Heng Li
|
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 |
|
Heng Li
|
b6006cbe9d
|
skip orientations that are much smaller than best
|
2013-02-11 13:44:39 -05:00 |
|
Heng Li
|
4431e359e2
|
analyze isize distribution
|
2013-02-11 12:15:12 -05:00 |
|
Heng Li
|
987d4b4205
|
fixed a stupid bug in fastq reading
|
2013-02-11 11:27:35 -05:00 |
|
Heng Li
|
59eaf650ac
|
code backup
|
2013-02-11 10:59:38 -05:00 |
|
Heng Li
|
f4c0672800
|
move sort_and_dedup() to worker1()
|
2013-02-10 12:55:19 -05:00 |
|
Heng Li
|
c310fb7424
|
a little refactoring for PE support
|
2013-02-10 12:24:33 -05:00 |
|
Heng Li
|
cb55617f50
|
added a new line
|
2013-02-08 22:12:18 -05:00 |
|
Heng Li
|
95a79afe71
|
command-line prompt
|
2013-02-08 22:11:44 -05:00 |
|
Heng Li
|
829664d6b5
|
missing identical hits; improved sub_n
|
2013-02-08 17:55:35 -05:00 |
|
Heng Li
|
b2c7148dc9
|
consider the number of suboptimal hits
|
2013-02-08 17:20:44 -05:00 |
|
Heng Li
|
39607065e0
|
allow more seeds to be seen (thus slower..)
|
2013-02-08 16:56:28 -05:00 |
|
Heng Li
|
2848d3045a
|
more accurate chain weight
|
2013-02-08 15:34:25 -05:00 |
|
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 |