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Commits on Jun 13, 2013
  1. update getHalGenomes to reflect commaless output of halStats which go…

    glennhickey committed Jun 13, 2013
    …t replaced in merge confusion
  2. update processing of halStats --genomes to reflect that list returned…

    glennhickey committed Jun 13, 2013
    … is not comma separated due to latest git merge. should eventually replace with the halStats.py methods
Commits on Jun 12, 2013
  1. add coding style blurb

    glennhickey committed Jun 12, 2013
  2. fix autoslice rounding

    glennhickey committed Jun 12, 2013
  3. revise rearrangement to prioritize duplication events so they dont ge…

    glennhickey committed Jun 12, 2013
    …t mislabled transpositions or inversions. also use the canonical paralog notion when iding dupes.
Commits on Jun 11, 2013
  1. add cleanResults function to cut off gaps between first and last bloc…

    glennhickey committed Jun 11, 2013
    …ks and to make sure the output thickstartend is the same as chrom startend
  2. remove cout

    glennhickey committed Jun 11, 2013
  3. remove couts

    glennhickey committed Jun 11, 2013
Commits on Jun 10, 2013
  1. clear ouput set

    glennhickey committed Jun 10, 2013
  2. revise bed12 logic and switch to block iterator. also keep output sor…

    glennhickey committed Jun 10, 2013
    …ted by source coordinates
Commits on Jun 8, 2013
Commits on Jun 7, 2013
  1. fix unique option

    glennhickey committed Jun 7, 2013
  2. work on append option

    glennhickey committed Jun 7, 2013
  3. add merge option

    glennhickey committed Jun 7, 2013
  4. get hal2mafmp running

    glennhickey committed Jun 7, 2013
  5. add append option

    glennhickey committed Jun 7, 2013
Commits on Jun 6, 2013
  1. merge development

    glennhickey committed Jun 6, 2013
Commits on Jun 5, 2013