aaron 647a367680 Made the size zero interval file checker emit a warnUser if we're not in unsafe mode. ... Also changed the default logger level from error to warn. Does anyone object? It makes sense for users to always get their warn user statements in the default logging level. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1451 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-21 14:40:57 +00:00
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gatk	Added detection of interval files with zero length to the GATK, and removed it from the interval merger walker: this was a critical blocking emergency issue for Eric.	2009-08-21 05:35:49 +00:00
playground	A most stupid bug. In cases when more than one indel variant was present in cleaned bam file, the "consensus" (max. # of occurences) call was computed incorrectly, and most of the times the call itself was not made at all. Fortunately, the locations where we see multiple indels are a minority, and many of them are suspicious anyway (manifestation of alignment problems?). Could change results of POOLED calls though.	2009-08-20 22:31:44 +00:00
secondarybase	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
utils	Made the size zero interval file checker emit a warnUser if we're not in unsafe mode.	2009-08-21 14:40:57 +00:00