9ce50a4e5e
dev-450: support diff ins/del penalties. NO TEST!!
2014-03-28 14:54:06 -04:00
2e9463ebf1
dev-r442: suppress exact full-length matches
2014-02-26 22:04:19 -05:00
4219e58623
r423: bugfix - SE hits not random
2013-11-23 09:36:26 -05:00
b51a66e4c1
r413: fixed an issue causing redundant alignment
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I have seen a fosmid aligned to the same position but with two slightly
different CIGARs: 30000M and 29900M50D100M, possibly caused by tandem repeats.
0.7.5a will regard them as two distinct alignments and generates a very small
mapping quality. However, these two are essentially the same. Although there is
ambiguity in aligning the end of the fosmid, we should not penalize the entire
alignment with a small mapQ. This commit fixes this issue. More testing is
needed, though.
2013-09-09 11:36:50 -04:00
623da055e1
alternative way to estimate mapQ
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the old mapQ estimate is too conservative
2013-09-06 12:31:47 -04:00
3b84c03c1e
r406: allow to use diff clipping penalties
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for 5'-end or for 3'-end
2013-08-28 15:59:05 -04:00
9735d7a31a
conform to the latest (unpublished) SAM spec
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for chimeric alignments
2013-05-22 19:45:16 -04:00
19cb7cd7ed
r388: cleanup mem_process_seqs() interface
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Print output outside the function and allow to feed insert size distribution.
2013-04-26 12:31:18 -04:00
53bb846407
r373: optionally distable mate rescue
2013-04-09 16:13:55 -04:00
9346acde1b
Release bwa-0.7.3a-r367
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In 0.7.3, the wrong CIGAR bug was only fixed in one scenario, but not fixed
in another corner case.
2013-03-15 21:26:37 -04:00
26f4c704ed
drop the old SAM writer
2013-03-11 22:24:54 -04:00
47952b6f3f
drop an unnecessary member from mem_aln_t
2013-03-11 21:35:32 -04:00
8f0d439913
prepare to replace the SAM printing code
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This move is dangerous as SAM printing is very complex, but it will benefit in
the long run. The planned change will reduce the redundancy, improves clarity
and most importantly makes it much easier to output multiple primary hits in an
optional tag.
2013-03-11 21:25:17 -04:00
5fbd454682
r332: added output threshold
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Otherwise there are far too many short hits
2013-03-05 22:49:38 -05:00
efd9769b07
r324: a little code cleanup
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The changes after r317 aim to improve the performance and accuracy for very
long query alignment. The short-read alignment should not be affected. The
changes include:
1) Z-dropoff. This is a variant of blast's X-dropoff. I orginally thought this
heuristic only improves speed, but now I realize it also reduces poor
alignment with long good flanking alignments. The difference from blast's
X-dropoff is that Z-dropoff allows big gaps, but X-dropoff does not.
2) Band width doubling. When band width is too small, we will get a poor
alignment in the middle. Sometimes such alignments cannot be fully excluded
with Z-dropoff. Band width doubling is an alternative heuristic. It is based
on the observation that the existing of close-to-boundary high score
possibly implies inadequate band width. When we see such a signal, we double
the band width.
2013-03-05 00:57:16 -05:00
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
35fb7f9fdf
r315: move kopen.o out of libbwa.a
2013-03-01 11:47:51 -05:00
3e4a178e08
r314: cleanup bwamem API
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Don't modify input sequences; more documentations
2013-03-01 11:14:51 -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
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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
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
c6b226d719
r292: fixed a very stupid bug on CLI
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I was thinking 0x10 or 16, but wrote 0x16...
2013-02-26 12:49:48 -05:00
20aa848b3c
r279: for PE mapq, consider the number of pairs
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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
5ead86acd3
optionally mark split hit as secondary
2013-02-25 11:18:35 -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
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Hide mem_seed_t and mem_chain_t. Don't expose unnecessary routines.
2013-02-24 12:17:29 -05:00
e613195e17
moved some common code to bwa.{c,h}
2013-02-23 15:30:46 -05:00
17c123d65a
pring paired-end SAM
2013-02-22 16:38:48 -05:00
a578688fa8
generate multiple alignments from one chain
2013-02-21 14:58:51 -05:00
54da54ffd4
extend more seeds (and thus slower...)
2013-02-21 12:52:00 -05:00
5626fe29b7
Well, at least output sth
2013-02-20 19:11:44 -05:00
688872fb1b
code backup
2013-02-19 00:50:39 -05:00
66585b7982
code backup
2013-02-18 16:33:06 -05:00
df1ff2b36e
better and proper way to infer orinentation
2013-02-14 12:59:32 -05:00
604e3d8da1
code backup; to upgrade ksw.{c,h}
2013-02-12 16:15:26 -05:00
cd0969332f
keep track of the "parent" of a secondary
2013-02-12 15:52:23 -05:00
22b79b3475
mark primary, instead of dropping secondary
2013-02-12 15:34:44 -05:00
95d18449b3
merge bseq.{h,c} to utils.{h,c}
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I do not like many small files.
2013-02-12 10:36:15 -05:00
99907c98fb
separated and improved SAM printing code
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This is for the PE mode. The routines may also be useful for bwa-sw, but
probably I won't change the old code.
2013-02-11 15:29:03 -05:00
59eaf650ac
code backup
2013-02-11 10:59:38 -05:00
829664d6b5
missing identical hits; improved sub_n
2013-02-08 17:55:35 -05:00
b2c7148dc9
consider the number of suboptimal hits
2013-02-08 17:20:44 -05:00
39607065e0
allow more seeds to be seen (thus slower..)
2013-02-08 16:56:28 -05:00
fdb0a7405f
better dealing with microrepeat
2013-02-08 14:46:57 -05:00
1bf1a674a8
minor improvement to mapQ
2013-02-08 13:43:15 -05:00
bfeb37c4de
code backup
2013-02-07 13:29:01 -05:00
5dc398cdef
start to write CLI
2013-02-07 13:13:43 -05:00
Heng Li