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Roger Zurawicki 4cbd1f0dec Reorganized the testing code and created ClipReadsTestUtils 
Tests are more rigorous and includes many more test cases.
We can tests custom cigars and the generated cigars.
     *Still needs debugging because code is not working.
Created test classes to be used across several tests.

Some cases are still commented out.

Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
 		2011-12-09 11:52:34 -05:00
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R scales=free shows variance within analysis better 2011-12-07 14:09:32 -05:00
c Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
chainFiles
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doc
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java Reorganized the testing code and created ClipReadsTestUtils 2011-12-09 11:52:34 -05:00
packages Revved Picard to incorporate tfennell's AsyncSAMFileWriter. 2011-12-06 10:37:42 -05:00
perl Update to the bindings for liftOverVCF.pl (to -V from -B) 2011-09-15 15:33:09 -04:00
scala Use optional() instead of required() to construct javaMemoryLimit argument in JavaCommandLineFunction 2011-12-05 14:06:00 -05:00
testdata Testdata for IntervalStratification 2011-11-10 11:08:34 -05:00