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Commits on Jul 19, 2011
  1. Version 0.9.11

    committed Jul 19, 2011
  2. Cleaned up comments

    committed Jul 19, 2011
Commits on Jul 18, 2011
Commits on Jul 15, 2011
  1. Increased version number to 0.9.10

    committed Jul 15, 2011
Commits on Jul 10, 2011
Commits on Jun 30, 2011
  1. Fixed cluster size computation

    committed Jun 30, 2011
  2. Added ability to cluster based on seed sequences that are not present…

    … in the FM-index.
    committed Jun 30, 2011
  3. Added example script for the Illumina MiSeq example data. Includes th…

    …e scaffolding component.
    committed Jun 30, 2011
  4. Cleaned up build. Added a Makefile to install the scripts the sga sca…

    …ffold pipeline requires (astat, bam2de).
    committed Jun 30, 2011
  5. Increased default minimum branch length in sga assemble to better han…

    …dle long (150+) reads.
    committed Jun 30, 2011
Commits on Jun 27, 2011
  1. Merge branch 'long-align'

    Conflicts:
    	src/Algorithm/Makefile.am
    	src/Util/Makefile.am
    committed Jun 27, 2011
Commits on Jun 21, 2011
Commits on Jun 20, 2011
Commits on Jun 17, 2011
  1. Fixed formatting of sga cluster help

    committed Jun 17, 2011
  2. Implemented extension mode for sga cluster. This required refactoring…

    … the SequenceProcessFramework to use a generic generator object.
    committed Jun 17, 2011
  3. Refactored cluster generation code into ReadCluster class. Added stub…

    … subprogram for cluster-extend.
    committed Jun 17, 2011
Commits on Jun 15, 2011
  1. Added early exit to kmerCorrect when the read sequence is shorter tha…

    …n the kmer length.
    
    Thanks to Dan Hughes for the bug report and test case.
    committed Jun 15, 2011
Commits on Jun 14, 2011
  1. Made the extension termination condition more robust. StringThreader …

    …now returns a trimmed alignment to avoid bad-tails of the long reads.
    committed Jun 14, 2011
Commits on Jun 13, 2011
  1. Implemented outputting corrected sequences from the StringThreader. S…

    …till a bit hacky.
    committed Jun 13, 2011
  2. Wrapped the long read correction process in a class to use in the Seq…

    …uenceProcessFramework.
    committed Jun 13, 2011
Commits on Jun 10, 2011
  1. Added a few more helper functions to the string threading code. Curre…

    …ntly, the search explodes when threading through repeats that are slightly
    
    divergent.
    committed Jun 10, 2011
  2. Full extension algorithm complete, including culling leaves once thei…

    …r error rate is too high.
    committed Jun 10, 2011