bcftools: Resurrect and update to 1.21

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: bcftools: Resurrect and update to 1.21
From: Jason W. Bacon <bacon%NetBSD.org@localhost>
Date: Sat, 28 Sep 2024 12:13:19 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Sep 28 07:12:34 2024 -0500
Changeset:	9643082cc7ae4342d2845471813cd94826bf4111

Added Files:
	bcftools/DESCR
	bcftools/Makefile
	bcftools/PLIST
	bcftools/distinfo
	bcftools/patches/patch-Makefile

Log Message:
bcftools: Resurrect and update to 1.21

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9643082cc7ae4342d2845471813cd94826bf4111

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

diffstat:
 bcftools/DESCR                  |  4 +++
 bcftools/Makefile               | 55 +++++++++++++++++++++++++++++++++++++++++
 bcftools/PLIST                  | 49 ++++++++++++++++++++++++++++++++++++
 bcftools/distinfo               |  6 +++++
 bcftools/patches/patch-Makefile | 23 +++++++++++++++++
 5 files changed, 137 insertions(+)

diffs:
diff --git a/bcftools/DESCR b/bcftools/DESCR
new file mode 100644
index 0000000000..d3bb50e44e
--- /dev/null
+++ b/bcftools/DESCR
@@ -0,0 +1,4 @@
+BCFtools is a set of utilities that manipulate variant calls in the
+Variant Call Format (VCF) and its binary counterpart BCF. All
+commands work transparently with both VCFs and BCFs, both
+uncompressed and BGZF-compressed.
diff --git a/bcftools/Makefile b/bcftools/Makefile
new file mode 100644
index 0000000000..4dc4ab83fe
--- /dev/null
+++ b/bcftools/Makefile
@@ -0,0 +1,55 @@
+# $NetBSD: Makefile,v 1.15 2022/06/30 11:18:04 nia Exp $
+
+DISTNAME=	bcftools-1.21
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=samtools/}
+GITHUB_RELEASE=	${PKGVERSION_NOREV}
+EXTRACT_SUFX=	.tar.bz2
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://www.htslib.org/
+COMMENT=	Tools for manipulating BCF and VCF variant call files
+LICENSE=	mit
+
+USE_TOOLS+=		autoconf automake autoreconf bash gmake perl
+GNU_CONFIGURE=		yes
+CONFIGURE_ARGS+=	--with-htslib=system
+MAKE_ENV+=		USE_GPL=1
+TEST_TARGET=		test
+
+SUBST_CLASSES+=		version
+SUBST_STAGE.version=	pre-configure
+SUBST_SED.version=	-e "s|m4_esyscmd_s(\[./version.sh 2>/dev/null\])|[${PKGVERSION_NOREV}]|"
+SUBST_FILES.version=	configure.ac
+
+SUBST_CLASSES+=		bash
+SUBST_STAGE.bash=	pre-configure
+SUBST_SED.bash+=	-e 's|/bin/bash|${TOOLS_PATH.bash}|'
+SUBST_SED.bash+=	-e 's|\\/bin\\/bash|${TOOLS_PATH.bash:S,/,\\\/,g}|'
+SUBST_FILES.bash=	test/test.pl
+
+REPLACE_PERL+=		misc/*.pl
+REPLACE_PERL+=		misc/fix-broken-GATK-Double-vs-Integer
+REPLACE_PERL+=		misc/plot-vcfstats
+REPLACE_PERL+=		test/test.pl
+REPLACE_PYTHON+=	misc/*.py
+
+pre-configure:
+	cd ${WRKSRC} && autoreconf -if
+
+post-install:
+	${MV} ${DESTDIR}${PREFIX}/bin/color-chrs.pl \
+		${DESTDIR}${PREFIX}/bin/color-chrs
+	${MV} ${DESTDIR}${PREFIX}/bin/guess-ploidy.py\
+	       ${DESTDIR}${PREFIX}/bin/guess-ploidy
+	${MV} ${DESTDIR}${PREFIX}/bin/plot-roh.py \
+		${DESTDIR}${PREFIX}/bin/plot-roh
+	${MV} ${DESTDIR}${PREFIX}/bin/run-roh.pl \
+		${DESTDIR}${PREFIX}/bin/run-roh
+	${MV} ${DESTDIR}${PREFIX}/bin/vcfutils.pl \
+		${DESTDIR}${PREFIX}/bin/vcfutils
+
+.include "../../biology/htslib/buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/bcftools/PLIST b/bcftools/PLIST
new file mode 100644
index 0000000000..f1f9897f9c
--- /dev/null
+++ b/bcftools/PLIST
@@ -0,0 +1,49 @@
+@comment $NetBSD$
+bin/bcftools
+bin/color-chrs
+bin/gff2gff.py
+bin/guess-ploidy
+bin/plot-roh
+bin/plot-vcfstats
+bin/run-roh
+bin/vcfutils
+libexec/bcftools/GTisec.so
+libexec/bcftools/GTsubset.so
+libexec/bcftools/ad-bias.so
+libexec/bcftools/add-variantkey.so
+libexec/bcftools/af-dist.so
+libexec/bcftools/allele-length.so
+libexec/bcftools/check-ploidy.so
+libexec/bcftools/check-sparsity.so
+libexec/bcftools/color-chrs.so
+libexec/bcftools/contrast.so
+libexec/bcftools/counts.so
+libexec/bcftools/dosage.so
+libexec/bcftools/fill-AN-AC.so
+libexec/bcftools/fill-from-fasta.so
+libexec/bcftools/fill-tags.so
+libexec/bcftools/fixploidy.so
+libexec/bcftools/fixref.so
+libexec/bcftools/frameshifts.so
+libexec/bcftools/guess-ploidy.so
+libexec/bcftools/gvcfz.so
+libexec/bcftools/impute-info.so
+libexec/bcftools/indel-stats.so
+libexec/bcftools/isecGT.so
+libexec/bcftools/mendelian2.so
+libexec/bcftools/missing2ref.so
+libexec/bcftools/parental-origin.so
+libexec/bcftools/prune.so
+libexec/bcftools/remove-overlaps.so
+libexec/bcftools/scatter.so
+libexec/bcftools/setGT.so
+libexec/bcftools/smpl-stats.so
+libexec/bcftools/split-vep.so
+libexec/bcftools/split.so
+libexec/bcftools/tag2tag.so
+libexec/bcftools/trio-dnm2.so
+libexec/bcftools/trio-stats.so
+libexec/bcftools/trio-switch-rate.so
+libexec/bcftools/variant-distance.so
+libexec/bcftools/variantkey-hex.so
+man/man1/bcftools.1
diff --git a/bcftools/distinfo b/bcftools/distinfo
new file mode 100644
index 0000000000..fb71bc1114
--- /dev/null
+++ b/bcftools/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+BLAKE2s (bcftools-1.21.tar.bz2) = 517b73f84870fa967e6f7f6241c446131cc54229e7ee446110955e39dfbe2563
+SHA512 (bcftools-1.21.tar.bz2) = f8fb2e50a1a9e7a7e8a4f71d71d052f6019d54c60ae060d0abfbd01ab61a2c44e04e069c479ea9f6156513b54a611a9a46930a0ff4454019bb715fdb9558d07d
+Size (bcftools-1.21.tar.bz2) = 7982173 bytes
+SHA1 (patch-Makefile) = 9dfe7b5dcf77deac6d248d7612440780ec8a3731
diff --git a/bcftools/patches/patch-Makefile b/bcftools/patches/patch-Makefile
new file mode 100644
index 0000000000..c1cae450ea
--- /dev/null
+++ b/bcftools/patches/patch-Makefile
@@ -0,0 +1,23 @@
+$NetBSD: patch-Makefile,v 1.4 2022/02/26 23:14:33 bacon Exp $
+
+# Respect pkgsrc env
+
+--- Makefile.orig	2021-03-19 17:42:33.842623449 +0000
++++ Makefile
+@@ -60,11 +60,11 @@ misc_bindir = $(bindir)
+ 
+ MKDIR_P = mkdir -p
+ INSTALL = install -p
+-INSTALL_DATA    = $(INSTALL) -m 644
+-INSTALL_DIR     = $(MKDIR_P) -m 755
+-INSTALL_MAN     = $(INSTALL_DATA)
+-INSTALL_PROGRAM = $(INSTALL)
+-INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
++INSTALL_DATA    = ${BSD_INSTALL_DATA}
++INSTALL_DIR     = $(MKDIR_P)
++INSTALL_MAN     = ${BSD_INSTALL_MAN}
++INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
++INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
+ 
+ PROGRAMS = bcftools
+ MISC_SCRIPTS = \
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