570e082b38
change CC back to gcc
2013-02-24 23:45:40 -05:00
29e41b592c
bugfix: isize is off by 1
2013-02-24 23:00:51 -05:00
0b4a40dc25
updated revision number; to merge into master
2013-02-24 13:34:20 -05:00
85775c3384
output multiple hits
2013-02-24 13:23:43 -05:00
6bdccf2a8a
added a bit documentation
2013-02-24 13:09:29 -05:00
ee59a13109
simplified bwamem.h
...
Hide mem_seed_t and mem_chain_t. Don't expose unnecessary routines.
2013-02-24 12:17:29 -05:00
cda85be059
fixed a couple bugs identified by gcc
...
Recent gcc is better.
2013-02-23 17:15:07 -05:00
6e7903e9f3
added kopen support
2013-02-23 17:09:23 -05:00
b4c38bcc1c
append fasta/q comment
2013-02-23 16:57:34 -05:00
33236de32e
a bit more error message
2013-02-23 16:44:02 -05:00
ee4540c394
support read group in bwa-mem
2013-02-23 16:41:44 -05:00
cfa7165036
cleanup index loading code
2013-02-23 16:10:48 -05:00
67543f19a1
code refactoring
2013-02-23 15:55:55 -05:00
e613195e17
moved some common code to bwa.{c,h}
2013-02-23 15:30:46 -05:00
3c330d5049
for another round of code cleanup
2013-02-23 15:12:26 -05:00
d460f2ec9e
bugfix in multi-threaded bwa-mem
2013-02-23 14:48:54 -05:00
a19ab654df
no effective change
2013-02-23 14:21:19 -05:00
dd85c528d6
an alternative bwt_invPsi() implementation
...
Cleaner, but not necessarily faster.
2013-02-23 13:59:18 -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
6230f86799
merged bwtmisc.c to bwtindex.c
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bwtmisc.c implements routines related to indexing
2013-02-22 17:23:34 -05:00
545fb87feb
removed another part related to color-space
2013-02-22 17:15:57 -05:00
f122fad562
minor code clean up
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bwtio.c is merged to bwt.c
2013-02-22 17:09:40 -05:00
17c123d65a
pring paired-end SAM
2013-02-22 16:38:48 -05:00
ba15b787cb
rework PE mapq; don't know if better
2013-02-22 14:47:57 -05:00
6c1a113753
mate-SW for all high-scoring hits
2013-02-22 13:26:23 -05:00
38fc5c8822
reduce mapQ when a read is moved
2013-02-22 12:54:42 -05:00
6a16edc15e
tuning PE mapQ
2013-02-22 12:47:26 -05:00
c0093264de
wrong logic: paired mapQ should <q_pe
2013-02-22 12:34:46 -05:00
c5ce72f593
scoring pairs by score, not by errors
...
This is important for bwa-mem which does local alignment. A short exact match
is worse than a long inexact match. Also fixed a bug in approximating mapping
quality.
2013-02-22 12:10:20 -05:00
ed08d08f36
fixed bugs caused by interger overflow
2013-02-22 11:17:31 -05:00
dfc63acc11
bugfix: another ">" vs. "<" bug
...
That hurts, as I am going to reverse all these again!
2013-02-22 11:06:36 -05:00
d5820177c6
bugfix: wrong mate-sw qry coor for rev
2013-02-22 11:02:14 -05:00
81fe6f8e38
bugfix: a typo leading to wrong pairing
2013-02-22 10:57:07 -05:00
58e4cc207f
bugfix: 1) fill seedcov; 2) pairing not working
2013-02-21 21:26:01 -05:00
d4cf6d97a6
bugfix: memory leak
2013-02-21 15:04:31 -05:00
a578688fa8
generate multiple alignments from one chain
2013-02-21 14:58:51 -05:00
cfbc4c89e3
perform extension when there are, say, 20bp tandem
2013-02-21 14:34:10 -05:00
54da54ffd4
extend more seeds (and thus slower...)
2013-02-21 12:52:00 -05:00
f8829318cf
weakened the chain filter
2013-02-21 12:25:20 -05:00
84a328764a
bugfix: mis-chaining caused by integer overflow
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I really need to rewrite kbtree some time.
2013-02-21 11:42:30 -05:00
a9cae8c9af
minor changes
2013-02-21 10:39:17 -05:00
41624fb347
bugfix: choosing the worse instead of the best
2013-02-20 20:43:22 -05:00
ea8f4f4d34
clean bill from valgrind
2013-02-20 20:26:57 -05:00
5626fe29b7
Well, at least output sth
2013-02-20 19:11:44 -05:00
a7d574d125
backup comments
2013-02-20 01:11:38 -05:00
688872fb1b
code backup
2013-02-19 00:50:39 -05:00
66585b7982
code backup
2013-02-18 16:33:06 -05:00
f0a6285aba
perform mate-SW for some suboptimal alignments
2013-02-16 11:52:04 -05:00
ea9fc7df48
keep the number of SW performed
2013-02-16 11:03:27 -05:00
8ee464478a
matesw working; for testing only
2013-02-16 10:48:50 -05:00
Heng Li