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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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	Bugfix for incorrect error messages for missing BAMs and VCFs	2012-01-23 09:52:07 -05:00