Ryan Poplin a4634624b7 There are now three triggering options in the HaplotypeCaller. The default (mismatches, insertions, deletions, high quality soft clips), an external alleles file (from the UG for example), or extended triggers which include low quality soft clips, bad mates and unmapped mates. Added better algorithm for band pass filtering an ActivityProfile and breaking them apart when they get too big. Greatly increased the specificity of the caller by battening down the hatches on things like base quality and mapping quality thresholds for both the assembler and the likelihood function.		2012-04-10 14:48:23 -04:00
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datasources	Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now.	2012-04-02 14:27:36 -04:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Taking care of bad cigars in the GATK	2012-03-20 14:32:57 -04:00
iterators	Removing extended event related unit tests	2012-04-02 14:40:36 -04:00
refdata	Merge with master	2011-11-19 09:56:06 -05:00
report	Added more primitives to GATK Report Column Type	2012-03-28 09:07:54 -04:00
samples	Added UnitTests for getFamilies() and getChildrenWithParents()	2011-12-09 15:57:07 +01:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	There are now three triggering options in the HaplotypeCaller. The default (mismatches, insertions, deletions, high quality soft clips), an external alleles file (from the UG for example), or extended triggers which include low quality soft clips, bad mates and unmapped mates. Added better algorithm for band pass filtering an ActivityProfile and breaking them apart when they get too big. Greatly increased the specificity of the caller by battening down the hatches on things like base quality and mapping quality thresholds for both the assembler and the likelihood function.	2012-04-10 14:48:23 -04:00
EngineFeaturesIntegrationTest.java	HierarchicalMicroScheduler no longer attempts to wrap exceptions	2012-03-23 11:27:21 -04:00
GenomeAnalysisEngineUnitTest.java	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00