4 Commits (2cd33b2f1f20abc481e7ab77d9a6650933a6e249)

Author	SHA1	Message	Date
Ryan Poplin	4d6312d4ea	HaplotypeCaller is now an ActiveRegionWalker.	2012-01-22 14:31:01 -05:00
Mauricio Carneiro	e89ff063fc	GATKSAMRecord refactor ... The GATK engine will now provide a GATKSAMRecord to all tools which incorporates the functionality used by the GATK to the bam file (ReadGroups, Reduced Reads, ...). * No tools should create SAMRecord anymore, use GATKSAMRecord instead *	2011-11-03 15:43:26 -04:00
Eric Banks	54331b44e9	New way of looking at the size of a pileup: there's a physical number of elements in the data structure and there's a representative depth of coverage (since a reduced read represents depth >= 1). The size() method has been removed because its meaning is ambiguous. Updated several annotations and the UG engine to make use of the representative depths.	2011-11-02 12:47:30 -04:00
Mark DePristo	034a997d07	Generalized Reads -> Fragment calculation ... -- Supports ReadBackedPileup -> FragmentCollection as before -- Added support for List<SAMRecord> -> FragmentCollection for Ryan's haplotype caller -- General cleanup, renaming, move to separate package, more extensive unit tests, etc. -- Added toFragment() function to ReadBackedPileup interface	2011-10-26 15:54:38 -04:00