biology/bedtools: Upgrade to 2.27.1

PR:             227272
Submitted by:   jwb
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15137

6 files changed, 36 insertions, 54 deletions

diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile
index 0b8640170ada..7047a703cf32 100644
--- a/biology/bedtools/Makefile
+++ b/biology/bedtools/Makefile
@@ -1,29 +1,30 @@
-# Created by: Scott Cheloha <scottcheloha@gmail.com>
 # $FreeBSD$
 
 PORTNAME=	bedtools
-PORTVERSION=	2.25.0
 DISTVERSIONPREFIX=	v
+DISTVERSION=	2.27.1
 CATEGORIES=	biology
-MASTER_SITES=	GITHUB
 
-MAINTAINER=	scottcheloha@gmail.com
-COMMENT=	Toolset for genome arithmetic
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Toolset for genome set arithmetic such as intersect, union
 
 LICENSE=	GPLv2
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
+USES=		gmake python
 USE_GITHUB=	yes
 GH_ACCOUNT=	arq5x
 GH_PROJECT=	bedtools2
 
-USES=		gmake python
-#NO_ARCH=	yes
-
-MAKE_JOBS_UNSAFE=	yes
+pre-build:
+	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' ${WRKSRC}/Makefile
+	@${REINPLACE_CMD} -e 's|@\$$(CXX)|$$(CXX)|g' \
+		${WRKSRC}/*/Makefile \
+		${WRKSRC}/*/*/Makefile \
+		${WRKSRC}/*/*/*/Makefile \
+		${WRKSRC}/*/*/*/*/Makefile
 
-post-patch:
-	@${REINPLACE_CMD} -e 's|python|${PYTHON_CMD}|g' \
-		${WRKSRC}/Makefile
+post-install:
+	${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/bedtools
 
 .include <bsd.port.mk>
diff --git a/biology/bedtools/distinfo b/biology/bedtools/distinfo
index 49d6b6491c63..bd752c979d56 100644
--- a/biology/bedtools/distinfo
+++ b/biology/bedtools/distinfo
@@ -1,2 +1,3 @@
-SHA256 (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 159122afb9978015f7ec85d7b17739b01415a5738086b20a48147eeefcf08cfb
-SIZE (arq5x-bedtools2-v2.25.0_GH0.tar.gz) = 19586049
+TIMESTAMP = 1519746174
+SHA256 (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = edcac089d84e63a51f85c3c189469daa7d42180272130b046856faad3cf79112
+SIZE (arq5x-bedtools2-v2.27.1_GH0.tar.gz) = 20003119
diff --git a/biology/bedtools/files/patch-Makefile b/biology/bedtools/files/patch-Makefile
index 3c479bc9f999..9ba6eaaccc4e 100644
--- a/biology/bedtools/files/patch-Makefile
+++ b/biology/bedtools/files/patch-Makefile
@@ -1,4 +1,4 @@
---- Makefile.orig	2015-11-14 00:48:48 UTC
+--- Makefile.orig	2017-12-14 17:15:02 UTC
 +++ Makefile
 @@ -4,7 +4,7 @@
  # (c) 2009 Aaron Quinlan
@@ -14,38 +14,28 @@
  export SRC_DIR	= src
  export UTIL_DIR	= src/utils
 -export CXX		= g++
-+export CXX	= c++
- #ifeq ($(DEBUG),1)
- #export CXXFLAGS = -Wall -O0 -g -fno-inline -fkeep-inline-functions -D_FILE_OFFSET_BITS=64 -fPIC -DDEBUG -D_DEBUG
- #else
++export CXX		?= g++
+ ifeq ($(DEBUG),1)
+-export CXXFLAGS = -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
++export CXXFLAGS += -Wall -Wextra -DDEBUG -D_DEBUG -g -O0 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+ else
 -export CXXFLAGS = -Wall -O2 -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
-+export CXXFLAGS += -Wall -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
- #endif
- export LIBS		= -lz
- export BT_ROOT  = src/utils/BamTools/
-@@ -129,20 +129,17 @@ INCLUDES =	-I$(SRC_DIR)/utils/bedFile \
- 				-I$(SRC_DIR)/utils/GenomeFile \
- 				-I$(SRC_DIR)/utils/RecordOutputMgr \
- 				-I$(SRC_DIR)/utils/ToolBase \
--				-I$(SRC_DIR)/utils/driver \
--				
-+				-I$(SRC_DIR)/utils/driver
++export CXXFLAGS += -D_FILE_OFFSET_BITS=64 -fPIC $(INCLUDES)
+ endif
+ 
+ # If the user has specified to do so, tell the compile to use rand() (instead of mt19937).
+@@ -143,8 +143,8 @@ INCLUDES =	-I$(SRC_DIR)/utils/bedFile \
  
  all: print_banner $(OBJ_DIR) $(BIN_DIR) autoversion $(UTIL_SUBDIRS) $(SUBDIRS)
  	@echo "- Building main bedtools binary."
- 	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
- 	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
- 	@echo "done."
--	
- 	@echo "- Creating executables for old CLI."
- 	@python scripts/makeBashScripts.py
- 	@chmod +x bin/*
+-	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
+-	@$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -c src/bedtools.cpp -o obj/bedtools.o $(INCLUDES)
++	$(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(BIN_DIR)/bedtools $(BUILT_OBJECTS) -L$(UTIL_DIR)/BamTools/lib/ -lbamtools $(LIBS) $(LDFLAGS) $(INCLUDES)
  	@echo "done."
--	
  
- .PHONY: all
- 
-@@ -183,7 +180,7 @@ clean:
+ 	@echo "- Creating executables for old CLI."
+@@ -193,7 +193,7 @@ clean:
  .PHONY: clean
  
  test: all
diff --git a/biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h b/biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h
deleted file mode 100644
index e5987e640cd0..000000000000
--- a/biology/bedtools/files/patch-src_utils_FileRecordTools_Records_StrandQueue.h
+++ /dev/null
@@ -1,11 +0,0 @@
---- src/utils/FileRecordTools/Records/StrandQueue.h.orig	2015-09-03 04:36:18 UTC
-+++ src/utils/FileRecordTools/Records/StrandQueue.h
-@@ -30,7 +30,7 @@ public:
- 
- private:
- //	static RecordPtrSortFunctor _recSortFunctor;
--	typedef priority_queue<Record *, vector<const Record *>, RecordPtrSortDescFunctor > queueType;
-+	typedef priority_queue<Record *, vector<Record *>, RecordPtrSortDescFunctor > queueType;
- 	vector<queueType *> _queues;
- 	static const int NUM_QUEUES = 3;
- 
diff --git a/biology/bedtools/pkg-descr b/biology/bedtools/pkg-descr
index 6eb2df9dab04..b4295c2fba7b 100644
--- a/biology/bedtools/pkg-descr
+++ b/biology/bedtools/pkg-descr
@@ -1,7 +1,7 @@
 The bedtools utilities are a suite of tools for performing a wide range of
 genomics analysis tasks.  The most widely-used of these tools enable genome
-arithmetic, i.e., set theory on the genome.  For example, with bedtools one
-can intersect, merge, count, complement, and shuffle genomic intervals from
+arithmetic, i.e., set theory on the genome.  For example, with bedtools one can
+intersect, merge, count, complement, and shuffle genomic intervals from
 multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
 
 Although each individual utility is designed to do a relatively simple task,
diff --git a/biology/bedtools/pkg-plist b/biology/bedtools/pkg-plist
index 3ad56455ec57..4768b1dc1de9 100644
--- a/biology/bedtools/pkg-plist
+++ b/biology/bedtools/pkg-plist
@@ -27,6 +27,7 @@ bin/nucBed
 bin/pairToBed
 bin/pairToPair
 bin/randomBed
+bin/shiftBed
 bin/shuffleBed
 bin/slopBed
 bin/sortBed