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1.6
date	2008.04.04.20.46.35;	author pav;	state Exp;
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1.5
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1.4
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1.3
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1.1
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desc
@@


1.6
log
@- 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)
@
text
@bin/primer3
%%PORTDOCS%%%%DOCSDIR%%/README.txt
%%PORTDOCS%%%%DOCSDIR%%/example
%%PORTDOCS%%%%EXAMPLESDIR%%/Makefile
%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_input
%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_long_input
%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_long_score_output
%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_output
%%PORTDOCS%%%%EXAMPLESDIR%%/dpal_score_output
%%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%%/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_list_last/AGAG.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/AGAG.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
%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-03.txt.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-06.txt.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-06.txt.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-19.txt.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-19.txt.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/SP01-21.txt.for
%%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
%%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/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
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%%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
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%%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_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/max_size_min_product.out
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.in
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/max_size_min_product_int.out
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm.in
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/min_opt_tm_int.in
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mishyb_obj_fn.in
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/mispr_obj_fn.out2
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_equal.in
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.in
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/no_terminal_equal.out
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_global_err/opt_max_size.in
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%%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/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
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_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
%%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/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-with-repeat1.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.int
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat1.rev
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat2.for
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat2.int
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_list_last/SP01-06-with-repeat2.rev
%%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_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%%/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
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_quality_boundary_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_rat_input
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_rat_output
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_repeat_boundary1_lib
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_repeat_boundary2_lib
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_repeat_long_lib
%%PORTDOCS%%%%EXAMPLESDIR%%/primer_start_codon_input
%%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_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
%%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%%
@


1.5
log
@- Update to 1.0.1
- Update MASTER_SITES
- Pass maintainership to submitter

PR:		ports/107246
Submitted by:	Fernan Aguero<fernan@@iib.unsam.edu.ar> (maintainer)
@
text
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_internal1_formatted_output
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%%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
a298 3
%%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
d308 3
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer_obj_fn_input
d343 1
a344 1
%%PORTDOCS%%%%EXAMPLESDIR%%/repeat_lib1
d363 4
d372 7
a378 1
%%DATADIR%%/Copyright.txt
a379 5
@@dirrm %%EXAMPLESDIR%%/primer1_list_last
@@dirrm %%EXAMPLESDIR%%/primer_global_err
@@dirrm %%EXAMPLESDIR%%/primer_list_last
@@dirrm %%EXAMPLESDIR%%
@@dirrm %%DATADIR%%
@


1.4
log
@- Update to 1.0.0
- Make DATADIR/EXAMPLESDIR/DOCSDIR safe
- Don't hardcode ${CPIO}

PR:		ports/82154
Submitted by:	George Hartzell <hartzell@@alerce.com>
Approved by:	maintainer
@
text
@d1 2
a2 1
%%PORTDOCS%%%%DOCSDIR%%/README
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%%PORTDOCS%%%%EXAMPLESDIR%%/primer1_list_last/included_test_w_middle.int
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%%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
a361 5
%%PORTDOCS%%@@dirrm %%DOCSDIR%%
%%PORTDOCS%%@@dirrm %%EXAMPLESDIR%%/primer1_list_last
%%PORTDOCS%%@@dirrm %%EXAMPLESDIR%%/primer_global_err
%%PORTDOCS%%@@dirrm %%EXAMPLESDIR%%/primer_list_last
%%PORTDOCS%%@@dirrm %%EXAMPLESDIR%%
@


1.3
log
@Cosmetic fix: use %%DOCSDIR%% macro.
No functionally changes.

Submitted by:	Oleg Karachevtsev <ok@@etrust.ru>
A part of PR:	57992
@
text
@d3 351
a353 344
%%PORTDOCS%%share/examples/primer3/dpal_gen.pl
%%PORTDOCS%%share/examples/primer3/dpal_input
%%PORTDOCS%%share/examples/primer3/dpal_long_input
%%PORTDOCS%%share/examples/primer3/dpal_long_score_output
%%PORTDOCS%%share/examples/primer3/dpal_output
%%PORTDOCS%%share/examples/primer3/dpal_score_output
%%PORTDOCS%%share/examples/primer3/dpal_test.pl
%%PORTDOCS%%share/examples/primer3/long_seq_input
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%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP01-06.txt.for
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%%PORTDOCS%%share/examples/primer3/primer1_list_last/SP04-07.txt.for
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%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test_w_middle.int
%%PORTDOCS%%share/examples/primer3/primer1_list_last/long_seq.for
%%PORTDOCS%%share/examples/primer3/primer1_list_last/included_test_w_middle.rev
%%PORTDOCS%%share/examples/primer3/primer1_list_last/long_seq.rev
%%PORTDOCS%%share/examples/primer3/primer1_list_last/targets_test.for
%%PORTDOCS%%share/examples/primer3/primer1_list_last/targets_test.rev
%%PORTDOCS%%share/examples/primer3/primer1_output
%%PORTDOCS%%share/examples/primer3/primer_boundary1_formated_output
%%PORTDOCS%%share/examples/primer3/primer_boundary1_input
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%%PORTDOCS%%share/examples/primer3/primer_boundary_formated_output
%%PORTDOCS%%share/examples/primer3/primer_boundary_input
%%PORTDOCS%%share/examples/primer3/primer_boundary_output
%%PORTDOCS%%share/examples/primer3/primer_check_input
%%PORTDOCS%%share/examples/primer3/primer_check_output
%%PORTDOCS%%share/examples/primer3/primer_end_pathology_input
%%PORTDOCS%%share/examples/primer3/primer_end_pathology_output
%%PORTDOCS%%share/examples/primer3/primer_global_err/MAX_PRIMER_LENGTH.in
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%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_salt_conc.in
%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_any_int.in
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%%PORTDOCS%%share/examples/primer3/primer_global_err/min_opt_tm_int.in
%%PORTDOCS%%share/examples/primer3/primer_global_err/mishyb_obj_fn.in
%%PORTDOCS%%share/examples/primer3/primer_global_err/mispr_obj_fn.in
%%PORTDOCS%%share/examples/primer3/primer_global_err/no=.in
%%PORTDOCS%%share/examples/primer3/primer_global_err/no_terminal=.in
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%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_err1.in
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%%PORTDOCS%%share/examples/primer3/primer_global_err/repeat_lib_int_err1.in
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%%PORTDOCS%%share/examples/primer3/primer_global_err/seq_quality2.in
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%%PORTDOCS%%share/examples/primer3/primer_global_err/zero_min_size.in
%%PORTDOCS%%share/examples/primer3/primer_global_err/zero_num_return.in
%%PORTDOCS%%share/examples/primer3/primer_global_err/MAX_PRIMER_LENGTH.out
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%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_2.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_float_3.out
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%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_any.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/empty_1.out
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%%PORTDOCS%%share/examples/primer3/primer_global_err/bad_self_end_int.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/empty_product_size.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/gc_clamp_min_size.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/incorrect_task.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/io_gc_content_obj_fn.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/io_obj_fn.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/max_min_tm.out
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%%PORTDOCS%%share/examples/primer3/primer_global_err/max_size_min_product_int.out
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%%PORTDOCS%%share/examples/primer3/primer_global_err/min_opt_tm_int.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/mishyb_obj_fn.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/mispr_obj_fn.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/no=.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/no_terminal=.out
%%PORTDOCS%%share/examples/primer3/primer_global_err/opt_max_size.out
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d355 7
a361 11
share/primer3/Copyright
share/primer3/primer3_www.cgi
share/primer3/primer3_www_help.html
share/primer3/primer3_www_results.cgi
share/primer3/primer3_www_results_help.html
@@dirrm share/primer3
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@


1.2
log
@Updated to fix problems as stated in PR ports/42915

PR:		ports/42915
Submitted by:	Tony Maher <tonym@@biolateral.com.au>
@
text
@d1 2
a2 2
%%PORTDOCS%%share/doc/primer3/README
%%PORTDOCS%%share/doc/primer3/example
d354 1
a354 1
%%PORTDOCS%%@@dirrm share/doc/primer3/
@


1.1
log
@add primer3 0.9
Primer3 helps to choose primers for PCR reactions

PR:		35298
Submitted by:	Tony Maher <tonym@@biolateral.com.au>
@
text
@a355 1
%%PORTDOCS%%@@dirrm share/examples/primer3/primer1_list_tmp
a357 1
%%PORTDOCS%%@@dirrm share/examples/primer3/primer_list_tmp
@

