aa92c720b5
cleanup bwt_occ()
2013-02-26 12:09:28 -05:00
80e1137a6c
move bwt_invPsi() from bwt.h to bwt.c
2013-02-26 11:57:36 -05:00
fd67064207
removed an unnecessary condition
2013-02-26 11:51:03 -05:00
264d5e42e5
simplified bwt_occ4() a little
2013-02-26 11:49:39 -05:00
c848b44481
code backup
2013-02-26 11:22:24 -05:00
174fe0f1d5
code backup: less dependent on gcc optimization
2013-02-26 11:14:19 -05:00
e70c7c2a71
r284: amend cross-reference hit
...
I really hate this: complex and twisted logic for a nasty scenario that almost
never happens to short reads - but it may become serious when the reference
genome consists of many contigs.
On toy examples, the code seems to work. Don't know if it really works...
2013-02-26 00:03:49 -05:00
61dd3bf13a
r283: prepare for fixing cross-ref aln
2013-02-25 22:49:15 -05:00
77b5b586ad
r282: set min split_len to read length
2013-02-25 17:29:35 -05:00
30cc8a95d1
fixed an unimportant memory leak
2013-02-25 16:34:19 -05:00
d19e834d84
r280: align two ends in the same thread
...
Otherwise odd-number threads may be of different speed from even-number threads.
2013-02-25 15:40:15 -05:00
20aa848b3c
r279: for PE mapq, consider the number of pairs
...
If there are a lot of proper pairs, it is more likely that the best pair is
wrong.
2013-02-25 13:00:35 -05:00
9957e04590
r278: don't perform too many mate-sw
2013-02-25 11:56:02 -05:00
e9e5ee6a3d
r277: updated the revision number
2013-02-25 11:34:06 -05:00
5092211d75
controllable scoring matrix
2013-02-25 11:24:21 -05:00
5ead86acd3
optionally mark split hit as secondary
2013-02-25 11:18:35 -05:00
514563bd0a
no poor hits with -a; reduce mapq for 2nd primary
2013-02-25 10:54:12 -05:00
4dc982a3c7
support interleaved fastq
2013-02-25 00:13:32 -05:00
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
...
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
...
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
Heng Li