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gatk-3.8/java/test/org/broadinstitute/sting/gatk
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hanna 5c3198520c A few minor modifications masquerading as significant changes according to 
svn's logs:
- Copied BAM indexing engine from Picard back into the GATK anticipating
  shard merging algorithm.  Tried to leave most of the building blocks in
  Picard.  If this turns into a logistical nightmare, I'll merge the building
  blocks into the GATK as well.
- Reorganized the org.broadinstitute.sting.gatk.datasources package, giving
  better separation of query and management functionality for reads, ref, rmd,
  and samples.  
- Merged Shard building blocks into org.broadinstitute.sting.gatk.datasources.
  reads package, indicating it's current strong relationship with the reads,
  rather than the general unifying element I wish this would be.
- Collapsed BAMFormatAwareShard into Shard.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5184 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-02-03 17:59:19 +00:00
..
arguments A significant refactoring of the ROD system, done largely to simplify the process of 2010-12-31 04:52:22 +00:00
contexts/variantcontext Remove the extra trailing tab at the end of the VCF ## header line. Unfortunately, this meant updating every freaking integration test. 2010-12-08 17:22:29 +00:00
datasources A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
executive Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00
filters Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
iterators A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
refdata Oops...forgot to commit the changes that allow primitive VCF streaming. 2011-01-12 21:54:51 +00:00
traversals A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
walkers NewEvaluationContext needs to be generated in the inner loop. Otherwise, multiple comp tracks end up getting routed to the same row of the output table. Added test to cover multiple comp tracks. 2011-02-03 07:04:53 +00:00
WalkerManagerUnitTest.java Changing testing framework from junit -> testng, for its enhanced configurability. 2010-11-01 21:31:44 +00:00