SeqAn is an open source C++ library of efficient algorithms

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.

WWW: http://www.seqan.de/

PR:		167571
Submitted by:	Hannes <h2+fbsdports@fsfe.org>

7 files changed, 2229 insertions, 0 deletions

diff --git a/biology/seqan/Makefile b/biology/seqan/Makefile
new file mode 100644
index 000000000000..96675e464607
--- /dev/null
+++ b/biology/seqan/Makefile
@@ -0,0 +1,49 @@
+# New ports collection makefile for:   seqan
+# Date created:        3 May 2012
+# Whom:                h2
+#
+# $FreeBSD$
+#
+
+PORTNAME=	seqan
+PORTVERSION=	1.3.1
+CATEGORIES=	biology
+MASTER_SITES=	http://ftp.seqan.de/releases/
+
+MAINTAINER=	h2+fsbdports@fsfe.org
+COMMENT=	C++ Sequence Analysis Library
+
+LICENSE=	BSD GPLv3
+LICENSE_COMB=	multi
+
+LICENSE_FILE_BSD=${WRKSRC}/seqan/LICENSE
+LICENSE_FILE_GPLv3=${WRKSRC}/apps/LICENSE
+
+USE_ZIP=	yes
+
+USE_CMAKE=	yes
+CMAKE_SOURCE_PATH=${WRKSRC}/cmake
+CMAKE_OUTSOURCE=yes
+USE_PYTHON_BUILD=yes
+MAKE_JOB_SAFE=	yes
+
+SUB_FILES=	pkg-message
+PKG_MESSAGE=	${WRKDIR}/pkg-message
+
+.include <bsd.port.pre.mk>
+
+.if ${ARCH} == i386
+# triggers internal error in system gcc
+USE_GCC=	4.4+
+.endif
+
+# unsafe workaround because FreeBSD lacks logl and expl
+# see "BUGS" in `man 3 math`
+post-patch:
+	@${REINPLACE_CMD} -e 's|expl|exp|g' ${WRKSRC}/apps/snp_store/snp_store.h
+	@${REINPLACE_CMD} -e 's|logl|log|g' ${WRKSRC}/apps/snp_store/snp_store.h
+
+post-install:
+	@${CAT} ${PKG_MESSAGE}
+
+.include <bsd.port.post.mk>
diff --git a/biology/seqan/distinfo b/biology/seqan/distinfo
new file mode 100644
index 000000000000..3e7a0a49d7b4
--- /dev/null
+++ b/biology/seqan/distinfo
@@ -0,0 +1,2 @@
+SHA256 (seqan-1.3.1.zip) = 87eebe73ace9ada2f4664a768ae212d4acc5fb3ce87702709c3d15bf2d153aeb
+SIZE (seqan-1.3.1.zip) = 8787521
diff --git a/biology/seqan/files/patch-cmake-CMakeLists.txt b/biology/seqan/files/patch-cmake-CMakeLists.txt
new file mode 100644
index 000000000000..8f39eebd62f6
--- /dev/null
+++ b/biology/seqan/files/patch-cmake-CMakeLists.txt
@@ -0,0 +1,13 @@
+--- 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
new file mode 100644
index 000000000000..21f5acf7b97f
--- /dev/null
+++ b/biology/seqan/files/patch-cmake-apps-CMakeLists.txt
@@ -0,0 +1,8 @@
+--- 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
new file mode 100644
index 000000000000..71fbb10d6371
--- /dev/null
+++ b/biology/seqan/files/pkg-message.in
@@ -0,0 +1,6 @@
+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
new file mode 100644
index 000000000000..298ab519446f
--- /dev/null
+++ b/biology/seqan/pkg-descr
@@ -0,0 +1,6 @@
+SeqAn is an open source C++ library of efficient algorithms
+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.
+
+WWW: http://www.seqan.de/
diff --git a/biology/seqan/pkg-plist b/biology/seqan/pkg-plist
new file mode 100644
index 000000000000..94398b23eb8c
--- /dev/null
+++ b/biology/seqan/pkg-plist
@@ -0,0 +1,2145 @@
+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_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
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+%%DATADIR%%/docs/index_sufarray.cpp
+%%DATADIR%%/docs/index_supermaxrepeats.cpp
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+%%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
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+@dirrm %%DATADIR%%/gapped_params
+@dirrm %%DATADIR%%/docs
+@dirrm %%DATADIR%%
+@dirrm include/seqan/system
+@dirrm include/seqan/store
+@dirrm include/seqan/statistics
+@dirrm include/seqan/sequence_journaled
+@dirrm include/seqan/sequence
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+@dirrm include/seqan/graph_align
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+@dirrm include/seqan/align
+@dirrm include/seqan