biology/bedtools: Upgrade to 2.30.0

Several bug fixes and performance enhancements

Reported by:    portscout

6 files changed, 46 insertions, 34 deletions

diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile
index c68f904b7570..93426f1b7a62 100644
--- a/biology/bedtools/Makefile
+++ b/biology/bedtools/Makefile
@@ -2,7 +2,7 @@
 
 PORTNAME=		bedtools
 DISTVERSIONPREFIX=	v
-DISTVERSION=		2.29.2
+DISTVERSION=		2.30.0
 CATEGORIES=		biology
 
 MAINTAINER=	jwb@FreeBSD.org
@@ -15,20 +15,12 @@ TEST_DEPENDS=	bash:shells/bash
 
 USES=		compiler:c++11-lang gmake python
 USE_GITHUB=	yes
+
 GH_ACCOUNT=	arq5x
 GH_PROJECT=	bedtools2
 
-post-extract:
-# Avoid conflict with C++20 <version> by adding .txt suffix
-	@${MV} ${WRKSRC}/src/utils/gzstream/version \
-		${WRKSRC}/src/utils/gzstream/version.txt
-
 pre-configure:
 	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile
-	@${REINPLACE_CMD} -e 's|@\$$(CXX)|$$(CXX)|g' \
-		${WRKSRC}/*/Makefile \
-		${WRKSRC}/*/*/Makefile \
-		${WRKSRC}/*/*/*/Makefile
 
 post-install:
 	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools
diff --git a/biology/bedtools/distinfo b/biology/bedtools/distinfo
index 05b0709901d3..7a106b0489f7 100644
--- a/biology/bedtools/distinfo
+++ b/biology/bedtools/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1576701335
-SHA256 (arq5x-bedtools2-v2.29.2_GH0.tar.gz) = bc2f36b5d4fc9890c69f607d54da873032628462e88c545dd633d2c787a544a5
-SIZE (arq5x-bedtools2-v2.29.2_GH0.tar.gz) = 20638840
+TIMESTAMP = 1611493289
+SHA256 (arq5x-bedtools2-v2.30.0_GH0.tar.gz) = c575861ec746322961cd15d8c0b532bb2a19333f1cf167bbff73230a7d67302f
+SIZE (arq5x-bedtools2-v2.30.0_GH0.tar.gz) = 20639858
diff --git a/biology/bedtools/files/patch-Makefile b/biology/bedtools/files/patch-Makefile
index 16159fa81527..7dac9b0f8b59 100644
--- a/biology/bedtools/files/patch-Makefile
+++ b/biology/bedtools/files/patch-Makefile
@@ -1,33 +1,36 @@
---- Makefile.orig	2019-09-07 21:14:56 UTC
+--- Makefile.orig	2021-01-23 19:33:26 UTC
 +++ Makefile
-@@ -4,7 +4,7 @@
+@@ -4,7 +4,8 @@
  # (c) 2009 Aaron Quinlan
  # ==========================
  
 -SHELL := /bin/bash -e
++# Use sh for portability and avoid bash extensions in shell commands
 +SHELL := /bin/sh -e
  
  VERSION_FILE=./src/utils/version/version_git.h
  RELEASED_VERSION_FILE=./src/utils/version/version_release.txt
-@@ -20,7 +20,7 @@ OBJ_DIR	= obj
+@@ -21,7 +22,8 @@ OBJ_DIR	= obj
  BIN_DIR	= bin
  SRC_DIR	= src
  
 -CXX     = g++
++# Default if not provided via the environment or make args
 +CXX     ?= g++
  
  ifeq ($(DEBUG),1)
  BT_CPPFLAGS = -DDEBUG -D_DEBUG -D_FILE_OFFSET_BITS=64 -DWITH_HTS_CB_API $(INCLUDES)
-@@ -40,7 +40,7 @@ endif
+@@ -41,7 +43,8 @@ endif
  BT_LDFLAGS =
  BT_LIBS    = -lz -lm -lbz2 -llzma -lpthread
  
 -prefix ?= /usr/local
++# Default if not provided via the environment or make args
 +PREFIX ?= /usr/local
  
  SUBDIRS = $(SRC_DIR)/annotateBed \
  		  $(SRC_DIR)/bamToBed \
-@@ -183,9 +183,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
+@@ -197,9 +200,9 @@ $(BIN_DIR)/intersectBed: | $(BIN_DIR)
  .PHONY: all
  
  install: all
diff --git a/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp b/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp
new file mode 100644
index 000000000000..10f628ad85b6
--- /dev/null
+++ b/biology/bedtools/files/patch-src_utils_BamTools_include_SamHeader.hpp
@@ -0,0 +1,23 @@
+--- src/utils/BamTools/include/SamHeader.hpp.orig	2021-01-24 16:15:06 UTC
++++ src/utils/BamTools/include/SamHeader.hpp
+@@ -7,6 +7,7 @@
+ #include <string.h>
+ #include <api/BamAux.h>
+ #include <stdlib.h>
++#include <sysexits.h>
+ 
+ 
+ #ifdef WITH_HTS_CB_API
+@@ -29,7 +30,11 @@ namespace htslib_future {
+ 		ops.cb_data = buffer;
+ 		samFile* fp = hts_open_callback(NULL, &ops, "w");
+ 
+-		sam_hdr_write(fp, hdr);
++		if ( sam_hdr_write(fp, hdr) != 0 )
++		{
++			fputs("sam_hdr_rebuild: Error: sam_hdr_write() failed.\n", stderr);
++			exit(EX_IOERR);
++		}
+ 
+ 		hts_close(fp);
+ 
diff --git a/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h b/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h
deleted file mode 100644
index 89f21e42296f..000000000000
--- a/biology/bedtools/files/patch-src_utils_Contexts_ContextBase.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/utils/Contexts/ContextBase.h.orig	2019-03-25 18:03:45 UTC
-+++ src/utils/Contexts/ContextBase.h
-@@ -44,7 +44,7 @@ public:
- 	FileRecordMgr *getFile(int fileIdx) { return _files[fileIdx]; }
- 	void setProgram(PROGRAM_TYPE program) { _program = program; }
- 
--	void addInputFile(const string &inputFile) { _fileNames.push_back(inputFile); }
-+	void addInputFile(const string &inputFile) { _fileNames.push_back(inputFile); cerr << "Adding " << inputFile << endl; }
- 
- 	int getNumInputFiles() const { return _fileNames.size(); }
- 	const string &getInputFileName(int fileNum) const { return _fileNames[fileNum]; }
diff --git a/biology/bedtools/files/patch-src_utils_htslib_Makefile b/biology/bedtools/files/patch-src_utils_htslib_Makefile
index 7ca62f5eb33a..45c973b23246 100644
--- a/biology/bedtools/files/patch-src_utils_htslib_Makefile
+++ b/biology/bedtools/files/patch-src_utils_htslib_Makefile
@@ -1,27 +1,32 @@
---- src/utils/htslib/Makefile.orig	2019-03-25 03:58:18 UTC
+--- src/utils/htslib/Makefile.orig	2021-01-23 19:33:26 UTC
 +++ src/utils/htslib/Makefile
-@@ -22,9 +22,9 @@
+@@ -22,20 +22,23 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  # DEALINGS IN THE SOFTWARE.
  
 -CC     = gcc
 -AR     = ar
 -RANLIB = ranlib
++# Defaults if not provided by the environment or make args
 +CC     ?= gcc
 +AR     ?= ar
 +RANLIB ?= ranlib
  
  # Default libraries to link if configure is not used
  htslib_default_libs = -lz -lm -lbz2 -llzma
-@@ -33,9 +33,9 @@ CPPFLAGS =
+ 
+-CPPFLAGS =
++# Defaults if not provided by the environment or make args
++CPPFLAGS ?=
++CFLAGS   ?= -g -Wall -O2
++LDFLAGS  ?=
++
  # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
  # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600
  #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__
 -CFLAGS   = -g -Wall -O2
-+CFLAGS   ?= -g -Wall -O2
  EXTRA_CFLAGS_PIC = -fpic
 -LDFLAGS  =
-+LDFLAGS  ?=
  LIBS     = $(htslib_default_libs)
  
  prefix      = /usr/local