-- This allows us to use -rf ReassignMappingQuality to reassign mapping qualities to 60 *before* the BQSR filters them out with MappingQualityUnassignedFilter.
-- delivers #50222251
-replace unnecessary uses of the UnifiedGenotyper by public integration tests
with PrintReads
-move NanoSchedulerIntegrationTest to protected, since it's completely dependent
on the UnifiedGenotyper
-- Renamed TraversalErrorManager to the more general MultiThreadedErrorTracker
-- ErrorTracker is now used throughout the NanoScheduler. In order to properly handle errors, the work previously done by main thread (submit jobs, block on reduce) is now handled in a separate thread. The main thread simply wakes up peroidically and checks whether the reduce result is available or if an error has occurred, and handles each appropriately.
-- EngineFeaturesIntegrationTest checks that -nt and -nct properly throw errors in Walkers
-- Added NanoSchedulerUnitTest for input errors
-- ThreadEfficiencyMonitoring is now disabled by default, and can be enabled with a GATK command line option. This is because the monitoring doesn't differentiate between threads that are supposed to do work, and those that are supposed to wait, and therefore gives misleading results.
-- Build.xml no longer copies the unittest results verbosely
-- Refactored error handling from HMS into utils.TraversalErrorManager, which is now used by HMS and will be usable by NanoScheduler
-- Generalized EngineFeaturesIntegrationTest to test map / reduce error throwing for nt 1, nt 2 and nct 2 (disabled)
-- Added unit tests for failing input iterator in NanoScheduler (fails)
-- Made ErrorThrowing NanoScheduable
-- Check if a traversal error occurred in the last shard
-- Catch ExecutionException from the TreeReducer and throw as our HMS execption
-- ShardTraverser just throws the exception as formatted by the HMS, rather than wrapping it as a RuntimeException itself
-- EngineFeaturesIntegrationTests now uses public exampleFASTA (faster), and does 1000x iterations (slower)
-- Better error message when a traveral error occurs (a real bug)
-- EngineFeaturesIntegrationTest runs the multi-threaded error testing routines 50x times
-- A bit of cleanup in WalkerTest
-- Cleanup some (but not all) VCF3 files. Turns out there are lots so...
-- Refactored gneotype parser from VCFCodec and VCF3Codec into a single shared version in AbstractVCFCodec. Now VCF3 properly handles the new GenotypeBuilder interface
-- Misc. bugfixes in GenotypeBuilder
-- Unfortunately the result of the multi-threaded test is non-deterministic so run the test 10x times to see if the right expection is always thrown
-- Now prints the stack trace and exception message of the caught exception of the wrong type, if this occurs
-- This behavior, which isn't obviously valuable at all, continued to grab and rethrow exceptions in the HMS that, if run without NT, would show up as more meaningful errors. Now HMS simply checks whether the throwable it received on error was a RuntimeException. If so, it is stored and rethrow without wrapping later. If it isn't, only in this case is the exception wrapped in a ReviewedStingException.
-- Added a QC walker ErrorThrowingWalker that will throw a UserException, ReviewedStingException, and NullPointerException from map as specified on the command line
-- Added IT that ensures that all three types are thrown properly (i.e., you catch a NullPointerException when you ask for one to be thrown) with and without threading enabled.
-- I believe this will finally put to rest all of these annoying HMS captures.
-- 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.
-- Cleaning up old interface to RMDT, docs and contracts added
-- Proper type checking for RodBinding for cases where the Tribble type isn't found or is the wrong type
-- support for explicit naming of bindings (-X:name,type x)
-- support for automatic naming of bindings in lists (-X:vcf foo.vcf -X:vcf bar.vcf will generate internal names X and X2)
-- ParserEngineUnitTest expanded to cover all of the Rodbinding cases
-- RodBindingUnitTest tests all of the low-level accessors
-- Parsing engine throws UserExceptions when bad bindings are provided on the command line
Mark DePristo
David Roazen
Mauricio Carneiro
Eric Banks