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gatk-3.8/public/java/test/org/broadinstitute/sting
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Mauricio Carneiro 7c3b3650bb BQSR bug triage 
* fixed bug where some keys were using the same recal datum objects
    * fixed quantization qual calculations when combining multiple reports
    * fixed rounding error with empirical quality reported when combining reports
    * fixed combine routine in the gatk reports due to the primary keys being out of order
    * added auto-recalibration option to BQSR scala script
    * reduced the size of the recalibration report by ~15%
    * updated md5's
 		2012-04-05 09:32:18 -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 BQSR bug triage 2012-04-05 09:32:18 -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 Moved the Smith-Watermaning of haplotypes to earlier in the process so that alleles sent to genotyping would have the exact genomic sequence of the active region they represent. As a side effect cleaned up some edge case problems with variants, both real and false, which show up on the edges of active regions. Removed code that was replicated between the Haplotype class and ReadUtils. Finally figured out how to ensure that the indel calls coming out of the HC were left aligned. 2012-04-04 16:04:29 -04:00
BaseTest.java Bug fix: BaseTest change shouldn't have been committed, first cleanup of SNP pool code (more to follow) 2012-04-03 18:55:52 -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 Minor: cleaner way of turning off index-on-the-fly checking in case we want to turn it back on. 2012-03-18 00:53:29 -04:00