Mark DePristo 80a4ce0edf Bugfix for incorrect error messages for missing BAMs and VCFs ... -- Missing BAMs were appearing as StingExceptions -- Missing VCFs were showing up as CommandLineErrors, but it's clearer for them to be CouldNotReadInputFile exceptions -- Added integration tests to ensure missing BAMs, VCFs, and -L files are properly thrown as CouldNotReadInputFile exceptions -- Added path to standard b37 BAM to BaseTest -- Cleaned up code in SAMDataSource, removing my parallel loading code as this just didn't prove to be useful.		2012-01-23 09:52:07 -05:00
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R	Protect ourselves when iteration is present but there's only a single iteration in queueJobReport.R	2011-12-19 10:08:38 -05:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
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	Bugfix for incorrect error messages for missing BAMs and VCFs	2012-01-23 09:52:07 -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	Be explicit about setting the snpEff -onlyCoding option in the pipeline	2012-01-17 20:04:27 -05:00
testdata	Data Processing Pipeline Test	2011-12-12 00:24:51 -05:00