Mauricio Carneiro 4a57add6d0 First implementation of DiagnoseTargets ... * calculates and interprets the coverage of a given interval track * allows to expand intervals by specified number of bases * classifies targets as CALLABLE, LOW_COVERAGE, EXCESSIVE_COVERAGE and POOR_QUALITY. * outputs text file for now (testing purposes only), soon to be VCF. * filters are overly aggressive for now.		2012-02-03 17:12:43 -05:00
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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	First implementation of DiagnoseTargets	2012-02-03 17:12:43 -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	Small script to chunk up a VCF into equal-sized chunks	2012-02-02 12:29:03 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00