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Commits on Oct 3, 2011
  1. v0.9.15

    committed Oct 3, 2011
  2. Added strict mode to scaffolder to only keep unambiguous connections …

    …in the scaffold graph
    committed Oct 3, 2011
Commits on Sep 28, 2011
  1. Added new filter to filterBAM to aggressively get rid of FR contamina…

    …tion in a mate pair library. Added new output to the Scaffold
    committed Sep 28, 2011
Commits on Sep 27, 2011
  1. Merge branch 'hapgen'

    Conflicts:
    	src/SGA/correct-long.cpp
    committed Sep 27, 2011
  2. Merge branch 'gapfill' into hapgen

    committed Sep 27, 2011
Commits on Sep 25, 2011
Commits on Sep 23, 2011
  1. hapgen: added function to MultiAlignment to construct an MA from loca…

    …l alignments. Added code to hapgen to pull out read pairs.
    committed Sep 23, 2011
  2. Write out beetl progress to a file.

    committed Sep 23, 2011
Commits on Sep 22, 2011
  1. Merge branch 'metagenomics' into gapfill

    Conflicts:
    	src/Algorithm/Makefile.am
    	src/SGA/Makefile.am
    	src/SGA/sga.cpp
    committed Sep 22, 2011
Commits on Sep 21, 2011
Commits on Sep 20, 2011
Commits on Sep 19, 2011
  1. sga metagenome: implement compare and swap logic to avoid outputting …

    …duplicate contigs when two threads assemble the same sequence simultaneously
    committed Sep 19, 2011
Commits on Sep 18, 2011
  1. Added descending kmer mode to gap filler and implemented first pass a…

    …t choosing the assembled sequence which best fits the gap
    committed Sep 18, 2011
  2. When patching a scaffold gap, remove the overlapping input sequence i…

    …nstead of the gap sequence.
    committed Sep 18, 2011
Commits on Sep 17, 2011
  1. gapfill: the gap sequence is now placed into the scaffold and the new…

    … scaffolds written. First functional build
    committed Sep 17, 2011
Commits on Sep 16, 2011
  1. Brand new long read error correction based on haplotype generation co…

    …de. The algorithm finds kmer anchors on the long reads, then builds putative haplotypes through a de Bruijn graph between them.
    committed Sep 16, 2011
  2. Merge branch 'small_repeat_rewrite'

    committed Sep 16, 2011
Commits on Sep 15, 2011
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