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freebayes: Up-to-date using bundled dependencies
Module Name: pkgsrc-wip
Committed By: Winston Weinert <winston%ml1.net@localhost>
Pushed By: winston
Date: Fri Mar 30 14:37:16 2018 -0500
Changeset: 94bd2857cb1249e8fb5f90e21cf463d56c95c476
Modified Files:
freebayes/Makefile
freebayes/distinfo
Added Files:
freebayes/buildlink3.mk
freebayes/patches/patch-Makefile
freebayes/patches/patch-SeqLib_bwa_Makefile
freebayes/patches/patch-SeqLib_bwa_bwt__lite.c
freebayes/patches/patch-SeqLib_bwa_bwtgap.h
freebayes/patches/patch-SeqLib_bwa_kthread.c
freebayes/patches/patch-SeqLib_fermi-lite_Makefile
freebayes/patches/patch-SeqLib_htslib_Makefile
freebayes/patches/patch-src_LargeFileSupport.h
freebayes/patches/patch-src_Makefile
freebayes/patches/patch-vcflib_Makefile
Log Message:
freebayes: Up-to-date using bundled dependencies
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=94bd2857cb1249e8fb5f90e21cf463d56c95c476
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
freebayes/Makefile | 50 +++---------
freebayes/buildlink3.mk | 11 +++
freebayes/distinfo | 18 ++++-
freebayes/patches/patch-Makefile | 23 ++++++
freebayes/patches/patch-SeqLib_bwa_Makefile | 17 ++++
freebayes/patches/patch-SeqLib_bwa_bwt__lite.c | 13 ++++
freebayes/patches/patch-SeqLib_bwa_bwtgap.h | 13 ++++
freebayes/patches/patch-SeqLib_bwa_kthread.c | 13 ++++
freebayes/patches/patch-SeqLib_fermi-lite_Makefile | 15 ++++
freebayes/patches/patch-SeqLib_htslib_Makefile | 32 ++++++++
freebayes/patches/patch-src_LargeFileSupport.h | 14 ++++
freebayes/patches/patch-src_Makefile | 90 ++++++++++++++++++++++
freebayes/patches/patch-vcflib_Makefile | 16 ++++
13 files changed, 283 insertions(+), 42 deletions(-)
diffs:
diff --git a/freebayes/Makefile b/freebayes/Makefile
index f061df0b3e..20bb8fb58a 100644
--- a/freebayes/Makefile
+++ b/freebayes/Makefile
@@ -1,51 +1,27 @@
# $NetBSD$
-#
-###########################################################
-# Generated by fbsd2pkg #
-###########################################################
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-# # FIXME: Do we need a version >= the submodules bamtools and vcflib?
-# BUILD_DEPENDS= ${LOCALBASE}/include/intervaltree/IntervalTree.h:/usr/wip/math/intervaltree \
-# ${LOCALBASE}/include/multichoose/multichoose.h:/usr/wip/math/multichoose
-# LIB_DEPENDS= libbamtools.so:/usr/wip/biology/bamtools \
-# libvcflib.so.1:/usr/wip/biology/vcflib \
-# libtabix.so.1:/usr/wip/biology/tabixpp \
-# libsw.so.1:/usr/wip/biology/smithwaterman \
-# libhts.so:/usr/ports/biology/htslib
-# Unknown tool: USE_TOOLS= compiler:c++11-lang
-# -I${LOCALBASE}/include/intervaltree \
-# -I${LOCALBASE}/include/vcflib \
-# -I${LOCALBASE}/include/multichoose \
-# -I${LOCALBASE}/include/smithwaterman
-
-DISTNAME= freebayes-${PORTVERSION}
+DISTNAME= freebayes-2018.03.23
CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_GITHUB:=outpaddling/}
-GITHUB_TAG= ${PORTVERSION}
+MASTER_SITES= https://acadix.biz/Ports/distfiles/
MAINTAINER= dsiercks%uwm.edu@localhost
HOMEPAGE= https://github.com/ekg/freebayes
COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping
LICENSE= mit
-# Just assuming C and C++: Adjust this!
+EXTRACT_SUFX= .tar.xz
+
USE_LANGUAGES= c c++
USE_LIBTOOL= yes
USE_TOOLS+= gmake
-MAKE_FILE= Makefile.external-libs
-INSTALL_TARGET= install-strip
+MAKE_JOBS_SAFE= no
# SUBST_CLASSES+= compile
# SUBST_FILES.compile= ${WRKSRC}/src/Makefile.external-libs
# SUBST_STAGE.compile= post-patch
# SUBST_SED.compile+= -e "s|-lm|-lm -rpath=${PREFIX}/lib|g"
-PORTVERSION= 65c4880d09ec21f7f2755eac9476b607011522f3
-
.include "../../mk/bsd.prefs.mk"
.if ${OPSYS} == Linux
@@ -54,14 +30,12 @@ MAKE_FLAGS= EXTRALIBS=${COMPILER_RPATH_FLAG}${PREFIX}/lib
MAKE_FLAGS+= EXTRALIBS=${COMPILER_RPATH_FLAG}${PREFIX}/lib
.endif
-.include "../../devel/libexecinfo/buildlink3.mk"
-.include "../../wip/filevercmp/buildlink3.mk"
+INSTALLATION_DIRS+= bin
+
+do-install:
+ ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${DESTDIR}${PREFIX}/bin
+
+.include "../../archivers/bzip2/buildlink3.mk"
+.include "../../archivers/xz/buildlink3.mk"
.include "../../devel/zlib/buildlink3.mk"
-.include "../../wip/intervaltree/buildlink3.mk"
-.include "../../wip/multichoose/buildlink3.mk"
-.include "../../wip/bamtools/buildlink3.mk"
-.include "../../wip/vcflib/buildlink3.mk"
-.include "../../wip/tabixpp/buildlink3.mk"
-.include "../../wip/smithwaterman/buildlink3.mk"
-.include "../../wip/htslib/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
diff --git a/freebayes/buildlink3.mk b/freebayes/buildlink3.mk
new file mode 100644
index 0000000000..0b6aff5038
--- /dev/null
+++ b/freebayes/buildlink3.mk
@@ -0,0 +1,11 @@
+# $NetBSD$
+BUILDLINK_TREE+= freebayes
+
+.if !defined(FREEBAYES_BUILDLINK3_MK)
+FREEBAYES_BUILDLINK3_MK:=
+
+BUILDLINK_API_DEPENDS.freebayes+= freebayes>=2018.03.23
+BUILDLINK_PKGSRCDIR.freebayes?= ../../wip/freebayes
+.endif # FREEBAYES_BUILDLINK3_MK
+
+BUILDLINK_TREE+= -freebayes
diff --git a/freebayes/distinfo b/freebayes/distinfo
index 7de36521ca..1aa6d4a556 100644
--- a/freebayes/distinfo
+++ b/freebayes/distinfo
@@ -1,6 +1,16 @@
$NetBSD$
-SHA1 (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 8e0ba1d24055f949a495f7de017298962367d6ab
-RMD160 (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 9b97eede39b7dd9bd9ae513274790567073d2dbb
-SHA512 (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 0b401c83a8667fe839d4ef8592b6de35bda33749e1ee448eb9e01613a4854703673c39943c87114ea5450cd46bcb96fa9ebe2f46c5c781149a56c97731680027
-Size (freebayes-65c4880d09ec21f7f2755eac9476b607011522f3-65c4880d09ec21f7f2755eac9476b607011522f3.tar.gz) = 2345427 bytes
+SHA1 (freebayes-2018.03.23.tar.xz) = f06f25c27cd24460146755430a5ae39d90db3f31
+RMD160 (freebayes-2018.03.23.tar.xz) = bde7a441c76c2a16c89600d8b3fe0ce843146b37
+SHA512 (freebayes-2018.03.23.tar.xz) = 04f386b24d623e4b818a2b3ce12042c30db877b9ab08744466702573730ff8f853f7f2720d9a23f3c7b3abae8dc50fba3912e1695ad7d04dbddc3682754952e4
+Size (freebayes-2018.03.23.tar.xz) = 89782932 bytes
+SHA1 (patch-Makefile) = aace859fb9e85a132386d510771c34f0b9a0d47b
+SHA1 (patch-SeqLib_bwa_Makefile) = 2822b4c3c8c612033fba165d918a790711e28bba
+SHA1 (patch-SeqLib_bwa_bwt__lite.c) = de4f9efd1485a4b6c20837584e65406267833ccd
+SHA1 (patch-SeqLib_bwa_bwtgap.h) = a8abe98b7f0ad65104a763c19fd128bbb05f2ed8
+SHA1 (patch-SeqLib_bwa_kthread.c) = 5170b400af2f1f835cfcf5dda3875242f227bc89
+SHA1 (patch-SeqLib_fermi-lite_Makefile) = 1f1d19792bcfca7cf76076243e2e0ee218e53e4a
+SHA1 (patch-SeqLib_htslib_Makefile) = f7d332c3defd580a44feaa479e5c17509f73e02d
+SHA1 (patch-src_LargeFileSupport.h) = 2efb9a247582c85b080a1e1346e687c99686749d
+SHA1 (patch-src_Makefile) = afd89cc38dd7cd94d0d4a698a54a1c2a6be87f29
+SHA1 (patch-vcflib_Makefile) = ce29ade87027b7e638f0472653cec6e9aa809b15
diff --git a/freebayes/patches/patch-Makefile b/freebayes/patches/patch-Makefile
new file mode 100644
index 0000000000..52e40e4f21
--- /dev/null
+++ b/freebayes/patches/patch-Makefile
@@ -0,0 +1,23 @@
+$NetBSD$
+
+Use correct make binary & do not download an unused file.
+--- 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 && $(MAKE) clean
diff --git a/freebayes/patches/patch-SeqLib_bwa_Makefile b/freebayes/patches/patch-SeqLib_bwa_Makefile
new file mode 100644
index 0000000000..a471484c89
--- /dev/null
+++ b/freebayes/patches/patch-SeqLib_bwa_Makefile
@@ -0,0 +1,17 @@
+$NetBSD$
+
+Allow makefile variable overrides.
+--- 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 $(WRAP_MALLOC)
+ ## moved is.o bwtiindex.o rope.o to LOBJS
+ LOBJS= utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o \
diff --git a/freebayes/patches/patch-SeqLib_bwa_bwt__lite.c b/freebayes/patches/patch-SeqLib_bwa_bwt__lite.c
new file mode 100644
index 0000000000..53f5b7dc48
--- /dev/null
+++ b/freebayes/patches/patch-SeqLib_bwa_bwt__lite.c
@@ -0,0 +1,13 @@
+$NetBSD$
+
+Add missing include.
+--- 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/freebayes/patches/patch-SeqLib_bwa_bwtgap.h b/freebayes/patches/patch-SeqLib_bwa_bwtgap.h
new file mode 100644
index 0000000000..e1cc56495e
--- /dev/null
+++ b/freebayes/patches/patch-SeqLib_bwa_bwtgap.h
@@ -0,0 +1,13 @@
+$NetBSD$
+
+Add missing include.
+--- 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/freebayes/patches/patch-SeqLib_bwa_kthread.c b/freebayes/patches/patch-SeqLib_bwa_kthread.c
new file mode 100644
index 0000000000..148fb653d8
--- /dev/null
+++ b/freebayes/patches/patch-SeqLib_bwa_kthread.c
@@ -0,0 +1,13 @@
+$NetBSD$
+
+Add missing include.
+--- 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/freebayes/patches/patch-SeqLib_fermi-lite_Makefile b/freebayes/patches/patch-SeqLib_fermi-lite_Makefile
new file mode 100644
index 0000000000..c7b746bb9b
--- /dev/null
+++ b/freebayes/patches/patch-SeqLib_fermi-lite_Makefile
@@ -0,0 +1,15 @@
+$NetBSD$
+
+Allow makefile variable overrides.
+--- 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/freebayes/patches/patch-SeqLib_htslib_Makefile b/freebayes/patches/patch-SeqLib_htslib_Makefile
new file mode 100644
index 0000000000..cd46441e98
--- /dev/null
+++ b/freebayes/patches/patch-SeqLib_htslib_Makefile
@@ -0,0 +1,32 @@
+$NetBSD$
+
+Allow makefile variable overrides
+--- SeqLib/htslib/Makefile.orig 2018-03-23 18:41:02 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 = $(htslib_default_libs)
+
+ prefix = /usr/local
diff --git a/freebayes/patches/patch-src_LargeFileSupport.h b/freebayes/patches/patch-src_LargeFileSupport.h
new file mode 100644
index 0000000000..039ceee11f
--- /dev/null
+++ b/freebayes/patches/patch-src_LargeFileSupport.h
@@ -0,0 +1,14 @@
+$NetBSD$
+
+Add macro-ifdef check for FreeBSD.
+--- 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/freebayes/patches/patch-src_Makefile b/freebayes/patches/patch-src_Makefile
new file mode 100644
index 0000000000..3a44086e6c
--- /dev/null
+++ b/freebayes/patches/patch-src_Makefile
@@ -0,0 +1,90 @@
+$NetBSD$
+
+Allow makefile variable overrides. Honor LDFLAGS. Honor make binary.
+--- src/Makefile.orig 2018-03-30 18:35:02.370636951 +0000
++++ 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 \
+@@ -92,19 +93,19 @@ HEADERS=multichoose.h version_git.h
+ # executables
+
+ freebayes ../bin/freebayes: freebayes.o $(OBJECTS) $(HEADERS) $(seqlib)
+- $(CXX) $(CXXFLAGS) $(INCLUDE) freebayes.o $(OBJECTS) -o ../bin/freebayes $(LIBS)
++ $(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) freebayes.o $(OBJECTS) -o ../bin/freebayes $(LIBS)
+
+ alleles ../bin/alleles: alleles.o $(OBJECTS) $(HEADERS) $(seqlib)
+- $(CXX) $(CXXFLAGS) $(INCLUDE) alleles.o $(OBJECTS) -o ../bin/alleles $(LIBS)
++ $(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) alleles.o $(OBJECTS) -o ../bin/alleles $(LIBS)
+
+ dummy ../bin/dummy: dummy.o $(OBJECTS) $(HEADERS) $(seqlib)
+- $(CXX) $(CXXFLAGS) $(INCLUDE) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
++ $(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) dummy.o $(OBJECTS) -o ../bin/dummy $(LIBS)
+
+ bamleftalign ../bin/bamleftalign: $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a bamleftalign.o Fasta.o LeftAlign.o IndelAllele.o split.o
+- $(CXX) $(CXXFLAGS) $(INCLUDE) bamleftalign.o $(OBJECTS) -o ../bin/bamleftalign $(LIBS)
++ $(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) bamleftalign.o $(OBJECTS) -o ../bin/bamleftalign $(LIBS)
+
+ bamfiltertech ../bin/bamfiltertech: $(SEQLIB_ROOT)/src/libseqlib.a $(HTSLIB_ROOT)/libhts.a bamfiltertech.o $(OBJECTS) $(HEADERS)
+- $(CXX) $(CXXFLAGS) $(INCLUDE) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
++ $(CXX) $(CXXFLAGS) $(INCLUDE) $(LDFLAGS) bamfiltertech.o $(OBJECTS) -o ../bin/bamfiltertech $(LIBS)
+
+
+ # objects
+@@ -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 $(VCFLIB_ROOT)/smithwaterman clean
diff --git a/freebayes/patches/patch-vcflib_Makefile b/freebayes/patches/patch-vcflib_Makefile
new file mode 100644
index 0000000000..cf0b91dbc8
--- /dev/null
+++ b/freebayes/patches/patch-vcflib_Makefile
@@ -0,0 +1,16 @@
+$NetBSD$
+
+Allow makefile variable overrides.
+--- 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
+
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