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Commits on Aug 15, 2011
  1. Version v0.9.13

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  2. Fixed rare bug in the scaffold builder where a contig could be added …

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

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    …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.
Commits on Jul 25, 2011
  1. Cleaned up unused files

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  2. Updated version to 0.9.12

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

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

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    …M format if the --sam option is given. This replaces --description-file.
Commits on Jul 19, 2011
  1. Version 0.9.11

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  2. Cleaned up comments

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

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

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  2. Added example script for the Illumina MiSeq example data. Includes th…

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    …e scaffolding component.
  3. Cleaned up build. Added a Makefile to install the scripts the sga sca…

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    …ffold pipeline requires (astat, bam2de).
  4. Increased default minimum branch length in sga assemble to better han…

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

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    Conflicts:
    	src/Algorithm/Makefile.am
    	src/Util/Makefile.am
Commits on Jun 21, 2011
Commits on Jun 20, 2011
Commits on Jun 17, 2011
  1. Implemented extension mode for sga cluster. This required refactoring…

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    … the SequenceProcessFramework to use a generic generator object.
  2. Refactored cluster generation code into ReadCluster class. Added stub…

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

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

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    …now returns a trimmed alignment to avoid bad-tails of the long reads.
Commits on Jun 13, 2011
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