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Commits on Sep 12, 2011
  1. Version 0.9.14

    committed Sep 12, 2011
  2. Track the number of vertices that have been merged into each vertex t…

    …o properly decide which walks to retain when removing bubbles.
    committed Sep 12, 2011
Commits on Sep 8, 2011
Commits on Sep 2, 2011
  1. Merge branch 'beetl'

    committed Sep 2, 2011
  2. Added human genome assembly instructions and updated c. elegans scrip…

    …t with the parameters used in the sga paper.
    committed Sep 2, 2011
  3. Fixed bug where the reverse index would not be used when the overlap …

    …method of correction is specified.
    committed Sep 2, 2011
Commits on Aug 17, 2011
Commits on Aug 16, 2011
Commits on Aug 15, 2011
  1. Version v0.9.13

    committed Aug 15, 2011
  2. Fixed rare bug in the scaffold builder where a contig could be added …

    …with the wrong orientation if a unique walk is found between the contig pair with orientation opposite to that of the link.
    committed Aug 15, 2011
Commits on Aug 6, 2011
  1. Fixed a bug in the suffix array validation code. The validator assume…

    …d that suffixes with the same string were sorted by read name when they are actually sorted by position in the file. Thanks to Tomas Larsson for the bug report and test data.
    committed Aug 6, 2011
Commits on Jul 25, 2011
  1. Cleaned up unused files

    committed Jul 25, 2011
  2. Updated version to 0.9.12

    committed Jul 25, 2011
Commits on Jul 21, 2011
  1. In sga filter, exit the homopolymer check if the read length is short…

    …er than the k-mer size. The homopolymer and complexity checks are now disabled by default.
    committed Jul 21, 2011
  2. Now sga walk will write out the reads making up the walk string in SA…

    …M format if the --sam option is given. This replaces --description-file.
    committed Jul 21, 2011
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