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biology/libgff: GFF/GTF parsing library based on GCLib

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This is an attempt to perform a simple "libraryfication" of the GFF/GTF
parsing code that is used in GFFRead codebase. There are not many
(any?) relatively lightweight GTF/GFF parsers exposing a C++ interface,
and the goal of this library is to provide this functionality without
the necessity of drawing in a heavy-weight dependency like SeqAn. Note:
This library draws directly from the code in GFFRead and GCLib, and
exists primarily to remove functionality (and hence code) that is
unnecessary for our downstream purposes. In the future, it may be
appropriate to just replace this library wholesale with GCLib.
This commit is contained in:
Jason W. Bacon 2021-12-05 14:50:42 -06:00
parent 316c372c7d
commit 864d4fdd18
5 changed files with 45 additions and 0 deletions
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1
biology/Makefile
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@ -78,6 +78,7 @@
SUBDIR += kallisto
SUBDIR += lamarc
SUBDIR += libbigwig
SUBDIR += libgff
SUBDIR += libgtextutils
SUBDIR += libneurosim
SUBDIR += libnuml

16
biology/libgff/Makefile Normal file
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@ -0,0 +1,16 @@
PORTNAME= libgff
DISTVERSIONPREFIX= v
DISTVERSION= 2.0.0
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= GFF/GTF parsing library based on GCLib
LICENSE= BSL
LICENSE_FILE= ${WRKSRC}/BoostLicense.txt
USES= cmake
USE_GITHUB= yes
GH_ACCOUNT= COMBINE-lab
.include <bsd.port.mk>

3
biology/libgff/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1631451501
SHA256 (COMBINE-lab-libgff-v2.0.0_GH0.tar.gz) = 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c
SIZE (COMBINE-lab-libgff-v2.0.0_GH0.tar.gz) = 102152

11
biology/libgff/pkg-descr Normal file
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@ -0,0 +1,11 @@
This is an attempt to perform a simple "libraryfication" of the GFF/GTF
parsing code that is used in GFFRead codebase. There are not many
(any?) relatively lightweight GTF/GFF parsers exposing a C++ interface,
and the goal of this library is to provide this functionality without
the necessity of drawing in a heavy-weight dependency like SeqAn. Note:
This library draws directly from the code in GFFRead and GCLib, and
exists primarily to remove functionality (and hence code) that is
unnecessary for our downstream purposes. In the future, it may be
appropriate to just replace this library wholesale with GCLib.
WWW: https://github.com/COMBINE-lab/libgff

14
biology/libgff/pkg-plist Normal file
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@ -0,0 +1,14 @@
include/GArgs.h
include/GBase.h
include/GFaSeqGet.h
include/GFastaIndex.h
include/GHash.hh
include/GList.hh
include/GStr.h
include/GVec.hh
include/codons.h
include/gdna.h
include/gff.h
lib/libgff.a
lib/libgff/cmake/libgffConfig.cmake
lib/libgff/cmake/libgffConfigVersion.cmake