578bb55c38
dev-449: unequal ins/del in global() and extend()
2014-03-28 14:15:38 -04:00
0c783399e8
dev-448: different ins/del penalties
2014-03-28 10:54:23 -04:00
f70d80a5a2
r427: fixed bugs in backtrack
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See comments in ksw_global() for details.
2013-12-30 15:40:18 -05:00
96e445d9e4
Reduce dependency on utils.h - new malloc wrapping scheme.
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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
4cb5110d03
Merge branch 'master' into master_fixes
2013-04-22 09:51:07 +01:00
db7a98636f
r380: er... another compiling error
2013-04-19 12:04:44 -04:00
f0c94d80d1
r379: fixed compiling error
2013-04-19 12:04:00 -04:00
be11e27e12
r378: bugfix - wrong CIGAR
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This is actually caused by a bug in SSE2-SW, where the query begin may be
smaller than the true one if there is an exact tandem repeat.
2013-04-19 12:00:37 -04:00
90ecd344ba
Merge branch 'master' into master_fixes. Merged up to master r375.
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Conflicts:
bwt.c
2013-04-11 11:15:39 +01:00
3d8a8c1e37
r374: fix - clipping penalty not always working
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This only happens to gaps where mem underestimates the bandwidth without
considering the clipping penalty.
2013-04-10 01:09:37 -04:00
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
8a078cc16d
Merge branch 'master' into master_fixes
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Conflicts:
bntseq.c
bwamem.c
2013-03-05 10:21:07 +00:00
e0991d6a45
r323: added Z-dropoff, a variant of blast's X-drop
2013-03-05 00:34:33 -05:00
59bc9341f6
code backup; more changes coming later
2013-03-04 17:29:07 -05:00
6beab5f765
Merge branch 'master' into master_fixes
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Merge changes to commit c5434ac
2013-03-01 10:22:49 +00:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
4bb0bdddca
r306: introduce clipping penalty
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More clipping leads to more severe reference bias. We should not clip the
alignment unless necessary.
2013-02-27 21:13:39 -05:00
b621d3ae38
r301: left-align indels
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Don't know why the change is working...
2013-02-27 00:42:19 -05:00
ea8f4f4d34
clean bill from valgrind
2013-02-20 20:26:57 -05:00
557daabf38
bugfix: bug in the new ksw.c
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On my test data, one alignment is different, caused by polyA
2013-02-12 17:48:46 -05:00
28a7d501f2
updated to the latest ksw; NOT TESTED YET!!!
2013-02-12 16:35:05 -05:00
d8e4d57956
Don't use narrow band.
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I may retry this feature if the profilter indicates that this greatly helps.
2013-02-07 21:22:54 -05:00
14e6a7bdb9
fixed a silly bug in ksw_extend()
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Query return value is assigned to the target variable and vice versa...
2013-02-05 17:29:03 -05:00
1e16f3e701
calling ksw_global(); ksw_extend() is buggy!
2013-02-05 17:13:12 -05:00
86caae811e
added comments
2013-02-05 16:58:35 -05:00
1bc9712cd8
explicitly use bit to keep bt matrix
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This also simplifies backtracking.
2013-02-05 16:28:15 -05:00
7e1466c885
implemented NW backtrack
2013-02-05 16:05:53 -05:00
d91e320972
towards reimplementing banded NW alignment
2013-02-05 12:06:56 -05:00
788e9d1e3d
fixed a couple of leaks; buggy atm
2013-02-04 15:40:26 -05:00
ba18db1a9f
sw extension works for the simplest case
2013-02-04 12:37:38 -05:00
f83dea36d8
no effective changes
2013-02-03 18:16:43 -05:00
2093398231
bugfix: the first line is wrong
2013-02-03 17:47:57 -05:00
e8a1962efe
code backup; it is wrong
2013-02-03 17:25:40 -05:00
92b084e553
reimplemented SW extension; not tested yet
2013-02-02 16:38:21 -05:00
55f1b36534
New wrapper for gzclose; added err_fflush calls and made it call fsync too.
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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
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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
182cb2e89c
use standard SW when no SSE2
2011-11-19 19:38:21 -05:00
c8c79ef024
mate rescue seems working (not MT)
2011-11-06 16:20:40 -05:00
Heng Li
Rob Davies
Heng Li