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207 lines
6.6 KiB
207 lines
6.6 KiB
--- samtools-0.1.20/bcftools/Makefile
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+++ samtools-0.1.20/bcftools/Makefile
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@@ -1,6 +1,6 @@
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-CC= gcc
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-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
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-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
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+CC?= gcc
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+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc
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+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
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LOBJS= bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
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OMISC= ..
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AOBJS= call1.o main.o $(OMISC)/kstring.o $(OMISC)/bgzf.o $(OMISC)/knetfile.o $(OMISC)/bedidx.o
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@@ -11,14 +11,14 @@
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.SUFFIXES:.c .o
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.c.o:
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- $(CC) -c $(CFLAGS) $(DFLAGS) -I.. $(INCLUDES) $< -o $@
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+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -I.. $(INCLUDES) $< -o $@
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all-recur lib-recur clean-recur cleanlocal-recur install-recur:
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@target=`echo $@ | sed s/-recur//`; \
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wdir=`pwd`; \
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list='$(SUBDIRS)'; for subdir in $$list; do \
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cd $$subdir; \
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- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
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INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
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cd $$wdir; \
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done;
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@@ -31,7 +31,7 @@
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$(AR) -csru $@ $(LOBJS)
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bcftools:lib $(AOBJS)
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- $(CC) $(CFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. $(LIBPATH) -lbcf -lm -lz -lpthread
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bcf.o:bcf.h
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vcf.o:bcf.h
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--- samtools-0.1.20/Makefile
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+++ samtools-0.1.20/Makefile
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@@ -4,10 +4,10 @@
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# make git-stamp
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VERSION=
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-CC= gcc
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-CFLAGS= -g -Wall $(VERSION) -O2
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-#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
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-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
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+CC?= gcc
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+CFLAGS?= -g -Wall $(VERSION) -O2
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+#LDFLAGS+= -Wl,-rpath,\$$ORIGIN/../lib
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+CPPFLAGS+= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
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KNETFILE_O= knetfile.o
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LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \
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bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
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@@ -28,14 +28,14 @@
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.PHONY: all lib
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.c.o:
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- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
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all-recur lib-recur clean-recur cleanlocal-recur install-recur:
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@target=`echo $@ | sed s/-recur//`; \
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wdir=`pwd`; \
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list='$(SUBDIRS)'; for subdir in $$list; do \
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cd $$subdir; \
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- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
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INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
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cd $$wdir; \
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done;
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@@ -48,22 +48,22 @@
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.PHONY:all lib clean cleanlocal
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.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
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-lib:libbam.a
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+lib:libbam-0.1-legacy.a
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-libbam.a:$(LOBJS)
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+libbam-0.1-legacy.a:$(LOBJS)
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$(AR) -csru $@ $(LOBJS)
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samtools:lib-recur $(AOBJS)
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- $(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) -L. -lbam-0.1-legacy -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
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razip:razip.o razf.o $(KNETFILE_O)
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- $(CC) $(CFLAGS) -o $@ $^ -lz
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz
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bgzip:bgzip.o bgzf.o $(KNETFILE_O)
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- $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $^ -lz -lpthread
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bgzf.o:bgzf.c bgzf.h
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- $(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
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+ $(CC) -c $(CFLAGS) $(CPPFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
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razip.o:razf.h
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bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
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@@ -90,17 +90,17 @@
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faidx_main.o:faidx.h razf.h
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-libbam.1.dylib-local:$(LOBJS)
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- libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
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+libbam-0.1-legacy.1.dylib-local:$(LOBJS)
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+ libtool -dynamic $(LOBJS) -o libbam-0.1-legacy.1.dylib -lc -lz
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-libbam.so.1-local:$(LOBJS)
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- $(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
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+libbam-0.1-legacy.so.1-local:$(LOBJS)
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+ $(CC) $(LDFLAGS) -shared -Wl,-soname,libbam-0.1-legacy.so -o libbam-0.1-legacy.so.1 $(LOBJS) -lc -lz -lm -lpthread
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dylib:
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@$(MAKE) cleanlocal; \
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case `uname` in \
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- Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
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- Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
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+ Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.so.1-local;; \
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+ Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam-0.1-legacy.1.dylib-local;; \
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*) echo 'Unknown OS';; \
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esac
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--- samtools-0.1.20/misc/Makefile
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+++ samtools-0.1.20/misc/Makefile
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@@ -1,8 +1,8 @@
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-CC= gcc
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-CXX= g++
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-CFLAGS= -g -Wall -O2 #-m64 #-arch ppc
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-CXXFLAGS= $(CFLAGS)
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-DFLAGS= -D_FILE_OFFSET_BITS=64
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+CC?= gcc
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+CXX?= g++
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+CFLAGS?= -g -Wall -O2 #-m64 #-arch ppc
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+CXXFLAGS?= $(CFLAGS)
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+CPPFLAGS+= -D_FILE_OFFSET_BITS=64
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OBJS=
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PROG= md5sum-lite md5fa maq2sam-short maq2sam-long ace2sam wgsim bamcheck
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INCLUDES= -I..
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@@ -11,7 +11,7 @@
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.SUFFIXES:.c .o
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.c.o:
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- $(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
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+ $(CC) -c $(CFLAGS) $(CPPFLAGS) $(INCLUDES) $< -o $@
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all:$(PROG)
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@@ -20,7 +20,7 @@
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wdir=`pwd`; \
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list='$(SUBDIRS)'; for subdir in $$list; do \
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cd $$subdir; \
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- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
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+ $(MAKE) CC="$(CC)" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" \
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INCLUDES="$(INCLUDES)" $$target || exit 1; \
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cd $$wdir; \
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done;
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@@ -28,31 +28,31 @@
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lib:
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bamcheck:bamcheck.o
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- $(CC) $(CFLAGS) -o $@ bamcheck.o -L.. -lm -lbam -lpthread -lz
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ bamcheck.o -L.. -lm -lbam-0.1-legacy -lpthread -lz
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bamcheck.o:bamcheck.c ../faidx.h ../khash.h ../sam.h ../razf.h
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$(CC) $(CFLAGS) -c -I.. -o $@ bamcheck.c
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ace2sam:ace2sam.o
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- $(CC) $(CFLAGS) -o $@ ace2sam.o -lz
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ ace2sam.o -lz
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wgsim:wgsim.o
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- $(CC) $(CFLAGS) -o $@ wgsim.o -lm -lz
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ wgsim.o -lm -lz
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md5fa:md5.o md5fa.o md5.h ../kseq.h
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- $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5.o md5fa.o -lz
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md5sum-lite:md5sum-lite.o
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- $(CC) $(CFLAGS) -o $@ md5sum-lite.o
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ md5sum-lite.o
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md5sum-lite.o:md5.c md5.h
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$(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
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maq2sam-short:maq2sam.c
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- $(CC) $(CFLAGS) -o $@ maq2sam.c -lz
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ maq2sam.c -lz
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maq2sam-long:maq2sam.c
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- $(CC) $(CFLAGS) -DMAQ_LONGREADS -o $@ maq2sam.c -lz
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+ $(CC) $(CFLAGS) -DMAQ_LONGREADS $(LDFLAGS) -o $@ maq2sam.c -lz
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md5fa.o:md5.h md5fa.c
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$(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
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--- samtools-0.1.20/misc/varfilter.py
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+++ samtools-0.1.20/misc/varfilter.py
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@@ -1,4 +1,4 @@
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-#!/software/bin/python
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+#!/usr/bin/env python
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# Author: lh3, converted to python and modified to add -C option by Aylwyn Scally
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#
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