biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15116

10 files changed, 200 insertions, 0 deletions

diff --git a/biology/freebayes/files/patch-Makefile b/biology/freebayes/files/patch-Makefile
new file mode 100644
index 000000000000..9c87b87ffbcb
--- /dev/null
+++ b/biology/freebayes/files/patch-Makefile
@@ -0,0 +1,20 @@
+--- Makefile.orig	2018-03-23 14:01:01 UTC
++++ Makefile
+@@ -5,7 +5,7 @@ wbamtools: vcflib/Makefile log
+ 	cd src && $(MAKE) -f Makefile.bamtools
+ 
+ log: src/version_git.h
+-	wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h | grep v | cut -f 3 -d\  | sed s/\"//g) &
++	# wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h | grep v | cut -f 3 -d\  | sed s/\"//g) &
+ 
+ src/version_git.h:
+ 	cd src && $(MAKE) autoversion
+@@ -27,7 +27,7 @@ uninstall:
+ 	rm /usr/local/bin/freebayes /usr/local/bin/bamleftalign
+ 
+ test:
+-	cd test && make test
++	cd test && ${MAKE} test
+ 
+ clean:
+ 	cd src && $(MAKE) clean
diff --git a/biology/freebayes/files/patch-SeqLib_bwa_Makefile b/biology/freebayes/files/patch-SeqLib_bwa_Makefile
new file mode 100644
index 000000000000..356ac3bd66ea
--- /dev/null
+++ b/biology/freebayes/files/patch-SeqLib_bwa_Makefile
@@ -0,0 +1,14 @@
+--- SeqLib/bwa/Makefile.orig	2018-03-23 18:47:04 UTC
++++ SeqLib/bwa/Makefile
+@@ -1,8 +1,8 @@
+-CC=			gcc
++CC ?=			gcc
+ #CC=			clang --analyze
+-CFLAGS=		-g -Wall -Wno-unused-function -O2
++CFLAGS ?=		-g -Wall -Wno-unused-function -O2
+ WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
+-AR=			ar
++AR ?=			ar
+ DFLAGS=		-DHAVE_PTHREAD $(WRAP_MALLOC)
+ ## moved is.o bwtiindex.o rope.o to LOBJS
+ LOBJS=		utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o \
diff --git a/biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c b/biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c
new file mode 100644
index 000000000000..f664bd55c48a
--- /dev/null
+++ b/biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c
@@ -0,0 +1,10 @@
+--- SeqLib/bwa/bwt_lite.c.orig	2018-03-23 18:49:48 UTC
++++ SeqLib/bwa/bwt_lite.c
+@@ -1,6 +1,7 @@
+ #include <stdlib.h>
+ #include <string.h>
+ #include <stdio.h>
++#include <sys/types.h>
+ #include "bwt_lite.h"
+ 
+ #ifdef USE_MALLOC_WRAPPERS
diff --git a/biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h b/biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h
new file mode 100644
index 000000000000..4b2e4322b70a
--- /dev/null
+++ b/biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h
@@ -0,0 +1,10 @@
+--- SeqLib/bwa/bwtgap.h.orig	2018-03-23 18:49:18 UTC
++++ SeqLib/bwa/bwtgap.h
+@@ -3,6 +3,7 @@
+ 
+ #include "bwt.h"
+ #include "bwtaln.h"
++#include <sys/types.h>
+ 
+ typedef struct { // recursion stack
+ 	u_int32_t info; // score<<21 | i
diff --git a/biology/freebayes/files/patch-SeqLib_bwa_kthread.c b/biology/freebayes/files/patch-SeqLib_bwa_kthread.c
new file mode 100644
index 000000000000..5193e4a2a2ab
--- /dev/null
+++ b/biology/freebayes/files/patch-SeqLib_bwa_kthread.c
@@ -0,0 +1,10 @@
+--- SeqLib/bwa/kthread.c.orig	2018-03-23 18:48:35 UTC
++++ SeqLib/bwa/kthread.c
+@@ -1,6 +1,7 @@
+ #include <pthread.h>
+ #include <stdlib.h>
+ #include <limits.h>
++#include <inttypes.h>
+ 
+ /************
+  * kt_for() *
diff --git a/biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile b/biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile
new file mode 100644
index 000000000000..ba795955ec76
--- /dev/null
+++ b/biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile
@@ -0,0 +1,12 @@
+--- SeqLib/fermi-lite/Makefile.orig	2018-03-23 18:50:25 UTC
++++ SeqLib/fermi-lite/Makefile
+@@ -1,6 +1,6 @@
+-CC=			gcc
+-CFLAGS=		-g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
+-CPPFLAGS=
++CC ?=			gcc
++CFLAGS ?=		-g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once
++CPPFLAGS ?=
+ INCLUDES=	
+ OBJS=		kthread.o misc.o \
+ 			bseq.o htab.o bfc.o \
diff --git a/biology/freebayes/files/patch-SeqLib_htslib_Makefile b/biology/freebayes/files/patch-SeqLib_htslib_Makefile
new file mode 100644
index 000000000000..e533e6ca5f45
--- /dev/null
+++ b/biology/freebayes/files/patch-SeqLib_htslib_Makefile
@@ -0,0 +1,38 @@
+--- SeqLib/htslib/Makefile.orig	2017-06-20 12:40:28 UTC
++++ SeqLib/htslib/Makefile
+@@ -22,20 +22,20 @@
+ # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ # DEALINGS IN THE SOFTWARE.
+ 
+-CC     = gcc
+-AR     = ar
+-RANLIB = ranlib
++CC     ?= gcc
++AR     ?= ar
++RANLIB ?= ranlib
+ 
+ # Default libraries to link if configure is not used
+ htslib_default_libs = -lz -lm -lbz2 -llzma
+ 
+-CPPFLAGS =
++CPPFLAGS ?=
+ # 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
+@@ -86,7 +86,7 @@ BUILT_THRASH_PROGRAMS = \
+ 	test/thrash_threads5 \
+ 	test/thrash_threads6
+ 
+-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
++all: lib-static $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
+ 
+ HTSPREFIX =
+ include htslib_vars.mk
diff --git a/biology/freebayes/files/patch-src_LargeFileSupport.h b/biology/freebayes/files/patch-src_LargeFileSupport.h
new file mode 100644
index 000000000000..60adfad0de8f
--- /dev/null
+++ b/biology/freebayes/files/patch-src_LargeFileSupport.h
@@ -0,0 +1,11 @@
+--- src/LargeFileSupport.h.orig	2018-03-23 21:15:04 UTC
++++ src/LargeFileSupport.h
+@@ -8,7 +8,7 @@ typedef __int64 off_type;
+ #define ftell64(a)     ftell(a)
+ #define fseek64(a,b,c) fseek(a,b,c)
+ typedef __int64_t off_type;
+-#elif defined(__APPLE__)
++#elif defined(__APPLE__) || defined(__FreeBSD__)
+ #define ftell64(a)     ftello(a)
+ #define fseek64(a,b,c) fseeko(a,b,c)
+ typedef off_t off_type;
diff --git a/biology/freebayes/files/patch-src_Makefile b/biology/freebayes/files/patch-src_Makefile
new file mode 100644
index 000000000000..cfe34b3b4ead
--- /dev/null
+++ b/biology/freebayes/files/patch-src_Makefile
@@ -0,0 +1,62 @@
+--- src/Makefile.orig	2018-03-23 14:01:01 UTC
++++ src/Makefile
+@@ -5,8 +5,9 @@
+ ################################################################################
+ 
+ # Compiler
+-CXX=g++ ${CXXFLAGS}
+-C=gcc
++CXX ?= g++
++# CXX += ${CXXFLAGS}
++CC ?= gcc
+ 
+ export CXXFLAGS
+ export C
+@@ -17,7 +18,7 @@ export LIBFLAGS
+ 
+ # Compiler flags
+ 
+-CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g
++CFLAGS += -D_FILE_OFFSET_BITS=64
+ #CFLAGS=-O3 -static -D VERBOSE_DEBUG  # enables verbose debugging via --debug2
+ 
+ SEQLIB_ROOT=../SeqLib
+@@ -25,7 +26,7 @@ VCFLIB_ROOT=../vcflib
+ TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp
+ HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib
+ 
+-LIBS = -lz -llzma -lbz2 -lm -lpthread
++LIBS = -lz -llzma -lbz2 -lm -lpthread -lexecinfo
+ INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) 
+ #INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib
+ 
+@@ -46,10 +47,10 @@ gprof:
+ .PHONY: all static debug profiling gprof
+ 
+ $(HTSLIB_ROOT)/libhts.a:
+-	cd $(HTSLIB_ROOT) && make
++	cd $(HTSLIB_ROOT) && ${MAKE}
+ 
+ $(SEQLIB_ROOT)/src/libseqlib.a:
+-	cd $(SEQLIB_ROOT) && ./configure && make 
++	cd $(SEQLIB_ROOT) && ./configure && ${MAKE} 
+ 
+ OBJECTS=BedReader.o \
+ 		CNV.o \
+@@ -122,7 +123,7 @@ freebayes.o: freebayes.cpp TryCatch.h $(
+ 	$(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp
+ 
+ fastlz.o: fastlz.c fastlz.h
+-	$(C) $(CFLAGS) $(INCLUDE) -c fastlz.c	
++	$(CC) $(CFLAGS) $(INCLUDE) -c fastlz.c	
+ 
+ Parameters.o: Parameters.cpp Parameters.h Version.h
+ 	$(CXX) $(CXXFLAGS) $(INCLUDE) -c Parameters.cpp
+@@ -277,5 +278,5 @@ autoversion:
+ 
+ clean:
+ 	rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp
+-	if [ -d $(BAMTOOLS_ROOT)/build ]; then make -C $(BAMTOOLS_ROOT)/build clean; fi
+-	make -C $(VCFLIB_ROOT)/smithwaterman clean
++	if [ -d $(BAMTOOLS_ROOT)/build ]; then ${MAKE} -C $(BAMTOOLS_ROOT)/build clean; fi
++	${MAKE} -C $(VCFLIB_ROOT)/smithwaterman clean
diff --git a/biology/freebayes/files/patch-vcflib_Makefile b/biology/freebayes/files/patch-vcflib_Makefile
new file mode 100644
index 000000000000..c3df0fb79e6c
--- /dev/null
+++ b/biology/freebayes/files/patch-vcflib_Makefile
@@ -0,0 +1,13 @@
+--- vcflib/Makefile.orig	2018-03-23 18:36:07 UTC
++++ vcflib/Makefile
+@@ -136,8 +136,8 @@ all: $(OBJECTS) $(BINS)
+ 
+ GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always)
+ 
+-CXX = g++
+-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x 
++CXX ?= g++
++CXXFLAGS += -D_FILE_OFFSET_BITS=64 -std=c++0x 
+ #CXXFLAGS = -O2
+ #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual
+