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gatk-3.8/java/test/org/broadinstitute/sting/utils
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chartl a79967d9af After extensive testing of MannWhitneyU: 
- Verified that exact calculations do agree with R's dwilcox()
 - Verified that exact calculations do not agree with R's wilcox.test
   + This is because R does a correction, and calculates CDFs rather than PDFs (e.g. sums over dwilcox() values)
 - Can now specify MWU to calculate cumulative exact tests, rather than point probabilities
 - Z-scores are now calculated properly for exact tests
   + Previously, z-values calculated by inverting normal CDF from U-statistic PDF
   + Now both inversions are done, with a smart heuristic (biased variance) to make the point-calculated Z-value more accurate
   + Additional tests



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5911 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-06-01 15:51:27 +00:00
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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 Make IntervalIntegrationTest aware of the new alignments in the MV1994.bam 2011-05-23 19:59:47 +00:00
pileup Stop RBP.getPileupBySample() from throwing a NullPointerException if the 2010-11-23 05:17:06 +00:00
report Removed old (and unused) reporting system, now that Kiran's VE reporting system is working. Refactors dictionary creation error messages into UserExceptions 2011-05-22 18:42:52 +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 GenomeLocParser and GenomeLoc are now fully implemented. 2011-05-21 02:01:59 +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
MWUnitTest.java After extensive testing of MannWhitneyU: 2011-06-01 15:51:27 +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
ReadUtilsUnitTest.java ClipReads now supports HARDCLIP_BASES, though in fact this turned out to be not necessary for my desired tests. In the process of developing the HARDCLIP mode, I added some proper ReadUtils unit tests, which would ideally be expanded to include other ReadUtil functions, as added 2011-05-27 11:42:22 +00:00
ReservoirDownsamplerUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
SimpleTimerUnitTest.java Contracts for SimpleTimer, as well as UnitTests 2011-05-22 19:45:31 +00:00
UtilsUnitTest.java Enabled the parameterize option for debugging PipelineTest MD5s. 2011-03-26 00:41:47 +00:00