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fast-bwa/Makefile

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Release bwa-0.7.9-r783
2014-05-19 21:09:11 +08:00
CC= gcc
#CC= clang --analyze
r766: removed useless code
2014-05-14 01:09:29 +08:00
CFLAGS= -g -Wall -Wno-unused-function -O2
r391: better method to resolve xref alignment The old method does not work when the alignment bridges three chr. This may actually happen often. The new method does not work all the time, either, but should be better than the old one. It is also simpler, arguably.
2013-05-23 06:57:51 +08:00
WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS
API: aln seems working
2012-04-07 12:23:01 +08:00
AR= ar
Reduce dependency on utils.h - new malloc wrapping scheme. Remove xmalloc, xcalloc, xrealloc and xstrdup from utils.h and revert calls to the normal malloc, calloc, realloc, strdup. Add new files malloc_wrap.[ch] with the wrapper functions. malloc_wrap.h #defines malloc etc. to the wrapper, but only if USE_MALLOC_WRAPPERS has been defined. Put #include "malloc_wrap.h" in any file that uses *alloc or strdup. This is also in a #ifdef USE_MALLOC_WRAPPERS ... #endif block to make using the wrappers optional. Add -DUSE_MALLOC_WRAPPERS into the makefile so they should normally get added. This is an improvement on the previous method as we now don't need to worry about stray function calls that were not changed to the wrapped version and the code will still work even if the wrapping is disabled. Other possible methods of doing this are using malloc_hook (glibc-specific), adding -include malloc_wrap.h to the gcc command-line (somewhat gcc-specific) or making our own malloc function and using dlopen (scary). This way is probably the most portable.
2013-05-02 22:12:01 +08:00
DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC)
moved indexing to libbwa
2016-02-14 07:48:46 +08:00
LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
bwape.o kopen.o pemerge.o maxk.o \
Imported from my local bwa repository, the master repository.
2011-01-14 09:52:12 +08:00
bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
r391: better method to resolve xref alignment The old method does not work when the alignment bridges three chr. This may actually happen often. The new method does not work all the time, either, but should be better than the old one. It is also simpler, arguably.
2013-05-23 06:57:51 +08:00
bwtsw2_chain.o fastmap.o bwtsw2_pair.o
r384: don't compile bwamem-lite by default
2013-04-23 23:27:30 +08:00
PROG= bwa
Imported from my local bwa repository, the master repository.
2011-01-14 09:52:12 +08:00
INCLUDES=
move bwt_gen/* to the root directory
2011-10-20 23:56:24 +08:00
LIBS= -lm -lz -lpthread
API: aln seems working
2012-04-07 12:23:01 +08:00
SUBDIRS= .
Imported from my local bwa repository, the master repository.
2011-01-14 09:52:12 +08:00
added -lrt on Linux
2014-10-16 11:23:01 +08:00
ifeq ($(shell uname -s),Linux)
LIBS += -lrt
endif
Imported from my local bwa repository, the master repository.
2011-01-14 09:52:12 +08:00
.SUFFIXES:.c .o .cc
.c.o:
Use $CPPFLAGS and $LDFLAGS if they are set The bwa makefile doesn't set these two itself, but the environment or make command line might set any of CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS. Use $(CPPFLAGS) when compiling and $(LDFLAGS) when linking so they can be used to customise the build. Remove $(DFLAGS) from link commands as these preprocessor options are irrelevant for linking.
2019-12-16 02:14:49 +08:00
$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $(CPPFLAGS) $< -o $@
Imported from my local bwa repository, the master repository.
2011-01-14 09:52:12 +08:00
all:$(PROG)
API: aln seems working
2012-04-07 12:23:01 +08:00
bwa:libbwa.a $(AOBJS) main.o
Use $CPPFLAGS and $LDFLAGS if they are set The bwa makefile doesn't set these two itself, but the environment or make command line might set any of CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS. Use $(CPPFLAGS) when compiling and $(LDFLAGS) when linking so they can be used to customise the build. Remove $(DFLAGS) from link commands as these preprocessor options are irrelevant for linking.
2019-12-16 02:14:49 +08:00
$(CC) $(CFLAGS) $(LDFLAGS) $(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
Use $CPPFLAGS and $LDFLAGS if they are set The bwa makefile doesn't set these two itself, but the environment or make command line might set any of CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS. Use $(CPPFLAGS) when compiling and $(LDFLAGS) when linking so they can be used to customise the build. Remove $(DFLAGS) from link commands as these preprocessor options are irrelevant for linking.
2019-12-16 02:14:49 +08:00
$(CC) $(CFLAGS) $(LDFLAGS) 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)
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
Use wrapper functions to catch system errors Use the wrapper functions in utils.c plus a few extra bits of error checking code to catch system errors and exit non-zero when they occur.
2012-12-16 18:34:57 +08:00
Merge branch 'master' into master_fixes Merged to master version b621d3a Conflicts: Makefile bntseq.c bwa.c bwase.c bwaseqio.c bwtaln.c bwtindex.c bwtio.c bwtmisc.c bwtsw2_aux.c cs2nt.c fastmap.c khash.h kseq.h ksw.c kvec.h simple_dp.c utils.c utils.h
2013-03-01 17:37:46 +08:00
depend:
Use $CPPFLAGS and $LDFLAGS if they are set The bwa makefile doesn't set these two itself, but the environment or make command line might set any of CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS. Use $(CPPFLAGS) when compiling and $(LDFLAGS) when linking so they can be used to customise the build. Remove $(DFLAGS) from link commands as these preprocessor options are irrelevant for linking.
2019-12-16 02:14:49 +08:00
( LC_ALL=C ; export LC_ALL; makedepend -Y -- $(CFLAGS) $(DFLAGS) $(CPPFLAGS) -- *.c )
Imported from my local bwa repository, the master repository.
2011-01-14 09:52:12 +08:00
Merge branch 'master' into master_fixes Merged to master version b621d3a Conflicts: Makefile bntseq.c bwa.c bwase.c bwaseqio.c bwtaln.c bwtindex.c bwtio.c bwtmisc.c bwtsw2_aux.c cs2nt.c fastmap.c khash.h kseq.h ksw.c kvec.h simple_dp.c utils.c utils.h
2013-03-01 17:37:46 +08:00
# DO NOT DELETE THIS LINE -- make depend depends on it.
r762: cleanup for the new release; unfinished It will take to make the documentation ready.
2014-05-12 03:15:44 +08:00
QSufSort.o: QSufSort.h
bamlite.o: bamlite.h malloc_wrap.h
updated dependency
2014-09-16 22:17:30 +08:00
bntseq.o: bntseq.h utils.h kseq.h malloc_wrap.h khash.h
added maxk: max unique k-mer at each position
2015-02-09 05:49:25 +08:00
bwa.o: bntseq.h bwa.h bwt.h ksw.h utils.h kstring.h malloc_wrap.h kvec.h
bwa.o: kseq.h
r762: cleanup for the new release; unfinished It will take to make the documentation ready.
2014-05-12 03:15:44 +08:00
bwamem.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h ksw.h kvec.h
bwamem.o: ksort.h utils.h kbtree.h
bwamem_extra.o: bwa.h bntseq.h bwt.h bwamem.h kstring.h malloc_wrap.h
bwamem_pair.o: kstring.h malloc_wrap.h bwamem.h bwt.h bntseq.h bwa.h kvec.h
bwamem_pair.o: utils.h ksw.h
bwape.o: bwtaln.h bwt.h kvec.h malloc_wrap.h bntseq.h utils.h bwase.h bwa.h
bwape.o: ksw.h khash.h
bwase.o: bwase.h bntseq.h bwt.h bwtaln.h utils.h kstring.h malloc_wrap.h
bwase.o: bwa.h ksw.h
bwaseqio.o: bwtaln.h bwt.h utils.h bamlite.h malloc_wrap.h kseq.h
added -lrt on Linux
2014-10-16 11:23:01 +08:00
bwashm.o: bwa.h bntseq.h bwt.h
r762: cleanup for the new release; unfinished It will take to make the documentation ready.
2014-05-12 03:15:44 +08:00
bwt.o: utils.h bwt.h kvec.h malloc_wrap.h
bwt_gen.o: QSufSort.h malloc_wrap.h
bwt_lite.o: bwt_lite.h malloc_wrap.h
bwtaln.o: bwtaln.h bwt.h bwtgap.h utils.h bwa.h bntseq.h malloc_wrap.h
bwtgap.o: bwtgap.h bwt.h bwtaln.h malloc_wrap.h
moved indexing to libbwa
2016-02-14 07:48:46 +08:00
bwtindex.o: bntseq.h bwa.h bwt.h utils.h rle.h rope.h malloc_wrap.h
r762: cleanup for the new release; unfinished It will take to make the documentation ready.
2014-05-12 03:15:44 +08:00
bwtsw2_aux.o: bntseq.h bwt_lite.h utils.h bwtsw2.h bwt.h kstring.h
bwtsw2_aux.o: malloc_wrap.h bwa.h ksw.h kseq.h ksort.h
bwtsw2_chain.o: bwtsw2.h bntseq.h bwt_lite.h bwt.h malloc_wrap.h ksort.h
bwtsw2_core.o: bwt_lite.h bwtsw2.h bntseq.h bwt.h kvec.h malloc_wrap.h
bwtsw2_core.o: khash.h ksort.h
bwtsw2_main.o: bwt.h bwtsw2.h bntseq.h bwt_lite.h utils.h bwa.h
bwtsw2_pair.o: utils.h bwt.h bntseq.h bwtsw2.h bwt_lite.h kstring.h
bwtsw2_pair.o: malloc_wrap.h ksw.h
example.o: bwamem.h bwt.h bntseq.h bwa.h kseq.h malloc_wrap.h
fastmap.o: bwa.h bntseq.h bwt.h bwamem.h kvec.h malloc_wrap.h utils.h kseq.h
is.o: malloc_wrap.h
kopen.o: malloc_wrap.h
kstring.o: kstring.h malloc_wrap.h
On ARM, rewrite SSE2 SIMD calls using Neon intrinsics Many Intel intrinsics have a corresponding Neon equivalent. Other cases are more interesting: * Neon's vmaxvq directly selects the maximum entry in a vector, so can be used to implement both the __max_16/__max_8 macros and the _mm_movemask_epi8 early loop exit. Introduce additional helper macros alongside __max_16/__max_8 so that the early loop exit can similarly be implemented differently on the two platforms. * Full-width shifts can be done via vextq. This is defined close to the ksw_u8()/ksw_i16() functions (rather than in neon_sse.h) as it implicitly uses one of their local variables. * ksw_i16() uses saturating *signed* 16-bit operations apart from _mm_subs_epu16; presumably the data is effectively still signed but we wish to keep it non-negative. The ARM intrinsics are more careful about type checking, so this requires an extra U16() helper macro.
2022-06-18 02:34:14 +08:00
ksw.o: ksw.h neon_sse.h malloc_wrap.h
r762: cleanup for the new release; unfinished It will take to make the documentation ready.
2014-05-12 03:15:44 +08:00
main.o: kstring.h malloc_wrap.h utils.h
malloc_wrap.o: malloc_wrap.h
added maxk: max unique k-mer at each position
2015-02-09 05:49:25 +08:00
maxk.o: bwa.h bntseq.h bwt.h bwamem.h kseq.h malloc_wrap.h
r762: cleanup for the new release; unfinished It will take to make the documentation ready.
2014-05-12 03:15:44 +08:00
pemerge.o: ksw.h kseq.h malloc_wrap.h kstring.h bwa.h bntseq.h bwt.h utils.h
updated dependencies
2016-01-27 02:54:47 +08:00
rle.o: rle.h
rope.o: rle.h rope.h
r762: cleanup for the new release; unfinished It will take to make the documentation ready.
2014-05-12 03:15:44 +08:00
utils.o: utils.h ksort.h malloc_wrap.h kseq.h