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
..
R	queueJobReport now compresses PDF when running R 2.13+.	2012-01-10 17:32:30 -05:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Weirdly, PicardException inherits from SAMException, which means that our specialty code for	2012-01-24 15:30:04 -05:00
packages	Revved Picard to incorporate tfennell's AsyncSAMFileWriter.	2011-12-06 10:37:42 -05:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	fixing bug with fastq extension	2012-01-24 11:02:15 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00