Heng Li
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017be45407
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r342: bugfix in bwasw - AS is off by one
but I do not understand why the old code does not have the same problem.
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2013-03-08 12:06:45 -05:00 |
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Heng Li
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e6c262594f
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bwa-sw: ditch stdaln
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2013-03-05 10:12:38 -05:00 |
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Heng Li
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086c9d0e7d
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bwa-sw: use bwa_gen_cigar() for cigar generation
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2013-03-05 09:54:49 -05:00 |
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Heng Li
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e613195e17
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moved some common code to bwa.{c,h}
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2013-02-23 15:30:46 -05:00 |
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Heng Li
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904c3205c0
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removed a few unused variables
These variables have been assigned but never actually used. Reported by
gcc-4.7. Lower version cannot give such warnings.
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2013-02-23 13:26:50 -05:00 |
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Heng Li
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95d18449b3
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merge bseq.{h,c} to utils.{h,c}
I do not like many small files.
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2013-02-12 10:36:15 -05:00 |
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Heng Li
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a09db69037
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In bwtsw, replace the batch seq-reader with bseq
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2013-02-06 17:12:27 -05:00 |
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Heng Li
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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
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292f9061ab
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r132: optionally copy FASTA/Q comment to SAM
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2012-10-26 12:54:32 -04:00 |
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Heng Li
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f44edd4fc9
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r128: more conservative chaining filter
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2012-06-28 14:51:02 -04:00 |
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Heng Li
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0ae318be0d
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resolve duphits after right extension as well
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2012-06-28 13:32:58 -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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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 |
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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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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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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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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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 |
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Heng Li
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06687a33b9
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bwasw: read and align two fastq at a time
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2011-11-05 14:00:01 -04:00 |
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Heng Li
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8f3c780552
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fixed a potential int overflow
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2011-10-24 14:22:39 -04:00 |
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Heng Li
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eed46e802a
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fixed a bug about reverse alignment
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2011-10-24 14:09:05 -04:00 |
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Heng Li
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b204437c7e
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fixed negative mapping quality; still byggy
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2011-10-24 14:00:36 -04:00 |
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Heng Li
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8512b55ce3
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bwasw works on a couple of sequences
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2011-10-24 13:42:32 -04:00 |
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Heng Li
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4c43c5914d
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this is better; but still buggy
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2011-10-24 11:50:11 -04:00 |
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Heng Li
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29c3acfb31
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not segfault immediately; but buggy
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2011-10-24 09:36:52 -04:00 |
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Heng Li
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b3397a1f14
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changes to bwa-sw for the 64-bit support; unfinish
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2011-10-21 13:32:45 -04:00 |
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Heng Li
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1cb409aaf2
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use forward-only pac to reduce memory
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2011-10-21 12:03:14 -04:00 |
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Heng Li
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8d6b859bf8
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speed up multi-threading
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2011-04-07 17:26:08 -04:00 |
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Heng Li
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5e30884730
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Update to the latest modfication 0.5.9rc1-2. Update ChangeLog
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2011-01-13 20:54:10 -05:00 |
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Heng Li
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007c3eb75d
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Imported from my local bwa repository, the master repository.
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2011-01-13 20:52:12 -05:00 |