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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
在gz_read部分加了异步读取
2025-01-13 20:24:20 +08:00
CFLAGS= -g -Wall -Wno-unused-function -mavx2 -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
添加了可同时读写的pipeline，优化了时间统计
2024-03-24 04:40:09 +08:00
SHOW_PERF= -DSHOW_PERF
在gz_read部分加了异步读取
2025-01-13 20:24:20 +08:00
SHOW_DATA_PERF= #-DSHOW_DATA_PERF
clean代码，结果正确
2024-07-26 04:15:55 +08:00
FILTER_FULL_MATCH= #-DFILTER_FULL_MATCH
解决了创建bwt索引时，一同创建fmt相关的索引相关的bug，现在可以正常一起创建索引了，接下来还可以将sa和bytesa一起创建来减小时间
2024-04-06 15:05:20 +08:00
USE_MT_READ= -DUSE_MT_READ
添加了可同时读写的pipeline，优化了时间统计
2024-03-24 04:40:09 +08:00
API: aln seems working
2012-04-07 12:23:01 +08:00
AR= ar
所有代码都合并了，还差一点建立索引的时候，一起都建立了
2024-04-02 07:42:37 +08:00
DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) $(SHOW_PERF) $(SHOW_DATA_PERF) $(FILTER_FULL_MATCH) $(USE_MT_READ) -DUSE_AVX2 -DKSW_EQUAL
moved indexing to libbwa
2016-02-14 07:48:46 +08:00
LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o \
添加了可同时读写的pipeline，优化了时间统计
2024-03-24 04:40:09 +08:00
QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o yarn.o
moved indexing to libbwa
2016-02-14 07:48:46 +08:00
AOBJS= bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \
修改了双线程解压读写fastq.gz的bug，修改了一些测试代码
2024-06-24 18:11:54 +08:00
bwape.o kopen.o pemerge.o maxk.o ksw_align_avx2.o \
Imported from my local bwa repository, the master repository.
2011-01-14 09:52:12 +08:00
bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o \
修改了双线程解压读写fastq.gz的bug，修改了一些测试代码
2024-06-24 18:11:54 +08:00
bwtsw2_chain.o fastmap.o bwtsw2_pair.o profiling.o \
fmt_idx.o ksw_extend2_avx2.o ksw_extend2_avx2_u8.o \
添加了共享内存支持，成功构建ert索引
2024-08-03 17:26:32 +08:00
debug.o ertindex.o ertseeding.o
所有代码都合并了，还差一点建立索引的时候，一起都建立了
2024-04-02 07:42:37 +08:00
PROG= fastbwa
Imported from my local bwa repository, the master repository.
2011-01-14 09:52:12 +08:00
INCLUDES=
解决了sa的bug，现在结果和原版一模一样
2024-02-21 15:21:56 +08:00
LIBS= -lm -lz -lpthread -ldl
API: aln seems working
2012-04-07 12:23:01 +08:00
SUBDIRS= .
清理一些fprintf
2024-04-06 16:08:43 +08:00
JE_MALLOC=/home/zzh/work/jemalloc/lib/libjemalloc.a
Imported from my local bwa repository, the master repository.
2011-01-14 09:52:12 +08:00
added -lrt on Linux
2014-10-16 11:23:01 +08:00
ifeq ($(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)
解决了sa的bug，现在结果和原版一模一样
2024-02-21 15:21:56 +08:00
#bwa:libbwa.a $(AOBJS) main.o
开始改成sbwa那种batch模式
2024-03-07 18:23:21 +08:00
# $(CC) $(CFLAGS) $(LDFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS)
所有代码都合并了，还差一点建立索引的时候，一起都建立了
2024-04-02 07:42:37 +08:00
$(PROG):libbwa.a $(AOBJS) main.o
开始改成sbwa那种batch模式
2024-03-07 18:23:21 +08:00
$(CC) $(CFLAGS) $(LDFLAGS) $(AOBJS) $(JE_MALLOC) main.o -o $@ -L. -lbwa $(LIBS)
解决了sa的bug，现在结果和原版一模一样
2024-02-21 15:21:56 +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 other platforms, emulate SSE2 SIMD calls using scalar code
2022-06-23 01:47:04 +08:00
ksw.o: ksw.h neon_sse.h scalar_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