Eric Banks e4ec899a87 First pass at adding unit tests for the RR framework: I have added 3 tests and all 3 uncovered RR bugs! ... One of the fixes was critical: SlidingWindow was not converting between global and relative positions correctly. Besides not being correct, it was resulting in a massive slow down of the RR traversal. That fix definitely breaks at least one of the integration tests, but it's not worth changing md5s now because I'll be changing things all over RR for the next few days, so I am going to let that test fail indefinitely until I can confirm general correctness of the tool.		2013-01-29 15:51:07 -05:00
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gatk	First pass at adding unit tests for the RR framework: I have added 3 tests and all 3 uncovered RR bugs!	2013-01-29 15:51:07 -05:00
utils	Unit tests for repeat covariates: generate 100 random reads consisting of tandem repeat units of random content and size, and check that covariates match expected values at all positions in reads.	2013-01-29 15:23:02 -05:00
package-info.java	Updated all JAVA file licenses accordingly	2013-01-10 17:06:41 -05:00