Guillermo del Angel c9c3f6b0fc Minor UG Engine refactoring/cleanup: instead of passing in the # of samples separately from sample set, pass in ploidy instead and compute # of chromosomes internally - will help later on with code clarity		2012-03-29 11:05:42 -04:00
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alignment	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
analyzecovariates	Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.	2012-02-03 17:13:52 -05:00
commandline	Merged bug fix from Stable into Unstable	2012-02-27 17:13:17 -05:00
gatk	Minor UG Engine refactoring/cleanup: instead of passing in the # of samples separately from sample set, pass in ploidy instead and compute # of chromosomes internally - will help later on with code clarity	2012-03-29 11:05:42 -04:00
jna	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00
queue	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00
utils	Refactoring so that ConsensusAlleleCounter can use regular pileups and can operate correctly. This involved adding utility functions to ReadBackedPileup to count # of insertions/deletions right after current position. Added unit test for IndelGenotypeLikelihoods, esp. ConsensusAlleleCounter logic	2012-03-28 21:01:31 -04:00