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Commits on Aug 24, 2012
  1. Added log directory link.

    roryk committed Aug 24, 2012
Commits on Aug 23, 2012
  1. Links to data.

    roryk committed Aug 23, 2012
  2. Organized the data directory.

    roryk committed Aug 23, 2012
  3. More setup.

    roryk committed Aug 23, 2012
  4. MACS up and running.

    roryk committed Aug 23, 2012
Commits on Aug 22, 2012
  1. Initial setup.

    roryk committed Aug 22, 2012
  2. Added .# to ignore emacs detritus.

    roryk committed Aug 22, 2012
  3. ENCODE downloading complete and functional.

    Rory Kirchner committed Aug 22, 2012
  4. QC and alignment complete.

    Rory Kirchner committed Aug 22, 2012
  5. complete project

    Rory Kirchner committed Aug 22, 2012
Commits on Aug 20, 2012
Commits on Aug 18, 2012
Commits on Aug 17, 2012
  1. Provide first pass at workflow for classification with downsampling o…

    chapmanb committed Aug 17, 2012
    …r reads at each position
  2. Avoid re-running minority variation calling if output file present. C…

    chapmanb committed Aug 17, 2012
    …orrectly pass along output file for protein change identification
  3. Include combined minority variant amino acid calling as part of stand…

    chapmanb committed Aug 17, 2012
    …ard calling pipeline
  4. Update VCF file of minority variant calls with combined amino acid ch…

    chapmanb committed Aug 17, 2012
    …anges and frequencies
Commits on Aug 16, 2012
  1. Continued work on calling amino acids with read phasing. Pull detecte…

    chapmanb committed Aug 16, 2012
    …d variants from original call VCF
Commits on Aug 15, 2012
  1. Generalize protein namespaces for move to read-based calling. Move to…

    chapmanb committed Aug 15, 2012
    … latest GATK/Picard/bcbio.variation. Add test data for read-based calling.
Commits on Jul 18, 2012
  1. Use majority base at each position to calculate amino acid change. Th…

    chapmanb committed Jul 18, 2012
    …is detects real minority variant cases where the population majority differs from the HXB2 consensus
  2. Avoid classification on larger percentage variants, restricting appli…

    chapmanb committed Jul 18, 2012
    …cation of filters to similarly trained reads.
  3. Update library dependencies and move to leiningen2. Update classifica…

    chapmanb committed Jul 18, 2012
    …tion configuration to avoid primer ends
Commits on Jul 6, 2012
  1. Bugfixes.

    roryk committed Jul 6, 2012
  2. Cleanup.

    roryk committed Jul 6, 2012
Commits on Jul 5, 2012