Heng Li
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99907c98fb
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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.
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2013-02-11 15:29:03 -05:00 |
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Heng Li
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987d4b4205
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fixed a stupid bug in fastq reading
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2013-02-11 11:27:35 -05:00 |
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Heng Li
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59eaf650ac
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code backup
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2013-02-11 10:59:38 -05:00 |
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Heng Li
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f4c0672800
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move sort_and_dedup() to worker1()
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2013-02-10 12:55:19 -05:00 |
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Heng Li
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c310fb7424
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a little refactoring for PE support
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2013-02-10 12:24:33 -05:00 |
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Heng Li
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829664d6b5
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missing identical hits; improved sub_n
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2013-02-08 17:55:35 -05:00 |
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Heng Li
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b2c7148dc9
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consider the number of suboptimal hits
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2013-02-08 17:20:44 -05:00 |
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Heng Li
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39607065e0
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allow more seeds to be seen (thus slower..)
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2013-02-08 16:56:28 -05:00 |
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Heng Li
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2848d3045a
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more accurate chain weight
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2013-02-08 15:34:25 -05:00 |
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Heng Li
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220fc39e9d
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the previous change does not work... Fixed.
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2013-02-08 14:51:24 -05:00 |
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Heng Li
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fdb0a7405f
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better dealing with microrepeat
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2013-02-08 14:46:57 -05:00 |
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Heng Li
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057b292dde
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exclude identical hits
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2013-02-08 14:18:39 -05:00 |
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Heng Li
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1bf1a674a8
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minor improvement to mapQ
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2013-02-08 13:43:15 -05:00 |
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Heng Li
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245505deed
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minor improvement to mapQ approx.
That is not good enough, but I am tired and need rest...
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2013-02-07 22:09:58 -05:00 |
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Heng Li
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d8e4d57956
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Don't use narrow band.
I may retry this feature if the profilter indicates that this greatly helps.
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2013-02-07 21:22:54 -05:00 |
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Heng Li
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d890c7997c
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better treatment for micro-repeat
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2013-02-07 21:20:36 -05:00 |
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Heng Li
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45b0d3423a
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bugfix: when no seed hits found
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2013-02-07 20:07:31 -05:00 |
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Heng Li
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cd6bd524d4
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discard internal seeds shorter than half
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2013-02-07 19:50:37 -05:00 |
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Heng Li
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83a49f3210
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compute mapQ; extend from the longest seed
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2013-02-07 17:15:45 -05:00 |
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Heng Li
|
6ba11ab68c
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no effective changes
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2013-02-07 16:42:01 -05:00 |
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Heng Li
|
ff3fea115c
|
write soft clip; added debugging code
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2013-02-07 16:27:11 -05:00 |
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Heng Li
|
27fdf6397d
|
single-end working! no mapQ, though
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2013-02-07 15:52:36 -05:00 |
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Heng Li
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49f2bcc015
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CIGAR is wrong, but the rest is okay
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2013-02-07 14:57:22 -05:00 |
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Heng Li
|
1fd51fc3f7
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code backup
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2013-02-07 14:36:18 -05:00 |
|
Heng Li
|
bfeb37c4de
|
code backup
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2013-02-07 13:29:01 -05:00 |
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Heng Li
|
5dc398cdef
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start to write CLI
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2013-02-07 13:13:43 -05:00 |
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Heng Li
|
5a0b32bfd2
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updated to the latest kseq.h
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2013-02-06 14:38:40 -05:00 |
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Heng Li
|
a9292d674d
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a bit code cleanup
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2013-02-06 13:59:32 -05:00 |
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Heng Li
|
797a8c147e
|
sorting chains while filtering chains
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2013-02-05 21:58:33 -05:00 |
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Heng Li
|
a61288c768
|
separate CIGAR generation
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2013-02-05 21:49:19 -05:00 |
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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 |
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Heng Li
|
1e16f3e701
|
calling ksw_global(); ksw_extend() is buggy!
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2013-02-05 17:13:12 -05:00 |
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Heng Li
|
7067af833d
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fixed a silly bug on sorted merge
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2013-02-05 00:41:07 -05:00 |
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Heng Li
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d6a73c9171
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chain filtering apparently working
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2013-02-05 00:17:20 -05:00 |
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Heng Li
|
9d0cdb2d3c
|
unfinished chain filter
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2013-02-04 17:23:06 -05:00 |
|
Heng Li
|
c589b42fb5
|
minor tuning for fewer identical hits
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2013-02-04 16:48:11 -05:00 |
|
Heng Li
|
29c8546679
|
better ref extraction
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2013-02-04 16:08:00 -05:00 |
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Heng Li
|
788e9d1e3d
|
fixed a couple of leaks; buggy atm
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2013-02-04 15:40:26 -05:00 |
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Heng Li
|
f27bd18f20
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check if every seed is included; not used for now
|
2013-02-04 15:09:47 -05:00 |
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Heng Li
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5bfa45a69b
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write the mem_aln_t struct
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2013-02-04 15:02:56 -05:00 |
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Heng Li
|
666638a953
|
changed the default scoring
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2013-02-04 14:51:51 -05:00 |
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Heng Li
|
ba18db1a9f
|
sw extension works for the simplest case
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2013-02-04 12:37:38 -05:00 |
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Heng Li
|
d25a87cc50
|
code backup
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2013-02-02 15:14:24 -05:00 |
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Heng Li
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00e5302219
|
routine to get subsequence from 2-bit pac
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2013-02-01 16:39:50 -05:00 |
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Heng Li
|
7ab4b3321f
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bugfix: memory leak
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2013-02-01 15:26:34 -05:00 |
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Heng Li
|
f8f3b7577a
|
code cleanup; added a missing file
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2013-02-01 14:38:44 -05:00 |
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Heng Li
|
620ad6e5b9
|
reseed long SMEMs
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2013-02-01 14:20:38 -05:00 |
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Heng Li
|
5d372cef65
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bugfix: wrong B-tree comparison
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2013-01-31 16:39:24 -05:00 |
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Heng Li
|
8977737460
|
basic chaining working
Definitely suboptimal in a lot of corner cases...
|
2013-01-31 16:26:05 -05:00 |
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Heng Li
|
6c19c9640c
|
code backup
|
2013-01-31 15:55:22 -05:00 |