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Commits on Oct 25, 2012
  1. Turned on semi-global alignment

    jts committed Oct 25, 2012
  2. Rewrote DindelHaplotype::extractVariants to use new MultipleAlignment…

    jts committed Oct 25, 2012
    … data structures
Commits on Oct 24, 2012
  1. Ported DindelRealignWindow to use new MultipleAlignment class instead…

    jts committed Oct 24, 2012
    … of deprecated MultiAlignment
Commits on Oct 23, 2012
  1. Code cleanup

    jts committed Oct 23, 2012
Commits on Oct 21, 2012
  1. Output read names in evidence BAM

    jts committed Oct 21, 2012
Commits on Oct 19, 2012
  1. Updateed third party code

    jts committed Oct 19, 2012
  2. When outputting a projected BAM, handle the case where the haplotype …

    jts committed Oct 19, 2012
    …and reference do not align end-to-end
Commits on Oct 15, 2012
  1. Code cleanup

    jts committed Oct 15, 2012
Commits on Oct 12, 2012
Commits on Oct 8, 2012
  1. code cleanup

    jts committed Oct 8, 2012
Commits on Oct 5, 2012
  1. Merge branch 'probcache' into new-overlap-hapgen

    jts committed Oct 5, 2012
    Conflicts:
    	src/Util/Makefile.am
Commits on Oct 3, 2012
Commits on Oct 2, 2012
  1. Built framework to abstract away the read extraction/overlap computat…

    jts committed Oct 2, 2012
    …ion during string graph hap gen
Commits on Oct 1, 2012
Commits on Sep 26, 2012
Commits on Sep 25, 2012
  1. v0.9.35

    jts committed Sep 25, 2012
  2. Implemented an upper limit on the number of edges we allow a vertex t…

    jts committed Sep 25, 2012
    …o have before giving up on using it in the assembly graph.
    
    This helps limit the memory usage in pathological cases, like when the genome contains a lot of satellite DNA.
Commits on Sep 24, 2012
  1. When building the FM-index using ropebwt the lexicographic index is b…

    jts committed Sep 24, 2012
    …uilt using openmp if the compiler supports it.
  2. github issue 27: added --no-primer-check option to preprocess. Also, …

    jts committed Sep 24, 2012
    …cleaned up help message.
Commits on Sep 7, 2012
  1. Fix divide-by-zero in sga-astat

    jts committed Sep 7, 2012
  2. Set the --mina option to abyss

    jts committed Sep 7, 2012
Commits on Aug 24, 2012
  1. Whitespace changes

    jts committed Aug 24, 2012
Commits on Aug 23, 2012
  1. v0.9.34

    jts committed Aug 23, 2012
  2. Explicitly construct the .sai file when using ropebwt since you canno…

    jts committed Aug 23, 2012
    …t get the lexicographic index from ropebwt when read lengths vary
Commits on Aug 21, 2012
  1. v0.9.33

    jts committed Aug 21, 2012