gatk-3.8/java/test/org/broadinstitute/sting/gatk
aaron 844cb2ed33 fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric!
Also putting more tolerance into the timing on the tibble index tests (that check to make sure we're deleting out of date indexes, and not deleting perfectly good indexes).  It seems that some of the farm nodes aren't great with a stopwatch.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3674 348d0f76-0448-11de-a6fe-93d51630548a
2010-06-29 21:38:55 +00:00
..
arguments Experimental versions of downsampler and Ryan's deduper are now available either 2010-05-19 05:40:05 +00:00
contexts/variantcontext JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout. 2010-06-07 00:33:02 +00:00
datasources Merging the sharding-specific inherited classes down into the base. 2010-06-17 22:36:13 +00:00
executive A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests. 2010-04-08 06:14:15 +00:00
filters A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests. 2010-04-08 06:14:15 +00:00
io A long overdue correction; all unit tests now end in 'UnitTest'. This was something we wanted to do for a while, and now with the performance tests coming, it was a good time to clean-up. Please label any new test appropriately: *UnitTest and *IntegrationTest are the two valid file name patterns for tests. 2010-04-08 06:14:15 +00:00
iterators First pass at eliminating the old sharding system. Classes required for the original sharding system 2010-06-17 20:17:31 +00:00
refdata fixing a bug that Eric found with RODs for reads, where some records could be omitted. Sorry Eric! 2010-06-29 21:38:55 +00:00
traversals Merging the sharding-specific inherited classes down into the base. 2010-06-17 22:36:13 +00:00
walkers An addition for Sendu since he can't seem to tell when his CountCovariate jobs die in the middle of writing the CSVs. We now write an EOF marker at the end of the covariates table and look for it when reading in the file in TableRecalibrationWalker. By default, we warn the user if the EOF marker isn't present, but we exception out if the user provides the --fail_with_no_eof_marker option. 2010-06-29 18:50:07 +00:00