vcf-split: Resurrect and update to 0.1.5.10

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

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue Oct 24 07:18:51 2023 -0500
Changeset:	608835a0318137b3d91ce7cf85e3f9808788c803

Modified Files:
	Makefile
Added Files:
	vcf-split/DESCR
	vcf-split/Makefile
	vcf-split/PLIST
	vcf-split/distinfo

Log Message:
vcf-split: Resurrect and update to 0.1.5.10

Updates for latest libxtend API

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=608835a0318137b3d91ce7cf85e3f9808788c803

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

diffstat:
 Makefile           |  1 +
 vcf-split/DESCR    |  6 ++++++
 vcf-split/Makefile | 19 +++++++++++++++++++
 vcf-split/PLIST    |  3 +++
 vcf-split/distinfo |  5 +++++
 5 files changed, 34 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 3d0f3ee1d3..12c8223e3c 100644
--- a/Makefile
+++ b/Makefile
@@ -5520,6 +5520,7 @@ SUBDIR+=	varnish-modules
 SUBDIR+=	varnish-slash
 SUBDIR+=	vault
 SUBDIR+=	vaultwarden-web-vault
+SUBDIR+=	vcf-split
 SUBDIR+=	vcflib
 SUBDIR+=	vcftools
 SUBDIR+=	vcg
diff --git a/vcf-split/DESCR b/vcf-split/DESCR
new file mode 100644
index 0000000000..37f7d39c7c
--- /dev/null
+++ b/vcf-split/DESCR
@@ -0,0 +1,6 @@
+Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
+of output files simultaneously.  Parsing the TOPMed human chromosome 1 BCF
+with bcftools takes two days, so extracting the 137,977 samples one at a time
+or using thousands of parallel readers of the same file is impractical.
+Vcf-split solves this by generating thousands of single-sample outputs during
+a single sweep through the multi-sample input.
diff --git a/vcf-split/Makefile b/vcf-split/Makefile
new file mode 100644
index 0000000000..50bcc8c1e2
--- /dev/null
+++ b/vcf-split/Makefile
@@ -0,0 +1,19 @@
+# $NetBSD$
+
+DISTNAME=	vcf-split-0.1.5.10
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=auerlab/}
+GITHUB_TAG=	0f2fd0a5051e058b82efd310679265bcda0b5b03
+
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/auerlab/vcf-split
+COMMENT=	Split a multi-sample VCF into single-sample VCFs
+LICENSE=	2-clause-bsd
+
+MAKE_ENV+=	VERSION=${PKGVERSION}
+
+pre-build:
+	cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend
+
+.include "../../wip/biolibc/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/vcf-split/PLIST b/vcf-split/PLIST
new file mode 100644
index 0000000000..b5e5d4f1d0
--- /dev/null
+++ b/vcf-split/PLIST
@@ -0,0 +1,3 @@
+@comment $NetBSD$
+bin/vcf-split
+man/man1/vcf-split.1
diff --git a/vcf-split/distinfo b/vcf-split/distinfo
new file mode 100644
index 0000000000..4429de5536
--- /dev/null
+++ b/vcf-split/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+BLAKE2s (vcf-split-0.1.5.10-0f2fd0a5051e058b82efd310679265bcda0b5b03.tar.gz) = de4d91fdcb9fe68d942e78f4819bf8a4437ac657d711c4348684f1a590462a59
+SHA512 (vcf-split-0.1.5.10-0f2fd0a5051e058b82efd310679265bcda0b5b03.tar.gz) = a6857dbfed03546d216302392b231ce29e7a9e320ceb18b1359bdede655bde2438e9235e109867cf7ba91334e384625bd9df635838f1bc1a156fc04c7819415f
+Size (vcf-split-0.1.5.10-0f2fd0a5051e058b82efd310679265bcda0b5b03.tar.gz) = 22560 bytes