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Commits on Oct 22, 2012
  1. ignore mac files

    committed Oct 22, 2012
  2. docu fix

    committed Oct 22, 2012
Commits on Sep 7, 2011
  1. Merge pull request #5 from tobiasmarschall/master

    xa2multi.pl: reverse sequence and phred if orientations differ between primary and secondary alignment
    Heng Li committed Sep 7, 2011
  2. Bugfix: reverse (complement) sequence and phred string if alternative…

    … alignment has different orientation than primary alignment
    Tobias Marschall committed Sep 7, 2011
Commits on Jul 10, 2011
  1. Merge pull request #2 from RoelKluin/master

    Filter Casava 1.8 flagged sequences with bwa aln -Y
    Heng Li committed Jul 10, 2011
  2. Remove sequences marked to be filtered by Casava-1.8 with bwa aln -Y

    In Casava 1.8 the fastq output changed. e.g.
    
    @EAS139:136:FC706VJ:2:5:1000:12850 1:Y:18:ATCACG
    AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
    +
    BBBBCCCC?<A?BC?7@@???????DBBA@@@@A@@
    
    The part after the space, treated as comment by bwa, contains the fields:
    <read number>:<is filtered>:<control number>:<barcode sequence>
    
    With `Y' Casava indicates that a sequence should be filtered. This patch
    enables bwa, with an -Y flag, to filter these sequences.
    
    Signed-off-by: Roel Kluin <roel.kluin@gmail.com>
    RoelKluin committed Jul 10, 2011
  3. Revert "In Casava 1.8 the fastq output changed, the name had a space …

    …which bwa"
    
    This reverts commit 36cd4f9.
    
    The comment shouldn't be included in the sequence name.
    RoelKluin committed Jul 10, 2011
Commits on Jul 8, 2011
  1. In Casava 1.8 the fastq output changed, the name had a space which bwa

    wasn't parsing correctly. This patch fixes that and enables bwa to filter
    sequences marked by Casava, removing this tag from the output.
    
    Signed-off-by: RoelKluin <roel.kluin@gmail.com>
    RoelKluin committed Jul 8, 2011
Commits on Jun 9, 2011
  1. convert XA to multiple lines

    Heng Li committed Jun 9, 2011
  2. automatically choose the algorithm for BWT

    Heng Li committed Jun 9, 2011
  3. increase maximum barcode length limit to 63bp

    Heng Li committed Jun 9, 2011
Commits on May 4, 2011
  1. applied patches from Alec Wysoker

    Heng Li committed May 4, 2011
  2. added -s to ar

    Heng Li committed May 4, 2011
Commits on Apr 7, 2011
  1. speed up multi-threading

    Heng Li committed Apr 7, 2011
Commits on Jan 25, 2011
  1. Release bwa-0.5.9 (r16)

    Heng Li committed Jan 25, 2011
Commits on Jan 22, 2011
  1. Added recommendation for PacBio reads

    Heng Li committed Jan 22, 2011
  2. fixed a typo in help

    Heng Li committed Jan 22, 2011
Commits on Jan 19, 2011
  1. update the manual page

    Heng Li committed Jan 19, 2011
  2. Put BC: to both ends

    Heng Li committed Jan 19, 2011
Commits on Jan 15, 2011
  1. Added barcode support

    Heng Li committed Jan 15, 2011
  2. Added an option to accept Illumina 1.3+ fastq

    Heng Li committed Jan 15, 2011
Commits on Jan 14, 2011
  1. Updated README

    Heng Li committed Jan 14, 2011
  2. Updated README

    Heng Li committed Jan 14, 2011
  3. Provided links to help information

    Heng Li committed Jan 14, 2011
  4. Added a few others to .gitignore

    Heng Li committed Jan 14, 2011
  5. Added .gitignore

    Heng Li committed Jan 14, 2011
  6. first commit

    Heng Li committed Jan 14, 2011