bwa/Makefile

CC=			gcc
CFLAGS=		-g -Wall -O2
CXXFLAGS=	$(CFLAGS)
AR=			ar
DFLAGS=		-DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64
LOBJS=		utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o
AOBJS=		QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
			is.o bwtindex.o bwape.o kopen.o \
			bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
			bwtsw2_chain.o fastmap.o bwtsw2_pair.o
PROG=		bwa bwamem-lite
INCLUDES=	
LIBS=		-lm -lz -lpthread
SUBDIRS=	.

.SUFFIXES:.c .o .cc

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

all:$(PROG)

bwa:libbwa.a $(AOBJS) main.o
		$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)

bwamem-lite:libbwa.a example.o
		$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)

libbwa.a:$(LOBJS)
		$(AR) -csru $@ $(LOBJS)

ksw.o:ksw.h
kstring.o:kstring.h
utils.o:utils.h ksort.h kseq.h
bntseq.o:bntseq.h
bwt.o:bwt.h utils.h
bwa.o:bwa.h bwt.h bntseq.h
bwamem.o:ksw.h kbtree.h ksort.h kvec.h kstring.h utils.h bwamem.h
bwamem_pair.o:ksw.h kvec.h kstring.h utils.h bwamem.h

QSufSort.o:QSufSort.h
bwt_gen.o:QSufSort.h

fastmap.o:bwt.h bwamem.h

bwtaln.o:bwt.h bwtaln.h kseq.h
bwtgap.o:bwtgap.h bwtaln.h bwt.h

bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h
bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h
bwtsw2_main.o:bwtsw2.h

clean:
		rm -f gmon.out *.o a.out $(PROG) *~ *.a
change CC back to gcc 2013-02-25 12:45:40 +08:00			`CC= gcc`
Imported from my local bwa repository, the master repository. 2011-01-14 09:52:12 +08:00			`CFLAGS= -g -Wall -O2`
			`CXXFLAGS= $(CFLAGS)`
API: aln seems working 2012-04-07 12:23:01 +08:00			`AR= ar`
use standard SW when no SSE2 2011-11-20 08:38:21 +08:00			`DFLAGS= -DHAVE_PTHREAD #-D_NO_SSE2 #-D_FILE_OFFSET_BITS=64`
r315: move kopen.o out of libbwa.a 2013-03-02 00:47:51 +08:00			`LOBJS= utils.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o`
r329: ditch stdaln.{c,h}; no changes to bwa-mem stdaln.{c,h} was written ten years ago. Its local and SW extension code are actually buggy (though that rarely happens and usually does not affect the results too much). ksw.{c,h} is more concise, potentially faster, less buggy, and richer in features. 2013-03-06 01:00:24 +08:00			`AOBJS= QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \`
r315: move kopen.o out of libbwa.a 2013-03-02 00:47:51 +08:00			`is.o bwtindex.o bwape.o kopen.o \`
Imported from my local bwa repository, the master repository. 2011-01-14 09:52:12 +08:00			`bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \`
API: aln seems working 2012-04-07 12:23:01 +08:00			`bwtsw2_chain.o fastmap.o bwtsw2_pair.o`
r308: added a new API to convert region to CIGAR and an example program demonstrating how to do single-end alignment in <50 lines of C code. 2013-02-28 11:28:29 +08:00			`PROG= bwa bwamem-lite`
Imported from my local bwa repository, the master repository. 2011-01-14 09:52:12 +08:00			`INCLUDES=`
move bwt_gen/* to the root directory 2011-10-20 23:56:24 +08:00			`LIBS= -lm -lz -lpthread`
API: aln seems working 2012-04-07 12:23:01 +08:00			`SUBDIRS= .`
Imported from my local bwa repository, the master repository. 2011-01-14 09:52:12 +08:00
			`.SUFFIXES:.c .o .cc`

			`.c.o:`
			`$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@`
			`.cc.o:`
			`$(CXX) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@`

			`all:$(PROG)`

API: aln seems working 2012-04-07 12:23:01 +08:00			`bwa:libbwa.a $(AOBJS) main.o`
Fixing problem with linking to libm on some Ubuntu systems (I see this on machine running 11.04, kernel 3.0.0-14-virtual). Changing order of -lm on the command line seems to do the trick and should be tolerated in other environments. 2013-03-06 04:48:16 +08:00			`$(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)`
API: aln seems working 2012-04-07 12:23:01 +08:00
r308: added a new API to convert region to CIGAR and an example program demonstrating how to do single-end alignment in <50 lines of C code. 2013-02-28 11:28:29 +08:00			`bwamem-lite:libbwa.a example.o`
Fixing problem with linking to libm on some Ubuntu systems (I see this on machine running 11.04, kernel 3.0.0-14-virtual). Changing order of -lm on the command line seems to do the trick and should be tolerated in other environments. 2013-03-06 04:48:16 +08:00			`$(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS)`
r308: added a new API to convert region to CIGAR and an example program demonstrating how to do single-end alignment in <50 lines of C code. 2013-02-28 11:28:29 +08:00
API: aln seems working 2012-04-07 12:23:01 +08:00			`libbwa.a:$(LOBJS)`
			`$(AR) -csru $@ $(LOBJS)`

moved some common code to bwa.{c,h} 2013-02-24 04:30:46 +08:00			`ksw.o:ksw.h`
more documentation in ksw.h 2013-02-28 10:40:46 +08:00			`kstring.o:kstring.h`
moved some common code to bwa.{c,h} 2013-02-24 04:30:46 +08:00			`utils.o:utils.h ksort.h kseq.h`
Imported from my local bwa repository, the master repository. 2011-01-14 09:52:12 +08:00			`bntseq.o:bntseq.h`
moved some common code to bwa.{c,h} 2013-02-24 04:30:46 +08:00			`bwt.o:bwt.h utils.h`
more documentation in ksw.h 2013-02-28 10:40:46 +08:00			`bwa.o:bwa.h bwt.h bntseq.h`
			`bwamem.o:ksw.h kbtree.h ksort.h kvec.h kstring.h utils.h bwamem.h`
			`bwamem_pair.o:ksw.h kvec.h kstring.h utils.h bwamem.h`

			`QSufSort.o:QSufSort.h`
			`bwt_gen.o:QSufSort.h`

			`fastmap.o:bwt.h bwamem.h`
moved some common code to bwa.{c,h} 2013-02-24 04:30:46 +08:00
			`bwtaln.o:bwt.h bwtaln.h kseq.h`
Imported from my local bwa repository, the master repository. 2011-01-14 09:52:12 +08:00			`bwtgap.o:bwtgap.h bwtaln.h bwt.h`

r329: ditch stdaln.{c,h}; no changes to bwa-mem stdaln.{c,h} was written ten years ago. Its local and SW extension code are actually buggy (though that rarely happens and usually does not affect the results too much). ksw.{c,h} is more concise, potentially faster, less buggy, and richer in features. 2013-03-06 01:00:24 +08:00			`bwtsw2_core.o:bwtsw2.h bwt.h bwt_lite.h`
			`bwtsw2_aux.o:bwtsw2.h bwt.h bwt_lite.h`
Imported from my local bwa repository, the master repository. 2011-01-14 09:52:12 +08:00			`bwtsw2_main.o:bwtsw2.h`

move bwt_gen/* to the root directory 2011-10-20 23:56:24 +08:00			`clean:`
Imported from my local bwa repository, the master repository. 2011-01-14 09:52:12 +08:00			`rm -f gmon.out .o a.out $(PROG) ~ *.a`