIR%%/docs/SPEC_P_Mode.html
-%%DATADIR%%/docs/SPEC_Packed+_Pair.html
-%%DATADIR%%/docs/SPEC_Packed+_String.html
-%%DATADIR%%/docs/SPEC_Packed+_Triple.html
-%%DATADIR%%/docs/SPEC_Pex.html
-%%DATADIR%%/docs/SPEC_Pizza+_26+_Chili+_Index.html
-%%DATADIR%%/docs/SPEC_Pizza+_26+_Chili+_String.html
-%%DATADIR%%/docs/SPEC_Pms1.html
-%%DATADIR%%/docs/SPEC_Pmsp.html
-%%DATADIR%%/docs/SPEC_Points+_Only+_Tree+_Node.html
-%%DATADIR%%/docs/SPEC_Pool_Config.html
-%%DATADIR%%/docs/SPEC_Pool_Config_Size.html
-%%DATADIR%%/docs/SPEC_Pool_Spec.html
-%%DATADIR%%/docs/SPEC_Position+_Iterator.html
-%%DATADIR%%/docs/SPEC_Prefix_Segment.html
-%%DATADIR%%/docs/SPEC_Priority_Heap.html
-%%DATADIR%%/docs/SPEC_Projection.html
-%%DATADIR%%/docs/SPEC_Rna.html
-%%DATADIR%%/docs/SPEC_Rna5.html
-%%DATADIR%%/docs/SPEC_Rng+_Functor.html
-%%DATADIR%%/docs/SPEC_Sampler.html
-%%DATADIR%%/docs/SPEC_Score+_Chain_So_P.html
-%%DATADIR%%/docs/SPEC_Score+_Manhattan.html
-%%DATADIR%%/docs/SPEC_Score+_Matrix.html
-%%DATADIR%%/docs/SPEC_Score+_Zero.html
-%%DATADIR%%/docs/SPEC_Scored+_Seed_Set.html
-%%DATADIR%%/docs/SPEC_Set_Horspool.html
-%%DATADIR%%/docs/SPEC_Shift_And.html
-%%DATADIR%%/docs/SPEC_Shift_Or.html
-%%DATADIR%%/docs/SPEC_Shifter.html
-%%DATADIR%%/docs/SPEC_Simple+_Allocator.html
-%%DATADIR%%/docs/SPEC_Simple+_Finder.html
-%%DATADIR%%/docs/SPEC_Simple+_Score.html
-%%DATADIR%%/docs/SPEC_Simple_Iterator.html
-%%DATADIR%%/docs/SPEC_Simple_Seed.html
-%%DATADIR%%/docs/SPEC_Simple_Shape.html
-%%DATADIR%%/docs/SPEC_Single+_Pool+_Allocator.html
-%%DATADIR%%/docs/SPEC_Skiplist.html
-%%DATADIR%%/docs/SPEC_Sorter_Config.html
-%%DATADIR%%/docs/SPEC_Sorter_Config_Size.html
-%%DATADIR%%/docs/SPEC_Sorter_Spec.html
-%%DATADIR%%/docs/SPEC_Source.html
-%%DATADIR%%/docs/SPEC_Store_Report.html
-%%DATADIR%%/docs/SPEC_Stream_Report.html
-%%DATADIR%%/docs/SPEC_Striped.html
-%%DATADIR%%/docs/SPEC_Suffix_Segment.html
-%%DATADIR%%/docs/SPEC_Sumlist_Gaps.html
-%%DATADIR%%/docs/SPEC_Super_Max_Repeats+_Iterator.html
-%%DATADIR%%/docs/SPEC_Super_Max_Repeats_Fast+_Iterator.html
-%%DATADIR%%/docs/SPEC_Swift.html
-%%DATADIR%%/docs/SPEC_Swift_Local.html
-%%DATADIR%%/docs/SPEC_Swift_Semi_Global.html
-%%DATADIR%%/docs/SPEC_Sync.html
-%%DATADIR%%/docs/SPEC_Top_Down+_Iterator.html
-%%DATADIR%%/docs/SPEC_Top_Down_History+_Iterator.html
-%%DATADIR%%/docs/SPEC_Trace_Back.html
-%%DATADIR%%/docs/SPEC_Tree.html
-%%DATADIR%%/docs/SPEC_Trie.html
-%%DATADIR%%/docs/SPEC_Tristate+_Holder.html
-%%DATADIR%%/docs/SPEC_Tupler.html
-%%DATADIR%%/docs/SPEC_Undirected+_Graph.html
-%%DATADIR%%/docs/SPEC_Ungapped_Shape.html
-%%DATADIR%%/docs/SPEC_Uniform+_Pdf.html
-%%DATADIR%%/docs/SPEC_V_S_Tree+_Iterator.html
-%%DATADIR%%/docs/SPEC_Vector_Set.html
-%%DATADIR%%/docs/SPEC_Vertex+_Iterator.html
-%%DATADIR%%/docs/SPEC_Wild_Shift_And.html
-%%DATADIR%%/docs/SPEC_Word+_Graph.html
-%%DATADIR%%/docs/SPEC_Wu_Manber.html
-%%DATADIR%%/docs/TAG.sort_Aligned_Read+_Tags.html
-%%DATADIR%%/docs/TAG_Alignment+_Graph+_Combination.html
-%%DATADIR%%/docs/TAG_Alignment+_Graph+_Format.html
-%%DATADIR%%/docs/TAG_Allocator+_Usage.html
-%%DATADIR%%/docs/TAG_Consensus+_Calling.html
-%%DATADIR%%/docs/TAG_Default.html
-%%DATADIR%%/docs/TAG_Distance+_Calculation.html
-%%DATADIR%%/docs/TAG_Dot_Drawing.html
-%%DATADIR%%/docs/TAG_E_S_A+_Index+_Fibres.html
-%%DATADIR%%/docs/TAG_Empty_Edges.html
-%%DATADIR%%/docs/TAG_External_Config.html
-%%DATADIR%%/docs/TAG_External_Config_Large.html
-%%DATADIR%%/docs/TAG_External_Config_Size.html
-%%DATADIR%%/docs/TAG_File+_Format.html
-%%DATADIR%%/docs/TAG_Find_Infix.html
-%%DATADIR%%/docs/TAG_Find_Prefix.html
-%%DATADIR%%/docs/TAG_Global+_Alignment+_Algorithms.html
-%%DATADIR%%/docs/TAG_Graph+_Iterator.html
-%%DATADIR%%/docs/TAG_Hamming_Distance.html
-%%DATADIR%%/docs/TAG_Hide_Empty_Edges.html
-%%DATADIR%%/docs/TAG_Index+_Find+_Algorithm.html
-%%DATADIR%%/docs/TAG_Interval_Tree+_Centers.html
-%%DATADIR%%/docs/TAG_Interval_Tree+_Node+_Types.html
-%%DATADIR%%/docs/TAG_Iterator+_Spec.html
-%%DATADIR%%/docs/TAG_Levenshtein_Distance.html
-%%DATADIR%%/docs/TAG_Local+_Alignment+_Algorithms.html
-%%DATADIR%%/docs/TAG_Logical+_Values.html
-%%DATADIR%%/docs/TAG_Mean_Std_Dev.html
-%%DATADIR%%/docs/TAG_Move+_Switch.html
-%%DATADIR%%/docs/TAG_Mu_Sigma.html
-%%DATADIR%%/docs/TAG_Nothing.html
-%%DATADIR%%/docs/TAG_Omops.html
-%%DATADIR%%/docs/TAG_Oops.html
-%%DATADIR%%/docs/TAG_Overflow+_Strategy.html
-%%DATADIR%%/docs/TAG_Pizza+_26+_Chili+_Index+_Fibres.html
-%%DATADIR%%/docs/TAG_Pizza+_26+_Chili+_Index+_Tags.html
-%%DATADIR%%/docs/TAG_Postorder.html
-%%DATADIR%%/docs/TAG_Postorder_Empty_Edges.html
-%%DATADIR%%/docs/TAG_Prefix+_Order.html
-%%DATADIR%%/docs/TAG_Preorder.html
-%%DATADIR%%/docs/TAG_Preorder_Empty_Edges.html
-%%DATADIR%%/docs/TAG_Q_Gram+_Index+_Fibres.html
-%%DATADIR%%/docs/TAG_Seed+_Adding.html
-%%DATADIR%%/docs/TAG_Seed+_Extension.html
-%%DATADIR%%/docs/TAG_Seed_Set.html
-%%DATADIR%%/docs/TAG_Segment+_Match+_Generation.html
-%%DATADIR%%/docs/TAG_Simple.html
-%%DATADIR%%/docs/TAG_Tag_List.html
-%%DATADIR%%/docs/TAG_Tcm.html
-%%DATADIR%%/docs/TAG_Upgma+_Configurator.html
-%%DATADIR%%/docs/TAG_W_O_T_D+_Index+_Fibres.html
-%%DATADIR%%/docs/TAG_Zoops.html
-%%DATADIR%%/docs/TYPEDEF_Aligned_Read_Store_Element_23_T_Gap_Anchors.html
-%%DATADIR%%/docs/TYPEDEF_Aligned_Read_Store_Element_23_T_Pos.html
-%%DATADIR%%/docs/TYPEDEF_Aligned_Read_Store_Element_23_T_Spec.html
-%%DATADIR%%/docs/TYPEDEF_Contig_Store_Element_23_T_Contig_Seq.html
-%%DATADIR%%/docs/TYPEDEF_Contig_Store_Element_23_T_Gap_Anchors.html
-%%DATADIR%%/docs/TYPEDEF_Contig_Store_Element_23_T_Pos.html
-%%DATADIR%%/docs/TYPEDEF_Contig_Store_Element_23_T_Spec.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Align_Quality_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Aligned_Read_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Aligned_Read_Tag_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Annotation_Name_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Annotation_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Contig_File_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Contig_Name_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Contig_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Library_Name_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Library_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Mate_Pair_Name_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Mate_Pair_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Read_Name_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Read_Seq_Store.html
-%%DATADIR%%/docs/TYPEDEF_Fragment_Store_23_T_Read_Store.html
-%%DATADIR%%/docs/alignment.cpp
-%%DATADIR%%/docs/alignmentGraph.png
-%%DATADIR%%/docs/alignment_local.cpp
-%%DATADIR%%/docs/allocator.cpp
-%%DATADIR%%/docs/alphabet.cpp
-%%DATADIR%%/docs/automatonGraph.png
-%%DATADIR%%/docs/blast_report.cpp
-%%DATADIR%%/docs/dddoc.js
-%%DATADIR%%/docs/dddoc_empty.gif
-%%DATADIR%%/docs/dddoc_html.css
-%%DATADIR%%/docs/dddoc_minus.gif
-%%DATADIR%%/docs/dddoc_plus.gif
-%%DATADIR%%/docs/directedGraph.png
-%%DATADIR%%/docs/file_format.cpp
-%%DATADIR%%/docs/find_approx.cpp
-%%DATADIR%%/docs/find_exact.cpp
-%%DATADIR%%/docs/find_motif.cpp
-%%DATADIR%%/docs/find_wild.cpp
-%%DATADIR%%/docs/graph_algo_bfs.cpp
-%%DATADIR%%/docs/graph_algo_dfs.cpp
-%%DATADIR%%/docs/graph_algo_flow_fordfulkerson.cpp
-%%DATADIR%%/docs/graph_algo_his.cpp
-%%DATADIR%%/docs/graph_algo_lcs.cpp
-%%DATADIR%%/docs/graph_algo_lis.cpp
-%%DATADIR%%/docs/graph_algo_path_allpairs.cpp
-%%DATADIR%%/docs/graph_algo_path_bellmanford.cpp
-%%DATADIR%%/docs/graph_algo_path_dag.cpp
-%%DATADIR%%/docs/graph_algo_path_dijkstra.cpp
-%%DATADIR%%/docs/graph_algo_path_floydwarshall.cpp
-%%DATADIR%%/docs/graph_algo_path_transitive.cpp
-%%DATADIR%%/docs/graph_algo_scc.cpp
-%%DATADIR%%/docs/graph_algo_topsort.cpp
-%%DATADIR%%/docs/graph_algo_tree_kruskal.cpp
-%%DATADIR%%/docs/graph_algo_tree_prim.cpp
-%%DATADIR%%/docs/graph_hmm.cpp
-%%DATADIR%%/docs/graph_hmm_silent.cpp
-%%DATADIR%%/docs/index.html
-%%DATADIR%%/docs/index_find.cpp
-%%DATADIR%%/docs/index_find_stringset.cpp
-%%DATADIR%%/docs/index_maxrepeats.cpp
-%%DATADIR%%/docs/index_mummy.cpp
-%%DATADIR%%/docs/index_mums.cpp
-%%DATADIR%%/docs/index_node_predicate.cpp
-%%DATADIR%%/docs/index_sufarray.cpp
-%%DATADIR%%/docs/index_supermaxrepeats.cpp
-%%DATADIR%%/docs/iterator.cpp
-%%DATADIR%%/docs/modifier_modreverse.cpp
-%%DATADIR%%/docs/modifier_modview.cpp
-%%DATADIR%%/docs/modifier_nested.cpp
-%%DATADIR%%/docs/pizzachili.cpp
-%%DATADIR%%/docs/rooted_iterator.cpp
-%%DATADIR%%/docs/searchfile.js
-%%DATADIR%%/docs/seqan_logo.gif
-%%DATADIR%%/docs/seqan_logo_large.png
-%%DATADIR%%/docs/shape_predefined.h
-%%DATADIR%%/docs/treeGraph.png
-%%DATADIR%%/docs/trieGraph.png
-%%DATADIR%%/docs/undirectedGraph.png
-%%DATADIR%%/gapped_params/results_N15_H.dat
-%%DATADIR%%/gapped_params/results_N15_L.dat
-%%DATADIR%%/gapped_params/results_N16_H.dat
-%%DATADIR%%/gapped_params/results_N16_L.dat
-%%DATADIR%%/gapped_params/results_N17_H.dat
-%%DATADIR%%/gapped_params/results_N17_L.dat
-%%DATADIR%%/gapped_params/results_N18_H.dat
-%%DATADIR%%/gapped_params/results_N18_L.dat
-%%DATADIR%%/gapped_params/results_N19_H.dat
-%%DATADIR%%/gapped_params/results_N19_L.dat
-%%DATADIR%%/gapped_params/results_N20_H.dat
-%%DATADIR%%/gapped_params/results_N20_L.dat
-%%DATADIR%%/gapped_params/results_N21_H.dat
-%%DATADIR%%/gapped_params/results_N21_L.dat
-%%DATADIR%%/gapped_params/results_N22_H.dat
-%%DATADIR%%/gapped_params/results_N22_L.dat
-%%DATADIR%%/gapped_params/results_N23_H.dat
-%%DATADIR%%/gapped_params/results_N23_L.dat
-%%DATADIR%%/gapped_params/results_N24_H.dat
-%%DATADIR%%/gapped_params/results_N24_L.dat
-%%DATADIR%%/gapped_params/results_N25_H.dat
-%%DATADIR%%/gapped_params/results_N25_L.dat
-%%DATADIR%%/gapped_params/results_N26_H.dat
-%%DATADIR%%/gapped_params/results_N26_L.dat
-%%DATADIR%%/gapped_params/results_N27_H.dat
-%%DATADIR%%/gapped_params/results_N27_L.dat
-%%DATADIR%%/gapped_params/results_N28_H.dat
-%%DATADIR%%/gapped_params/results_N28_L.dat
-%%DATADIR%%/gapped_params/results_N29_H.dat
-%%DATADIR%%/gapped_params/results_N29_L.dat
-%%DATADIR%%/gapped_params/results_N30_H.dat
-%%DATADIR%%/gapped_params/results_N30_L.dat
-%%DATADIR%%/gapped_params/results_N31_H.dat
-%%DATADIR%%/gapped_params/results_N31_L.dat
-%%DATADIR%%/gapped_params/results_N32_H.dat
-%%DATADIR%%/gapped_params/results_N32_L.dat
-%%DATADIR%%/gapped_params/results_N33_H.dat
-%%DATADIR%%/gapped_params/results_N33_L.dat
-%%DATADIR%%/gapped_params/results_N34_H.dat
-%%DATADIR%%/gapped_params/results_N34_L.dat
-%%DATADIR%%/gapped_params/results_N35_H.dat
-%%DATADIR%%/gapped_params/results_N35_L.dat
-%%DATADIR%%/gapped_params/results_N36_H.dat
-%%DATADIR%%/gapped_params/results_N36_L.dat
-%%DATADIR%%/gapped_params/results_N37_H.dat
-%%DATADIR%%/gapped_params/results_N37_L.dat
-%%DATADIR%%/gapped_params/results_N38_H.dat
-%%DATADIR%%/gapped_params/results_N38_L.dat
-%%DATADIR%%/gapped_params/results_N39_H.dat
-%%DATADIR%%/gapped_params/results_N39_L.dat
-%%DATADIR%%/gapped_params/results_N40_H.dat
-%%DATADIR%%/gapped_params/results_N40_L.dat
-%%DATADIR%%/gapped_params/results_N41_H.dat
-%%DATADIR%%/gapped_params/results_N41_L.dat
-%%DATADIR%%/gapped_params/results_N42_H.dat
-%%DATADIR%%/gapped_params/results_N42_L.dat
-%%DATADIR%%/gapped_params/results_N43_H.dat
-%%DATADIR%%/gapped_params/results_N43_L.dat
-%%DATADIR%%/gapped_params/results_N44_H.dat
-%%DATADIR%%/gapped_params/results_N44_L.dat
-%%DATADIR%%/gapped_params/results_N45_H.dat
-%%DATADIR%%/gapped_params/results_N45_L.dat
-%%DATADIR%%/gapped_params/results_N46_H.dat
-%%DATADIR%%/gapped_params/results_N46_L.dat
-%%DATADIR%%/gapped_params/results_N47_H.dat
-%%DATADIR%%/gapped_params/results_N47_L.dat
-%%DATADIR%%/gapped_params/results_N48_H.dat
-%%DATADIR%%/gapped_params/results_N48_L.dat
-%%DATADIR%%/gapped_params/results_N49_H.dat
-%%DATADIR%%/gapped_params/results_N49_L.dat
-%%DATADIR%%/gapped_params/results_N50_H.dat
-%%DATADIR%%/gapped_params/results_N50_L.dat
-%%DATADIR%%/gapped_params/results_N51_H.dat
-%%DATADIR%%/gapped_params/results_N51_L.dat
-%%DATADIR%%/gapped_params/results_N52_H.dat
-%%DATADIR%%/gapped_params/results_N52_L.dat
-%%DATADIR%%/gapped_params/results_N53_H.dat
-%%DATADIR%%/gapped_params/results_N53_L.dat
-%%DATADIR%%/gapped_params/results_N54_H.dat
-%%DATADIR%%/gapped_params/results_N54_L.dat
-%%DATADIR%%/gapped_params/results_N55_H.dat
-%%DATADIR%%/gapped_params/results_N55_L.dat
-%%DATADIR%%/gapped_params/results_N56_H.dat
-%%DATADIR%%/gapped_params/results_N56_L.dat
-%%DATADIR%%/gapped_params/results_N57_H.dat
-%%DATADIR%%/gapped_params/results_N57_L.dat
-%%DATADIR%%/gapped_params/results_N58_H.dat
-%%DATADIR%%/gapped_params/results_N58_L.dat
-%%DATADIR%%/gapped_params/results_N59_H.dat
-%%DATADIR%%/gapped_params/results_N59_L.dat
-%%DATADIR%%/gapped_params/results_N60_H.dat
-%%DATADIR%%/gapped_params/results_N60_L.dat
-%%DATADIR%%/gapped_params/results_N61_H.dat
-%%DATADIR%%/gapped_params/results_N61_L.dat
-%%DATADIR%%/gapped_params/results_N62_H.dat
-%%DATADIR%%/gapped_params/results_N62_L.dat
-%%DATADIR%%/gapped_params/results_N63_H.dat
-%%DATADIR%%/gapped_params/results_N63_L.dat
-%%DATADIR%%/gapped_params/results_N64_H.dat
-%%DATADIR%%/gapped_params/results_N64_L.dat
-%%DATADIR%%/gapped_params/results_N65_H.dat
-%%DATADIR%%/gapped_params/results_N65_L.dat
-%%DATADIR%%/gapped_params/results_N66_H.dat
-%%DATADIR%%/gapped_params/results_N67_H.dat
-%%DATADIR%%/gapped_params/results_N68_H.dat
-%%DATADIR%%/gapped_params/results_N69_H.dat
-%%DATADIR%%/gapped_params/results_N70_H.dat
-%%DATADIR%%/gapped_params/results_N71_H.dat
-%%DATADIR%%/gapped_params/results_N72_H.dat
-%%DATADIR%%/gapped_params/results_N73_H.dat
-%%DATADIR%%/gapped_params/results_N74_H.dat
-%%DATADIR%%/gapped_params/results_N75_H.dat
+%%PORTDOCS%%%%DOCSDIR%%/CHANGELOG.rst
+%%PORTDOCS%%%%DOCSDIR%%/LICENSE
+%%PORTDOCS%%%%DOCSDIR%%/README.rst
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AFScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Accumulator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Align.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignCols.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignQualityStoreElement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignTraceback.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignedReadLayout.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignedReadStoreElement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AlignmentStats.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Allocator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AlphabetExpansion.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AnnotationStoreElement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ArgParseArgument.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ArgumentParser.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_AsyncRequest.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BadAlloc.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BadCast.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BamAlignmentRecord.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BamHeader.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BamHeaderRecord.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BamIOContext.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BamIndex.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BamTagsDict.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BedRecord.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BedRgb.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BetaDistribution.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastIOContext.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastMatch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastMatchField.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastProgramSelector.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastRecord.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastReport.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastScoringScheme.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastTabular.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastTabularLL.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BlastTabularSpecSelector.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_BufferedStream.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Bundle2.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Bundle3.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Bundle5.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_CigarElement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_CompressedSA.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ConcatenatorManyToOne.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ConcurrentQueue.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ConsensusAlignerIllegalArgumentException.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ConsensusAlignmentOptions.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ConsensusScoreSequenceEntry.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ContainerView.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ContigFile.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ContigStoreElement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_CyclicShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_DPBandConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_DefaultJstConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_DefaultSeedConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_DeltaMap.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Deque.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_EdgeStump.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Exception.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ExternalConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ExternalConfigLarge.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ExternalConfigSize.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FMIndexConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FaiIndex.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_File.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FileMapping.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FormattedFile.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FormattedNumber.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Fragment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FragmentStore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FunctorComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FunctorConvert.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FunctorLowcase.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_FunctorUpcase.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_GapAnchor.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_GapsIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_GenomicRegion.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_GffRecord.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Holder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_IOError.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_IdManager.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_InternalPointerPropertyMap.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_InternalPropertyMap.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_IntervalAndCargo.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_IntervalTree.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_IntervalTreeNode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Iter.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_JoinConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_JournaledStringTree.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_LF.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Lexical.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_LibraryStoreElement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_LocalAlignmentEnumerator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_LocalMatch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_LocalMatchStore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_LocalMatchStoreConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_LogProb.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Loop.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_LoopReverse.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_MMapConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_MarkovModel.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_MatePairStoreElement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Matrix.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ModifiedAlphabet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ModifiedIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ModifiedString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_MsaOptions.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_NameStoreCache.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Pair.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Pattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_PigeonholeParameters.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Pipe.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_PointAndCargo.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Pool.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_PriorityType.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ProfileChar.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Proxy.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Range.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_RankDictionary.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_RankSupportBitString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ReadStoreElement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Repeat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_RightArrayBinaryTree.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_RuntimeError.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_SeedDiagonal.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_SeedSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Segment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_SentinelRankDictionary.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_SequenceOutputOptions.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_SimpleIntervalsIOContext.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_SimpleType.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_SparseString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Splitter.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_StreamBuffer.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_String.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_StringEnumerator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_StringSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_SwiftParameters.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_TabixIndex.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Tag.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_TagList.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_TagSelector.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ToStdAllocator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_ToolDoc.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Triple.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_Tuple.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_UcscIOContext.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_UcscRecord.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_UnionFind.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_VcfHeader.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_VcfHeaderRecord.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_VcfIOContext.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_VcfRecord.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_VirtualStream.html
+%%PORTDOCS%%%%DOCSDIR%%/html/class_VolatilePtr.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_AggregateConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_AlphabetConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_AlphabetWithGapsConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_AlphabetWithQualitiesConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_AlphabetWithUnknownValueConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_AssignableConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_BidirectionalIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_BidirectionalStreamConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_ComparableConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_ContainerConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_ConvertibleConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_CopyConstructibleConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_DefaultConstructibleConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_DestructibleConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_EqualityComparableConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_FiniteOrderedAlphabetConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_FormattedFileHeaderConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_FormattedFileRecordConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_ForwardContainerConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_ForwardIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_GraphOverAlphabetConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_HostedConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_InputIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_InputStreamConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_IntegerConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_IteratorAssociatedTypesConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_LessThanComparableConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_MutableBidirectionalIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_MutableForwardIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_MutableRandomAccessIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_MutableRootedIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_MutableRootedRandomAccessIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_NumberConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_OrderedAlphabetConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_OutputIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_OutputStreamConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_PropertyMapConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_RandomAccessContainerConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_RandomAccessIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_ReversibleContainerConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_RootedIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_RootedRandomAccessIteratorConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_SegmentableConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_SignedIntegerConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_StreamConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_StringConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_StringIndexConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_StringTreeConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_StringTrieConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_TextConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/concept_UnsignedIntegerConcept.html
+%%PORTDOCS%%%%DOCSDIR%%/html/css/common.less
+%%PORTDOCS%%%%DOCSDIR%%/html/css/common.less.css
+%%PORTDOCS%%%%DOCSDIR%%/html/css/custom.css
+%%PORTDOCS%%%%DOCSDIR%%/html/css/full_list.css
+%%PORTDOCS%%%%DOCSDIR%%/html/css/main.css
+%%PORTDOCS%%%%DOCSDIR%%/html/css/reset.css
+%%PORTDOCS%%%%DOCSDIR%%/html/css/rules.less
+%%PORTDOCS%%%%DOCSDIR%%/html/css/style.css
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/blast/blast_in_lowlevel.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/blast/blast_in_lowlevel.cpp.stdout_
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/align.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/align.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/compute_alignment_stats.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/compute_alignment_stats.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/gaps_example.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/gaps_example.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/global_alignment_banded.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/global_alignment_banded.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/global_alignment_unbanded.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/global_alignment_unbanded.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/integrate_align.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align/integrate_align.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align_extend/extend_alignment.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align_extend/extend_alignment.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align_profile/profile_seq_frac_score.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align_profile/profile_seq_score.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align_split/split_alignment.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/align_split/split_alignment.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/arg_parse/argument_parser.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/bam_io/bam_tags_dict.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/bam_io/bam_tags_dict.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/basic/enable_if.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/basic/metaprogramming_control.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/basic/metaprogramming_logic.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/basic/metaprogramming_math.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/basic/metaprogramming_switch.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/basic/simple_type_construction.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/basic/zip_iterator.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/basic/zip_iterator.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/consensus/consensus_alignment.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/consensus/consensus_alignment.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/find/finder_aho_corasick.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/find/finder_index.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/find/finder_index.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/find/finder_online.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/find/finder_online.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/all_pairs_shortest_path.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/all_pairs_shortest_path.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/bellman_ford_algorithm.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/bellman_ford_algorithm.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/breadth_first_search.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/breadth_first_search.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/dag_shortest_path.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/dag_shortest_path.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/depth_first_search.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/depth_first_search.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/dijkstra.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/dijkstra.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/floyd_warshall_algorithm.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/ford_fulkerson_algorithm.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/heaviest_increasing_subsequence.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/kruskals_algorithm.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/kruskals_algorithm.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/longest_common_subsequence.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/longest_increasing_subsequence.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/prims_algorithm.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/prims_algorithm.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/strongly_connected_components.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/strongly_connected_components.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/topological_sort.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/topological_sort.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/transitive_closure.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_algorithms/transitive_closure.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_align/graph_align.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_types/graph_algo_dijkstra.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/graph_types/graph_algo_dijkstra.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/begin_atEnd_representative.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/begin_atEnd_representative.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/begin_atEnd_representative_bottomUp.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/begin_range_goDown_representative_repLength.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/counting.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/counting.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/find_repeats.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/finder.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/finder.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/getOccurrences_getFrequency_range_getFibre.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/iterator.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/iterator.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/iterator_short.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/iterator_short.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/length_countSequences.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/length_countSequences.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/maxrepeats.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/mummy.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/mums.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/node_predicate.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/open_save.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/open_save.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/shape_hash_init.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/sufarray.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/supermaxrepeats.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/textAt_indexText_saAt_indexRequire.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/index/textAt_indexText_saAt_indexRequire.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/misc/enumerate_strings.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/misc/enumerate_strings.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/misc/get_terminal_size.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/misc/interval_tree_example.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/misc/name_store_cache.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/misc/name_store_cache.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/modifier/cyclic_shape.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/modifier/cyclic_shape.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/modifier/cyclic_shape_snippets.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/modifier/modified_string.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/modifier/modified_string.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/modifier/modified_string_mod_view.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/modifier/modified_string_mod_view.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/modifier/modified_string_nested.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/modifier/modified_string_nested.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/parallel/queue_example.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/parallel/queue_example.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/parallel/splitter_example.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/parallel/splitter_example.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/pipe/pool_sorter.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/score/score.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/score/score.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/seeds/seeds_add_seed.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/seeds/seeds_chaining.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/seeds/seeds_chaining.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/seeds/seeds_extension.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/seeds/seeds_extension.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/seq_io/fai_index_example.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/seq_io/fai_index_example.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/sequence/container_view_zip.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/sequence/container_view_zip.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/sequence/segment.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/sequence/string.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/sequence/string2.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/sequence/string2.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/sequence/stringset.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/sequence/stringset.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/statistics/build_markov_model.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/statistics/load_markov_model.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/store/store_example.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/stream/lexical_cast.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/dox/stream/lexical_cast.cpp.stdout
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/tutorial/sam_and_bam_io/example.sam
+%%PORTDOCS%%%%DOCSDIR%%/html/demos/tutorial/sam_and_bam_io/solution1.cpp
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_ArgParseArgument_58_58ArgumentType.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_ArgumentParser_58_58ParseResult.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_BamFlags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_BamHeaderRecordType.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_BamSortOrder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_BlastMatchField_58_58Enum.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_BlastProgram.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_BlastTabularSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_DeltaType.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_ExtensionDirection.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_FileMappingAdvise.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_FileMappingMode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_FileOpenMode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_FragmentStore_58_58PredefinedAnnotationTypes.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_GeneticCodeSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/enum_TranslationFrames.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_TView.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_addToProfile.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_alignmentEvaluation.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_alignmentFreeComparison.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_allPairsShortestPath.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayClearSpace.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayConstruct.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayConstructCopy.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayConstructMove.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayCopy.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayCopyBackward.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayCopyForward.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayDestruct.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayFill.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayMove.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayMoveBackward.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_arrayMoveForward.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_assignQualities.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_assignTagsBamToSam.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_assignTagsSamToBam.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_atomicMax.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_atomicMin.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_bandedChainAlignment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_bellmanFordAlgorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_bitScanForward.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_bitScanReverse.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_breadthFirstSearch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_buildAlignmentGraph.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_bundle2.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_bundle3.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_bundle5.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_calcBetaDistParam.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_calcLogNormalDistParam.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_calculateCovariance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_calculateOverlapIndicator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_calculatePeriodicity.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_calculateProbability.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_calculateVariance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_chainSeedsGlobally.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_clearAllBits.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_clearBit.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_complement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_computeAlignmentStats.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_computeSplitters.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_connectedComponents.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_consensusAlignment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_convert.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_convertImpl.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_convertQuality.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_countKmers.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_cpuTime.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_createBWTable.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_createInvSuffixArray.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_createLcpTable.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_createSuffixArray.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_cutNs.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_dagShortestPath.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_defaultRng.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_depthFirstSearch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_dijkstra.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_endsWith.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_expectation.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_extendAlignment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_findRepeats.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_floydWarshallAlgorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_fordFulkersonAlgorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_getAbsolutePath.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_getBamTypeChar.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_getBamTypeSize.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_getTerminalSize.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_globalAlignment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_globalAlignmentScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_globalMsaAlignment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_guessFormatFromFilename.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_heaviestIncreasingSubsequence.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_ignoreUnusedVariableWarning.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_integrateAlign.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_isAnsiColorTerminal.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_isBitSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_isTerminal.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_kruskalsAlgorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_lexicalCast.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_lexicalCastWithException.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_localAlignment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_log2.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_longestCommonSubsequence.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_longestIncreasingSubsequence.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_lowerBoundAlignedReads.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_makeZipIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_makeZipView.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_matchRefinement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_memset.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_njTree.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_orderOccurrences.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_partialSum.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_popCount.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_primsAlgorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_printDebugLevel.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_progressiveAlignment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_reAlign.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_reAlignment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_readEmblHeader.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_reverseComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_setBit.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_setBitTo.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_shareResources.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_shuffle.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_sortAlignedReads.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_splitAlignment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_splitGenBankHeader.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_startsWith.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_stringToStringSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_stronglyConnectedComponents.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_sum.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_sumOfPairsScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_sysTime.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_testAllOnes.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_testAllZeros.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_toLower.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_toUpper.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_topologicalSort.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_transitiveClosure.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_translate.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_tripletLibraryExtension.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_upgmaTree.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_upperBoundAlignedReads.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_valueConstruct.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_valueDestruct.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_variance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_weaklyConnectedComponents.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_function_zscore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_AllowsFastRandomAccess.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_BasicStream.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_BytesPerValue.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Chunk.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Comparator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_CompareType.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_CompareTypeImpl.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Convert.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_DeepestSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_DefaultFindBeginPatternSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_DefaultFinder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_DefaultOverflowExplicit.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_DefaultOverflowImplicit.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_DefaultPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_DefaultPrefixOrder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Device.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Difference.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Fibre.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_FileExtensions.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Find.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_GappedValueType.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_GetDefaultRng.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_GetValue.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_HasMoveConstructor.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IntegralForValue.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IosOpenMode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Is.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsCharType.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsContiguous.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsDevice.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsInteger.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsIntegral.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsLightWeight.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsSameType.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsSequence.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsSimple.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_IsView.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Key.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_LENGTH.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_MagicHeader.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_MakePacked.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_MakeSigned.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_MakeUnsigned.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Member.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Reference.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_RemoveConst.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_RemovePointer.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_RemoveReference.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_RemoveView.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_SAValue.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Size.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_VertexDescriptor.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_View.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_metafunction_WEIGHT.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Blosum30.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Blosum45.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Blosum62.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Blosum80.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_CharIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_CharString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_DPBand.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Dna5Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Dna5QString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Dna5String.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Dna5StringComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Dna5StringReverse.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Dna5StringReverseComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_DnaIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_DnaQString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_DnaString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_DnaStringComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_DnaStringReverse.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_DnaStringReverseComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_EditDistanceScoreTypedef.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_IupacIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_IupacString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_MyersUkkonen.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_MyersUkkonenBanded.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_MyersUkkonenGlobal.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_MyersUkkonenGlobalBanded.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Pam120.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Pam200.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Pam250.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Pam40.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Peptide.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_PeptideIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Rna5Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Rna5String.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Rna5StringComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Rna5StringReverse.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Rna5StringReverseComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaStringComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaStringReverse.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_RnaStringReverseComplement.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_SimpleScoreTypedef.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_TraceBack.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_UnicodeString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/global_typedef_Vtml200.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_AggregateTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_AlignmentAlgorithmTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_AlignmentGraphCombinationTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_AlignmentGraphFormatTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_AllocatorUsageTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_ApproximateFinderSearchTypeTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_AssertMacros.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_AtomicPrimitives.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_BamIOContextMemberTag.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_BottomUp.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_CompressedSAFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_ConceptChecking.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_ContainerIteratorTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_DPBandSwitch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_DeltaTypeTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_DfiIndexFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_DfsOrder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_DirectionTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_DistanceCalculationTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_EnableIfFunctionality.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_ExceptionHandling.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_FMIndexCompressionSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_FMIndexFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_FMIndexRankDictionarySpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_FileCompressionTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_FileFormats.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_GapDirectionTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_GapsSpecTag.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_GlobalChainingTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_GraphIteratorTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_HmmAlgorithms.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_IndexEsaFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_IndexFindAlgorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_IntervalTreeNodeTypeTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_JoinStrategiesTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_LFTableFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_LocalChainingTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_LogicMetaprogramming.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_LogicalValuesTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_MetafunctionSwitch.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_MetaprogrammingMath.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_MultipleSequenceAlignmentTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_OpenAdressingTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_OverflowStrategyTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_PairwiseLocalAlignmentAlgorithms.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_ParallelismTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_PizzaChiliIndexFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_PizzaChiliIndexTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_PositionCalculation.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_PrefixOrderTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_QGramIndexFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_RankDictionaryFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_RankSupportBitStringFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_RightArrayBinaryTreeFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_SeedExtensionTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_SegmentMatchGenerationTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_SentinelRankDictionaryFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_SortAlignedReadTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_SparseStringFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_StandardIntegers.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_StreamFormats.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_TestSystemMacros.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_TopDown.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_UpgmaConfiguratorTags.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_WOTDIndexFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/group_WaveletTreeFibres.html
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_class.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_concept.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_enum.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_function.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_group.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_macro.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_metafunction.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_page.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_tag.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_typedef.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/icon_variable.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/list-small.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/list.pdf
+%%PORTDOCS%%%%DOCSDIR%%/html/img/list.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/seqan_logo.highres.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/seqan_logo.png
+%%PORTDOCS%%%%DOCSDIR%%/html/img/seqan_strands.svg
+%%PORTDOCS%%%%DOCSDIR%%/html/img/strands.png
+%%PORTDOCS%%%%DOCSDIR%%/html/include/seqan/index/shape_predefined.h
+%%PORTDOCS%%%%DOCSDIR%%/html/index.html
+%%PORTDOCS%%%%DOCSDIR%%/html/js/app.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/autocomplete.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/common.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/full_list.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/jquery.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/jquery.smooth-scroll.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/lang_entities.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/less.min.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/link.data.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/rubydoc_custom.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/search.data.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/search.engine.js
+%%PORTDOCS%%%%DOCSDIR%%/html/js/version.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/3L.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/CHANGELOG.md
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/LICENCES.md
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/assets/animations/animation1.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/assets/animations/animation2.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/assets/animations/animation3.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/assets/animations/animation4.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/assets/animations/animation5.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/3L/assets/less.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/README.md
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/ZeroClipboard/ZeroClipboard.min.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/ZeroClipboard/ZeroClipboard.swf
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/README.md
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/css/bootstrap-3.0.0.min.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/css/bootstrap-multiselect.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/css/prettify.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/custom.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/fonts/glyphicons-halflings-regular.eot
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/fonts/glyphicons-halflings-regular.svg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/fonts/glyphicons-halflings-regular.ttf
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/fonts/glyphicons-halflings-regular.woff
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/index.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/bootstrap-3.0.0.min.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/bootstrap-multiselect.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/jquery-2.0.3.min.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/knockout-2.3.0.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/js/prettify.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/knockout-examples.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/less/bootstrap-multiselect.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap-multiselect/tests.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/css/bootstrap.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/css/bootstrap.min.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/fonts/glyphicons-halflings-regular.eot
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/fonts/glyphicons-halflings-regular.svg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/fonts/glyphicons-halflings-regular.ttf
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/fonts/glyphicons-halflings-regular.woff
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/js/bootstrap.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bootstrap/js/bootstrap.min.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/bower.json
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/css/font-awesome.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/css/font-awesome.min.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/fonts/FontAwesome.otf
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/fonts/fontawesome-webfont.eot
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/fonts/fontawesome-webfont.svg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/fonts/fontawesome-webfont.ttf
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/fonts/fontawesome-webfont.woff
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/bordered-pulled.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/core.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/fixed-width.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/font-awesome.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/icons.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/larger.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/list.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/mixins.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/path.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/rotated-flipped.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/spinning.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/stacked.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/less/variables.less
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_bordered-pulled.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_core.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_fixed-width.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_icons.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_larger.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_list.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_mixins.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_path.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_rotated-flipped.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_spinning.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_stacked.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/_variables.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/font-awesome/scss/font-awesome.scss
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/LICENSE-GPL
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/LICENSE-MIT
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/README.markdown
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/files/jquery-ba-bbq-js.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/Events.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/Files.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/Functions.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/General.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/index/Properties.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/javascript/main.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/javascript/searchdata.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/ClassHierarchy.nd
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/ConfigFileInfo.nd
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/FileInfo.nd
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/ImageFileInfo.nd
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/ImageReferenceTable.nd
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/IndexInfo.nd
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/PreviousMenuState.nd
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/PreviousSettings.nd
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Data/SymbolTable.nd
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Languages.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Menu.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/nd/Topics.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/EventsH.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FilesJ.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsA.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsD.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsE.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsF.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsG.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsH.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsN.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsP.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsQ.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsR.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/FunctionsS.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralA.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralD.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralE.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralF.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralG.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralH.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralJ.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralK.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralL.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralN.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralP.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralQ.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralR.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/GeneralS.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/NoResults.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/PropertiesD.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/search/PropertiesS.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/styles/1.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/styles/2.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/docs/styles/main.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/config.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/deparam/index.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/donate.gif
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/bbq.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/burger.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/burger.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/chicken.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/chicken.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/index.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/kebabs.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/kebabs.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/kielbasa.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/kielbasa.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/ribs.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/ribs.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/steak.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-advanced/steak.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/XMLpage.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/bbq.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/burger.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/chicken.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/index.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/kebabs.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/kielbasa.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/page.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/pages.xml
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/ribs.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-ajax-crawlable/steak.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/bbq.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/burger.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/burger.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/chicken.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/chicken.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/index.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/kebabs.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/kebabs.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/kielbasa.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/kielbasa.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/ribs.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/ribs.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/steak.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-basic/steak.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/bbq.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/burger.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/chicken.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/index.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/kebabs.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/kielbasa.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/ribs.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/fragment-jquery-ui-tabs/steak.jpg
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/index.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/examples/index.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/jquery.ba-bbq.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/jquery.ba-bbq.min.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/LGPLv3.txt
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/clipboard.swf
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushAS3.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushBash.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushCSharp.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushCpp.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushCss.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushDelphi.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushDiff.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushGroovy.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushJScript.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushJava.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushJavaFX.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushPerl.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushPhp.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushPlain.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushPowerShell.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushPython.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushRuby.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushScala.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushSql.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushVb.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shBrushXml.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shCore.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/scripts/shLegacy.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/src/shCore.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/src/shLegacy.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/help.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/magnifier.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/page_white_code.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/page_white_copy.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/printer.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/shCore.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/shThemeDefault.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/shThemeDjango.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/shThemeEmacs.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/shThemeFadeToGrey.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/shThemeMidnight.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/shThemeRDark.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/styles/wrapping.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/SyntaxHighlighter/test.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/ba-debug.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-1.3.2.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-1.4.1.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-1.4.2.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/cowboy_hat.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-bg_diagonals-medium_18_b81900_40x40.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-bg_diagonals-medium_20_FF7F00_40x40.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-bg_diagonals-small_35_FF7F00_40x40.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-bg_flat_10_000000_40x100.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-bg_highlight-soft_100_FDEBDC_1x100.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-bg_highlight-soft_100_FFD6AF_1x100.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-bg_highlight-soft_100_dddddd_1x100.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-bg_highlight-soft_75_C4884F_1x100.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-bg_inset-soft_100_dddddd_1x100.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-icons_222222_256x240.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-icons_228ef1_256x240.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-icons_333333_256x240.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-icons_913D00_256x240.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-icons_FF7F00_256x240.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-icons_ffd27a_256x240.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/images/ui-icons_ffffff_256x240.png
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/css/benalman/jquery-ui-1.7.2.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/jquery-ui-1.7.2/js/jquery-ui-1.7.2.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/json2.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/json_echo.php
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/shared/qunit.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/unit/ie7-compat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/unit/index.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/unit/jquery-1.3.2.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/unit/jquery-1.4.1.html
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/unit/qunit.css
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/jquery-bbq/unit/unit.js
+%%PORTDOCS%%%%DOCSDIR%%/html/lib/styles.less
+%%PORTDOCS%%%%DOCSDIR%%/html/list.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_PLATFORM_95CUDA.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_PLATFORM_95GCC.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95DEVICE.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95ENABLE_95PARALLELISM.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95GLOBAL.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95HAS_95BZIP2.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95HAS_95ZLIB.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95HOST.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95HOST_95DEVICE.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95IS_9532_95BIT.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95IS_9564_95BIT.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95OMP_95PRAGMA.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95PATH_95TO_95ROOT.html
+%%PORTDOCS%%%%DOCSDIR%%/html/macro_SEQAN_95TEMP_95FILENAME.html
+%%PORTDOCS%%%%DOCSDIR%%/html/page_DemoConstraintIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/page_DemoIndexCountChildren.html
+%%PORTDOCS%%%%DOCSDIR%%/html/page_DemoMaximalRepeats.html
+%%PORTDOCS%%%%DOCSDIR%%/html/page_DemoMaximalUniqueMatches.html
+%%PORTDOCS%%%%DOCSDIR%%/html/page_DemoMummy.html
+%%PORTDOCS%%%%DOCSDIR%%/html/page_DemoSuffixArray.html
+%%PORTDOCS%%%%DOCSDIR%%/html/page_DemoSupermaximalRepeats.html
+%%PORTDOCS%%%%DOCSDIR%%/html/page_LanguageEntities.html
+%%PORTDOCS%%%%DOCSDIR%%/html/page_mainpage.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AbndmAlgoPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AdaptorIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AdjacencyIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AhoCorasickPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AlignColIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AlignmentGraph.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AllocString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AminoAcid.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AnchorGaps.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AnnotationTreeIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ArgParseOption.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ArrayGaps.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ArrayString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AsyncFile.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AutoSeqFormat.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Automaton.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_AverageAccumulator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BadLexicalCast.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BaiBamIndex.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BamFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BamFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BandedLocalAlignmentEnumerator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Bed12Record.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Bed3Record.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Bed4Record.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Bed5Record.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Bed6Record.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BedFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BedFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BfamPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BfsIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BitPackedPair.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BitPackedTuple.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BlastReportFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BlastTabularFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BlastTabularFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BlockString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BndmAlgoPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_BottomUpIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_CStyleString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Caster.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ChainedSeed.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ConcatDirectStringSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ConcatVirtualIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ConcurrentSuspendableQueue.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Counter.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_CountingIdManager.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_D2AFScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_D2StarAFScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_D2zAFScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_DPSearchPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_DeltaMapIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_DependentStringSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_DfsPreorderIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_DirectedGraph.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Dna.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Dna5.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Dna5Q.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_DnaQ.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Echoer.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_EdgeIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_EditDistanceScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_EditEnvironment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_EmptyFieldError.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Equidistant.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ExactFragment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ExactReversableFragment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ExternalString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_FMIndex.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Filter.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Finite.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_FixedCyclicShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_FormattedFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_FormattedFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_GappedShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_GenericCyclicShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_GenericShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_GenerousDependentStringSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_GffFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_GffFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_GlobalAlign.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_GlobalChain.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_HammingSimplePattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_HammingStringEnumerator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_HardwiredShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_HierarchicalPexPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_HmmGraph.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_HorspoolPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_IndexDfi.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_IndexEsa.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_IndexQGram.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_IndexSa.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_IndexWotd.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_InfixSegment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_InputStreamIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_IteratorProxy.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Iupac.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Joiner.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_JournaledSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_JournaledString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_LevenshteinStringEnumerator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MMapString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MapperConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MapperConfigSize.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MapperSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MatrixScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MaxRepeatsIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModCyclicShapeModifiedIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModCyclicShapeModifiedString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModReverseIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModReverseString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModViewModifiedIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ModViewModifiedString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MultiBfamPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MultiMemsIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MultiPoolAllocator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MultipleShiftAndPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MumsIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_MyersPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_N2AFScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Namer.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_NonHierarchicalPexPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OneGappedShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OpenAddressingQGramIndex.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OracleBfamPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OracleMultiBfamPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OutEdgeIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OutputStreamIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_OwnerStringSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PackedPair.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PackedString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PackedTriple.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ParseError.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PexPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PigeonholeFinder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PigeonholePattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PizzaChiliIndex.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PizzaChiliString.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PoolConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PoolConfigSize.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PoolSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PositionIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PrefixSegment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_PriorityHeap.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ProfileSeqFracScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ProfileSeqScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ReducedAminoAcid.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ResizableContainerView.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RightArrayBinaryTreeIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Rna.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Rna5.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_RoiFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Sampler.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SeqFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SeqFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SetHorspoolPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ShiftAndPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ShiftOrPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Shifter.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleAllocator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleHolder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleIntervalsFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleIntervalsFileInOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimplePattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleScore.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleSeed.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SimpleShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SinglePoolAllocator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Skiplist.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SorterConfig.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SorterConfigSize.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SorterSpec.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StdAdaptorIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StoreIntervalsIntervalTreeNode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StorePointsOnlyIntervalTreeNode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_StreamIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SuffixSegment.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SuperMaxRepeatsFastIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SuperMaxRepeatsIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftFinder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftLocalFinder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftLocalPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftSemiGlobalFinder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SwiftSemiGlobalPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_SyncFile.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TightDependentStringSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TopDownHistoryIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TopDownIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Tree.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TrieBfamPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TristateHolder.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_Tupler.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_TwoLevelRankDictionary.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UcscFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UcscFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UnbandedLocalAlignmentEnumerator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UndirectedGraph.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UnexpectedEnd.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_UngappedShape.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VSTreeIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VcfFileIn.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VcfFileOut.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VectorSet.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_VertexIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WaveletTree.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WildShiftAndPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WordGraph.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_WuManberPattern.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ZipContainerView.html
+%%PORTDOCS%%%%DOCSDIR%%/html/specialization_ZipIterator.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Default.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_DotDrawing.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_EditDistance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_GeneticCode.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_HammingDistance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_LevenshteinDistance.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Move.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Murphy10.html
+%%PORTDOCS%%%%DOCSDIR%%/html/tag_Nothing.html
+%%PORTDOCS%%%%DOCSDIR%%/html/variable_BAM_95FLAG_95SUPPLEMENTARY_32_61_320x0800.html
+%%PORTDOCS%%%%DOCSDIR%%/html/variable_LibraryStoreElementstd.html
+%%PORTDOCS%%@dir %%DOCSDIR%%/html/docs/seqan
+%%PORTDOCS%%@dir %%DOCSDIR%%/html/lists
diff --git a/biology/seqan1/Makefile b/biology/seqan1/Makefile
new file mode 100644
index 000000000000..d5222cac07b2
--- /dev/null
+++ b/biology/seqan1/Makefile
@@ -0,0 +1,31 @@
+# Created by: h2
+# $FreeBSD$
+
+PORTNAME=	seqan
+PORTVERSION=	1.3.1
+PORTREVISION=	3
+CATEGORIES=	biology
+MASTER_SITES=	http://ftp.seqan.de/releases/
+PKGNAMESUFFIX=	1
+
+MAINTAINER=	h2+fbsdports@fsfe.org
+COMMENT=	C++ Sequence Analysis Library
+
+LICENSE=	BSD3CLAUSE
+LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE
+
+USES=		zip
+NO_BUILD=	yes
+
+CONFLICTS=	seqan-[2-9]*
+
+do-install:
+	${MKDIR} ${STAGEDIR}/${PREFIX}/include/${PORTNAME}
+	cd ${WRKSRC} && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include
+	cd ${WRKSRC} && ${INSTALL_DATA} ./${PORTNAME}.h ${STAGEDIR}/${PREFIX}/include
+
+post-install:
+	${MKDIR} ${STAGEDIR}${DOCSDIR}
+	cd ${WRKSRC}/docs && ${COPYTREE_SHARE} ./ ${STAGEDIR}${DOCSDIR}
+
+.include <bsd.port.mk>
diff --git a/biology/seqan1/distinfo b/biology/seqan1/distinfo
new file mode 100644
index 000000000000..3e7a0a49d7b4
--- /dev/null
+++ b/biology/seqan1/distinfo
@@ -0,0 +1,2 @@
+SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb
+SIZE (seqan-1.3.1.zip) = 8787521
diff --git a/biology/seqan1/pkg-descr b/biology/seqan1/pkg-descr
new file mode 100644
index 000000000000..5f27809a1ba8
--- /dev/null
+++ b/biology/seqan1/pkg-descr
@@ -0,0 +1,10 @@
+SeqAn is an open source C++ library of efficient algorithms
+and data structures for the analysis of sequences with the
+focus on biological data.
+
+This port includes only the library, the apps have been
+moved to biology/seqan-apps. This is the last release of
+the version 1 API, it is highly recommended to upgrade to 
+biology/seqan (version 2).
+
+WWW: http://www.seqan.de/
diff --git a/biology/seqan1/pkg-plist b/biology/seqan1/pkg-plist
new file mode 100644
index 000000000000..e6c2faed81f0
--- /dev/null
+++ b/biology/seqan1/pkg-plist
@@ -0,0 +1,1983 @@
+include/seqan.h
+include/seqan/LICENSE
+include/seqan/align.h
+include/seqan/align/align_algorithms.h
+include/seqan/align/align_base.h
+include/seqan/align/align_cols_base.h
+include/seqan/align/align_dynprog.h
+include/seqan/align/align_generated_forwards.h
+include/seqan/align/align_hirschberg.h
+include/seqan/align/align_iterator_base.h
+include/seqan/align/align_local_dynprog.h
+include/seqan/align/align_local_dynprog_banded.h
+include/seqan/align/align_myers.h
+include/seqan/align/align_trace.h
+include/seqan/align/gaps_array.h
+include/seqan/align/gaps_base.h
+include/seqan/align/gaps_iterator_base.h
+include/seqan/align/gaps_sumlist.h
+include/seqan/align/hirschberg_set.h
+include/seqan/align/matrix_base.h
+include/seqan/basic.h
+include/seqan/basic/basic_aggregates.h
+include/seqan/basic/basic_allocator_chunkpool.h
+include/seqan/basic/basic_allocator_interface.h
+include/seqan/basic/basic_allocator_multipool.h
+include/seqan/basic/basic_allocator_simple.h
+include/seqan/basic/basic_allocator_singlepool.h
+include/seqan/basic/basic_allocator_to_std.h
+include/seqan/basic/basic_alphabet_interface.h
+include/seqan/basic/basic_alphabet_interface2.h
+include/seqan/basic/basic_alphabet_simple.h
+include/seqan/basic/basic_alphabet_simple_tabs.h
+include/seqan/basic/basic_alphabet_trait_basic.h
+include/seqan/basic/basic_compare.h
+include/seqan/basic/basic_converter.h
+include/seqan/basic/basic_counted_ptr.h
+include/seqan/basic/basic_debug.h
+include/seqan/basic/basic_definition.h
+include/seqan/basic/basic_forwards.h
+include/seqan/basic/basic_generated_forwards.h
+include/seqan/basic/basic_holder.h
+include/seqan/basic/basic_holder_dynamic.h
+include/seqan/basic/basic_host.h
+include/seqan/basic/basic_iterator.h
+include/seqan/basic/basic_iterator_adapt_std.h
+include/seqan/basic/basic_iterator_adaptor.h
+include/seqan/basic/basic_iterator_base.h
+include/seqan/basic/basic_iterator_position.h
+include/seqan/basic/basic_iterator_simple.h
+include/seqan/basic/basic_logvalue.h
+include/seqan/basic/basic_metaprogramming.h
+include/seqan/basic/basic_operator.h
+include/seqan/basic/basic_parallelism.h
+include/seqan/basic/basic_pointer.h
+include/seqan/basic/basic_profchar.h
+include/seqan/basic/basic_profile.h
+include/seqan/basic/basic_proxy.h
+include/seqan/basic/basic_sse2.h
+include/seqan/basic/basic_tag.h
+include/seqan/basic/basic_testing.h
+include/seqan/basic/basic_transport.h
+include/seqan/basic/basic_type.h
+include/seqan/basic/basic_volatile_ptr.h
+include/seqan/blast.h
+include/seqan/blast/blast_base.h
+include/seqan/blast/blast_generated_forwards.h
+include/seqan/blast/blast_hit.h
+include/seqan/blast/blast_hit_iterator.h
+include/seqan/blast/blast_hsp.h
+include/seqan/blast/blast_hsp_iterator.h
+include/seqan/blast/blast_iterator.h
+include/seqan/blast/blast_parsing.h
+include/seqan/blast/blast_report.h
+include/seqan/blast/blast_run.h
+include/seqan/blast/blast_stream_hit.h
+include/seqan/blast/blast_stream_hit_iterator.h
+include/seqan/blast/blast_stream_hsp_iterator.h
+include/seqan/blast/blast_stream_report.h
+include/seqan/chaining.h
+include/seqan/chaining/chain_base.h
+include/seqan/chaining/chain_generic.h
+include/seqan/chaining/chain_meta_fragment.h
+include/seqan/chaining/chain_point.h
+include/seqan/chaining/chain_wrapper_point.h
+include/seqan/chaining/chaining_generated_forwards.h
+include/seqan/chaining/fragment.h
+include/seqan/chaining/geom_distribution.h
+include/seqan/chaining/range_max_tree.h
+include/seqan/chaining/range_tree.h
+include/seqan/chaining/rmt_base.h
+include/seqan/chaining/rmt_common_algos.h
+include/seqan/chaining/rmt_compl_algos.h
+include/seqan/chaining/rmt_def_algos.h
+include/seqan/chaining/rmt_skip_base_element.h
+include/seqan/chaining/rmt_skip_element.h
+include/seqan/chaining/rt_base.h
+include/seqan/chaining/rt_common_algos.h
+include/seqan/chaining/rt_impl.h
+include/seqan/chaining/rt_skip_base_element.h
+include/seqan/chaining/rt_skip_element.h
+include/seqan/chaining/rt_sl_base.h
+include/seqan/chaining/rt_sl_compl_algos.h
+include/seqan/chaining/rt_sl_def_algos.h
+include/seqan/chaining/rt_sl_impl.h
+include/seqan/chaining/score_chain.h
+include/seqan/chaining/score_chain_sop.h
+include/seqan/chaining/score_manhattan.h
+include/seqan/chaining/score_zero.h
+include/seqan/chaining/skip_base_element.h
+include/seqan/chaining/skip_element.h
+include/seqan/chaining/skip_list.h
+include/seqan/chaining/skip_list_base.h
+include/seqan/chaining/skip_list_dynamic.h
+include/seqan/chaining/skip_list_impl.h
+include/seqan/chaining/skip_list_iterator.h
+include/seqan/chaining/skip_list_type.h
+include/seqan/chaining/skip_pool_alloc.h
+include/seqan/chaining/tree_chain.h
+include/seqan/chaining/tree_chain_sop.h
+include/seqan/chaining/tree_chain_utils.h
+include/seqan/consensus.h
+include/seqan/consensus/consensus_base.h
+include/seqan/consensus/consensus_generated_forwards.h
+include/seqan/consensus/consensus_library.h
+include/seqan/consensus/consensus_realign.h
+include/seqan/consensus/consensus_score.h
+include/seqan/file.h
+include/seqan/file/chunk_collector.h
+include/seqan/file/cstream.h
+include/seqan/file/file_array.h
+include/seqan/file/file_base.h
+include/seqan/file/file_cstyle.h
+include/seqan/file/file_filereader.h
+include/seqan/file/file_filereaderiterator.h
+include/seqan/file/file_format.h
+include/seqan/file/file_format_cgviz.h
+include/seqan/file/file_format_embl.h
+include/seqan/file/file_format_fasta.h
+include/seqan/file/file_format_fasta_align.h
+include/seqan/file/file_format_genbank.h
+include/seqan/file/file_format_guess.h
+include/seqan/file/file_format_mmap.h
+include/seqan/file/file_format_raw.h
+include/seqan/file/file_forwards.h
+include/seqan/file/file_generated_forwards.h
+include/seqan/file/file_page.h
+include/seqan/file/file_page_raid0.h
+include/seqan/file/meta.h
+include/seqan/file/stream.h
+include/seqan/file/stream_algorithms.h
+include/seqan/file/string_external.h
+include/seqan/file/string_mmap.h
+include/seqan/find.h
+include/seqan/find/find_abndm.h
+include/seqan/find/find_ahocorasick.h
+include/seqan/find/find_base.h
+include/seqan/find/find_begin.h
+include/seqan/find/find_bndm.h
+include/seqan/find/find_bom.h
+include/seqan/find/find_generated_forwards.h
+include/seqan/find/find_hamming_simple.h
+include/seqan/find/find_horspool.h
+include/seqan/find/find_multi.h
+include/seqan/find/find_multiple_bfam.h
+include/seqan/find/find_multiple_shiftand.h
+include/seqan/find/find_myers_ukkonen.h
+include/seqan/find/find_pattern_base.h
+include/seqan/find/find_pex.h
+include/seqan/find/find_score.h
+include/seqan/find/find_set_horspool.h
+include/seqan/find/find_shiftand.h
+include/seqan/find/find_shiftor.h
+include/seqan/find/find_simple.h
+include/seqan/find/find_wild_shiftand.h
+include/seqan/find/find_wumanber.h
+include/seqan/find2.h
+include/seqan/find2/find2_generated_forwards.h
+include/seqan/find2/find_approx_dpsearch.h
+include/seqan/find2/find_approx_find_begin.h
+include/seqan/find2/find_base.h
+include/seqan/find2/find_exact_shiftand.h
+include/seqan/find2/find_exact_simple.h
+include/seqan/find2/find_finder_default.h
+include/seqan/find2/find_hamming_simple.h
+include/seqan/find2/find_multiple_exact_simple.h
+include/seqan/find2/find_pattern_wild_shiftand.h
+include/seqan/find_motif.h
+include/seqan/find_motif/em_algorithm.h
+include/seqan/find_motif/find_motif_base.h
+include/seqan/find_motif/find_motif_epatternbranching.h
+include/seqan/find_motif/find_motif_generated_forwards.h
+include/seqan/find_motif/find_motif_pms1.h
+include/seqan/find_motif/find_motif_pmsp.h
+include/seqan/find_motif/find_motif_projection.h
+include/seqan/find_motif/frequency_distribution.h
+include/seqan/find_motif/profile.h
+include/seqan/find_motif/pseudocount_base.h
+include/seqan/find_motif/pseudocount_mode_c.h
+include/seqan/find_motif/pseudocount_mode_p.h
+include/seqan/find_motif/sequence_model_types.h
+include/seqan/graph_algorithms.h
+include/seqan/graph_algorithms/graph_algorithm.h
+include/seqan/graph_algorithms/graph_algorithm_heap_tree.h
+include/seqan/graph_algorithms/graph_algorithm_hmm.h
+include/seqan/graph_algorithms/graph_algorithm_lis_his.h
+include/seqan/graph_algorithms/graph_algorithms_generated_forwards.h
+include/seqan/graph_align.h
+include/seqan/graph_align/graph_align_banded_gotoh.h
+include/seqan/graph_align/graph_align_banded_needleman_wunsch.h
+include/seqan/graph_align/graph_align_banded_smith_waterman_clump.h
+include/seqan/graph_align/graph_align_base.h
+include/seqan/graph_align/graph_align_config.h
+include/seqan/graph_align/graph_align_generated_forwards.h
+include/seqan/graph_align/graph_align_gotoh.h
+include/seqan/graph_align/graph_align_hirschberg.h
+include/seqan/graph_align/graph_align_interface.h
+include/seqan/graph_align/graph_align_needleman_wunsch.h
+include/seqan/graph_align/graph_align_smith_waterman.h
+include/seqan/graph_align/graph_align_smith_waterman_clump.h
+include/seqan/graph_msa.h
+include/seqan/graph_msa/graph_align_tcoffee_base.h
+include/seqan/graph_msa/graph_align_tcoffee_distance.h
+include/seqan/graph_msa/graph_align_tcoffee_guidetree.h
+include/seqan/graph_msa/graph_align_tcoffee_io.h
+include/seqan/graph_msa/graph_align_tcoffee_kmer.h
+include/seqan/graph_msa/graph_align_tcoffee_library.h
+include/seqan/graph_msa/graph_align_tcoffee_msa.h
+include/seqan/graph_msa/graph_align_tcoffee_progressive.h
+include/seqan/graph_msa/graph_align_tcoffee_refinement.h
+include/seqan/graph_msa/graph_msa_generated_forwards.h
+include/seqan/graph_types.h
+include/seqan/graph_types/graph_base.h
+include/seqan/graph_types/graph_drawing.h
+include/seqan/graph_types/graph_edgestump.h
+include/seqan/graph_types/graph_idmanager.h
+include/seqan/graph_types/graph_impl_automaton.h
+include/seqan/graph_types/graph_impl_directed.h
+include/seqan/graph_types/graph_impl_fragment.h
+include/seqan/graph_types/graph_impl_hmm.h
+include/seqan/graph_types/graph_impl_oracle.h
+include/seqan/graph_types/graph_impl_tree.h
+include/seqan/graph_types/graph_impl_trie.h
+include/seqan/graph_types/graph_impl_undirected.h
+include/seqan/graph_types/graph_impl_wordgraph.h
+include/seqan/graph_types/graph_interface.h
+include/seqan/graph_types/graph_iterator.h
+include/seqan/graph_types/graph_iterator_adjacency.h
+include/seqan/graph_types/graph_iterator_bfs.h
+include/seqan/graph_types/graph_iterator_dfs.h
+include/seqan/graph_types/graph_iterator_edge.h
+include/seqan/graph_types/graph_iterator_outedge.h
+include/seqan/graph_types/graph_iterator_vertex.h
+include/seqan/graph_types/graph_property.h
+include/seqan/graph_types/graph_types_generated_forwards.h
+include/seqan/graph_types/graph_utility_parsing.h
+include/seqan/index.h
+include/seqan/index/find_index.h
+include/seqan/index/find_index_approx.h
+include/seqan/index/find_index_esa.h
+include/seqan/index/find_index_qgram.h
+include/seqan/index/find_quasar.h
+include/seqan/index/find_swift.h
+include/seqan/index/index_base.h
+include/seqan/index/index_bwt.h
+include/seqan/index/index_childtab.h
+include/seqan/index/index_dfi.h
+include/seqan/index/index_esa_algs.h
+include/seqan/index/index_esa_algs_multi.h
+include/seqan/index/index_esa_base.h
+include/seqan/index/index_esa_drawing.h
+include/seqan/index/index_esa_stree.h
+include/seqan/index/index_generated_forwards.h
+include/seqan/index/index_lcp.h
+include/seqan/index/index_lcp_tree.h
+include/seqan/index/index_manual_forwards.h
+include/seqan/index/index_pizzachili.h
+include/seqan/index/index_pizzachili_find.h
+include/seqan/index/index_pizzachili_string.h
+include/seqan/index/index_qgram.h
+include/seqan/index/index_qgram_openaddressing.h
+include/seqan/index/index_sa_btree.h
+include/seqan/index/index_sa_bwtwalk.h
+include/seqan/index/index_sa_lss.h
+include/seqan/index/index_sa_mm.h
+include/seqan/index/index_sa_qsort.h
+include/seqan/index/index_shawarma.h
+include/seqan/index/index_shims.h
+include/seqan/index/index_skew3.h
+include/seqan/index/index_skew7.h
+include/seqan/index/index_skew7_multi.h
+include/seqan/index/index_wotd.h
+include/seqan/index/pipe_merger3.h
+include/seqan/index/pipe_merger7.h
+include/seqan/index/pizzachili_api.h
+include/seqan/index/pump_extender3.h
+include/seqan/index/pump_extender7.h
+include/seqan/index/pump_lcp_core.h
+include/seqan/index/pump_separator7.h
+include/seqan/index/radix.h
+include/seqan/index/repeat_base.h
+include/seqan/index/shape_base.h
+include/seqan/index/shape_gapped.h
+include/seqan/index/shape_onegapped.h
+include/seqan/index/shape_predefined.h
+include/seqan/index/shape_threshold.h
+include/seqan/map.h
+include/seqan/map/map_adapter_stl.h
+include/seqan/map/map_base.h
+include/seqan/map/map_chooser.h
+include/seqan/map/map_generated_forwards.h
+include/seqan/map/map_skiplist.h
+include/seqan/map/map_vector.h
+include/seqan/map/sumlist.h
+include/seqan/map/sumlist_mini.h
+include/seqan/map/sumlist_skip.h
+include/seqan/misc/edit_environment.h
+include/seqan/misc/misc_base.h
+include/seqan/misc/misc_cmdparser.h
+include/seqan/misc/misc_dequeue.h
+include/seqan/misc/misc_generated_forwards.h
+include/seqan/misc/misc_interval_tree.h
+include/seqan/misc/misc_long_word.h
+include/seqan/misc/misc_map.h
+include/seqan/misc/misc_parsing.h
+include/seqan/misc/misc_random.h
+include/seqan/misc/misc_set.h
+include/seqan/misc/misc_svg.h
+include/seqan/misc/priority_type_base.h
+include/seqan/misc/priority_type_heap.h
+include/seqan/modifier.h
+include/seqan/modifier/modifier_alphabet.h
+include/seqan/modifier/modifier_alphabet_expansion.h
+include/seqan/modifier/modifier_functors.h
+include/seqan/modifier/modifier_generated_forwards.h
+include/seqan/modifier/modifier_iterator.h
+include/seqan/modifier/modifier_reverse.h
+include/seqan/modifier/modifier_shortcuts.h
+include/seqan/modifier/modifier_string.h
+include/seqan/modifier/modifier_view.h
+include/seqan/parallel.h
+include/seqan/parallel/parallel_atomic_misc.h
+include/seqan/parallel/parallel_atomic_primitives.h
+include/seqan/parallel/parallel_generated_forwards.h
+include/seqan/parallel/parallel_macros.h
+include/seqan/pipe.h
+include/seqan/pipe/pipe_base.h
+include/seqan/pipe/pipe_caster.h
+include/seqan/pipe/pipe_counter.h
+include/seqan/pipe/pipe_echoer.h
+include/seqan/pipe/pipe_edit_environment.h
+include/seqan/pipe/pipe_filter.h
+include/seqan/pipe/pipe_generated_forwards.h
+include/seqan/pipe/pipe_iterator.h
+include/seqan/pipe/pipe_joiner.h
+include/seqan/pipe/pipe_namer.h
+include/seqan/pipe/pipe_sampler.h
+include/seqan/pipe/pipe_shifter.h
+include/seqan/pipe/pipe_source.h
+include/seqan/pipe/pipe_tupler.h
+include/seqan/pipe/pool_base.h
+include/seqan/pipe/pool_mapper.h
+include/seqan/pipe/pool_sorter.h
+include/seqan/platform.h
+include/seqan/platform/platform_gcc.h
+include/seqan/platform/platform_generated_forwards.h
+include/seqan/platform/platform_mingw.h
+include/seqan/platform/platform_solaris.h
+include/seqan/platform/platform_windows.h
+include/seqan/random.h
+include/seqan/random/ext_MersenneTwister.h
+include/seqan/random/random_base.h
+include/seqan/random/random_generated_forwards.h
+include/seqan/random/random_geometric.h
+include/seqan/random/random_lognormal.h
+include/seqan/random/random_mt19937.h
+include/seqan/random/random_normal.h
+include/seqan/random/random_rng_functor.h
+include/seqan/random/random_shuffle.h
+include/seqan/random/random_uniform.h
+include/seqan/refinement.h
+include/seqan/refinement/graph_algorithm_refine_align.h
+include/seqan/refinement/graph_algorithm_refine_aligngraph.h
+include/seqan/refinement/graph_algorithm_refine_annotation.h
+include/seqan/refinement/graph_algorithm_refine_exact.h
+include/seqan/refinement/graph_algorithm_refine_exact_iterative.h
+include/seqan/refinement/graph_algorithm_refine_fragment.h
+include/seqan/refinement/graph_algorithm_refine_inexact.h
+include/seqan/refinement/graph_algorithm_refine_scoring.h
+include/seqan/refinement/graph_impl_align.h
+include/seqan/refinement/graph_impl_align_adapt.h
+include/seqan/refinement/refinement_generated_forwards.h
+include/seqan/score.h
+include/seqan/score/score_base.h
+include/seqan/score/score_edit.h
+include/seqan/score/score_generated_forwards.h
+include/seqan/score/score_matrix.h
+include/seqan/score/score_matrix_data.h
+include/seqan/score/score_simple.h
+include/seqan/seeds.h
+include/seqan/seeds/banded_align.h
+include/seqan/seeds/banded_chain_align.h
+include/seqan/seeds/banded_chain_align_affine.h
+include/seqan/seeds/global_seed_chain.h
+include/seqan/seeds/memoryManager_base.h
+include/seqan/seeds/memoryManager_int.h
+include/seqan/seeds/propertyMap.h
+include/seqan/seeds/seedHandlingTags.h
+include/seqan/seeds/seedSet_base.h
+include/seqan/seeds/seedSet_iterator.h
+include/seqan/seeds/seedSet_score.h
+include/seqan/seeds/seed_base.h
+include/seqan/seeds/seed_multi.h
+include/seqan/seeds/seeds_generated_forwards.h
+include/seqan/seeds2.h
+include/seqan/seeds2/align_chain_banded.h
+include/seqan/seeds2/align_dynprog_affine.h
+include/seqan/seeds2/align_dynprog_banded_affine.h
+include/seqan/seeds2/align_dynprog_banded_linear.h
+include/seqan/seeds2/align_dynprog_linear.h
+include/seqan/seeds2/basic_iter_indirect.h
+include/seqan/seeds2/seeds2_generated_forwards.h
+include/seqan/seeds2/seeds_base.h
+include/seqan/seeds2/seeds_combination.h
+include/seqan/seeds2/seeds_extension.h
+include/seqan/seeds2/seeds_global_chaining.h
+include/seqan/seeds2/seeds_global_chaining_base.h
+include/seqan/seeds2/seeds_global_chaining_gusfield.h
+include/seqan/seeds2/seeds_seed_base.h
+include/seqan/seeds2/seeds_seed_chained.h
+include/seqan/seeds2/seeds_seed_diagonal.h
+include/seqan/seeds2/seeds_seed_set_base.h
+include/seqan/seeds2/seeds_seed_set_non_scored.h
+include/seqan/seeds2/seeds_seed_set_scored.h
+include/seqan/seeds2/seeds_seed_set_unordered.h
+include/seqan/seeds2/seeds_seed_simple.h
+include/seqan/sequence.h
+include/seqan/sequence/adapt_array_pointer.h
+include/seqan/sequence/adapt_std_list.h
+include/seqan/sequence/adapt_std_string.h
+include/seqan/sequence/adapt_std_vector.h
+include/seqan/sequence/iter_concat_virtual.h
+include/seqan/sequence/segment_base.h
+include/seqan/sequence/segment_infix.h
+include/seqan/sequence/segment_prefix.h
+include/seqan/sequence/segment_suffix.h
+include/seqan/sequence/sequence_concatenator.h
+include/seqan/sequence/sequence_forwards.h
+include/seqan/sequence/sequence_generated_forwards.h
+include/seqan/sequence/sequence_interface.h
+include/seqan/sequence/sequence_lexical.h
+include/seqan/sequence/sequence_shortcuts.h
+include/seqan/sequence/sequence_stream.h
+include/seqan/sequence/string_alloc.h
+include/seqan/sequence/string_array.h
+include/seqan/sequence/string_base.h
+include/seqan/sequence/string_block.h
+include/seqan/sequence/string_cstyle.h
+include/seqan/sequence/string_packed.h
+include/seqan/sequence/string_set_base.h
+include/seqan/sequence/string_set_concat_direct.h
+include/seqan/sequence/string_set_dependent_generous.h
+include/seqan/sequence/string_set_dependent_tight.h
+include/seqan/sequence/string_set_owner.h
+include/seqan/sequence_journaled.h
+include/seqan/sequence_journaled/journal_entries_sorted_array.h
+include/seqan/sequence_journaled/journal_entries_unbalanced_tree.h
+include/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h
+include/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h
+include/seqan/sequence_journaled/journal_entry.h
+include/seqan/sequence_journaled/sequence_journaled.h
+include/seqan/sequence_journaled/sequence_journaled_forwards.h
+include/seqan/sequence_journaled/sequence_journaled_generated_forwards.h
+include/seqan/sequence_journaled/sequence_journaled_iterator.h
+include/seqan/statistics.h
+include/seqan/statistics/statistics_base.h
+include/seqan/statistics/statistics_generated_forwards.h
+include/seqan/statistics/statistics_markov_model.h
+include/seqan/store.h
+include/seqan/store/store_align.h
+include/seqan/store/store_align_intervals.h
+include/seqan/store/store_all.h
+include/seqan/store/store_annotation.h
+include/seqan/store/store_base.h
+include/seqan/store/store_contig.h
+include/seqan/store/store_generated_forwards.h
+include/seqan/store/store_intervaltree.h
+include/seqan/store/store_io.h
+include/seqan/store/store_io_bam.h
+include/seqan/store/store_io_gff.h
+include/seqan/store/store_io_sam.h
+include/seqan/store/store_io_ucsc.h
+include/seqan/store/store_library.h
+include/seqan/store/store_matepair.h
+include/seqan/store/store_read.h
+include/seqan/system.h
+include/seqan/system/file_async.h
+include/seqan/system/file_directory.h
+include/seqan/system/file_manual_forwards.h
+include/seqan/system/file_sync.h
+include/seqan/system/system_base.h
+include/seqan/system/system_event.h
+include/seqan/system/system_generated_forwards.h
+include/seqan/system/system_manual_forwards.h
+include/seqan/system/system_mutex.h
+include/seqan/system/system_sema.h
+include/seqan/system/system_thread.h
+include/seqan/version.h
+%%PORTDOCS%%%%DOCSDIR%%/ADAPTION.char+array.html
+%%PORTDOCS%%%%DOCSDIR%%/ADAPTION.std_3a_3a_F_I_L_E+_2a.html
+%%PORTDOCS%%%%DOCSDIR%%/ADAPTION.std_3a_3abasic__string.html
+%%PORTDOCS%%%%DOCSDIR%%/ADAPTION.std_3a_3aiostream.html
+%%PORTDOCS%%%%DOCSDIR%%/ADAPTION.std_3a_3alist.html
+%%PORTDOCS%%%%DOCSDIR%%/ADAPTION.std_3a_3avector.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Align.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Align_Cols.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Align_Config.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Align_Quality_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Aligned_Read_Layout.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Aligned_Read_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Allocator.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Async_Request.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Auto_Seq_Format.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Blast_Hit.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Blast_Hsp.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Blast_Report.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Bundle2.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Bundle3.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Bundle5.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Command_Line_Option.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Command_Line_Parser.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Concatenator_Many_To_One.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Contig_File.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Contig_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Dequeue.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Edge_Stump.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_External+_Property+_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_File.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_File_Format.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Fragment.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Fragment_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Frequency_Distribution.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Functor_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Functor_Convert.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Functor_Lowcase.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Functor_Upcase.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Gap_Anchor.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Hardwired_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Holder.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Id_Manager.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Internal_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Internal_Pointer_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Internal_Raw_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Interval_And_Cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Interval_Tree.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Interval_Tree_Node.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Iter.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Lexical.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Library_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Local_Alignment_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Markov_Model.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Mate_Pair_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Matrix.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Memory_Manager.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Modified_Alphabet.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Modified_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Modified_String.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Motif_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Name_Store_Cache.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Pair.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Pattern.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Pdf.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Pipe.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Point_And_Cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Pool.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Priority_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Property_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Proxy.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Pseudocount.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Read_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Rng.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Seed_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Segment.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Simple_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_String.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_String_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Tag_Selector.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_To_Std_Allocator.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Triple.html
+%%PORTDOCS%%%%DOCSDIR%%/CLASS_Tuple.html
+%%PORTDOCS%%%%DOCSDIR%%/CONCEPT_Allocator.html
+%%PORTDOCS%%%%DOCSDIR%%/CONCEPT_Container.html
+%%PORTDOCS%%%%DOCSDIR%%/CONCEPT_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/CONCEPT_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/CONCEPT_Pattern.html
+%%PORTDOCS%%%%DOCSDIR%%/CONCEPT_Rooted+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/CONCEPT_Simple+_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_All+_Pairs+_Shortest+_Path.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Allocators.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Alphabets.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Approximate+_Searching.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Bellman-_Ford+_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Blast+_Reports.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Breadth-_First+_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Constraint+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Depth-_First+_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Dijkstras+_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Exact+_Searching.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_File+_Format+_I_2f_O.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Floyd-_Warshall+_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Global+_Alignments.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_H_M_M+_Silent+_States.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_H_M_M.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Heaviest+_Increasing+_Subsequence.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Index+_Finder+_String_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Index+_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Iterator+_Basics.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Kruskals+_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Local+_Alignments.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Longest+_Common+_Subsequence.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Longest+_Increasing+_Subsequence.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Maximal+_Repeats.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Maximal+_Unique+_Matches.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Maximum+_Flow.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Mod_Reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Mod_View.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Motif+_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Mummy.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Nested+_Modifiers.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Pizza+_26+_Chili+_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Prims+_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Rooted+_Iterators.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Shortest+_Path+in+_D_A_Gs.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_String+_Basics.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Strongly+_Connected+_Components.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Suffix+_Array.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Supermaximal+_Repeats.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Topological+_Sort.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Transitive+_Closure.html
+%%PORTDOCS%%%%DOCSDIR%%/DEMO_Wildcard+_Searching.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.abs_Freq_Of_Letters_In_Seq.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.abs_Freq_Of_Letters_In_Set_Of_Seqs.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Argument_Text.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Child.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Edge.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Help_Line.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Interval.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Line.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Option.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Section.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Seeds.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Title_Line.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Usage_Line.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Version_Line.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.add_Vertex.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.adjust_Top.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.alignment_Evaluation.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.all_Pairs_Shortest_Path.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.allocate.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.append.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.append_Aligned_Read.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.append_Diag.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.append_Mate_Pair.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.append_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.append_Read.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.append_Seqs.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.append_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.argument_Count.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.argument_Text.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Clear_Space.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Construct.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Construct_Copy.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Construct_Move.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Copy.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Copy_Backward.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Copy_Forward.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Destruct.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Fill.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Move.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Move_Backward.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.array_Move_Forward.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Begin_State.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Cropped_Seq_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Emission_Probability.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_End_State.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Next_S.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Next_T.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Property.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Qual.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Qual_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Qualities.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Quality_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Root.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Seq.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Seq_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Silent_Status.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_String_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Target.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Transition_Probability.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.assign_Value_By_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.async_Read_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.async_Write_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.at_Begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.at_End.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.at_End_Of_Sequence.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.at_Nil.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.atomic_Add.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.atomic_Cas.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.atomic_Dec.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.atomic_Inc.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.atomic_Max.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.atomic_Min.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.atomic_Or.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.atomic_Xor.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.back.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.background_Frequency.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.backward_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.banded_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.banded_Chain_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.begin_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.begin_Read.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.begin_State.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.begin_Write.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.bellman_Ford_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.binomial_Coefficient.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.blast_23get_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.breadth_First_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.bundle2.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.bundle3.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.bundle5.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.bwt_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.calculate_Insert_Sizes.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.calculate_Mate_Indices.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.can_Parse_String.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.cancel.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.capacity.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.child_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.child_Vertex.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.children_Are_Leaves.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.clear.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.clear_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.clear_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.clear_Reads.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.clear_Vertices.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.clipped_Begin_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.clipped_End_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.close.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.col.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.collect_Leaves.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.cols.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.compact_Aligned_Reads.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.compact_Pair_Match_Ids.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.compare.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.complement.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.complete_Profile.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.compute_Generous_Capacity.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.concat.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.connected_Components.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.container.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.convert.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.convert_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.convert_Impl.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.convert_Matches_To_Global_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.convert_Pair_Wise_To_Global_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.convert_Pattern_To_Profile.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.convert_Residue_To_Frequency_Dist.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.convert_Set_Of_Patterns_To_Profile.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.count_Characters.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.count_Children.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.count_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.count_Occurrences.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.count_Occurrences_Multiple.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.cpu_Time.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_B_W_Table.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Childtab.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Count_Array.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Interval_Tree.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Lcp_Table.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Oracle.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Oracle_On_Reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Q_Gram_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Q_Gram_Index_Dir_Only.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Q_Gram_Index_S_A_Only.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Root.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Suffix_Array.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Suffix_Trie.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Trie.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Trie_On_Reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.create_Wotd_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.dag_Shortest_Path.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.database_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.database_Orientation_Plus.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.deallocate.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.degree.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.dependent.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.dependent_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.depth_First_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.detach.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.determine_Consensus_Seq.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.difference.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.dijkstra.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.dimension.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.dir_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.display.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.display_Result.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.em.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.emission_Probability.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.empty.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.empty_Parent_Edge.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.empty_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.end.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.end_Diagonal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.end_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.end_Read.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.end_State.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.end_Write.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.erase.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.erase_Back.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.expectation.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.extend_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.extend_Seed_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.extend_Seeds.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.extend_Seeds_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.factorial.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.find.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.find_Begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.find_Edge.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.find_Intervals.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.find_Intervals_Exclude_Touching.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.find_Motif.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.find_Vertex.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.flatten.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.floyd_Warshall_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.flush.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.ford_Fulkerson_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.forward_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.fragment_Begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.fragment_Length.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.front.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.gap_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.gap_Value_Impl.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.generate_Sequence.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Adjacency_Matrix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Argument_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Argument_Values.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Begin_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Begin_State.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Bit_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Database_Begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Database_End.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Database_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Distance_Matrix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_E_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_E_Value_Cutoff.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Emission_Probability.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_End_State.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Fibre.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_First_Covered_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Frequency.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Gapped_Kappa.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Gapped_Lambda.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Get_Extension.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Get_Open.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Id_By_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Id_Lower_Bound.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Id_Upper_Bound.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Kappa.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Kmer_Similarity_Matrix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Lambda.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Last_Covered_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Left_Boundary.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Mate_No.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Motif.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Next.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Next_S.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Next_T.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Nil.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Num_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Occurrence.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Occurrences.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Occurrences_Bwt.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Option_Value_Long.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Option_Value_Short.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Option_Values_Long.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Option_Values_Short.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Projected_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Property.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Query_Begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Query_End.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Query_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Read.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Right_Boundary.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Root.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Seq_No.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Seq_Offset.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Step_Size.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_String_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Successor.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Swift_Hits.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Target.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Transition_Probability.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.get_Value_By_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.global_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.global_Chaining.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.global_Msa_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_Begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_Down.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_End.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_Further.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_Next.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_Nil.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_Previous.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_Right.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_Root.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.go_Up.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.guess_File_Format.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.guess_Format.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.guess_Format_From_Filename.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.hamming_Distance.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.has_Option_Long.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.has_Option_Short.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.has_Prefix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.hash.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.hash2.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.hash2_Next.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.hash2_Upper.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.hash_Next.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.hash_Upper.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.haystack.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.heaviest_Increasing_Subsequence.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.help.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.help_Text.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.host.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.host_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.host_Hit.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.host_Report.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.id_Count.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.id_In_Use.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.id_To_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.in_Degree.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Bucket_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Bwt.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Childtab.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Counts.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Counts_Dir.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Create.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Dir.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Lcp.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Lcpe.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Raw_S_A.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Raw_Text.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Require.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_S_A.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Supplied.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.index_Text.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.infimum_Value_Impl.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.infix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.infix_With_Length.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.insert.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.insert_Gap.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.insert_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.insert_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.integrate_Align.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.inverse_Hash.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Boolean_Option.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Double_Option.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Equal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Gap.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Greater.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Greater_Or_Equal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Hidden_Option.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Int_Option.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Label_Option.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Left_Maximal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Less.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Less_Or_Equal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Not_Equal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Option_List.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Option_Mandatory.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Partially_Left_Extensible.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Prefix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Reversed.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Right_Terminal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Root.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Set_Long.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Set_Short.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Silent.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_String_Option.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.is_Unique.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.iter.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.key.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.kruskals_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.label.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.layout_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.lca.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.lcp.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.lcp_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.lcp_Length.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.lcpe_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.left_Boundary.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.left_Diagonal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.left_Dim0.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.left_Dim1.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.left_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.length.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.load_Contig.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.load_Contigs.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.load_Reads.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.load_Score_Matrix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.local_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.lock_Contig.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.lock_Contigs.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.log2.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.logarithmize.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.long_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.longest_Common_Subsequence.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.longest_Increasing_Subsequence.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.lower_Bound_Aligned_Reads.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.map_23add.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.map_23cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.map_23erase.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.map_23erase_All.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.map_23find.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.map_23has_Key.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.map_23insert.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.map_23value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.map_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.match_Refinement.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.max_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.maximum_Distance.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.min_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.motif_Count.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.move.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.move_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.move_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.mt_Rand.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.mt_Rand_Double.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.mt_Rand_Init.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.multi_Local_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.needle.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.next_S.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.next_T.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.node_Depth.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.node_Hull_Predicate.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.node_Predicate.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.node_Up.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.normalize.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.num_Children.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.num_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.num_Hits.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.num_Hsps.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.num_Tree_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.num_Vertices.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.obtain_I_D.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.obtain_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.open.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.open_Temp.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.ord_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.order_Occurrences.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.out_Degree.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.parent_Edge_First_Char.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.parent_Edge_Label.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.parent_Edge_Length.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.parent_Rep_Length.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.parent_Vertex.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.parse.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.parse_String.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.pick_Random_Number.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.pop.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.pos_Globalize.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.pos_Local_To_X.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.pos_Localize.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.pos_Of_Max.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.position_Range.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.position_Range_No_Clip.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.position_To_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.prefix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.prepend_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.prims_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.print_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.print_Debug_Level.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.progressive_Alignment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.property.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.push.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.quality_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.query_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.query_Orientation_Plus.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.range.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.rawsa_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.rawtext_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.re_Align.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.read.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.read_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.read_Feature.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.read_Line_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.read_Meta.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.refresh.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.release_All.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.release_I_D.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.release_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.remove_All_Children.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.remove_Child.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.remove_Edge.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.remove_Gap.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.remove_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.remove_In_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.remove_Out_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.remove_Value_By_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.remove_Vertex.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.rep_Length.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.replace.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.representative.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.required_Arguments.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.reserve.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.resize.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.resize_Edge_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.resize_Space.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.resize_Vertex_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.reverse_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.rewind.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.right_Boundary.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.right_Diagonal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.right_Dim0.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.right_Dim1.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.right_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.root.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.row.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.rows.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.sa_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Gap.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Gap_Extend.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Gap_Extend_Horizontal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Gap_Extend_Vertical.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Gap_Horizontal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Gap_Open.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Gap_Open_Horizontal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Gap_Open_Vertical.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Gap_Vertical.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Limit.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Match.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Mismatch.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.score_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.scoring_Scheme.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.seed_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.seek.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.sequence_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Begin_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Default_Score_Matrix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_End.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_End_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Eof.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Haystack.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Help_Text.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Host.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Left_Diagonal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Left_Dim0.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Left_Dim1.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Left_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Long_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Maximum_Distance.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Needle.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Option_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Quality_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Right_Diagonal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Right_Dim0.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Right_Dim1.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Right_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Score_Gap.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Score_Gap_Extend.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Score_Gap_Open.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Score_Limit.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Score_Match.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Score_Mismatch.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Scoring_Scheme.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Short_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Step_Size.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Strings.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.set_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.shape_To_String.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.share_Resources.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.short_Help.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.short_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.shrink_To_Fit.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.shuffle.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.silent_Status.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.size.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.slow_Nj_Tree.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.sort_Aligned_Reads.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.source.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.source_Begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.source_End.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.source_Length.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.source_Segment.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.source_Vertex.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.split.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.start_Diagonal.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.string_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.string_Set_Limits.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.string_To_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.strongly_Connected_Components.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.suffix.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.sum.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.sum_Of_Pairs_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.supremum_Value_Impl.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.swap.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.sys_Time.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.target.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.target_Vertex.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.tell.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.text_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.to_C_String.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.to_Lower.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.to_Source_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.to_Upper.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.to_View_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.topological_Sort.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.transition_Probability.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.transitive_Closure.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.transpose.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.triplet_Library_Extension.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.unlock_And_Free_Contig.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.unlock_And_Free_Contigs.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.unlock_Contig.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.unlock_Contigs.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.upgma_Tree.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.upper_Bound_Aligned_Reads.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.value.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.value_By_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.value_Construct.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.value_Construct_Move.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.value_Destruct.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.variance.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.version.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.viterbi_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.wait_For.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.weight.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.window_Find_Begin.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.window_Find_End.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.window_Find_Next.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.write.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.write_At.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.write_Contigs.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION.zscore.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Allocator_23clear.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Automaton_23label.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Blast_23get_Blast_Match_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Fileformat_23read.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Fileformat_23write.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Graph_23assign_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Graph_23is_Leaf.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Graph_23is_Root.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Index_23is_Leaf.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Pipelining_23front.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Priority_Type_23pop.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Priority_Type_23push.html
+%%PORTDOCS%%%%DOCSDIR%%/FUNCTION_Priority_Type_23top.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEXPAGE_Adaption.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEXPAGE_Class.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEXPAGE_Concept.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEXPAGE_Demo.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEXPAGE_Function.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEXPAGE_Metafunction.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEXPAGE_Shortcut.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEXPAGE_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEXPAGE_Tag.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Adaption.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Aggregates.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Alignments.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Basic.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Blast.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Fragment+_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Input_2f_Output.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Markov_Model.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Miscellaneous.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Modifier.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Motif+_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Pipelining.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Random.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Searching.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Seed+_Handling.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Class_Sequences.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Concept.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Demo.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Demo_Basics.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Demo_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Demo_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Demo_Miscellaneous.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Demo_Modifier.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Demo_Motif+_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Demo_Searching.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Demo_System.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function.sequences.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Alignments.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Alphabets.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Array+_Handling.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Atomic+_Operations.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Blast.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Chaining.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Class._Align.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Class.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Comparisons.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Containers.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Content+_Manipulation.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Dependent+_Objects.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Fragment+_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Input_2f_Output.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Iteration.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Memory.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Misc.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Miscellaneous.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Miscellaneous_3a.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Modifier.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Modifiers.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Motif+_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Pipelining.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Random.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Scoring.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Searching.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Seed+_Handling.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Function_Sequences.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Metafunction.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Metafunction_Basic.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Metafunction_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Metafunction_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Metafunction_Miscellaneous.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Metafunction_Searching.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Metafunction_Sequences.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Page.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Shortcut.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Shortcut_Input_2f_Output.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Shortcut_Iterators.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Shortcut_Modifier.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Shortcut_Pattern+_Matching.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Shortcut_Scoring.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Shortcut_Strings.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Aggregates.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Alignments.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Allocators.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Alphabets.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Blast.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Chaining.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Files.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Holders.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Iterators.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Map.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Miscellaneous.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Modifier.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Motif+_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Pattern+_Matching.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Pipelining.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Proxies.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Random.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Scoring.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Searching.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Seed+_Handling.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Segments.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Sequences.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Spec_Strings.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag_Fragment+_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag_Miscellaneous.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag_Motif+_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag_Random.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag_Scoring.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag_Searching.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag_Seed+_Handling.html
+%%PORTDOCS%%%%DOCSDIR%%/INDEX_Tag_Strings.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC.~_Holder.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Adaptor_Iterator_23_Iter.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Align_Quality_Store_Element_23_Align_Quality_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Aligned_Read_Store_Element_23_Aligned_Read_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Bottom_Up+_Iterator_23_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Chained_Seed_23_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Command_Line_Option_23_Command_Line_Option.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Command_Line_Parser_23_Command_Line_Parser.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Concat_Virtual+_Iterator_23_Iter.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Concatenator_Many_To_One_23_Concatenator_Many_To_One.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Contig_Store_Element_23_Contig_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Ext_String_23_String.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Filter_23_Pipe.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Finder_23_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Fragment_23_Fragment.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Gap_Anchor_23_Gap_Anchor.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Gaps_23_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Generic_Shape_23_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Geometric+_Pdf_23_Pdf.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Holder.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Infix_Segment_23_Segment.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Interval_And_Cargo_23_Interval_And_Cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Interval_Tree_23_Interval_Tree.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Interval_Tree_Node_23_Interval_Tree_Node.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Library_Store_Element_23_Library_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Local_Alignment_Finder_23_Local_Alignment_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Log-_Normal+_Pdf_23_Pdf.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Markov_Model_23_Markov_Model.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Markov_Model_23build.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Markov_Model_23emitted_Probability.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Markov_Model_23read.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Markov_Model_23set.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Markov_Model_23write.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Mate_Pair_Store_Element_23_Mate_Pair_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Max_Repeats+_Iterator_23_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Mersenne+_Twister+_Rng_23_Rng.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Multi_Mems+_Iterator_23_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Mums+_Iterator_23_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Namer_23_Pipe.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Normal+_Pdf_23_Pdf.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_One_Gapped_Shape_23_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Pair_23_Pair.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Pipe_23_Pipe.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Point_And_Cargo_23_Point_And_Cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Position_Iterator_23_Iter.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Prefix_Segment_23_Segment.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Read_Store_Element_23_Read_Store_Element.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Rng+_Functor_23_Rng.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Rng_23operator_28_29.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Score+_Matrix_23_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Score_23_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Seed_Set_23_Seed_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Shape_23_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Simple_Seed_23_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Simple_Shape_23_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Suffix_Segment_23_Segment.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Super_Max_Repeats+_Iterator_23_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Super_Max_Repeats_Fast+_Iterator_23_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_To_Std_Allocator.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Top_Down+_Iterator_23_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Top_Down_History+_Iterator_23_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMFUNC_Triple_23_Triple.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Align_Quality_Store_Element_23errors.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Align_Quality_Store_Element_23pair_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Align_Quality_Store_Element_23score.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Aligned_Read_Layout_23contig_Rows.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Aligned_Read_Store_Element_23_I_N_V_A_L_I_D___I_D.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Aligned_Read_Store_Element_23begin_Pos.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Aligned_Read_Store_Element_23contig_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Aligned_Read_Store_Element_23end_Pos.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Aligned_Read_Store_Element_23gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Aligned_Read_Store_Element_23id.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Aligned_Read_Store_Element_23pair_Match_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Aligned_Read_Store_Element_23read_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle2_23in1.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle2_23in2.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle3_23in1.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle3_23in2.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle3_23in3.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle5_23in1.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle5_23in2.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle5_23in3.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle5_23in4.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Bundle5_23in5.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Concat_Direct_23concat.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_File_23file_Name.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_File_23first_Contig_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_File_23format.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_Store_Element_23_I_N_V_A_L_I_D___I_D.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_Store_Element_23file_Begin_Pos.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_Store_Element_23file_End_Pos.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_Store_Element_23file_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_Store_Element_23gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_Store_Element_23seq.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Contig_Store_Element_23usage.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23align_Quality_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23aligned_Read_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23aligned_Read_Tag_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23annotation_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23annotation_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23contig_File_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23contig_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23contig_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23library_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23library_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23mate_Pair_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23mate_Pair_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23read_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23read_Seq_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Fragment_Store_23read_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Gap_Anchor_23gap_Pos.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Gap_Anchor_23seq_Pos.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Interval_And_Cargo_23cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Interval_And_Cargo_23i1.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Interval_And_Cargo_23i2.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Interval_Tree_Node_23center.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Interval_Tree_Node_23list1.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Interval_Tree_Node_23list2.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Library_Store_Element_23mean.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Library_Store_Element_23std.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Markov_Model_23order.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Markov_Model_23stationary_Distribution.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Markov_Model_23transition.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Mate_Pair_Store_Element_23_I_N_V_A_L_I_D___I_D.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Mate_Pair_Store_Element_23lib_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Mate_Pair_Store_Element_23read_Id[2].html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Name_Store_Cache_23_Name_Store_Cache.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Open_Addressing_23alpha.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Pair_23i1.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Pair_23i2.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Point_And_Cargo_23cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Point_And_Cargo_23point.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Read_Store_Element_23_I_N_V_A_L_I_D___I_D.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Read_Store_Element_23mate_Pair_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Tag_Selector_23tag_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Triple_23i1.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Triple_23i2.html
+%%PORTDOCS%%%%DOCSDIR%%/MEMVAR_Triple_23i3.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Allows_Fast_Random_Access.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Alphabet.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Bits_Per_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Bytes_Per_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Cargo.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Col.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Cols.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Comparator.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Compare_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Concatenator.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Container.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Convert.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Deepest_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Find_Begin_Pattern_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Get_Iterator_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Index_Creator.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Index_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Index_String_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Iterator_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Overflow_Explicit.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Overflow_Implicit.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Pattern.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Default_Prefix_Order.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Difference.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Edge_Descriptor.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Edge_Id_Handler.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Edge_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Fibre.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Gapped_Value_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Get_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Get_V_S_Tree_Iterator_Traits.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Get_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Haystack.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Hit.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Host.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Hsp.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Id.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Infix.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Insertion_Buffer.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Integral_For_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Is_Contiguous.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Is_Integral.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Is_Sequence.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Is_Simple.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Iter_Complement_Const.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Iter_Make_Const.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Journal_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Key.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_L_E_N_G_T_H.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_List_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Map_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Max_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Min_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Motif.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Needle.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Pex_Multi_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Position.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Prefix.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Reference.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Row.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Rows.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_S_A_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Scoring_Scheme.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Size.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Std_Container_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_String_Set_Type.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Suffix.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Value.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Value_Size.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Vertex_Descriptor.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Vertex_Id_Handler.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_W_E_I_G_H_T.html
+%%PORTDOCS%%%%DOCSDIR%%/METAFUNCTION_Weight.html
+%%PORTDOCS%%%%DOCSDIR%%/PAGE.dddoc.html
+%%PORTDOCS%%%%DOCSDIR%%/PAGE_Glossary.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Blosum30.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Blosum45.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Blosum62.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Blosum80.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Char_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Char_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna5_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna5_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna5_String_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna5_String_Reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna5_String_Reverse_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna_String_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna_String_Reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Dna_String_Reverse_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Edit_Distance_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Iupac_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Iupac_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Mod_Complement_Dna.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Mod_Complement_Dna5.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Mod_Complement_Rna.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Mod_Complement_Rna5.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Multi_Fasta.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Multi_Seq_File.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Myers_Ukkonen.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Myers_Ukkonen_Banded.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Myers_Ukkonen_Global.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Myers_Ukkonen_Global_Banded.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Pam120.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Pam200.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Pam250.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Pam40.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Peptide.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Peptide_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna5_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna5_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna5_String_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna5_String_Reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna5_String_Reverse_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna_String_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna_String_Reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Rna_String_Reverse_Complement.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Simple_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Unicode_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Unicode_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SHORTCUT_Vtml200.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Abndm_Algo.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Adaptor+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Adjacency+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Aho_Corasick.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Align_Col_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Alignment+_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Alloc+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Alphabet+_Expansion.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Amino_Acid.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Anchor_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Array+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Array_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Async.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Automaton.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Basic_Info.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Bfam.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Bfam_3c_Oracle_3e.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Bfam_3c_Trie_3e.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Bfs+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Bit+_Compressed+_Pair.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Bit+_Packed+_Tuple.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Blast_N.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Blast_P.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Block+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Bndm_Algo.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Bottom_Up+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_C_Mode.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_C_Style+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Caster.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Chained.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Chained_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Chunk+_Pool+_Allocator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Concat_Direct.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Concat_Virtual+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Counter.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Counting+_Id_Manager.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_D_P_Search.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Dependent.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Dfs+_Preorder+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Directed+_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Dna.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Dna5.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Dna5_Q.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Dna_Q.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_E_Pattern_Branching.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Echoer.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Edge+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Edit_Distance.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Edit_Environment.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Exact_Fragment.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Exact_Reversable_Fragment.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_External+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_File+_Reader+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Filter.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Finite.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Full_Info.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Gapped_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Generic_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Geometric+_Pdf.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Hamming_Simple_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Hierarchical.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Hit_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Hmm.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Horspool.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Hsp_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Index_Dfi.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Index_Esa.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Index_Q_Gram.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Index_Wotd.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Infix_Segment.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Interval+_Tree+_Node.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Iterator+_Proxy.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Iupac.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Joiner.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Journaled+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Log-_Normal+_Pdf.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_M_Map+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Mapper_Config.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Mapper_Config_Size.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Mapper_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Max_Repeats+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Memory_Manager_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Memory_Manager_Pointer.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Mersenne+_Twister+_Rng.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Mod_Reverse.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Mod_View.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Multi+_Pool+_Allocator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Multi_Bfam.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Multi_Bfam_3c_Oracle_3e.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Multi_Mems+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Multi_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Multiple_Shift_And.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Mums+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Myers.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Namer.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Non_Hierarchical.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Non_Scored+_Seed_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Normal+_Pdf.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_One_Gapped_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Open_Addressing.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Oracle.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Out-_Edge+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Owner.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_P_Mode.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Packed+_Pair.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Packed+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Packed+_Triple.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Pex.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Pizza+_26+_Chili+_Index.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Pizza+_26+_Chili+_String.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Pms1.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Pmsp.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Points+_Only+_Tree+_Node.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Pool_Config.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Pool_Config_Size.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Pool_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Position+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Prefix_Segment.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Priority_Heap.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Projection.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Rna.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Rna5.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Rng+_Functor.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Sampler.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Score+_Chain_So_P.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Score+_Manhattan.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Score+_Matrix.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Score+_Zero.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Scored+_Seed_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Set_Horspool.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Shift_And.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Shift_Or.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Shifter.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Simple+_Allocator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Simple+_Finder.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Simple+_Score.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Simple_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Simple_Seed.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Simple_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Single+_Pool+_Allocator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Skiplist.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Sorter_Config.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Sorter_Config_Size.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Sorter_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Source.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Store_Report.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Stream_Report.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Striped.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Suffix_Segment.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Sumlist_Gaps.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Super_Max_Repeats+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Super_Max_Repeats_Fast+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Swift.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Swift_Local.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Swift_Semi_Global.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Sync.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Top_Down+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Top_Down_History+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Trace_Back.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Tree.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Trie.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Tristate+_Holder.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Tupler.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Undirected+_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Ungapped_Shape.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Uniform+_Pdf.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_V_S_Tree+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Vector_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Vertex+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Wild_Shift_And.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Word+_Graph.html
+%%PORTDOCS%%%%DOCSDIR%%/SPEC_Wu_Manber.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG.sort_Aligned_Read+_Tags.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Alignment+_Graph+_Combination.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Alignment+_Graph+_Format.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Allocator+_Usage.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Consensus+_Calling.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Default.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Distance+_Calculation.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Dot_Drawing.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_E_S_A+_Index+_Fibres.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Empty_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_External_Config.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_External_Config_Large.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_External_Config_Size.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_File+_Format.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Find_Infix.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Find_Prefix.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Global+_Alignment+_Algorithms.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Graph+_Iterator.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Hamming_Distance.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Hide_Empty_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Index+_Find+_Algorithm.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Interval_Tree+_Centers.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Interval_Tree+_Node+_Types.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Iterator+_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Levenshtein_Distance.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Local+_Alignment+_Algorithms.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Logical+_Values.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Mean_Std_Dev.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Move+_Switch.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Mu_Sigma.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Nothing.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Omops.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Oops.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Overflow+_Strategy.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Pizza+_26+_Chili+_Index+_Fibres.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Pizza+_26+_Chili+_Index+_Tags.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Postorder.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Postorder_Empty_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Prefix+_Order.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Preorder.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Preorder_Empty_Edges.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Q_Gram+_Index+_Fibres.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Seed+_Adding.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Seed+_Extension.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Seed_Set.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Segment+_Match+_Generation.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Simple.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Tag_List.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Tcm.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Upgma+_Configurator.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_W_O_T_D+_Index+_Fibres.html
+%%PORTDOCS%%%%DOCSDIR%%/TAG_Zoops.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Aligned_Read_Store_Element_23_T_Gap_Anchors.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Aligned_Read_Store_Element_23_T_Pos.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Aligned_Read_Store_Element_23_T_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Contig_Store_Element_23_T_Contig_Seq.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Contig_Store_Element_23_T_Gap_Anchors.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Contig_Store_Element_23_T_Pos.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Contig_Store_Element_23_T_Spec.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Align_Quality_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Aligned_Read_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Aligned_Read_Tag_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Annotation_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Annotation_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Contig_File_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Contig_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Contig_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Library_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Library_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Mate_Pair_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Mate_Pair_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Read_Name_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Read_Seq_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/TYPEDEF_Fragment_Store_23_T_Read_Store.html
+%%PORTDOCS%%%%DOCSDIR%%/alignment.cpp
+%%PORTDOCS%%%%DOCSDIR%%/alignmentGraph.png
+%%PORTDOCS%%%%DOCSDIR%%/alignment_local.cpp
+%%PORTDOCS%%%%DOCSDIR%%/allocator.cpp
+%%PORTDOCS%%%%DOCSDIR%%/alphabet.cpp
+%%PORTDOCS%%%%DOCSDIR%%/automatonGraph.png
+%%PORTDOCS%%%%DOCSDIR%%/blast_report.cpp
+%%PORTDOCS%%%%DOCSDIR%%/dddoc.js
+%%PORTDOCS%%%%DOCSDIR%%/dddoc_empty.gif
+%%PORTDOCS%%%%DOCSDIR%%/dddoc_html.css
+%%PORTDOCS%%%%DOCSDIR%%/dddoc_minus.gif
+%%PORTDOCS%%%%DOCSDIR%%/dddoc_plus.gif
+%%PORTDOCS%%%%DOCSDIR%%/directedGraph.png
+%%PORTDOCS%%%%DOCSDIR%%/file_format.cpp
+%%PORTDOCS%%%%DOCSDIR%%/find_approx.cpp
+%%PORTDOCS%%%%DOCSDIR%%/find_exact.cpp
+%%PORTDOCS%%%%DOCSDIR%%/find_motif.cpp
+%%PORTDOCS%%%%DOCSDIR%%/find_wild.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_bfs.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_dfs.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_flow_fordfulkerson.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_his.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_lcs.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_lis.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_path_allpairs.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_path_bellmanford.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_path_dag.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_path_dijkstra.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_path_floydwarshall.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_path_transitive.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_scc.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_topsort.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_tree_kruskal.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_algo_tree_prim.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_hmm.cpp
+%%PORTDOCS%%%%DOCSDIR%%/graph_hmm_silent.cpp
+%%PORTDOCS%%%%DOCSDIR%%/index.html
+%%PORTDOCS%%%%DOCSDIR%%/index_find.cpp
+%%PORTDOCS%%%%DOCSDIR%%/index_find_stringset.cpp
+%%PORTDOCS%%%%DOCSDIR%%/index_maxrepeats.cpp
+%%PORTDOCS%%%%DOCSDIR%%/index_mummy.cpp
+%%PORTDOCS%%%%DOCSDIR%%/index_mums.cpp
+%%PORTDOCS%%%%DOCSDIR%%/index_node_predicate.cpp
+%%PORTDOCS%%%%DOCSDIR%%/index_sufarray.cpp
+%%PORTDOCS%%%%DOCSDIR%%/index_supermaxrepeats.cpp
+%%PORTDOCS%%%%DOCSDIR%%/iterator.cpp
+%%PORTDOCS%%%%DOCSDIR%%/modifier_modreverse.cpp
+%%PORTDOCS%%%%DOCSDIR%%/modifier_modview.cpp
+%%PORTDOCS%%%%DOCSDIR%%/modifier_nested.cpp
+%%PORTDOCS%%%%DOCSDIR%%/pizzachili.cpp
+%%PORTDOCS%%%%DOCSDIR%%/rooted_iterator.cpp
+%%PORTDOCS%%%%DOCSDIR%%/searchfile.js
+%%PORTDOCS%%%%DOCSDIR%%/seqan_logo.gif
+%%PORTDOCS%%%%DOCSDIR%%/seqan_logo_large.png
+%%PORTDOCS%%%%DOCSDIR%%/shape_predefined.h
+%%PORTDOCS%%%%DOCSDIR%%/treeGraph.png
+%%PORTDOCS%%%%DOCSDIR%%/trieGraph.png
+%%PORTDOCS%%%%DOCSDIR%%/undirectedGraph.png