carneiro e2e435d52c GenotypeAndValidate: now looks at annotations in the INFO field instead of filter field. Better output and filters repetitive calls to indel extended events. ... IndelUtils: added a isInsideExtendedIndel() method to filter the above mentioned. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5449 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-15 21:54:40 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	GenotypeAndValidate: now looks at annotations in the INFO field instead of filter field. Better output and filters repetitive calls to indel extended events.	2011-03-15 21:54:40 +00:00
test	Removing some debug code from VQSRv2. VariantEval can now be stratified by contig with -ST Contig. New hidden option in CombineVariants for overlapping records to take the info fields from the record with the highest AC (while still updating AC/AN/AF correctly) instead of dropping info fields which aren't exactly the same.	2011-03-15 21:28:10 +00:00