kshakir 2ef66af903 Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high. ... Moved the BamListWriter from FCP to ListWriterFunction in the Queue core. Added an ExampleCountLoci QScript along with an example pipeline integration test which checks MD5s. Added a few more utility methods to PipelineTest including a currentGATK variable that points to the GATK jar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5121 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-28 23:33:58 +00:00
..
baq	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
bed	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
collections	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
fasta	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
genotype	Moving GLF code to archive	2011-01-15 22:42:42 +00:00
interval	Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.	2011-01-28 23:33:58 +00:00
pileup	Stop RBP.getPileupBySample() from throwing a NullPointerException if the	2010-11-23 05:17:06 +00:00
report	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
sam	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
threading	Documentation and cleanup of the distributed GATK implementation. Detailed documentation -- given that Matt will be extending the system in the near future -- about how the locking and processing trackers work. Added error trapping to note that distributed, shared-memory parallelism isn't yet implemented, instead of just not working silently. General utility function for the analysis of distributedGATK operation in the analysis directory	2011-01-28 03:40:09 +00:00
BaseUtilsUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
GenomeLocParserUnitTest.java	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
GenomeLocSortedSetUnitTest.java	vastly improved progress meter that estimates % of work done and time until the job finishes and time remaining. Reordered GATK core initialization order -- intervals are created before the scheduler.	2011-01-12 17:32:27 +00:00
GenomeLocUnitTest.java	Getting back to '-L unmapped':	2010-12-14 18:24:18 +00:00
MathUtilsUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
PathUtilsUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
ReservoirDownsamplerUnitTest.java	Changing testing framework from junit -> testng, for its enhanced configurability.	2010-11-01 21:31:44 +00:00
UtilsUnitTest.java	Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.	2010-11-22 22:59:42 +00:00