depristo e16bc2cbd9 Contracts for Java now write for GenomeLoc and GenomeLocParser. The semantics of GenomeLoc are now much clearer. It is no longer allowed to create invalid GenomeLocs -- you can only create them with well formed start, end, and contigs, with respect to the mater dictionary. Where one previously created an invalid GenomeLoc, and asked is this valid, you must now provide the raw arguments to helper functions to assess this. Providing bad arguments to GenomeLoc generates UserExceptions now. Added utilty functions contigIsInDictionary and indexIsInDictionary to help with this. ... Refactored several Interval utilties from GenomeLocParser to IntervalUtils, as one might expect they go Removed GenomeLoc.clone() method, as this was not correctly implemented, and actually unnecessary, as GenomeLocs are immutable. Several iterator classes have changed to remove their use of clone() Removed misc. unnecessary imports Disabled, temporarily, the validating pileup integration test, as it uses reads mapped to an different reference sequence for ecoli, and this now does not satisfy the contracts for GenomeLoc git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5827 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-20 15:43:27 +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
broad	Fixed import.	2011-05-09 18:07:40 +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	Contracts for Java now write for GenomeLoc and GenomeLocParser. The semantics of GenomeLoc are now much clearer. It is no longer allowed to create invalid GenomeLocs -- you can only create them with well formed start, end, and contigs, with respect to the mater dictionary. Where one previously created an invalid GenomeLoc, and asked is this valid, you must now provide the raw arguments to helper functions to assess this. Providing bad arguments to GenomeLoc generates UserExceptions now. Added utilty functions contigIsInDictionary and indexIsInDictionary to help with this.	2011-05-20 15:43:27 +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
text	A 'fat shard' finder. Cranks through the indices of a BAM file or list of	2011-05-10 12:56:47 +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	Contracts for Java now write for GenomeLoc and GenomeLocParser. The semantics of GenomeLoc are now much clearer. It is no longer allowed to create invalid GenomeLocs -- you can only create them with well formed start, end, and contigs, with respect to the mater dictionary. Where one previously created an invalid GenomeLoc, and asked is this valid, you must now provide the raw arguments to helper functions to assess this. Providing bad arguments to GenomeLoc generates UserExceptions now. Added utilty functions contigIsInDictionary and indexIsInDictionary to help with this.	2011-05-20 15:43:27 +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