-- 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.
Creating a single temporary directory per ant test run instead of a putting temp files across all runs in the same directory.
Updated various tests for above items and other small fixes.
PreQC parses file with spaces in sample names by using tabs only.
PostQC allows passing the file names for the evals so that flanks can be evaled.
BaseTest's network temp dir now adds the user name to the path so files aren't created in the root.
HybridSelectionPipeline:
- Updated to latest versions of reference data.
- Refactored Picard parsing code replacing YAML.
-- VariantSummary now includes novelty of CNVs by reciprocal overlap detection using the standard variant eval -knownCNVs argument
-- Genericizes loading for intervals into interval tree by chromosome
-- GenomeLoc methods for reciprocal overlap detection, with unit tests
System has the concept of a local and a global MD5 db. The local one is like it operated previously. The global one lives in /humgen/gsa-hpprojects/GATK/data/integrationtests. If the system can find this directory then MD5s will also be read / written to this location. This means that gsabamboo will print differences as appropriate. And all users will in effect have access to a complete history of MD5 file results.
A few minor code reshuffles changed VariantRecalibration and VCFHeader test files.
printSummaryReport now uses GATKReport for nice formating
Moved print formatting arguments into inner class provided to printing functions themselves, not the class
BAMDiffableReader only reads 1000 entries to avoid performance issue. Work around for BAM files with non-unique names
Uncommented all of the incorrectly commented out CombineVariants integrationtests
BaseTest now uses DiffEngine to provide inline differences to VCF and BAM files
Mark DePristo
Khalid Shakir
Ryan Poplin
David Roazen