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Commits on Jan 9, 2012
  1. Updated third party code

    committed Jan 9, 2012
  2. Integrated new overlap method which extends an existing alignment. Co…

    …nsiderably faster than previous method.
    committed Jan 9, 2012
  3. Updated third party code

    committed Jan 9, 2012
Commits on Jan 6, 2012
Commits on Jan 5, 2012
  1. Refined the kmer matching portion of the overlap calculation for the …

    …new corrector.
    
    Previously, we called SampledSuffixArray::calcSA to get the read ID for every kmer match.
    This was very expensive as usually reads would share multiple kmers, making the calculation
    very redundant. Now we cache the indices as we visit them which is two orders of magnitude
    faster. The DP overlap calculation is now the bottleneck.
    committed Jan 5, 2012
Commits on Jan 4, 2012
  1. First implementation of new correction algorithm, which allows arbitr…

    …ary overlaps between reads. Not for production use
    committed Jan 4, 2012
Commits on Jan 3, 2012
  1. Implemented --longest-n parameter for sga-walk --component-walk.

    This option limits the number of walks that are output for complex components.
    committed Jan 3, 2012
Commits on Dec 31, 2011
  1. Merge pull request #11 from hyphaltip/patch-1

    use -t option in sga-align in the example
    committed Dec 31, 2011
  2. Seems like sga-align could be run with threads so that bwa uses multi…

    …threaded to be faster. Is there any reason not to do this?
    hyphaltip committed Dec 31, 2011
Commits on Dec 15, 2011
  1. Modified sga-cluster-extend to warn instead of exit when some seed th…

    …at is passed in is a substring of a read.
    committed Dec 15, 2011
Commits on Dec 2, 2011
  1. Added error message when a sequence with a given ID cannot be found i…

    …n the input scaffold/contig collection
    committed Dec 2, 2011
Commits on Nov 30, 2011
  1. Bumped version to v0.9.18

    committed Nov 30, 2011
  2. Fixed configure script to properly handle bamtools include/lib paths …

    …in the case where it was installed with make install
    committed Nov 30, 2011
Commits on Nov 28, 2011
  1. Fixed two performance issues in sga assemble.

    For very complex graphs with repetitive genomes, Myers' transitive
    reduction algorithm can take a very long time to complete.
    Since sga overlap does not output transitive edges, in the
    general use case Myers' algorithm is not needed. So it is now
    turned off by default.
    
    Second, the small repeat resolution algorithm can also take a long time
    to run. I'm attempting a fix here where I limit to run on not-too-
    complex vertices.
    committed Nov 28, 2011
Commits on Nov 11, 2011
  1. In configure, specify -lbamtools in LIBS instead of LDFLAGS. This cor…

    …rects the library link ordering and fixes the build in the case --as-needed is used in ld, as in newer versions of gcc.
    committed Nov 11, 2011
Commits on Nov 10, 2011
  1. Fixed usage message for sga filter

    committed Nov 10, 2011
Commits on Nov 8, 2011
  1. Changed sga walk to remove contained reads and lingering transitive e…

    …dges when --component-walks is specified.
    committed Nov 8, 2011
Commits on Oct 28, 2011
  1. Merged Albert Villela's change which allows adding a suffix to each r…

    …ead ID in sga preprocess
    committed Oct 28, 2011
Commits on Oct 19, 2011
  1. Removed some cruft from sga-asqg2dot

    committed Oct 19, 2011
  2. Set the bamtools link flag in the case that bamtools is installed in …

    …a standard directory and --with-bamtools is not needed.
    committed Oct 19, 2011
Commits on Oct 12, 2011
  1. v0.9.17

    committed Oct 12, 2011
Commits on Oct 10, 2011
  1. v0.9.16

    committed Oct 10, 2011
Commits on Oct 4, 2011
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