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Commits on Mar 26, 2013
Commits on Mar 25, 2013
Commits on Mar 22, 2013
  1. added specs RC2.0.

    committed Mar 22, 2013
  2. removed UNKNOWN read group, -1 is used for no read group index;

    NS -1 is used for no mate.
    committed Mar 22, 2013
Commits on Mar 21, 2013
  1. fixed AP to slice context.

    committed Mar 21, 2013
Commits on Mar 20, 2013
Commits on Mar 19, 2013
Commits on Mar 18, 2013
Commits on Mar 15, 2013
Commits on Mar 14, 2013
  1. 'small.cram' reading test is ok.

    fixed '*' QS in Sam2BamRecordFactory.addInsertions.
    committed Mar 14, 2013
Commits on Mar 11, 2013
  1. initial commit for 2.0;

    changed version and build number;
    added preliminary cram2 files for testing.
    committed Mar 11, 2013
Commits on Mar 7, 2013
Commits on Mar 6, 2013
  1. fixed cram2bam random access (in crai first offset was 0).

    fixed merge tool to work with crai. 
    removed ref requirement from indexing tool.
    committed Mar 6, 2013
Commits on Feb 14, 2013
Commits on Feb 12, 2013
  1. fixed missing NM tag

    committed Feb 12, 2013
Commits on Feb 7, 2013
Commits on Feb 5, 2013
  1. minor fixes

    committed Feb 5, 2013
Commits on Feb 4, 2013
Commits on Feb 1, 2013
  1. in progress dibify

    committed Feb 1, 2013
Commits on Jan 31, 2013
  1. added SAMSelector.

    committed Jan 31, 2013
Commits on Jan 30, 2013
  1. added SamRecordComparision;

    minor fixes reported by JB.
    committed Jan 30, 2013
Commits on Jan 24, 2013
Commits on Jan 22, 2013
  1. fixed lossless QS alias, tested.

    fixed null read bases bug.
    committed Jan 22, 2013
Commits on Jan 21, 2013
  1. BAM indexing tested;

    renamed 'view' to 'merge' because 'bam' tools does most of the 'view'
    functions.
    committed Jan 21, 2013
Commits on Jan 11, 2013
  1. added View to view and merge BAM/CRAM files, not tested;

    fixed BAM indexing, nearly complete, briefly tested.
    committed Jan 11, 2013
Commits on Jan 9, 2013
  1. pre-built jar

    committed Jan 9, 2013
  2. fix: lower case ref bases carried over to reads;

    fix: fails if first read is unmapped;
    added: BAM index, preliminary, works;
    committed Jan 9, 2013
Commits on Dec 11, 2012
  1. minor fixes;

    added crai;
    brai in progress (beyond alignment query returns all records instead of
    none).
    committed Dec 11, 2012
Commits on Dec 7, 2012
Commits on Dec 4, 2012
  1. added fastq writer.

    improved performance of both bam2cram and cram2bam by caching reference
    bytes between containers.
    committed Dec 4, 2012