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Commits on Sep 12, 2016
  1. Merge pull request #52 from douglasgscofield/patch-1

    Fix typo in README.md, mammals.maf to mammals.hal
    committed on GitHub Sep 12, 2016
Commits on Sep 1, 2016
  1. Merge remote-tracking branch 'origin/development'

    Glenn Hickey committed Sep 1, 2016
  2. refactor last change so that gap flip gets done once per line instead…

    … of once per chunk
    Glenn Hickey committed Sep 1, 2016
  3. Fix maf2hal bug where any reverse-strand alignment in a gapped block …

    …is mishandled
    Glenn Hickey committed Sep 1, 2016
Commits on Jul 26, 2016
Commits on Jun 30, 2016
  1. hal2maf --refTargets fixes

    As a side effect, no longer supports exporting only part of the BED
    using --refSequence, --start, and --length.
    joelarmstrong committed Jun 30, 2016
Commits on Apr 28, 2016
Commits on Apr 15, 2016
  1. Merge pull request #44 from harvardinformatics/master

    Updated phast installation instructions.
    committed Apr 15, 2016
  2. Updated phast installation instructions. svn no longer works and PHAS…

    …T var is set by Makefile
    aaronk committed Apr 15, 2016
Commits on Apr 13, 2016
Commits on Apr 10, 2016
Commits on Apr 7, 2016
Commits on Mar 29, 2016
Commits on Mar 22, 2016
Commits on Mar 19, 2016
Commits on Mar 17, 2016
  1. use absolute paths

    joelarmstrong committed Mar 17, 2016
Commits on Mar 14, 2016
Commits on Mar 5, 2016
Commits on Feb 13, 2016
Commits on Feb 12, 2016
Commits on Jan 31, 2016
Commits on Jan 28, 2016
Commits on Jan 26, 2016
  1. Merge pull request #39 from ifiddes/master

    Added option to run phyloFit model on subset of an alignment
    joelarmstrong committed Jan 26, 2016
  2. forgot aggregate stats

    ifiddes committed Jan 26, 2016
Commits on Nov 11, 2015
  1. remove the "prefetch LOD levels" feature

    Not clear that it provides a large improvement from just caching indices
    and the root genome, and it was slowing down first accesses in
    high-latency situations.
    joelarmstrong committed Nov 11, 2015
Commits on Sep 10, 2015
Commits on Jun 26, 2015
  1. Merge pull request #32 from diekhans/pslStatsBug

    PSL statistics bug
    joelarmstrong committed Jun 26, 2015
  2. fix incorrect computation of psl nCount field. While ucsc does not do…

    …cument it, it is an exclusive count from the other counts
    diekhans committed Jun 25, 2015