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Commits on Oct 11, 2013
  1. fix merge from dev

    committed Oct 11, 2013
Commits on Oct 10, 2013
  1. @joelarmstrong
  2. @joelarmstrong
Commits on Oct 4, 2013
  1. @ngannguyen
Commits on Oct 2, 2013
  1. @ngannguyen
Commits on Oct 1, 2013
  1. @joelarmstrong
  2. @joelarmstrong
  3. fix typo in error message

    committed Oct 1, 2013
Commits on Sep 30, 2013
  1. @ngannguyen
Commits on Sep 29, 2013
  1. @ngannguyen
Commits on Sep 27, 2013
  1. @ngannguyen

    Fixed indexing bug

    ngannguyen committed Sep 27, 2013
Commits on Sep 26, 2013
  1. @ngannguyen
Commits on Sep 10, 2013
  1. @ngannguyen

    Fix track labeling

    ngannguyen committed Sep 10, 2013
Commits on Aug 30, 2013
  1. @ngannguyen

    Added conservation track

    ngannguyen committed Aug 30, 2013
Commits on Aug 14, 2013
  1. move halBlockMapper from chain to liftover to break circular dependen…

    …cy created by adding maf function to chain
    committed Aug 14, 2013
Commits on Aug 13, 2013
  1. change recursive traversal in columnIterator and mappedSegment to not…

    … visit paralogy edges when parent genome is not within scope. thus hopefully correcting a longstanding bug.
    committed Aug 13, 2013
Commits on Jul 26, 2013
  1. fix bug in halAlignability and halPhyloPMain where more than the tota…

    …l length could be computed due to a bug in chopping into sequence coordinates
    committed Jul 26, 2013
Commits on Jul 24, 2013
  1. keep bitset in order to only write mapped positions. no more writing …

    …default values in gaps
    committed Jul 24, 2013
  2. @ngannguyen
  3. Revert "pass inmemory option throught hal2maf"

    This reverts commit 6af7c4a.
    committed Jul 24, 2013
  4. @joelarmstrong

    fix metadata rewrite bug

    joelarmstrong committed Jul 24, 2013
  5. merge phyloP

    committed Jul 24, 2013
  6. fix bug with how refbed gets passed. refactor to not use recursive ca…

    …lls for tree traversal. parallelize bigwig generation
    committed Jul 24, 2013