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Commits on Oct 11, 2013
Commits on Sep 30, 2013
  1. fixed makefile

    joelarmstrong committed Sep 30, 2013
Commits on Aug 22, 2013
  1. Add "merge" option to halAppendSubtree

    joelarmstrong committed Aug 22, 2013
    Using the option will merge the appended node and the node which is
    appended to.
    
    This makes halAddToNode unnecessary (this is more general) so I
    removed it.
Commits on Aug 16, 2013
Commits on Aug 13, 2013
  1. Fix insertion behavior

    joelarmstrong committed Aug 13, 2013
    (hopefully)
  2. change recursive traversal in columnIterator and mappedSegment to not…

    glennhickey committed Aug 13, 2013
    … visit paralogy edges when parent genome is not within scope. thus hopefully correcting a longstanding bug.
Commits on Aug 1, 2013
  1. Merge remote-tracking branch 'refs/remotes/origin/development' into m…

    joelarmstrong committed Aug 1, 2013
    …odificationTools
    
    Conflicts:
    	stats/impl/halStatsMain.cpp
Commits on Jul 26, 2013
  1. fix bug in halAlignability and halPhyloPMain where more than the tota…

    glennhickey committed Jul 26, 2013
    …l length could be computed due to a bug in chopping into sequence coordinates
  2. Replacing a genome should work with all genomes now

    joelarmstrong committed Jul 26, 2013
    (Other than single-genome "alignments")
Commits on Jul 25, 2013
  1. Fix halReplaceGenome bug

    joelarmstrong committed Jul 25, 2013
Commits on Jul 24, 2013
  1. keep bitset in order to only write mapped positions. no more writing …

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

    glennhickey committed Jul 24, 2013
    This reverts commit 6af7c4a.
  3. fix metadata rewrite bug

    joelarmstrong committed Jul 24, 2013
  4. merge phyloP

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

    glennhickey committed Jul 24, 2013
    …lls for tree traversal. parallelize bigwig generation
  6. add refbed option

    glennhickey committed Jul 24, 2013
  7. Append subtree utility

    joelarmstrong committed Jul 24, 2013