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Commits on Nov 12, 2013
  1. Revert "try moving phast includes out of hal headers"

    This reverts commit cb78499.
    glennhickey committed Nov 12, 2013
Commits on Nov 7, 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
  1. Clarify column iterator usage

    getColumnIterator expects position in sequence coordinates (genome coordinates if the sequence is a genome), but ColumnIterator->toSite expects the position exclusively in genome coordinates.
    joelarmstrong committed Oct 15, 2013
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

    Conflicts:
    	lod/halLodInterpolate.py
    	lod/impl/halLodExtractMain.cpp
    glennhickey committed Sep 30, 2013
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…

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

    ngannguyen committed Sep 27, 2013