samtools: Remove, same version already in biology

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat May 4 11:22:50 2019 -0500
Changeset:	2ab60451a27509204fa57a9679beb553daddd857

Modified Files:
	Makefile
	ddocent/Makefile
Removed Files:
	samtools/DESCR
	samtools/Makefile
	samtools/PLIST
	samtools/TODO
	samtools/distinfo

Log Message:
samtools: Remove, same version already in biology

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2ab60451a27509204fa57a9679beb553daddd857

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

diffstat:
 Makefile          |  1 -
 ddocent/Makefile  |  2 +-
 samtools/DESCR    |  3 ---
 samtools/Makefile | 28 ----------------------------
 samtools/PLIST    | 24 ------------------------
 samtools/TODO     |  3 ---
 samtools/distinfo |  6 ------
 7 files changed, 1 insertion(+), 66 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index 8d141e95f0..f84007a498 100644
--- a/Makefile
+++ b/Makefile
@@ -4346,7 +4346,6 @@ SUBDIR+=	sais
 SUBDIR+=	sais-demo-data
 SUBDIR+=	salmon
 SUBDIR+=	samhain
-SUBDIR+=	samtools
 SUBDIR+=	samtools0119
 SUBDIR+=	sara
 SUBDIR+=	sarf
diff --git a/ddocent/Makefile b/ddocent/Makefile
index ae37e968fc..33fcefb6dc 100644
--- a/ddocent/Makefile
+++ b/ddocent/Makefile
@@ -27,7 +27,7 @@ DEPENDS=	mawk>=0:../../lang/mawk \
 		parallel>=0:../../parallel/parallel \
 		bwa>=0.7.13:../../biology/bwa \
 		cdhit>=0:../../biology/cdhit \
-		samtools>=1.3:../../wip/samtools \
+		samtools>=1.3:../../biology/samtools \
 		vcftools>=0.1.15:../../wip/vcftools \
 		Trimmomatic>=0:../../biology/trimmomatic \
 		stacks>=0:../../biology/stacks \
diff --git a/samtools/DESCR b/samtools/DESCR
deleted file mode 100644
index 23d11d1c81..0000000000
--- a/samtools/DESCR
+++ /dev/null
@@ -1,3 +0,0 @@
-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
deleted file mode 100644
index 933bec8d2d..0000000000
--- a/samtools/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-# $NetBSD: Makefile,v 1.3 2018/11/06 10:49:41 adam Exp $
-
-DISTNAME=	samtools-1.9
-CATEGORIES=	biology
-MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
-EXTRACT_SUFX=	.tar.bz2
-GITHUB_RELEASE=	${PKGVERSION_NOREV}
-
-MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	http://www.htslib.org/
-COMMENT=	Tools for manipulating next-generation sequencing data
-LICENSE=	mit
-
-USE_TOOLS+=		gmake perl:run
-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
-
-.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
deleted file mode 100644
index 7b812362b5..0000000000
--- a/samtools/PLIST
+++ /dev/null
@@ -1,24 +0,0 @@
-@comment $NetBSD: PLIST,v 1.1 2018/05/07 18:37:31 bacon Exp $
-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/varfilter.py
-bin/wgsim
-bin/wgsim_eval.pl
-bin/zoom2sam.pl
-man/man1/samtools.1
-man/man1/wgsim.1
diff --git a/samtools/TODO b/samtools/TODO
deleted file mode 100644
index f1db9acbd6..0000000000
--- a/samtools/TODO
+++ /dev/null
@@ -1,3 +0,0 @@
-Figure out who removed zlib/bl3 in biology/samtools
-
-Address vulnerability
diff --git a/samtools/distinfo b/samtools/distinfo
deleted file mode 100644
index 5100c09cb1..0000000000
--- a/samtools/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD: distinfo,v 1.2 2018/11/06 10:49:41 adam Exp $
-
-SHA1 (samtools-1.9.tar.bz2) = 267191dc2f5d24eb0b22c0094138270ed5384241
-RMD160 (samtools-1.9.tar.bz2) = b7f49e1bdd569f63ec53330f43df7e5566ba8a16
-SHA512 (samtools-1.9.tar.bz2) = 6c8207754615ae8dad84b278f93e7d57eb40b818efb80f6aff6aba22fde5772247724e86596e765791e3175ffbb683393dd3ddfe7681c73eef4eb4f2342bf68f
-Size (samtools-1.9.tar.bz2) = 4440405 bytes