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
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
220fc39e9d
the previous change does not work... Fixed.
2013-02-08 14:51:24 -05:00
fdb0a7405f
better dealing with microrepeat
2013-02-08 14:46:57 -05:00
057b292dde
exclude identical hits
2013-02-08 14:18:39 -05:00
1bf1a674a8
minor improvement to mapQ
2013-02-08 13:43:15 -05:00
245505deed
minor improvement to mapQ approx.
...
That is not good enough, but I am tired and need rest...
2013-02-07 22:09:58 -05:00
d8e4d57956
Don't use narrow band.
...
I may retry this feature if the profilter indicates that this greatly helps.
2013-02-07 21:22:54 -05:00
d890c7997c
better treatment for micro-repeat
2013-02-07 21:20:36 -05:00
45b0d3423a
bugfix: when no seed hits found
2013-02-07 20:07:31 -05:00
cd6bd524d4
discard internal seeds shorter than half
2013-02-07 19:50:37 -05:00
83a49f3210
compute mapQ; extend from the longest seed
2013-02-07 17:15:45 -05:00
6ba11ab68c
no effective changes
2013-02-07 16:42:01 -05:00
ff3fea115c
write soft clip; added debugging code
2013-02-07 16:27:11 -05:00
27fdf6397d
single-end working! no mapQ, though
2013-02-07 15:52:36 -05:00
49f2bcc015
CIGAR is wrong, but the rest is okay
2013-02-07 14:57:22 -05:00
1fd51fc3f7
code backup
2013-02-07 14:36:18 -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
5a0b32bfd2
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
a9292d674d
a bit code cleanup
2013-02-06 13:59:32 -05:00
797a8c147e
sorting chains while filtering chains
2013-02-05 21:58:33 -05:00
a61288c768
separate CIGAR generation
2013-02-05 21:49:19 -05:00
14e6a7bdb9
fixed a silly bug in ksw_extend()
...
Query return value is assigned to the target variable and vice versa...
2013-02-05 17:29:03 -05:00
1e16f3e701
calling ksw_global(); ksw_extend() is buggy!
2013-02-05 17:13:12 -05:00
7067af833d
fixed a silly bug on sorted merge
2013-02-05 00:41:07 -05:00
d6a73c9171
chain filtering apparently working
2013-02-05 00:17:20 -05:00
9d0cdb2d3c
unfinished chain filter
2013-02-04 17:23:06 -05:00
c589b42fb5
minor tuning for fewer identical hits
2013-02-04 16:48:11 -05:00
29c8546679
better ref extraction
2013-02-04 16:08:00 -05:00
788e9d1e3d
fixed a couple of leaks; buggy atm
2013-02-04 15:40:26 -05:00
f27bd18f20
check if every seed is included; not used for now
2013-02-04 15:09:47 -05:00
5bfa45a69b
write the mem_aln_t struct
2013-02-04 15:02:56 -05:00
666638a953
changed the default scoring
2013-02-04 14:51:51 -05:00
ba18db1a9f
sw extension works for the simplest case
2013-02-04 12:37:38 -05:00
d25a87cc50
code backup
2013-02-02 15:14:24 -05:00
00e5302219
routine to get subsequence from 2-bit pac
2013-02-01 16:39:50 -05:00
7ab4b3321f
bugfix: memory leak
2013-02-01 15:26:34 -05:00
f8f3b7577a
code cleanup; added a missing file
2013-02-01 14:38:44 -05:00
620ad6e5b9
reseed long SMEMs
2013-02-01 14:20:38 -05:00
5d372cef65
bugfix: wrong B-tree comparison
2013-01-31 16:39:24 -05:00
8977737460
basic chaining working
...
Definitely suboptimal in a lot of corner cases...
2013-01-31 16:26:05 -05:00
6c19c9640c
code backup
2013-01-31 15:55:22 -05:00
91debf412b
move smem iterators to bwamem.{c,h}
2013-01-31 13:59:48 -05:00
Heng Li