- Update to 1.1.3

PR:		ports/122374
Submitted by:	Wen heping <wenheping@gmail.com>
Patch revised:	Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)

3 files changed, 203 insertions, 185 deletions

diff --git a/biology/primer3/Makefile b/biology/primer3/Makefile
index 6b1350f9a00f..527b546f7841 100644
--- a/biology/primer3/Makefile
+++ b/biology/primer3/Makefile
@@ -6,17 +6,17 @@
 #
 
 PORTNAME=	primer3
-PORTVERSION=	1.0.1
+PORTVERSION=	1.1.3
 CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
-MASTER_SITE_SUBDIR=	${PORTNAME}
-DISTNAME=	${PORTNAME}_${PORTVERSION}
+MASTER_SITES=	SF
+DISTNAME=	${PORTNAME}-${PORTVERSION}
 
 MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	Primer3 helps to choose primers for PCR reactions
 
+USE_GMAKE=	yes
 WRKSRC=		${WRKDIR}/${DISTNAME}/src
-DOCUMENTS=	README.${PORTNAME}_${PORTVERSION}.txt example
+DOCUMENTS=	README.txt example
 
 post-patch:
 	@${REINPLACE_CMD} \
@@ -29,7 +29,7 @@ post-patch:
 do-install:
 	@${INSTALL_PROGRAM} ${WRKSRC}/primer3_core ${PREFIX}/bin/primer3
 	@${MKDIR} ${DATADIR}
-	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright.txt ${DATADIR}
+	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/COPYING.txt ${DATADIR}
 .if !defined(NOPORTDOCS)
 	@${MKDIR} ${DOCSDIR}
 .for file in ${DOCUMENTS}
@@ -42,6 +42,6 @@ do-install:
 .endif
 
 post-install:
-	@${CAT} ${DATADIR}/Copyright.txt
+	@${CAT} ${DATADIR}/COPYING.txt
 
 .include <bsd.port.mk>
diff --git a/biology/primer3/distinfo b/biology/primer3/distinfo
index 7098986592c7..2c91a55672f3 100644
--- a/biology/primer3/distinfo
+++ b/biology/primer3/distinfo
@@ -1,3 +1,3 @@
-MD5 (primer3_1.0.1.tar.gz) = 4fa33b8667cec1b88f1516d175eb1bed
-SHA256 (primer3_1.0.1.tar.gz) = 2f7641d66d75b4830a01d31dbc96c61ffad2b1f047287009906902558a9e165e
-SIZE (primer3_1.0.1.tar.gz) = 902576
+MD5 (primer3-1.1.3.tar.gz) = 3d027d5dcbdb88c0f9622938f9d38534
+SHA256 (primer3-1.1.3.tar.gz) = ad3071fd1a8da8caae6f30b799cae4b7e53f00476ca0441b37bddf8995d1fa38
+SIZE (primer3-1.1.3.tar.gz) = 943678
diff --git a/biology/primer3/pkg-plist b/biology/primer3/pkg-plist
index 06fd055664b8..8bbd779a715a 100644
--- a/biology/primer3/pkg-plist
+++ b/biology/primer3/pkg-plist
@@ -1,7 +1,7 @@
 bin/primer3
-%%PORTDOCS%%%%DOCSDIR%%/README.primer3_1.0.1.txt
+%%PORTDOCS%%%%DOCSDIR%%/README.txt
 %%PORTDOCS%%%%DOCSDIR%%/example
-%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_gen.pl
+%%PORTDOCS%%%%EXAMPLESDIR%%/Makefile
 %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_long_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_long_score_output
@@ -14,20 +14,14 @@ bin/primer3
 %%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production.lib
 %%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Ns.lib
 %%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Xs.lib
+%%PORTDOCS%%%%EXAMPLESDIR%%/oligotm.txt
+%%PORTDOCS%%%%EXAMPLESDIR%%/oligotm_test.pl
 %%PORTDOCS%%%%EXAMPLESDIR%%/p3-tmpl-mispriming_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/p3-tmpl-mispriming_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/p3test.pl
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/AGAG.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/AGAG.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-02.txt.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-02.txt.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-03.txt.for
@@ -40,8 +34,16 @@ bin/primer3
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-21.txt.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP04-07.txt.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP04-07.txt.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/long_seq.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/targets_test.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/targets_test.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_formatted_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_output
@@ -52,224 +54,236 @@ bin/primer3
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_check_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_end_pathology_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_end_pathology_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_1.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_1.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_1.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_2.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_2.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_2.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_3.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_3.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_3.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_4.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_4.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_divalent_dntp_conc_4.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_dna_conc.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_4.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_int_3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_num_ns.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_product_size.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/gc_clamp_min_size.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/incorrect_task.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_gc_content_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/io_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/MAX_PRIMER_LENGTH.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_limit_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pair_mispr.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err6.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality1.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality4.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/too_many_product_sizes.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_min_size.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/zero_num_return.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_formatted_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_input
@@ -278,22 +292,10 @@ bin/primer3
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/AGAG.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/AGAG.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-02.txt.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-02.txt.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-03.txt.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-03.txt.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.rev
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.int
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.rev
@@ -303,18 +305,29 @@ bin/primer3
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.int
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat3.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06.txt.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-19.txt.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-21.txt.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-21.txt.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP04-07.txt.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP04-07.txt.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/case_problem_test.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/included_test_w_middle.rev
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.for
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/long_seq.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/targets_test.for
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/targets_test.rev
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_formatted_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_formatted_output
@@ -327,8 +340,8 @@ bin/primer3
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_num_best_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_num_best_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib1
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_formatted_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_input
@@ -347,15 +360,20 @@ bin/primer3
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_formatted_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_tm_lc_masking_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib1
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib2
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib3
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib4
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib5
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib6
-%%DATADIR%%/Copyright.txt
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-@dirrm %%EXAMPLESDIR%%/primer1_list_last
-@dirrm %%EXAMPLESDIR%%/primer_global_err
-@dirrm %%EXAMPLESDIR%%/primer_list_last
-@dirrm %%EXAMPLESDIR%%
+%%PORTDOCS%%%%EXAMPLESDIR%%/vgrep.pl
+%%DATADIR%%/COPYING.txt
 @dirrm %%DATADIR%%
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_list_last
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_global_err
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer1_list_last
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
+%%PORTDOCS%%@dirrm %%DOCSDIR%%