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Commits on Feb 26, 2014
  1. Fix crash on some snake tracks with dups

    (range1 was null for all but the first iteration of the inner loop.)
    joelarmstrong committed Feb 26, 2014
Commits on Nov 20, 2013
  1. revert last change

    glennhickey committed Nov 20, 2013
  2. add header to empty maf

    glennhickey committed Nov 20, 2013
  3. change exception to warning when running hal2maf with default params …

    …on empty genome or seuqnce
    glennhickey committed Nov 20, 2013
Commits on Nov 18, 2013
  1. Update README.md

    add contributors list
    glennhickey committed Nov 18, 2013
Commits on Nov 16, 2013
  1. Fix not being able to reuse WiggleLiftover classes

    WiggleLiftover calls WiggleTiles.clear() after one conversion, but
    clear() didn't set the genome length to 0, which caused WiggleLiftover
    not to re-initialize the tiles properly.
    joelarmstrong committed Nov 16, 2013
Commits on Nov 15, 2013
  1. Fix 4dExtract problem w/ intra-exon duplication

    (hopefully)
    joelarmstrong committed Nov 15, 2013
Commits on Nov 14, 2013
  1. conserved 4d site extraction

    Also reading frame preservation, fixes, and tests
    joelarmstrong committed Nov 14, 2013
Commits on Nov 7, 2013
Commits on Nov 6, 2013
Commits on Nov 5, 2013
  1. change halBlockViz lib to return target seq

    (breaks existing code, but hopefully just the genome browser, since I
    renamed "sequence" to "qSequence.")
    joelarmstrong committed Nov 5, 2013
Commits on Nov 2, 2013
  1. Revert "dont run phylop on inserts in leaves. they will just be 0 any…

    …way"
    
    (I changed my mind.  We want those zeros.  Keeping them allows us to have fewer headers, which can be a bigger win in terms of size of resulting wigs and bigwigs)
    This reverts commit e789f92.
    glennhickey committed Nov 2, 2013
  2. remove logic where defaultValues were not lifted. this had the nasty …

    …side effect of creating lots of headers around zero values
    glennhickey committed Nov 2, 2013
Commits on Nov 1, 2013
  1. add --prec option to halPhlyoP to control number of digits to write i…

    …n wigs. default remains 3
    glennhickey committed Nov 1, 2013
Commits on Oct 31, 2013
  1. subtree conservation for halPhyloP (thanks Melissa)

    and halPhyloP mask option fix
    joelarmstrong committed Oct 31, 2013
Commits on Oct 25, 2013
  1. deleted unneeded file

    joelarmstrong committed Oct 25, 2013
  2. OS X Mavericks compatibility

    (Benedict's code, closes #3)
    joelarmstrong committed Oct 25, 2013
Commits on Oct 22, 2013
  1. Fix wiggleLiftover segfault

    (hopefully!)
    joelarmstrong committed Oct 22, 2013
Commits on Oct 16, 2013
  1. add --tab option and enable by passing a custom locale pointer to all…

    … functions reading bed streams
    glennhickey committed Oct 16, 2013
Commits on Oct 15, 2013