Heng Li
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bb7a97f68c
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update about bwa.kit
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2014-11-19 09:36:56 -05:00 |
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Heng Li
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82ef0500e6
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Merge branch 'dev'
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2014-11-18 23:29:11 -05:00 |
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Heng Li
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56f1056b49
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don't type empty files
This causes errors.
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2014-11-18 23:28:46 -05:00 |
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Heng Li
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61ab329639
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fine tune the wrapper scripts
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2014-11-18 15:40:58 -05:00 |
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Heng Li
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80e4ecfa79
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r998: smart pairing; allow mixture of SE/PE reads
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2014-11-18 14:30:22 -05:00 |
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Heng Li
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6f9bf9a4ae
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minor change
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2014-11-17 15:23:38 -05:00 |
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Heng Li
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eb664c2fe8
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added an evaluation section
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2014-11-17 14:54:24 -05:00 |
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Heng Li
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cee8149b12
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Updated README for ALT mapping
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2014-11-17 13:20:23 -05:00 |
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Heng Li
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ad9d12c04d
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Removed a comment on hs38 lacking EBV
as is pointed out by Martin Pollard
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2014-11-17 11:08:07 -05:00 |
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Heng Li
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bf053c779b
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polish
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2014-11-17 10:54:16 -05:00 |
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Heng Li
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0071c4ab22
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polish the run script
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2014-11-17 10:44:54 -05:00 |
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Heng Li
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792be78a80
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replace run-gen-hs38* with run-gen-ref
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2014-11-16 00:46:02 -05:00 |
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Heng Li
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050482ef77
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fine tune
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2014-11-13 19:52:47 -05:00 |
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Heng Li
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65c637b036
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smarter prefix finder
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2014-11-13 16:16:21 -05:00 |
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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 |