samtools: Resurrect for upgradr to 1.10

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu May 21 13:52:11 2020 -0500
Changeset:	f1db7bc4a952cb573e51891fce2ad479f71e5246

Modified Files:
	Makefile
Added Files:
	samtools/DESCR
	samtools/Makefile
	samtools/PLIST
	samtools/distinfo

Log Message:
samtools: Resurrect for upgradr to 1.10

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f1db7bc4a952cb573e51891fce2ad479f71e5246

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile          |  1 +
 samtools/DESCR    |  3 +++
 samtools/Makefile | 29 +++++++++++++++++++++++++++++
 samtools/PLIST    | 53 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 samtools/distinfo |  6 ++++++
 5 files changed, 92 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 2f33897bba..9195a4b3c1 100644
--- a/Makefile
+++ b/Makefile
@@ -4438,6 +4438,7 @@ SUBDIR+=	sais
 SUBDIR+=	sais-demo-data
 SUBDIR+=	salmon
 SUBDIR+=	samhain
+SUBDIR+=	samtools
 SUBDIR+=	samtools0119
 SUBDIR+=	sara
 SUBDIR+=	sarf
diff --git a/samtools/DESCR b/samtools/DESCR
new file mode 100644
index 0000000000..23d11d1c81
--- /dev/null
+++ b/samtools/DESCR
@@ -0,0 +1,3 @@
+Samtools implements various utilities for post-processing alignments in the
+SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
+with bcftools), and a simple alignment viewer.
diff --git a/samtools/Makefile b/samtools/Makefile
new file mode 100644
index 0000000000..ad66069a74
--- /dev/null
+++ b/samtools/Makefile
@@ -0,0 +1,29 @@
+# $NetBSD: Makefile,v 1.7 2020/01/26 17:30:46 rillig Exp $
+
+DISTNAME=	samtools-1.10
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://www.htslib.org/
+COMMENT=	Tools for manipulating next-generation sequencing data
+LICENSE=	mit
+
+USE_TOOLS+=		autoconf automake autoreconf gmake perl
+GNU_CONFIGURE=		yes
+CONFIGURE_ARGS+=	--with-htslib=system
+TEST_TARGET=		test
+
+REPLACE_PERL=		misc/*.pl
+REPLACE_PERL+=		misc/plot-bamstats
+REPLACE_PERL+=		test/test.pl
+REPLACE_PYTHON=		misc/*.py
+
+pre-configure:
+	(cd ${WRKSRC} && autoreconf)
+
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../wip/htslib/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/curses.buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/samtools/PLIST b/samtools/PLIST
new file mode 100644
index 0000000000..31dfd1eeaf
--- /dev/null
+++ b/samtools/PLIST
@@ -0,0 +1,53 @@
+@comment $NetBSD$
+bin/ace2sam
+bin/blast2sam.pl
+bin/bowtie2sam.pl
+bin/export2sam.pl
+bin/interpolate_sam.pl
+bin/maq2sam-long
+bin/maq2sam-short
+bin/md5fa
+bin/md5sum-lite
+bin/novo2sam.pl
+bin/plot-bamstats
+bin/psl2sam.pl
+bin/sam2vcf.pl
+bin/samtools
+bin/samtools.pl
+bin/seq_cache_populate.pl
+bin/soap2sam.pl
+bin/wgsim
+bin/wgsim_eval.pl
+bin/zoom2sam.pl
+man/man1/samtools-addreplacerg.1
+man/man1/samtools-bedcov.1
+man/man1/samtools-calmd.1
+man/man1/samtools-cat.1
+man/man1/samtools-collate.1
+man/man1/samtools-depad.1
+man/man1/samtools-depth.1
+man/man1/samtools-dict.1
+man/man1/samtools-faidx.1
+man/man1/samtools-fasta.1
+man/man1/samtools-fastq.1
+man/man1/samtools-fixmate.1
+man/man1/samtools-flags.1
+man/man1/samtools-flagstat.1
+man/man1/samtools-fqidx.1
+man/man1/samtools-idxstats.1
+man/man1/samtools-index.1
+man/man1/samtools-markdup.1
+man/man1/samtools-merge.1
+man/man1/samtools-mpileup.1
+man/man1/samtools-phase.1
+man/man1/samtools-quickcheck.1
+man/man1/samtools-reheader.1
+man/man1/samtools-rmdup.1
+man/man1/samtools-sort.1
+man/man1/samtools-split.1
+man/man1/samtools-stats.1
+man/man1/samtools-targetcut.1
+man/man1/samtools-tview.1
+man/man1/samtools-view.1
+man/man1/samtools.1
+man/man1/wgsim.1
diff --git a/samtools/distinfo b/samtools/distinfo
new file mode 100644
index 0000000000..05156ee999
--- /dev/null
+++ b/samtools/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (samtools-1.10.tar.gz) = 98b24393629d63f2203f59c108b840b1e046f209
+RMD160 (samtools-1.10.tar.gz) = e8d91dfc0970a0faa85d45962f76f831af331007
+SHA512 (samtools-1.10.tar.gz) = 7760a1e8a89780ac80053b136930a8ed0cc130b72c9f66cdc9c211e93b6bcc8923140e7caae9824c81caa4a2bfab3a14280e3e7d7245abeaa6f91f0f96123fda
+Size (samtools-1.10.tar.gz) = 4457760 bytes