Heng Li
|
220fc39e9d
|
the previous change does not work... Fixed.
|
2013-02-08 14:51:24 -05:00 |
|
Heng Li
|
fdb0a7405f
|
better dealing with microrepeat
|
2013-02-08 14:46:57 -05:00 |
|
Heng Li
|
057b292dde
|
exclude identical hits
|
2013-02-08 14:18:39 -05:00 |
|
Heng Li
|
1bf1a674a8
|
minor improvement to mapQ
|
2013-02-08 13:43:15 -05:00 |
|
Heng Li
|
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 |
|
Heng Li
|
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 |
|
Heng Li
|
d890c7997c
|
better treatment for micro-repeat
|
2013-02-07 21:20:36 -05:00 |
|
Heng Li
|
45b0d3423a
|
bugfix: when no seed hits found
|
2013-02-07 20:07:31 -05:00 |
|
Heng Li
|
cd6bd524d4
|
discard internal seeds shorter than half
|
2013-02-07 19:50:37 -05:00 |
|
Heng Li
|
83a49f3210
|
compute mapQ; extend from the longest seed
|
2013-02-07 17:15:45 -05:00 |
|
Heng Li
|
6ba11ab68c
|
no effective changes
|
2013-02-07 16:42:01 -05:00 |
|
Heng Li
|
ff3fea115c
|
write soft clip; added debugging code
|
2013-02-07 16:27:11 -05:00 |
|
Heng Li
|
27fdf6397d
|
single-end working! no mapQ, though
|
2013-02-07 15:52:36 -05:00 |
|
Heng Li
|
49f2bcc015
|
CIGAR is wrong, but the rest is okay
|
2013-02-07 14:57:22 -05:00 |
|
Heng Li
|
1fd51fc3f7
|
code backup
|
2013-02-07 14:36:18 -05:00 |
|
Heng Li
|
bfeb37c4de
|
code backup
|
2013-02-07 13:29:01 -05:00 |
|
Heng Li
|
5dc398cdef
|
start to write CLI
|
2013-02-07 13:13:43 -05:00 |
|
Heng Li
|
a09db69037
|
In bwtsw, replace the batch seq-reader with bseq
|
2013-02-06 17:12:27 -05:00 |
|
Heng Li
|
901d28d5f5
|
code backup
|
2013-02-06 15:03:09 -05:00 |
|
Heng Li
|
5a0b32bfd2
|
updated to the latest kseq.h
|
2013-02-06 14:38:40 -05:00 |
|
Heng Li
|
a9292d674d
|
a bit code cleanup
|
2013-02-06 13:59:32 -05:00 |
|
Heng Li
|
e65b2096f7
|
removed useless members
|
2013-02-06 12:25:49 -05:00 |
|
Heng Li
|
797a8c147e
|
sorting chains while filtering chains
|
2013-02-05 21:58:33 -05:00 |
|
Heng Li
|
a61288c768
|
separate CIGAR generation
|
2013-02-05 21:49:19 -05:00 |
|
Heng Li
|
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 |
|
Heng Li
|
1e16f3e701
|
calling ksw_global(); ksw_extend() is buggy!
|
2013-02-05 17:13:12 -05:00 |
|
Heng Li
|
86caae811e
|
added comments
|
2013-02-05 16:58:35 -05:00 |
|
Heng Li
|
1bc9712cd8
|
explicitly use bit to keep bt matrix
This also simplifies backtracking.
|
2013-02-05 16:28:15 -05:00 |
|
Heng Li
|
7e1466c885
|
implemented NW backtrack
|
2013-02-05 16:05:53 -05:00 |
|
Heng Li
|
d91e320972
|
towards reimplementing banded NW alignment
|
2013-02-05 12:06:56 -05:00 |
|
Heng Li
|
7067af833d
|
fixed a silly bug on sorted merge
|
2013-02-05 00:41:07 -05:00 |
|
Heng Li
|
d6a73c9171
|
chain filtering apparently working
|
2013-02-05 00:17:20 -05:00 |
|
Heng Li
|
9d0cdb2d3c
|
unfinished chain filter
|
2013-02-04 17:23:06 -05:00 |
|
Heng Li
|
c589b42fb5
|
minor tuning for fewer identical hits
|
2013-02-04 16:48:11 -05:00 |
|
Heng Li
|
29c8546679
|
better ref extraction
|
2013-02-04 16:08:00 -05:00 |
|
Heng Li
|
788e9d1e3d
|
fixed a couple of leaks; buggy atm
|
2013-02-04 15:40:26 -05:00 |
|
Heng Li
|
f27bd18f20
|
check if every seed is included; not used for now
|
2013-02-04 15:09:47 -05:00 |
|
Heng Li
|
5bfa45a69b
|
write the mem_aln_t struct
|
2013-02-04 15:02:56 -05:00 |
|
Heng Li
|
666638a953
|
changed the default scoring
|
2013-02-04 14:51:51 -05:00 |
|
Heng Li
|
ba18db1a9f
|
sw extension works for the simplest case
|
2013-02-04 12:37:38 -05:00 |
|
Heng Li
|
f83dea36d8
|
no effective changes
|
2013-02-03 18:16:43 -05:00 |
|
Heng Li
|
2093398231
|
bugfix: the first line is wrong
|
2013-02-03 17:47:57 -05:00 |
|
Heng Li
|
e8a1962efe
|
code backup; it is wrong
|
2013-02-03 17:25:40 -05:00 |
|
Heng Li
|
92b084e553
|
reimplemented SW extension; not tested yet
|
2013-02-02 16:38:21 -05:00 |
|
Heng Li
|
d25a87cc50
|
code backup
|
2013-02-02 15:14:24 -05:00 |
|
Heng Li
|
00e5302219
|
routine to get subsequence from 2-bit pac
|
2013-02-01 16:39:50 -05:00 |
|
Heng Li
|
7ab4b3321f
|
bugfix: memory leak
|
2013-02-01 15:26:34 -05:00 |
|
Heng Li
|
f8f3b7577a
|
code cleanup; added a missing file
|
2013-02-01 14:38:44 -05:00 |
|
Heng Li
|
620ad6e5b9
|
reseed long SMEMs
|
2013-02-01 14:20:38 -05:00 |
|
Heng Li
|
abc675f278
|
typo in comments
|
2013-02-01 13:14:16 -05:00 |