f3cff1c609
r311: even tighter bw for CIGAR
2013-02-27 23:59:50 -05:00
a33b9c0633
tighter bw for cigar SW
2013-02-27 23:40:46 -05:00
6a4d8c79d8
r309: bugfix - soft clipping missing in example.c
2013-02-27 22:45:18 -05:00
df7c3f0000
r308: added a new API to convert region to CIGAR
...
and an example program demonstrating how to do single-end alignment in <50
lines of C code.
2013-02-27 22:28:29 -05:00
64d92d26df
more documentation in ksw.h
2013-02-27 21:40:46 -05:00
4bb0bdddca
r306: introduce clipping penalty
...
More clipping leads to more severe reference bias. We should not clip the
alignment unless necessary.
2013-02-27 21:13:39 -05:00
b7791105bc
r305: in NEWS, convert TAB to space
2013-02-27 16:56:54 -05:00
aef179a580
r304: prepare release notes (not released yet)
2013-02-27 16:55:07 -05:00
292e92b602
r303: bugfix - wrong band width when CIGAR
2013-02-27 15:39:15 -05:00
e620f0ff4e
r302: updated the manpage
2013-02-27 13:16:22 -05:00
b621d3ae38
r301: left-align indels
...
Don't know why the change is working...
2013-02-27 00:42:19 -05:00
65e099df34
r300: fixed an out-of-boundary bug in rare case
2013-02-27 00:37:17 -05:00
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
...
This is particularly important for long sequences
2013-02-26 16:26:46 -05:00
54ab3bbec7
Dropped solid2fastq.pl
...
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
...
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
Heng Li