3 files changed, 98 insertions, 97 deletions

diff --git a/biology/primer3/Makefile b/biology/primer3/Makefile
index bb8506a0ee46..6b1350f9a00f 100644
--- a/biology/primer3/Makefile
+++ b/biology/primer3/Makefile
@@ -6,16 +6,17 @@
 #
 
 PORTNAME=	primer3
-PORTVERSION=	1.0.0
+PORTVERSION=	1.0.1
 CATEGORIES=	biology
-MASTER_SITES=	http://frodo.wi.mit.edu/primer3/
+MASTER_SITES=	${MASTER_SITE_SOURCEFORGE}
+MASTER_SITE_SUBDIR=	${PORTNAME}
 DISTNAME=	${PORTNAME}_${PORTVERSION}
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	fernan@iib.unsam.edu.ar
 COMMENT=	Primer3 helps to choose primers for PCR reactions
 
 WRKSRC=		${WRKDIR}/${DISTNAME}/src
-DOCUMENTS=	README example
+DOCUMENTS=	README.${PORTNAME}_${PORTVERSION}.txt example
 
 post-patch:
 	@${REINPLACE_CMD} \
@@ -28,7 +29,7 @@ post-patch:
 do-install:
 	@${INSTALL_PROGRAM} ${WRKSRC}/primer3_core ${PREFIX}/bin/primer3
 	@${MKDIR} ${DATADIR}
-	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright ${DATADIR}
+	@${INSTALL_DATA} ${WRKDIR}/${DISTNAME}/Copyright.txt ${DATADIR}
 .if !defined(NOPORTDOCS)
 	@${MKDIR} ${DOCSDIR}
 .for file in ${DOCUMENTS}
@@ -41,6 +42,6 @@ do-install:
 .endif
 
 post-install:
-	@${CAT} ${DATADIR}/Copyright
+	@${CAT} ${DATADIR}/Copyright.txt
 
 .include <bsd.port.mk>
diff --git a/biology/primer3/distinfo b/biology/primer3/distinfo
index 69847f87228b..7098986592c7 100644
--- a/biology/primer3/distinfo
+++ b/biology/primer3/distinfo
@@ -1,3 +1,3 @@
-MD5 (primer3_1.0.0.tar.gz) = 58605ee607f6218a2a775345b10d15fa
-SHA256 (primer3_1.0.0.tar.gz) = fcbcf2e540e0062f3fa0d723b443b04a1c31e3e03e3aa5d97e3b2f910499f34b
-SIZE (primer3_1.0.0.tar.gz) = 936696
+MD5 (primer3_1.0.1.tar.gz) = 4fa33b8667cec1b88f1516d175eb1bed
+SHA256 (primer3_1.0.1.tar.gz) = 2f7641d66d75b4830a01d31dbc96c61ffad2b1f047287009906902558a9e165e
+SIZE (primer3_1.0.1.tar.gz) = 902576
diff --git a/biology/primer3/pkg-plist b/biology/primer3/pkg-plist
index 9641035d99d8..06fd055664b8 100644
--- a/biology/primer3/pkg-plist
+++ b/biology/primer3/pkg-plist
@@ -1,4 +1,5 @@
-%%PORTDOCS%%%%DOCSDIR%%/README
+bin/primer3
+%%PORTDOCS%%%%DOCSDIR%%/README.primer3_1.0.1.txt
 %%PORTDOCS%%%%DOCSDIR%%/example
 %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_gen.pl
 %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_input
@@ -9,10 +10,24 @@
 %%PORTDOCS%%%%EXAMPLESDIR%%/dpal_test.pl
 %%PORTDOCS%%%%EXAMPLESDIR%%/long_seq_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/long_seq_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/long_seq_tm_test.pl
 %%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production.lib
+%%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Ns.lib
+%%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Xs.lib
+%%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
@@ -25,24 +40,18 @@
 %%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/long_seq.for
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.rev
-%%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
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_formatted_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_check_input
 %%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/bad_dna_conc.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_1.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_float_2.in
@@ -60,8 +69,8 @@
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_2.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_3.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_product_sizes_4.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_salt_conc.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end_int.in
@@ -75,15 +84,16 @@
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.in
 %%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_size_limit_int.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no=.in
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal=.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.in
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size_int.in
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_min_size.in
@@ -92,91 +102,91 @@
 %%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_err.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_int_err.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/MAX_PRIMER_LENGTH.out
+%%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_1.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.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.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/empty_1.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.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.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.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.out
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.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=.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal=.out
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.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_min_size.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_err.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_int_err.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
@@ -184,70 +194,70 @@
 %%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/MAX_PRIMER_LENGTH.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_gc_1.out2
 %%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.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.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_any_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/bad_self_end.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.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_min_tm_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_opt_tm.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.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.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=.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal=.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.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_min_size.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.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/pr_gc_content_obj_fn.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_size_obj_fn.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/product_tm_obj_fn.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err1.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err2.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err3.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err4.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err5.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err6.out2
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err.out2
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_err.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err1.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err2.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err3.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err4.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/repeat_lib_int_err5.out2
 %%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.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality2.out2
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/seq_quality3.out2
@@ -259,14 +269,31 @@
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_human_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_input
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_formatted_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_formatted_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_input
+%%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
@@ -276,40 +303,34 @@
 %%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
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_long_lib_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_long_lib_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_formatted_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_input
 %%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
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_quality_boundary_input
@@ -323,39 +344,18 @@
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_start_codon_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_syntax_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_syntax_output
+%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_formatted_output
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_input
 %%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_test.pl
-%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib1
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib2
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib3
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib4
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib5
 %%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib6
-%%PORTDOCS%%%%EXAMPLESDIR%%/long_seq_tm_test.pl
-%%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Ns.lib
-%%PORTDOCS%%%%EXAMPLESDIR%%/not_for_production_Xs.lib
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary1_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_boundary_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_lib_amb_codes_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary1_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_boundary2_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_mispriming_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_must_use_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_position_penalty_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_task_formatted_output
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_template_mispriming_input
-%%PORTDOCS%%%%EXAMPLESDIR%%/primer_template_mispriming_output
-bin/primer3
-%%DATADIR%%/Copyright
-@dirrm %%DATADIR%%
+%%DATADIR%%/Copyright.txt
 %%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer1_list_last
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_global_err
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%/primer_list_last
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
+@dirrm %%EXAMPLESDIR%%/primer1_list_last
+@dirrm %%EXAMPLESDIR%%/primer_global_err
+@dirrm %%EXAMPLESDIR%%/primer_list_last
+@dirrm %%EXAMPLESDIR%%
+@dirrm %%DATADIR%%