Heng Li
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904afefbc6
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r985: fix bug due to the lack of _pri contigs d6
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2014-11-13 12:12:41 -05:00 |
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Heng Li
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a81603217e
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mate chr is sometimes wrong
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2014-11-10 10:16:53 -05:00 |
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Heng Li
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b2b42cea7e
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removed contig weight & code cleanup
Contig weight was calculated based on a false assumption. It is actually not useful.
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2014-11-07 12:45:01 -05:00 |
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Heng Li
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6db2fd98aa
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r960: merge changes from the master branch
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2014-10-28 13:46:40 -04:00 |
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Heng Li
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0f8a164bd3
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bugfix: .ctw not generated properly
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2014-10-25 23:08:29 -04:00 |
|
Heng Li
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2bfcc421d9
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bugfix: alignments not outputted
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2014-10-25 22:13:31 -04:00 |
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Heng Li
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7327f8fa10
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output all overlapping HLA hits
A contig longer than HLA genes may not get hits to HLA and thus won't be used
in typing.
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2014-10-25 12:00:15 -04:00 |
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Heng Li
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33938e1ed0
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save reads mapped to each HLA gene
for downstream typing
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2014-10-24 16:54:48 -04:00 |
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Heng Li
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ba3ab0ca98
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removed hla typing - not good enough
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2014-10-24 14:52:16 -04:00 |
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Heng Li
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7a8019e6ee
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removed debugging code
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2014-10-24 14:51:05 -04:00 |
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Heng Li
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f005ea4bf3
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coarse HLA typing and doc
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2014-10-23 14:42:45 -04:00 |
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Heng Li
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2bfa3c767b
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CLI help
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2014-10-21 00:22:59 -04:00 |
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Heng Li
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497913d404
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working largely as expected
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2014-10-21 00:16:41 -04:00 |
|
Heng Li
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25d45512d9
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code backup
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2014-10-20 14:17:56 -04:00 |
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Heng Li
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6f41a27e27
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towards adding "-r" to postprocessing
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2014-10-19 20:53:47 -04:00 |
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Heng Li
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3370ae9e35
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r926: prepare to move -g to bwa-postalt.js
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2014-10-19 20:43:53 -04:00 |
|
Heng Li
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647b0e828a
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wrong flag in the SAM output
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2014-10-14 16:57:57 -04:00 |
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Heng Li
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c79427a22d
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improved CLI
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2014-10-14 16:31:40 -04:00 |
|
Heng Li
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15becdd3df
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use weight1 by default
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2014-10-14 14:50:37 -04:00 |
|
Heng Li
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2485a3ca02
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bug in the last commit
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2014-10-12 18:24:40 -04:00 |
|
Heng Li
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bf08f76a3c
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requiring full overlap
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2014-10-12 17:17:29 -04:00 |
|
Heng Li
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4356fd485c
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changed weighting
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2014-10-10 13:41:53 -04:00 |
|
Heng Li
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2d7ec6b051
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ALT genotyping semi-working, but ...
... the result is not good.
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2014-10-05 22:18:07 -04:00 |
|
Heng Li
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2c3619d569
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code backup
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2014-10-02 23:48:03 -04:00 |
|
Heng Li
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7026b3ec68
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code backup
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2014-10-02 21:49:29 -04:00 |
|
Heng Li
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cd44ac48cd
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code backup
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2014-10-02 18:04:36 -04:00 |
|
Heng Li
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c4bdf1678d
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code backup
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2014-10-02 17:11:37 -04:00 |
|
Heng Li
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0a526c698a
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code backup
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2014-10-02 16:23:55 -04:00 |
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Heng Li
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7b62fbb4ba
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r880: bug in writing .ann file
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2014-10-02 15:34:49 -04:00 |
|
Heng Li
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d802cfb7f5
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code backup
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2014-09-30 20:50:26 -04:00 |
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Heng Li
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8d61316cc8
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more comments
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2014-09-23 10:33:15 -04:00 |
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Heng Li
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5fc0f44e27
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mapQ is not quite right
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2014-09-19 23:39:59 -04:00 |
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Heng Li
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a33ca20499
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separate postalt to a separate script
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2014-09-19 23:23:54 -04:00 |