Heng Li
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72f1a95448
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Merge branch 'master' into api
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2012-04-17 20:44:30 -04:00 |
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Heng Li
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cd818687ac
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r115: added -I and -S to bwasw
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2012-04-17 20:43:43 -04:00 |
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Heng Li
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4f61e2b7f5
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unnecessary large .sai output
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2012-04-17 19:31:37 -04:00 |
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Heng Li
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9c486fa41e
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updated APIs abit
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2012-04-08 00:55:52 -04:00 |
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Heng Li
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3b5a9e5595
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simplified bwa_se() interface
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2012-04-08 00:12:34 -04:00 |
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Heng Li
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ca93a71e6e
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complete single-end alignment
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2012-04-08 00:02:06 -04:00 |
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Heng Li
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080726cb47
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preliminary doc
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2012-04-07 22:50:07 -04:00 |
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Heng Li
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1cef219667
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compute CIGAR; rev seq not working
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2012-04-07 22:00:03 -04:00 |
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Heng Li
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66154ff5d2
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towards refined gapped; unfinished
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2012-04-07 01:25:39 -04:00 |
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Heng Li
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a1abfe9977
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API: aln seems working
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2012-04-07 00:23:01 -04:00 |
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Heng Li
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cff473393c
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commented out debugging code
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2012-04-02 12:05:15 -04:00 |
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Heng Li
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790df95e1a
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updated revision number
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2012-04-02 11:43:32 -04:00 |
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Heng Li
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36f2fd6238
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bugfix: incorrect bandwidth
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2012-04-02 11:39:40 -04:00 |
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Heng Li
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d3169804f6
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debugging; bug persistant
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2012-04-02 10:45:42 -04:00 |
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Heng Li
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173b93dfd4
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debugging code: bwasw has a rare bug
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2012-04-02 09:37:02 -04:00 |
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Heng Li
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d33abf127f
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check *.64.bwt first and then *.bwt
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2012-03-29 14:45:00 -04:00 |
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Heng Li
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c875085b2b
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do not use .64 suffix by default
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2012-03-29 12:31:01 -04:00 |
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Heng Li
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bdc953cad9
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Tim's suggestion suffix file name with .64
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2012-03-29 12:22:51 -04:00 |
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Heng Li
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a471f1918b
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bugfix: long-existing out-of-boundary bug
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2012-03-19 13:45:09 -04:00 |
Heng Li
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91a4a0c8ea
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Release bwa-0.6.1
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2011-11-28 09:52:07 -05:00 |
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Heng Li
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64e353ce49
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bugfix: bwa-sw PE segfault in rare case
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2011-11-28 09:12:21 -05:00 |
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Heng Li
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bf65b6463a
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fastmap: optionally output the original query seq
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2011-11-24 19:44:21 -05:00 |
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Heng Li
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150bfbdef4
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fixed a deadlock; SMEM iterator
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2011-11-24 19:15:14 -05:00 |
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Heng Li
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b5170e0efa
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output the NM tag
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2011-11-24 11:51:38 -05:00 |
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Heng Li
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717959e819
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fixed a minor issue in trimming
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2011-11-24 10:39:41 -05:00 |
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Heng Li
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eeedda105d
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perhaps improves samse/sampe
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2011-11-24 01:22:02 -05:00 |
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Heng Li
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196b50dde3
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optionally mark multi-part hits as secondary
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2011-11-23 23:39:59 -05:00 |
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Heng Li
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9f84384ed2
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reordering BWA-SW command-line prompt
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2011-11-23 23:36:08 -05:00 |
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Heng Li
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b17b6577ac
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removed a useless bwa-sw CMD option
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2011-11-23 23:30:14 -05:00 |
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Heng Li
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107a9870ef
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incorrect mate pos in BWA-SW SE mode
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2011-11-23 23:18:51 -05:00 |
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Heng Li
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dec584d50b
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fixed a long-existing bug in trimming
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2011-11-23 23:11:50 -05:00 |
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Heng Li
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84aa3fa696
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useless script
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2011-11-19 21:48:54 -05:00 |
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Heng Li
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182cb2e89c
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use standard SW when no SSE2
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2011-11-19 19:38:21 -05:00 |
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Heng Li
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dc4008936c
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avoid duplicated XA tags
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2011-11-19 14:52:47 -05:00 |
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Heng Li
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8f89f55484
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fixed a segfault when there are too few good bases.
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2011-11-17 22:13:38 -05:00 |
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Heng Li
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c8edcafb44
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added SEAL
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2011-11-12 20:48:35 -05:00 |
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Heng Li
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162f220deb
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updated README
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2011-11-12 20:26:52 -05:00 |
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Heng Li
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9f2c77880d
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remove a useless file
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2011-11-12 20:06:37 -05:00 |
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Heng Li
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770a5f2ae0
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Release BWA-0.6.0
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2011-11-12 20:04:39 -05:00 |
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Heng Li
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f1517b845c
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updated manual
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2011-11-12 18:35:04 -05:00 |
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Heng Li
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7544aca718
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updated revision number
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2011-11-12 16:56:21 -05:00 |
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Heng Li
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2f3cdcd55b
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bugfix: bwa-short MT does not work (by Peter)
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2011-11-12 16:54:38 -05:00 |
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Heng Li
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56a18659b6
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crash under non-typical setting (by John Marshall)
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2011-11-12 16:53:53 -05:00 |
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Heng Li
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8060693411
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multithreading works again
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2011-11-12 16:50:58 -05:00 |
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Heng Li
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fa8cfe5567
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bugfix: wrong mapping quality
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2011-11-12 12:12:45 -05:00 |
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Heng Li
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b42910ada6
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proper mate information
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2011-11-12 00:49:21 -05:00 |
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Heng Li
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e06685db45
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bwa-sw PE seems working (SAM is incorrect)
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2011-11-07 00:51:43 -05:00 |
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Heng Li
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c8c79ef024
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mate rescue seems working (not MT)
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2011-11-06 16:20:40 -05:00 |
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Heng Li
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17eaac5a21
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compute insert size distribution
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2011-11-05 23:17:52 -04:00 |
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Heng Li
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a29b179045
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further preparation for pairing
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2011-11-05 14:31:30 -04:00 |