hanna 9b182e3063 Prep for documenting command-line arguments: delete some arguments that don't make sense any more given ... the state of the traversals and GATK input requirements: all_loci (replaced by walker annotation), max OTF sorts (bam files must be sorted and indexed), threaded io (replaced by data sharding framework). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1144 348d0f76-0448-11de-a6fe-93d51630548a		2009-07-01 18:23:35 +00:00
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datasources	When you get the reference string for a read that is mapped partially off the end of a contig, the string is masked with X's for base positions without corresponding reference positions.	2009-06-29 20:51:55 +00:00
executive	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00
iterators	changes to fix and test the interval based traversals	2009-06-25 17:54:15 +00:00
refdata	Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.	2009-06-22 14:39:41 +00:00
traversals	changes to fix and test the interval based traversals	2009-06-25 17:54:15 +00:00
walkers	a fix to make the test run	2009-06-29 20:24:32 +00:00
GATKArgumentCollectionTest.java	Prep for documenting command-line arguments: delete some arguments that don't make sense any more given	2009-07-01 18:23:35 +00:00
OutputTrackerTest.java	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +00:00