From aa8e14f1c183bdc57940de974b9773b498595974 Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Tue, 23 Mar 2021 15:15:00 +0000
Subject: biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF
 file

ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file.  SAM input is read via stdin and the VCF
input file is taken as a command-line argument. This allows expensive BAM/CRAM
decoding to be performed in parallel by a separate samtools process.
---
 biology/Makefile         |  1 +
 biology/ad2vcf/Makefile  | 26 ++++++++++++++++++++++++++
 biology/ad2vcf/distinfo  |  3 +++
 biology/ad2vcf/pkg-descr |  6 ++++++
 4 files changed, 36 insertions(+)
 create mode 100644 biology/ad2vcf/Makefile
 create mode 100644 biology/ad2vcf/distinfo
 create mode 100644 biology/ad2vcf/pkg-descr

(limited to 'biology')

diff --git a/biology/Makefile b/biology/Makefile
index cba970a40784..260d2763d896 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -4,6 +4,7 @@
     COMMENT = Biology
 
     SUBDIR += abyss
+    SUBDIR += ad2vcf
     SUBDIR += artemis
     SUBDIR += avida
     SUBDIR += babel
diff --git a/biology/ad2vcf/Makefile b/biology/ad2vcf/Makefile
new file mode 100644
index 000000000000..e3703746263e
--- /dev/null
+++ b/biology/ad2vcf/Makefile
@@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME=	ad2vcf
+DISTVERSION=	0.1.2
+CATEGORIES=	biology
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Add allelic depth info from a SAM stream to a VCF file
+
+LICENSE=	BSD2CLAUSE
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+BUILD_DEPENDS=	biolibc>=0.1.1:biology/biolibc
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	auerlab
+
+PLIST_FILES=	bin/ad2vcf man/man1/ad2vcf.1.gz
+
+pre-build:
+	(cd ${WRKSRC} && ${MAKE} LOCALBASE=${LOCALBASE} depend)
+
+do-test:
+	(cd ${WRKSRC}/Test && ./run-test.sh)
+
+.include <bsd.port.mk>
diff --git a/biology/ad2vcf/distinfo b/biology/ad2vcf/distinfo
new file mode 100644
index 000000000000..649dbb04a74c
--- /dev/null
+++ b/biology/ad2vcf/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1616510305
+SHA256 (auerlab-ad2vcf-0.1.2_GH0.tar.gz) = e85e221c69748082799f5b048412136d28a0395290b16728500fe30190eaea84
+SIZE (auerlab-ad2vcf-0.1.2_GH0.tar.gz) = 15204
diff --git a/biology/ad2vcf/pkg-descr b/biology/ad2vcf/pkg-descr
new file mode 100644
index 000000000000..21df7c875513
--- /dev/null
+++ b/biology/ad2vcf/pkg-descr
@@ -0,0 +1,6 @@
+ad2vdf extracts allelic depth info from a SAM stream and adds it to a
+corresponding single-sample VCF file.  SAM input is read via stdin and the VCF
+input file is taken as a command-line argument. This allows expensive BAM/CRAM
+decoding to be performed in parallel by a separate samtools process.
+
+WWW: https://github.com/auerlab/ad2vcf
-- 
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