kshakir 45ebbf725c Instead of always merging Picard interval files they are optionally merged by Sting Utils. ... Disabled the MFCP while the FCP gets an update. Minor updates to email messages for upcoming scala 2.9. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5588 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-06 21:12:05 +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	Instead of always merging Picard interval files they are optionally merged by Sting Utils.	2011-04-06 21:12:05 +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	Following up Mark's recent commit: hooking up the --maxPositionalMoveAllowed argument into the indel realigner and through to the SAM writer. We now ensure that no read is realigned more than N bases (200 by default, which is nowhere close to realistically possible). If anyone ever sees a warning message about this with the default value then please let me know because I need to see it for myself.	2011-02-28 04:40:54 +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	Enabled the parameterize option for debugging PipelineTest MD5s.	2011-03-26 00:41:47 +00:00