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Commits on Nov 5, 2013
  1. change halBlockViz lib to return target seq

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

    glennhickey committed Nov 2, 2013
    …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.
  2. remove logic where defaultValues were not lifted. this had the nasty …

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

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

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

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

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

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

    glennhickey committed Oct 16, 2013
    … functions reading bed streams
Commits on Oct 15, 2013
  1. Clarify column iterator usage

    joelarmstrong committed Oct 15, 2013
    getColumnIterator expects position in sequence coordinates (genome coordinates if the sequence is a genome), but ColumnIterator->toSite expects the position exclusively in genome coordinates.
Commits on Oct 11, 2013
Commits on Oct 10, 2013
Commits on Oct 4, 2013
Commits on Oct 2, 2013
Commits on Oct 1, 2013
  1. fix typo in error message

    glennhickey committed Oct 1, 2013
Commits on Sep 30, 2013
  1. Merge branch 'development' into lod

    glennhickey committed Sep 30, 2013
    Conflicts:
    	lod/halLodInterpolate.py
    	lod/impl/halLodExtractMain.cpp
Commits on Sep 29, 2013
  1. add missing includes

    glennhickey committed Sep 29, 2013
  2. change step parameter to scale in halLodExtract. this way different s…

    glennhickey committed Sep 29, 2013
    …ubtrees can get different steps
Commits on Sep 27, 2013
  1. Fixed indexing bug

    ngannguyen committed Sep 27, 2013
Commits on Sep 26, 2013
Commits on Sep 10, 2013
  1. Fix track labeling

    ngannguyen committed Sep 10, 2013