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gatk-3.8/public/java/test/org/broadinstitute/sting
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Mark DePristo fb1911a1b6 -- Convenience constructor for VariantContextBuilder that creates a new one based on an existing builder 
-- Convenience routine for creating alleles from strings of bases
-- Convenience constructor for VCFFilterHeader line whose description is the same as name
-- VariantContextTestProvider creates all sorts of types of VariantContexts for testing purposes.  Can be reused throughtout code for BCF, VCF, etc.
-- Created basic BCF2WriterCodec tests that consumes VariantContextTestProvider contexts, writes them to disk with BCF2 writer, and checks that they come back equals to the original VariantContexts. Actually worked for some complex tests in the first go
 		2012-05-24 10:57:01 -04:00
..
alignment Reinitialize random seed in the bwa bindings from the fixed seed stored in the 2011-07-22 13:41:53 -04:00
commandline Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
gatk Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each. 2012-05-21 15:41:56 -04:00
jna When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter. 2011-12-16 18:09:25 -05:00
utils -- Convenience constructor for VariantContextBuilder that creates a new one based on an existing builder 2012-05-24 10:57:01 -04:00
BaseTest.java Revert bad part of last commit that shouldn't have been pushed 2012-05-10 10:41:08 -04:00
MD5DB.java Merged bug fix from Stable into Unstable 2011-10-13 18:02:06 -04:00
MedianUnitTest.java Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably. 2012-03-05 08:28:42 -05:00
StingTextReporter.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
WalkerTest.java Rev'ing Tribble from 53 to 94 2012-05-03 07:31:47 -04:00