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

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Commits on Oct 24, 2012
  1. Ported DindelRealignWindow to use new MultipleAlignment class instead…

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

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

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

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  2. When outputting a projected BAM, handle the case where the haplotype …

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

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Commits on Oct 12, 2012
Commits on Oct 8, 2012
  1. code cleanup

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

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    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…

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    …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

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  2. Implemented an upper limit on the number of edges we allow a vertex t…

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    …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…

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

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

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  2. Set the --mina option to abyss

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Commits on Aug 24, 2012
  1. Whitespace changes

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Commits on Aug 23, 2012
  1. v0.9.34

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  2. Explicitly construct the .sai file when using ropebwt since you canno…

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

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