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

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.

biology/Makefile

@@ -6,6 +6,7 @@
     SUBDIR += avida
     SUBDIR += babel
     SUBDIR += bamtools
+    SUBDIR += bamutil
     SUBDIR += bbmap
     SUBDIR += bcftools
     SUBDIR += bedtools

biology/bamutil/Makefile

@@ -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>

biology/bamutil/distinfo

@@ -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

biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib

@@ -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)
+ 

biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain

@@ -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

biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp

@@ -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));

biology/bamutil/pkg-descr

@@ -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