Matt Hanna c312bd5960 Weirdly, PicardException inherits from SAMException, which means that our specialty code for ... reporting malformed BAMs was actually misreporting any error that happened in the Picard layer as a BAM ERROR. Specifically changing PicardException to report as a ReviewedStingException; we might want to change it in the future. I'll followup with the Picard team to make sure they really, really want PicardException to inherit from SAMException.		2012-01-24 15:30:04 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Weirdly, PicardException inherits from SAMException, which means that our specialty code for	2012-01-24 15:30:04 -05:00
test	Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.	2012-01-23 16:17:04 -05:00