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Commits on Oct 3, 2011
  1. v0.9.15

    authored
Commits on Sep 28, 2011
  1. Added new filter to filterBAM to aggressively get rid of FR contamina…

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

    authored
    Conflicts:
    	src/SGA/correct-long.cpp
  2. Merge branch 'gapfill' into hapgen

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

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    …l alignments. Added code to hapgen to pull out read pairs.
Commits on Sep 22, 2011
  1. Merge branch 'metagenomics' into gapfill

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    Conflicts:
    	src/Algorithm/Makefile.am
    	src/SGA/Makefile.am
    	src/SGA/sga.cpp
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 …

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

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

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

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

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    …de. The algorithm finds kmer anchors on the long reads, then builds putative haplotypes through a de Bruijn graph between them.
Commits on Sep 15, 2011
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