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Commits on Nov 18, 2011
Commits on Nov 1, 2011
Commits on Oct 31, 2011
  1. If the best candidate haplotype is to the reverse strand of the refer…

    committed Oct 31, 2011
    …ence reverse-complement everything so the variants are on the right strand
Commits on Oct 29, 2011
Commits on Oct 28, 2011
Commits on Oct 27, 2011
  1. Changed dindel assertion to a throw; modified the post-assembly walk …

    committed Oct 27, 2011
    …finding algorithm to avoid performing enormous walks in the case that the graph has loops
Commits on Oct 26, 2011
Commits on Oct 25, 2011
  1. More debugging output in VCFTester

    committed Oct 25, 2011
  2. DindelRealign code now outputs to a stream instead of a file. Also, a…

    committed Oct 25, 2011
    …dded more debug output in VCFTester
Commits on Oct 24, 2011
  1. Added extra information in the vcf testing mode of graph-diff to help…

    committed Oct 24, 2011
    … understand why some variants were not found
  2. The previous commits that changed the represtation of lexicographic i…

    committed Oct 24, 2011
    …ndex in the SampleSuffixArray broke binary compatability with previous files. Updated the magic number to catch these old binaries.
  3. Adding functionality to graph-diff to test existing variants passed i…

    committed Oct 24, 2011
    …n via a VCF file
Commits on Oct 21, 2011
  1. Added code to perform a fairly basic selection of the best alignment …

    committed Oct 21, 2011
    …position from a set of possibilities
Commits on Oct 20, 2011
  1. Fixed bug in read pair extraction

    committed Oct 20, 2011
Commits on Oct 19, 2011
  1. Revised SampledSuffixArray to using a uint32_t to store the ids of th…

    committed Oct 19, 2011
    …e lexicographically sorted reads. This cuts the memory of the data structure in half but limits it to 2**32 strings.
  2. Implemented function to get the edges of the de Bruijn graph from the…

    committed Oct 19, 2011
    … FM-index using a single (forward) index. This can be used to cut the memory usage of some subprograms in half.
Commits on Oct 18, 2011
  1. Initial merge and integration of Kees' dindel code

    committed Oct 18, 2011
    Conflicts:
    	src/Algorithm/Makefile.am
Commits on Oct 17, 2011
  1. Refactored code into HapgenUtil

    committed Oct 17, 2011
  2. Fixed addSNP to candidate haplotypes.

    Cornelis Arnout Albers committed Oct 17, 2011
Commits on Oct 13, 2011
  1. Changed calling to ModelSelection. Added EM haplotype frequency estim…

    Cornelis Arnout Albers committed Oct 13, 2011
    …ation. Seems to work.
Commits on Oct 12, 2011
  1. v0.9.17

    committed Oct 12, 2011
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