Heng Li
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4373a077d5
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wrapper for bwa-mem
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2014-11-13 15:51:00 -05:00 |
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Heng Li
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a5c144db4d
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added scripts to generate hs38a.fa and hs38d6.fa
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2014-11-13 12:53:29 -05:00 |
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Heng Li
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fffe52a45b
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move bwa-typeHLA back to this repo
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2014-11-13 12:50:56 -05:00 |
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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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c5fe18438a
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r984: updated to the latest kseq.h
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2014-11-13 11:12:23 -05:00 |
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Heng Li
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7eabcf42c4
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r983: bugfix - wrong mate info
Picard now gives a clean bill.
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2014-11-10 13:15:11 -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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4e97cdfde8
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move to a new project bwa-typeHLA
The two scripts cannot be used standalone anyway.
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2014-11-06 09:13:15 -05:00 |
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Heng Li
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c2f2cb03ce
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to be moved to a separate project
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2014-11-06 09:12:53 -05:00 |
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Heng Li
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1bee29ef44
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map to individual HLA ALT for meaningful mapQ
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2014-11-06 00:37:59 -05:00 |
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Heng Li
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10de1e0b74
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optionally output debegging info
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2014-11-05 13:20:33 -05:00 |
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Heng Li
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0eee4fa1b0
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nothing, really
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2014-11-04 16:00:25 -05:00 |
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Heng Li
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2a41772d0a
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more command line help
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2014-11-04 15:41:18 -05:00 |
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Heng Li
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e5d7f4fc30
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change the default max_len
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2014-11-04 15:31:33 -05:00 |
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Heng Li
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ccf03ffd22
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control min-match-length
we still need this to kill false mapping/alignment
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2014-11-04 15:26:10 -05:00 |
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Heng Li
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de268247db
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type primary exons first and then the rest
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2014-11-04 15:09:21 -05:00 |
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Heng Li
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12fff1ad57
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a bit code cleanup
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2014-11-04 14:30:31 -05:00 |
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Heng Li
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96fba0f2f4
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proper homozygous typing; fixed a low-level bug
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2014-11-04 11:38:05 -05:00 |
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Heng Li
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ace18171b0
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backup
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2014-11-04 10:07:14 -05:00 |
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Heng Li
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4cbb0cb829
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polished the run script
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2014-11-03 15:29:02 -05:00 |
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Heng Li
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9dbf152e31
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added the pipeline script
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2014-11-03 15:16:14 -05:00 |
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Heng Li
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40c4a6ffe1
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better CLI; more comments
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2014-11-03 12:09:29 -05:00 |
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Heng Li
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4bc01e90c8
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not used any more
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2014-11-03 11:51:25 -05:00 |
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Heng Li
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b7d0a2d537
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first HLA typing script
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2014-11-03 11:47:23 -05:00 |
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Heng Li
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9bf898fa10
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r963: expose mask_level
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2014-10-30 11:33:43 -04:00 |
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Heng Li
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6b4e6bf7dd
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Merge branch 'dev'
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2014-10-28 13:47:02 -04:00 |
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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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9867634f72
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r960: XA tags occasionally missing for PE
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2014-10-28 13:43:26 -04:00 |
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Heng Li
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6f39715e6e
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keep mate positions
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2014-10-28 13:03:33 -04:00 |
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Heng Li
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5c87869d91
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keep RG
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2014-10-27 10:45:07 -04:00 |
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Heng Li
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dbe74ca9b8
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Merge branch 'dev'
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2014-10-25 23:10:25 -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 |
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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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7c362bef69
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added another paper
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2014-10-23 15:15:20 -04:00 |
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Heng Li
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3a1da27c1c
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added Bai et al. Seems good, too.
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2014-10-23 15:08:18 -04:00 |
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Heng Li
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d61a1226a8
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highlight Liu et al. It seems good.
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2014-10-23 14:52:48 -04:00 |
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Heng Li
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b45442fbc1
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Merge branch 'dev'
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2014-10-23 14:43:06 -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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af606fc31a
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Merge branch 'dev'
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2014-10-22 16:17:36 -04:00 |
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Heng Li
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3d129be642
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r943: change the default -y to 20, but ...
for GRCh38 ALT, this is not enough. We need -y at least 40 to get high accuracy
because a locus at chr19 has 35 copies.
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2014-10-22 12:42:58 -04:00 |
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Heng Li
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4177d6c2c7
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r942: ignore ALT hits when counting n_sub for ...
non-ALT hits. Counting leads to underestimated mapQ.
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2014-10-22 10:24:16 -04:00 |
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Heng Li
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60b728487a
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r941: set a min length for 3rd-round seeding
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2014-10-21 13:15:42 -04:00 |
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Heng Li
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282130a64e
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r940: fixed a bug - missing primary hit
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2014-10-21 12:57:49 -04:00 |
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Heng Li
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5e00d08346
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r939: fixed a memory leak (issue #35)
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2014-10-21 09:26:19 -04:00 |
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Heng Li
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574098d034
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updated directory name
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2014-10-21 00:57:06 -04:00 |