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
77b5b586ad
r282: set min split_len to read length
2013-02-25 17:29:35 -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
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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
514563bd0a
no poor hits with -a; reduce mapq for 2nd primary
2013-02-25 10:54:12 -05:00
29e41b592c
bugfix: isize is off by 1
2013-02-24 23:00:51 -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
cda85be059
fixed a couple bugs identified by gcc
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Recent gcc is better.
2013-02-23 17:15:07 -05:00
b4c38bcc1c
append fasta/q comment
2013-02-23 16:57:34 -05:00
ee4540c394
support read group in bwa-mem
2013-02-23 16:41:44 -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
d460f2ec9e
bugfix in multi-threaded bwa-mem
2013-02-23 14:48:54 -05:00
904c3205c0
removed a few unused variables
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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
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
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
d4cf6d97a6
bugfix: memory leak
2013-02-21 15:04:31 -05:00
a578688fa8
generate multiple alignments from one chain
2013-02-21 14:58:51 -05:00
cfbc4c89e3
perform extension when there are, say, 20bp tandem
2013-02-21 14:34:10 -05:00
54da54ffd4
extend more seeds (and thus slower...)
2013-02-21 12:52:00 -05:00
f8829318cf
weakened the chain filter
2013-02-21 12:25:20 -05:00
84a328764a
bugfix: mis-chaining caused by integer overflow
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I really need to rewrite kbtree some time.
2013-02-21 11:42:30 -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
a7d574d125
backup comments
2013-02-20 01:11:38 -05:00
688872fb1b
code backup
2013-02-19 00:50:39 -05:00
66585b7982
code backup
2013-02-18 16:33:06 -05:00
ea9fc7df48
keep the number of SW performed
2013-02-16 11:03:27 -05:00
5f8c6efbc3
forbid x-bounary bns_get_seq(); code backup
2013-02-16 09:48:44 -05:00
604e3d8da1
code backup; to upgrade ksw.{c,h}
2013-02-12 16:15:26 -05:00
325ba8213b
move mark primary to worker1()
2013-02-12 15:54:55 -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
2fc469d0c9
code backup
2013-02-12 12:09:36 -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
13288e2dcd
code backup
2013-02-12 09:22:47 -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
987d4b4205
fixed a stupid bug in fastq reading
2013-02-11 11:27:35 -05:00
59eaf650ac
code backup
2013-02-11 10:59:38 -05:00
f4c0672800
move sort_and_dedup() to worker1()
2013-02-10 12:55:19 -05:00
c310fb7424
a little refactoring for PE support
2013-02-10 12:24:33 -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
2848d3045a
more accurate chain weight
2013-02-08 15:34:25 -05:00
Heng Li