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Commits on Feb 10, 2012
  1. v0.9.19

Commits on Feb 6, 2012
  1. Merge branch 'new-indexer'

Commits on Feb 3, 2012
  1. Merge pull request #12 from drio/master

    OSX not implementing certain semaphore functions
Commits on Feb 2, 2012
  1. @drio

    Warning the user about the fact he will have issues merging

    drio authored
    BWTs on disk since OSX doesn't implement certain semaphores'
Commits on Jan 25, 2012
Commits on Jan 23, 2012
Commits on Jan 20, 2012
  1. sga-rmdup now writes out the number of copies of each sequence in the…

    … header line of the fasta file.
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.
Commits on Dec 31, 2011
  1. Merge pull request #11 from hyphaltip/patch-1

    use -t option in sga-align in the example
  2. @hyphaltip

    Seems like sga-align could be run with threads so that bwa uses multi…

    hyphaltip authored
    …threaded to be faster. Is there any reason not to do this?
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.
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
Commits on Nov 30, 2011
  1. Bumped version to v0.9.18

  2. Fixed configure script to properly handle bamtools include/lib paths …

    …in the case where it was installed with make install
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.
Commits on Nov 15, 2011
  1. Removed print from BCR

  2. BCR algorithm now writes out the reverse index. Made the algorithm ch…

    …oice a command line argument
  3. Started to integrate BCR into index. Made it more efficient by using …

    …2-bit encoded strings everywhere
  4. BCR cleanup

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.
  2. Skeleton code for new indexer

Commits on Nov 10, 2011
  1. Fixed usage message for sga filter

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

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

    …ead ID in sga preprocess
Commits on Oct 19, 2011
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