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locks; strict;
comment	@# @;


1.3
date	2025.01.18.13.52.23;	author bacon;	state Exp;
branches;
next	1.2;
commitid	KkoV4qIVTtmdkYFF;

1.2
date	2022.03.17.23.49.08;	author bacon;	state Exp;
branches;
next	1.1;
commitid	oWjTYz3E37mjYCwD;

1.1
date	2018.12.22.21.52.06;	author bacon;	state Exp;
branches;
next	;
commitid	goNC4TSVvkt8jQ4B;


desc
@@


1.3
log
@biology/stacks: Update to 2.68

Numerous fixes and improvements since 2.6
Changes: http://catchenlab.life.illinois.edu/stacks/changelog.php
@
text
@@@comment $NetBSD$
bin/clone_filter
bin/cstacks
bin/denovo_map.pl
bin/gstacks
bin/kmer_filter
bin/phasedstacks
bin/populations
bin/process_radtags
bin/process_shortreads
bin/ref_map.pl
bin/sstacks
bin/stacks-count-reads-per-sample-per-locus
bin/stacks-dist-extract
bin/stacks-gdb
bin/stacks-hist2d-loci-samples-coverage
bin/stacks-integrate-alignments
bin/stacks-private-alleles
bin/stacks-samtools-tview
bin/tsv2bam
bin/ustacks
@


1.2
log
@biology/stacks: Update to 2.60

Numerous bug fixes and enhancements since 2.2
Unbreak build on Darwin
@
text
@d18 1
@


1.1
log
@biology/stacks: import stacks-2.2

Stacks is a software pipeline for building loci from short-read sequences, such
as those generated on the Illumina platform. Stacks was developed to work with
restriction enzyme-based data, such as RAD-seq, for the purpose of building
genetic maps and conducting population genomics and phylogeography.
@
text
@a2 1
bin/count_fixed_catalog_snps.py
a5 1
bin/integrate_alignments.py
d13 1
d16 1
d18 1
a20 47
share/stacks/php/CatalogClass.php
share/stacks/php/Locus.php
share/stacks/php/ajax.js
share/stacks/php/annotate.js
share/stacks/php/annotate_marker.php
share/stacks/php/catalog.php
share/stacks/php/catalog_genotypes.php
share/stacks/php/constants.php.dist
share/stacks/php/correct_genotype.php
share/stacks/php/correct_genotypes.php
share/stacks/php/db_functions.php
share/stacks/php/export.js
share/stacks/php/export_batch.php
share/stacks/php/fst_view.php
share/stacks/php/hapstat_view.php
share/stacks/php/header.php
share/stacks/php/images/caret-d.png
share/stacks/php/images/caret-u.png
share/stacks/php/images/excel_icon.png
share/stacks/php/images/l-arrow-disabled.png
share/stacks/php/images/l-arrow.png
share/stacks/php/images/r-arrow-disabled.png
share/stacks/php/images/r-arrow.png
share/stacks/php/images/stacks_bg.png
share/stacks/php/images/stacks_logo_rev_small.png
share/stacks/php/index.php
share/stacks/php/last_modified.php
share/stacks/php/phist_view.php
share/stacks/php/pop_view.php
share/stacks/php/population_view.js
share/stacks/php/samples.php
share/stacks/php/sequence_blast.php
share/stacks/php/stack_view.php
share/stacks/php/stacks.css
share/stacks/php/stacks.js
share/stacks/php/stacks_functions.php
share/stacks/php/sumstat_view.php
share/stacks/php/tag.php
share/stacks/php/tags.php
share/stacks/php/version.php
share/stacks/php/view_sequence.php
share/stacks/sql/catalog_index.sql
share/stacks/sql/chr_index.sql
share/stacks/sql/mysql.cnf.dist
share/stacks/sql/stacks.sql
share/stacks/sql/tag_index.sql
@@pkgdir share/stacks/php/export
@