<commit_before>CC=			gcc
# CFLAGS=		-ggdb -Wall -O0 #-m64 #-arch ppc
CFLAGS=		-Wall -O2 -ggdb #-m64 #-arch ppc
DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 \
			-DGIT_VERSION="$(shell git describe --always)"
KNETFILE_O=	knetfile.o
LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
AOBJS=		bam_tview.o bam_plcmd.o sam_view.o	\
			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
			cut_target.o phase.o bam2depth.o
PROG=		samtools razip faidx bgzip
INCLUDES=	-I.
SUBDIRS=	. bcftools misc
LIBPATH=
LIBCURSES=	-lcurses # -lXCurses

.SUFFIXES:.c .o

.c.o:
		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

all-recur lib-recur clean-recur cleanlocal-recur install-recur:
		@target=`echo $@ | sed s/-recur//`; \
		wdir=`pwd`; \
		list='$(SUBDIRS)'; for subdir in $$list; do \
			cd $$subdir; \
			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
			cd $$wdir; \
		done;

all:$(PROG)

install: all-recur
	install -d -m 755 $(prefix)/bin
	install -d -m 755 $(prefix)/include/bam
	install -d -m 755 $(prefix)/lib
	install -d -m 755 $(prefix)/share/man/man1
	install -s -m 755 -b samtools $(prefix)/bin
	install -s -m 755 -b samtools $(prefix)/bin/sam
	install -s -m 755 -b razip $(prefix)/bin
	install -s -m 755 -b bgzip $(prefix)/bin
	install -s -m 755 -b faidx $(prefix)/bin
	install    -m 644 -b libbam.a $(prefix)/lib
	install    -m 644    *.h $(prefix)/include/bam/
	install -s -m 755 -b bcftools/bcftools $(prefix)/bin
	install    -m 755    bcftools/vcfutils.pl $(prefix)/bin
	install    -m 644    samtools.1 $(prefix)/share/man/man1
	install -s -m 755 -b misc/seqtk $(prefix)/bin
	install -s -m 755 -b misc/wgsim $(prefix)/bin

<commit_msg>let some file copies fail silently<commit_after>CC=			gcc
# CFLAGS=		-ggdb -Wall -O0 #-m64 #-arch ppc
CFLAGS=		-Wall -O2 -ggdb #-m64 #-arch ppc
DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 \
			-DGIT_VERSION="$(shell git describe --always)"
KNETFILE_O=	knetfile.o
LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
AOBJS=		bam_tview.o bam_plcmd.o sam_view.o	\
			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o	\
			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
			cut_target.o phase.o bam2depth.o
PROG=		samtools razip faidx bgzip
INCLUDES=	-I.
SUBDIRS=	. bcftools misc
LIBPATH=
LIBCURSES=	-lcurses # -lXCurses

.SUFFIXES:.c .o

.c.o:
		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@

all-recur lib-recur clean-recur cleanlocal-recur install-recur:
		@target=`echo $@ | sed s/-recur//`; \
		wdir=`pwd`; \
		list='$(SUBDIRS)'; for subdir in $$list; do \
			cd $$subdir; \
			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
			cd $$wdir; \
		done;

all:$(PROG)

install: all-recur
	install -d -m 755 $(prefix)/bin
	install -d -m 755 $(prefix)/include/bam
	install -d -m 755 $(prefix)/lib
	install -d -m 755 $(prefix)/share/man/man1
	-install -s -m 755 -b samtools $(prefix)/bin
	-install -s -m 755 -b samtools $(prefix)/bin/sam
	install -s -m 755 -b razip $(prefix)/bin
	install -s -m 755 -b bgzip $(prefix)/bin
	install -s -m 755 -b faidx $(prefix)/bin
	install    -m 644 -b libbam.a $(prefix)/lib
	install    -m 644    *.h $(prefix)/include/bam/
	-install -s -m 755 -b bcftools/bcftools $(prefix)/bin
	-install    -m 755    bcftools/vcfutils.pl $(prefix)/bin
	install    -m 644    samtools.1 $(prefix)/share/man/man1
	-install -s -m 755 -b misc/seqtk $(prefix)/bin
	-install -s -m 755 -b misc/wgsim $(prefix)/bin


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{'dir': 'git-commits-cleaned', 'id': '1382297', 'n_tokens_mistral': 2020, 'n_tokens_neox': 1828, 'n_words': 439}