7 files changed, 79 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index ba430926041c..c779368ef1d2 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -6,6 +6,7 @@
     SUBDIR += avida
     SUBDIR += babel
     SUBDIR += bamtools
+    SUBDIR += bamutil
     SUBDIR += bbmap
     SUBDIR += bcftools
     SUBDIR += bedtools
diff --git a/biology/bamutil/Makefile b/biology/bamutil/Makefile
new file mode 100644
index 000000000000..1df27f50678d
--- /dev/null
+++ b/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>
diff --git a/biology/bamutil/distinfo b/biology/bamutil/distinfo
new file mode 100644
index 000000000000..4f76b5616521
--- /dev/null
+++ b/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
diff --git a/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.lib
new file mode 100644
index 000000000000..7f8d5a434e94
--- /dev/null
+++ b/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)
+ 
diff --git a/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain b/biology/bamutil/files/patch-libStatGen_Makefiles_Makefile.toolchain
new file mode 100644
index 000000000000..447be2125380
--- /dev/null
+++ b/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
diff --git a/biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp b/biology/bamutil/files/patch-libStatGen_vcf_VcfRecordGenotype.cpp
new file mode 100644
index 000000000000..db31c78ab9d7
--- /dev/null
+++ b/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));
diff --git a/biology/bamutil/pkg-descr b/biology/bamutil/pkg-descr
new file mode 100644
index 000000000000..6eb44e52fcb7
--- /dev/null
+++ b/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