samtools: Resurrect for upgradr to 1.10
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Makefile
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Makefile
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@ -4438,6 +4438,7 @@ SUBDIR+= sais
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SUBDIR+= sais-demo-data
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SUBDIR+= salmon
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SUBDIR+= samhain
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SUBDIR+= samtools
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SUBDIR+= samtools0119
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SUBDIR+= sara
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SUBDIR+= sarf
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@ -0,0 +1,3 @@
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Samtools implements various utilities for post-processing alignments in the
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SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
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with bcftools), and a simple alignment viewer.
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@ -0,0 +1,29 @@
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# $NetBSD: Makefile,v 1.7 2020/01/26 17:30:46 rillig Exp $
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DISTNAME= samtools-1.10
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=samtools/}
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MAINTAINER= bacon@NetBSD.org
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HOMEPAGE= https://www.htslib.org/
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COMMENT= Tools for manipulating next-generation sequencing data
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LICENSE= mit
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USE_TOOLS+= autoconf automake autoreconf gmake perl
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GNU_CONFIGURE= yes
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CONFIGURE_ARGS+= --with-htslib=system
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TEST_TARGET= test
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REPLACE_PERL= misc/*.pl
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REPLACE_PERL+= misc/plot-bamstats
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REPLACE_PERL+= test/test.pl
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REPLACE_PYTHON= misc/*.py
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pre-configure:
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(cd ${WRKSRC} && autoreconf)
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.include "../../devel/zlib/buildlink3.mk"
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.include "../../wip/htslib/buildlink3.mk"
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.include "../../lang/python/application.mk"
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.include "../../mk/curses.buildlink3.mk"
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.include "../../mk/bsd.pkg.mk"
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@ -0,0 +1,53 @@
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@comment $NetBSD$
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bin/ace2sam
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bin/blast2sam.pl
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bin/bowtie2sam.pl
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bin/export2sam.pl
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bin/interpolate_sam.pl
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bin/maq2sam-long
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bin/maq2sam-short
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bin/md5fa
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bin/md5sum-lite
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bin/novo2sam.pl
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bin/plot-bamstats
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bin/psl2sam.pl
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bin/sam2vcf.pl
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bin/samtools
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bin/samtools.pl
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bin/seq_cache_populate.pl
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bin/soap2sam.pl
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bin/wgsim
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bin/wgsim_eval.pl
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bin/zoom2sam.pl
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man/man1/samtools-addreplacerg.1
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man/man1/samtools-bedcov.1
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man/man1/samtools-calmd.1
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man/man1/samtools-cat.1
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man/man1/samtools-collate.1
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man/man1/samtools-depad.1
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man/man1/samtools-depth.1
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man/man1/samtools-dict.1
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man/man1/samtools-faidx.1
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man/man1/samtools-fasta.1
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man/man1/samtools-fastq.1
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man/man1/samtools-fixmate.1
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man/man1/samtools-flags.1
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man/man1/samtools-flagstat.1
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man/man1/samtools-fqidx.1
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man/man1/samtools-idxstats.1
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man/man1/samtools-index.1
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man/man1/samtools-markdup.1
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man/man1/samtools-merge.1
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man/man1/samtools-mpileup.1
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man/man1/samtools-phase.1
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man/man1/samtools-quickcheck.1
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man/man1/samtools-reheader.1
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man/man1/samtools-rmdup.1
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man/man1/samtools-sort.1
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man/man1/samtools-split.1
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man/man1/samtools-stats.1
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man/man1/samtools-targetcut.1
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man/man1/samtools-tview.1
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man/man1/samtools-view.1
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man/man1/samtools.1
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man/man1/wgsim.1
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@ -0,0 +1,6 @@
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$NetBSD$
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SHA1 (samtools-1.10.tar.gz) = 98b24393629d63f2203f59c108b840b1e046f209
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RMD160 (samtools-1.10.tar.gz) = e8d91dfc0970a0faa85d45962f76f831af331007
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SHA512 (samtools-1.10.tar.gz) = 7760a1e8a89780ac80053b136930a8ed0cc130b72c9f66cdc9c211e93b6bcc8923140e7caae9824c81caa4a2bfab3a14280e3e7d7245abeaa6f91f0f96123fda
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Size (samtools-1.10.tar.gz) = 4457760 bytes
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