zzh
7d085962a2
开始改成sbwa那种batch模式
2024-03-07 18:23:21 +08:00
96e445d9e4
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 15:12:01 +01:00
90ecd344ba
Merge branch 'master' into master_fixes. Merged up to master r375.
...
Conflicts:
bwt.c
2013-04-11 11:15:39 +01:00
47520134e7
r375: fixed compiling errors by the last change
2013-04-10 11:04:32 -04:00
9228e48efd
Merge branch 'master' into master_fixes
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Conflicts:
Makefile
2013-03-11 13:50:49 +00:00
017be45407
r342: bugfix in bwasw - AS is off by one
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but I do not understand why the old code does not have the same problem.
2013-03-08 12:06:45 -05:00
aabd990e8f
Merge branch 'master' into master_fixes
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Conflicts:
Makefile
bwape.c
bwase.c
bwtsw2_aux.c
stdaln.c
2013-03-08 16:46:45 +00:00
e6c262594f
bwa-sw: ditch stdaln
2013-03-05 10:12:38 -05:00
086c9d0e7d
bwa-sw: use bwa_gen_cigar() for cigar generation
2013-03-05 09:54:49 -05:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
e613195e17
moved some common code to bwa.{c,h}
2013-02-23 15:30:46 -05:00
904c3205c0
removed a few unused variables
...
These variables have been assigned but never actually used. Reported by
gcc-4.7. Lower version cannot give such warnings.
2013-02-23 13:26:50 -05:00
95d18449b3
merge bseq.{h,c} to utils.{h,c}
...
I do not like many small files.
2013-02-12 10:36:15 -05:00
a09db69037
In bwtsw, replace the batch seq-reader with bseq
2013-02-06 17:12:27 -05:00
5a0b32bfd2
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
55f1b36534
New wrapper for gzclose; added err_fflush calls and made it call fsync too.
...
Added a new utils.c wrapper err_gzclose and changed gzclose calls to use it.
Put in some more err_fflush calls before files being written are closed.
Made err_fflush call fsync. This is useful for remote filesystems where
errors may not be reported on fflush or fclose as problems at the server
end may only be detected after they have returned. If bwa is being used
only to write to local filesystems, calling fsync is not really necessary.
To disable it, comment out #define FSYNC_ON_FLUSH in utils.c.
2013-01-03 16:57:37 +00:00
b081ac9b8b
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 10:34:57 +00:00
292f9061ab
r132: optionally copy FASTA/Q comment to SAM
2012-10-26 12:54:32 -04:00
f44edd4fc9
r128: more conservative chaining filter
2012-06-28 14:51:02 -04:00
0ae318be0d
resolve duphits after right extension as well
2012-06-28 13:32:58 -04:00
cd818687ac
r115: added -I and -S to bwasw
2012-04-17 20:43:43 -04:00
cff473393c
commented out debugging code
2012-04-02 12:05:15 -04:00
790df95e1a
updated revision number
2012-04-02 11:43:32 -04:00
36f2fd6238
bugfix: incorrect bandwidth
2012-04-02 11:39:40 -04:00
d3169804f6
debugging; bug persistant
2012-04-02 10:45:42 -04:00
173b93dfd4
debugging code: bwasw has a rare bug
2012-04-02 09:37:02 -04:00
b5170e0efa
output the NM tag
2011-11-24 11:51:38 -05:00
196b50dde3
optionally mark multi-part hits as secondary
2011-11-23 23:39:59 -05:00
b17b6577ac
removed a useless bwa-sw CMD option
2011-11-23 23:30:14 -05:00
107a9870ef
incorrect mate pos in BWA-SW SE mode
2011-11-23 23:18:51 -05:00
8f89f55484
fixed a segfault when there are too few good bases.
2011-11-17 22:13:38 -05:00
8060693411
multithreading works again
2011-11-12 16:50:58 -05:00
fa8cfe5567
bugfix: wrong mapping quality
2011-11-12 12:12:45 -05:00
b42910ada6
proper mate information
2011-11-12 00:49:21 -05:00
e06685db45
bwa-sw PE seems working (SAM is incorrect)
2011-11-07 00:51:43 -05:00
c8c79ef024
mate rescue seems working (not MT)
2011-11-06 16:20:40 -05:00
17eaac5a21
compute insert size distribution
2011-11-05 23:17:52 -04:00
a29b179045
further preparation for pairing
2011-11-05 14:31:30 -04:00
06687a33b9
bwasw: read and align two fastq at a time
2011-11-05 14:00:01 -04:00
8f3c780552
fixed a potential int overflow
2011-10-24 14:22:39 -04:00
eed46e802a
fixed a bug about reverse alignment
2011-10-24 14:09:05 -04:00
b204437c7e
fixed negative mapping quality; still byggy
2011-10-24 14:00:36 -04:00
8512b55ce3
bwasw works on a couple of sequences
2011-10-24 13:42:32 -04:00
4c43c5914d
this is better; but still buggy
2011-10-24 11:50:11 -04:00
29c3acfb31
not segfault immediately; but buggy
2011-10-24 09:36:52 -04:00
b3397a1f14
changes to bwa-sw for the 64-bit support; unfinish
2011-10-21 13:32:45 -04:00
1cb409aaf2
use forward-only pac to reduce memory
2011-10-21 12:03:14 -04:00
8d6b859bf8
speed up multi-threading
2011-04-07 17:26:08 -04:00
5e30884730
Update to the latest modfication 0.5.9rc1-2. Update ChangeLog
2011-01-13 20:54:10 -05:00
007c3eb75d
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
zzh
Rob Davies
Heng Li
Heng Li