90ecd344ba
Merge branch 'master' into master_fixes. Merged up to master r375.
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Conflicts:
bwt.c
2013-04-11 11:15:39 +01:00
53bb846407
r373: optionally distable mate rescue
2013-04-09 16:13:55 -04:00
c862a1a396
Merge branch 'master' into master_fixes
2013-03-18 13:35:12 +00:00
e5355fe3a0
r364: bug in mem pairing (no effect with -A=1)
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Forgot to adjust for matching score. This bug has no effect when -A takes the
default value.
2013-03-14 22:01:26 -04:00
cca27c1ef5
Merge branch 'master' into master_fixes
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Conflicts:
bwamem.c
bwamem_pair.c
example.c
2013-03-13 12:12:28 +00:00
aa7cdf4bb3
r361: flag proper pair even if multi-primary
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Up to here, all the features in my checklist have been implemented.
2013-03-12 00:00:04 -04:00
6c665189ad
r359: identical output to 0.7.2 (without -a)
2013-03-11 23:16:18 -04:00
26f4c704ed
drop the old SAM writer
2013-03-11 22:24:54 -04:00
0b0455ca51
replace PE; BUGGY right now!!
2013-03-11 22:18:23 -04:00
9228e48efd
Merge branch 'master' into master_fixes
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Conflicts:
Makefile
2013-03-11 13:50:49 +00:00
2d01a297fb
Improving 'properly paired' flag.
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If one end has a low quality tail that happens to have a score-20 hit,
the pair won't be flagged as properly paired because bwa-mem thought it has
multiple hits. By filtering with -T, we won't have this problem.
2013-03-09 18:05:50 -05:00
274c0ac96c
r343: bugfix in mem - wrong mate info for unmap
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SAM generation is always among the nastiest bits. I would need to refactor at
some point (hardly happening).
2013-03-08 12:40:31 -05:00
aabd990e8f
Merge branch 'master' into master_fixes
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Conflicts:
Makefile
bwape.c
bwase.c
bwtsw2_aux.c
stdaln.c
2013-03-08 16:46:45 +00:00
b5b50ac8da
r341: bugfix - wrong mate position
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when one end is mapped with a score less than -T. Caused by the -T option.
2013-03-07 21:35:57 -05:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
e70c7c2a71
r284: amend cross-reference hit
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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
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
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
b4c38bcc1c
append fasta/q comment
2013-02-23 16:57:34 -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
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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
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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
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
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
fe2236f6fe
code backup
2013-02-16 10:09:30 -05:00
5f8c6efbc3
forbid x-bounary bns_get_seq(); code backup
2013-02-16 09:48:44 -05:00
df1ff2b36e
better and proper way to infer orinentation
2013-02-14 12:59:32 -05:00
688b524cdf
code backup; tired..
2013-02-13 23:55:56 -05:00
87d619a21f
minor code simplification
2013-02-13 23:16:16 -05:00
604e3d8da1
code backup; to upgrade ksw.{c,h}
2013-02-12 16:15:26 -05:00
2fc469d0c9
code backup
2013-02-12 12:09:36 -05:00
e5ab59db53
Multiple changes:
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1. Removed bwa.{h,c}. I am not going to finish them anyway.
2. Updated to the latest khash.h, which should be faster.
3. Define 64-bit vector and 128-bit integer/vector in utils.h.
2013-02-12 09:50:28 -05:00
13288e2dcd
code backup
2013-02-12 09:22:47 -05:00
Rob Davies
Heng Li