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Commits on Aug 13, 2013
  1. change recursive traversal in columnIterator and mappedSegment to not…

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

    authored
    …l length could be computed due to a bug in chopping into sequence coordinates
Commits on Jul 24, 2013
  1. @ngannguyen
  2. Revert "pass inmemory option throught hal2maf"

    authored
    This reverts commit 6af7c4a.
  3. @joelarmstrong

    fix metadata rewrite bug

    joelarmstrong authored
  4. merge phyloP

    authored
  5. fix bug with how refbed gets passed. refactor to not use recursive ca…

    authored
    …lls for tree traversal. parallelize bigwig generation
  6. add refbed option

    authored
  7. add halTreePhyloP script

    authored
Commits on Jul 23, 2013
  1. @ngannguyen
  2. change phyloP bed reader to slice by command line interval if specifi…

    authored
    …ed. will make parallelizing easier once debugged. need to do the same for hal2maf
Commits on Jul 22, 2013
  1. refactor phyloP class substantially to adopt hal coding style and to …

    authored
    …prepare for bed subselection support
Commits on Jul 19, 2013
Commits on Jul 18, 2013
Commits on Jul 17, 2013
  1. @ngannguyen
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