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
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
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
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
...
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
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
...
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
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
...
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
...
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
...
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}
...
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
...
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
Heng Li