chartl f7d1b8f5de CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive. ... Also, I can't be bothered to fix the spelling of "oldepthofcoverage" to contain the necessary number of D's. Be content that it does, however, contain the requisite number of O's. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3109 348d0f76-0448-11de-a6fe-93d51630548a		2010-04-01 16:27:23 +00:00
..
arguments	Bug fix in variant eval 2. Preliminary (slow and buggy) support for -XL exclude lists.	2010-03-12 19:23:12 +00:00
contexts/variantcontext	add a new JEXLContext that lazy-evaluates JEXL expressions given the VariantContext.	2010-03-15 16:00:55 +00:00
datasources	the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.	2010-03-31 22:39:56 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
filters	Added an optional argument -rgbl --read_group_black_list to filter read groups.	2010-03-26 19:38:57 +00:00
io	Fix for problem where err stream remapped to output stream in certain cases, (hopefully) completing Matt's hat trick of fail. Thanks, unit tests.	2009-09-16 08:33:56 +00:00
iterators	Fix off-by-one error in original implementation of read sharding. Tested by	2010-03-06 18:52:53 +00:00
refdata	the last-mile commit for Tribble integration. The system is now ready for Tribble to be turned on, as soon as we've removed any dependencies in the ROD code on interfaces that aren't in the Tribble library (i.e. the Variation or Genotype interface on RODs). All of the walkers should be up to date.	2010-03-31 22:39:56 +00:00
traversals	Rework the way the MicroScheduler handles locus shards to handle intervals that span shards	2010-03-11 18:40:31 +00:00
walkers	CoverageStatistics has now replaced DepthOfCoverage -- old DoC is in the archive.	2010-04-01 16:27:23 +00:00