0b533385ef
r299: better way to exclude seed
2013-02-27 00:29:11 -05:00
ee80fb8bd0
Test each seed to see if extension is needed
...
The old version wastefully extends many seeds contained in an aligned region
found before. While this wastes little time for short reads, it becomes a
serious defect for long query sequences.
This is an attempt to fix this problem, but more tuning are needed.
2013-02-26 22:55:44 -05:00
acd1ab607b
r297: reduce wasteful SW extension
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This is particularly important for long sequences
2013-02-26 16:26:46 -05:00
54ab3bbec7
Dropped solid2fastq.pl
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SOLiD is not supported any more.
2013-02-26 14:35:03 -05:00
98787f0ae0
r295: generate NM
2013-02-26 13:36:01 -05:00
32f2d60a2e
r294: bugfix - -M not working
2013-02-26 13:14:33 -05:00
619ac4f93d
r293: bugfix - wrong RG type in SAM output
2013-02-26 13:03:35 -05:00
c6b226d719
r292: fixed a very stupid bug on CLI
...
I was thinking 0x10 or 16, but wrote 0x16...
2013-02-26 12:49:48 -05:00
bfb2583d7f
r291: summary - bwt.c micro optimization
2013-02-26 12:10:19 -05:00
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
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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
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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
...
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
Heng Li