Valentin Ruano-Rubio fc5ce4b662 Created the stand-alone AC and AF annotation AlleleCountBySample ... Story: https://www.pivotaltracker.com/story/show/77250524 Changes: - Remove the annotating code in GeneralPloidyExactAFCalc (GPEAFC) class. - Added the asAlleleList to GenotypeAlleleCounts class and get (GPEAFC) to use that instead of implementing its own (nicer and more reusable code). - Removed the explicit addition of AlleleCountBySample fields to the VCF header by the walker initialize - Added utility methods in Utils to wrap and int[] array into a List<Integer>, and double[] array into a List<Double> efficiently. Test: - Added unit-testing for asAlleleList in GenotypeAlleleCountsUnitTest (within testFirst and testNext). - Added unit-testing for new methods in Utils : asList(int[]) and asList(double[]) - Changed UG General Ploidy test to add explicitly those annotations. - Non-trivial changes in integration tests involving non-diploid runs (namelly haploid and tetraploid) as they are not showing those annotations anylonger, so the MD5s have been changed accordingly.		2014-08-22 20:33:25 -04:00
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src	Created the stand-alone AC and AF annotation AlleleCountBySample	2014-08-22 20:33:25 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.3 development	2014-07-17 12:09:33 -04:00