ports/122374: [Update] biology/primer3 : update to 1.1.3
Fernan Aguero
fernan at iib.unsam.edu.ar
Wed Apr 2 17:20:03 UTC 2008
The following reply was made to PR ports/122374; it has been noted by GNATS.
From: Fernan Aguero <fernan at iib.unsam.edu.ar>
To: bug-followup at FreeBSD.ORG
Cc: edwin at FreeBSD.ORG, wenheping at gmail.com
Subject: Re: ports/122374: [Update] biology/primer3 : update to 1.1.3
Date: Wed, 2 Apr 2008 14:06:34 -0300
--9amGYk9869ThD9tj
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> Maintainer of biology/primer3,
>
> Please note that PR ports/122374 has just been submitted.
>
> If it contains a patch for an upgrade, an enhancement or a bug fix
> you agree on, reply to this email stating that you approve the patch
> and a committer will take care of it.
>
> The full text of the PR can be found at:
> http://www.freebsd.org/cgi/query-pr.cgi?pr=ports/122374
>
> --
> Edwin Groothuis via the GNATS Auto Assign Tool
> edwin at FreeBSD.org
Please find a revised patch using PLIST macros.
Thanks!
--9amGYk9869ThD9tj
Content-Type: text/x-diff; charset=us-ascii
Content-Disposition: attachment; filename="primer3.diff"
diff -ruN --exclude CVS /usr/ports/biology/primer3/Makefile primer3/Makefile
--- /usr/ports/biology/primer3/Makefile Fri Dec 29 20:40:53 2006
+++ primer3/Makefile Wed Apr 2 14:01:15 2008
@@ -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 at 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:
@${REINPLACE_CMD} \
@@ -29,7 +29,7 @@
do-install:
@${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 ${DOCUMENTS}
@@ -42,6 +42,6 @@
.endif
post-install:
- @${CAT} ${DATADIR}/Copyright.txt
+ @${CAT} ${DATADIR}/COPYING.txt
.include <bsd.port.mk>
diff -ruN --exclude CVS /usr/ports/biology/primer3/distinfo primer3/distinfo
--- /usr/ports/biology/primer3/distinfo Fri Dec 29 20:40:53 2006
+++ primer3/distinfo Wed Apr 2 14:01:15 2008
@@ -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 -ruN --exclude CVS /usr/ports/biology/primer3/pkg-plist primer3/pkg-plist
--- /usr/ports/biology/primer3/pkg-plist Fri Dec 29 20:40:53 2006
+++ primer3/pkg-plist Wed Apr 2 14:02:01 2008
@@ -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 @@
%%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 @@
%%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 @@
%%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 @@
%%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 @@
%%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 @@
%%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 @@
%%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%%
- at dirrm %%EXAMPLESDIR%%/primer1_list_last
- at dirrm %%EXAMPLESDIR%%/primer_global_err
- at dirrm %%EXAMPLESDIR%%/primer_list_last
- at dirrm %%EXAMPLESDIR%%
+%%PORTDOCS%%%%EXAMPLESDIR%%/vgrep.pl
+%%DATADIR%%/COPYING.txt
@dirrm %%DATADIR%%
+ at dirrm %%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last
+ at dirrm %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err
+ at dirrm %%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last
+ at dirrm %%PORTDOCS%%%%EXAMPLESDIR%%
+ at dirrm %%PORTDOCS%%%%DOCSDIR%%
--9amGYk9869ThD9tj--
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