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biology/bamutil: Utilities for working with SAM/BAM files

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Utilities for working on SAM/BAM files from The Center for Statistical
Genetics at the University of Michigan School of Public Health.  It
includes numerous functions such as splitting, merging, trimming reads,
filtering, validation, diff, etc.
This commit is contained in:
Jason W. Bacon 2021-10-12 11:40:35 -05:00
parent ec07fc5b07
commit cdf2ff2f68
7 changed files with 79 additions and 0 deletions
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1
biology/Makefile
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@ -6,6 +6,7 @@
SUBDIR += avida
SUBDIR += babel
SUBDIR += bamtools
SUBDIR += bamutil
SUBDIR += bbmap
SUBDIR += bcftools
SUBDIR += bedtools

26
biology/bamutil/Makefile Normal file
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@ -0,0 +1,26 @@
PORTNAME= bamutil
DISTVERSIONPREFIX= v
DISTVERSION= 1.0.14
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org
COMMENT= Utilities for working with SAM/BAM files
LICENSE= GPLv3
LICENSE_FILE= ${WRKSRC}/copyrights/COPYING
USES= gmake
USE_GITHUB= yes
GH_ACCOUNT= statgen
GH_PROJECT= bamUtil
# Build needs access to libStatGen Makefiles, so can't install separately
GH_TUPLE= statgen:libStatGen:v${DISTVERSION}:statgen/libStatGen
MAKE_ENV= LIB_PATH_GENERAL=${WRKSRC}/libStatGen
MAKE_ENV+= INSTALLDIR=${STAGEDIR}${PREFIX}/bin
PLIST_FILES= bin/bam
.include <bsd.port.mk>

5
biology/bamutil/distinfo Normal file
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@ -0,0 +1,5 @@
TIMESTAMP = 1634051641
SHA256 (statgen-bamUtil-v1.0.14_GH0.tar.gz) = f5ec8d5e98a3797742106c3413a4ab1622d8787e38b29b3df4cddb59d77efda5
SIZE (statgen-bamUtil-v1.0.14_GH0.tar.gz) = 1916953
SHA256 (statgen-libStatGen-v1.0.14_GH0.tar.gz) = 70a504c5cc4838c6ac96cdd010644454615cc907df4e3794c999baf958fa734b
SIZE (statgen-libStatGen-v1.0.14_GH0.tar.gz) = 558924

17
biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib Normal file
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@ -0,0 +1,17 @@
--- libStatGen/Makefiles/Makefile.lib.orig 2021-10-12 15:28:34 UTC
+++ libStatGen/Makefiles/Makefile.lib
@@ -34,11 +34,11 @@ profile: $(STAT_GEN_LIB_PROFILE)
# To build the library, build the objects
# Then add them to the library
$(STAT_GEN_LIB_OPT): $(OBJECTS_OPT)
- ar -cru $@ $(OBJECTS_OPT)
+ ar -cr $@ $(OBJECTS_OPT)
$(STAT_GEN_LIB_DEBUG): $(OBJECTS_DEBUG)
- ar -cru $@ $(OBJECTS_DEBUG)
+ ar -cr $@ $(OBJECTS_DEBUG)
$(STAT_GEN_LIB_PROFILE): $(OBJECTS_PROFILE)
- ar -cru $@ $(OBJECTS_PROFILE)
+ ar -cr $@ $(OBJECTS_PROFILE)
UNAME=$(shell uname)

13
biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain Normal file
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@ -0,0 +1,13 @@
--- libStatGen/Makefiles/Makefile.toolchain.orig 2021-10-12 15:09:29 UTC
+++ libStatGen/Makefiles/Makefile.toolchain
@@ -51,8 +51,8 @@ endif
# CPP0X=-std=c++0x
-CXX = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)g++ $(CPP0X)
-CC = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)gcc
+CXX = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)c++ $(CPP0X)
+CC = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)cc
LD = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ld
AR = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ar
RANLIB = $(TOOLCHAIN_DIR)$(TOOLCHAIN_PREFIX)ranlib

11
biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp Normal file
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@ -0,0 +1,11 @@
--- libStatGen/vcf/VcfRecordGenotype.cpp.orig 2021-10-12 15:13:03 UTC
+++ libStatGen/vcf/VcfRecordGenotype.cpp
@@ -176,7 +176,7 @@ bool VcfRecordGenotype::setString(const std::string& k
if(sampleNum >= mySamples.size())
{
// Out of range sample index.
- return(NULL);
+ return(false);
}
// Set the field in the sample.
return(mySamples.get(sampleNum).setString(key, value));

6
biology/bamutil/pkg-descr Normal file
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@ -0,0 +1,6 @@
Utilities for working on SAM/BAM files from The Center for Statistical
Genetics at the University of Michigan School of Public Health. It
includes numerous functions such as splitting, merging, trimming reads,
filtering, validation, diff, etc.
WWW: https://github.com/statgen/bamUtil