sjia ada4c5a13c Small change to debug printing code ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1521 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-03 18:31:21 +00:00
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examples	Update naming for consistency.	2009-06-30 22:03:21 +00:00
gatk	Small change to debug printing code	2009-09-03 18:31:21 +00:00
indels	change paths to new ones	2009-07-24 07:28:43 +00:00
piecemealannotator	Cleanup...deprecate FastaSequenceFile2 in favor of IndexedFastaSequenceFile or ReferenceSequenceFile from Picard, depending on the application.	2009-07-08 18:49:08 +00:00
somaticcoverage	Cleanup: GATKEngine no longer needs to be lazy loaded, b/c the plugin directory no longer exists.	2009-07-21 18:50:51 +00:00
tools	Improvements to make this work with uncompressed fastq files. Pulled the fastq parser out into it's own SAMFileReader-like entity.	2009-09-03 17:20:16 +00:00
utils	Changed to use AlignmentUtils.isReadUnmapped() for better consistency with SAM spec; also, it is now explicitly enforced that unmapped reads have <NO_...> values set for ref contig and start upon "remapping"	2009-09-03 16:45:07 +00:00