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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Valentin Ruano-Rubio 08f92bb6f9 Added AnalyzeCovariates tool to generate BQSR assessment quality plots. 
Implemtation details:

* Added tool class *.AnalyzeCovariates
* Added convenient addAll method to Utils to be able to add elements of an array.
* Added parameter comparison methods to RecalibrationArgumentCollection class in order to verify that multiple imput recalibration report are compatible and comparable.
* Modified the BQSR.R script to handle up to 3 different recalibration tables (-BQSR, -before and -after) and removed some irrelevant arguments (or argument values) from the output.
* Added an integration test class.
 		2013-06-19 14:38:02 -04:00
..
annotator Fixes to several of the annotations for reduced reads (and other issues). 2013-06-16 01:18:20 -04:00
beagle Simpler FILTER and info field encoding for BeagleOutputToVCF 2013-06-14 15:56:13 -04:00
bqsr Added AnalyzeCovariates tool to generate BQSR assessment quality plots. 2013-06-19 14:38:02 -04:00
compression/reducereads Fix error in merging code in HC 2013-05-31 16:29:29 -04:00
diagnostics Update MD5s and the Diagnose Target scala script 2013-05-13 12:06:17 -04:00
diffengine Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec). 2013-04-05 00:52:32 -04:00
genotyper Swapping in logless Pair HMM for default usage with UG: 2013-06-18 10:06:27 -04:00
haplotypecaller Adding new pruning parameter to ReadThreadingAssembler 2013-06-17 16:46:40 -04:00
indels Secondary alignments were not handled correctly in IndelRealigner 2013-05-06 19:09:10 -04:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods 2013-03-29 14:52:10 -04:00
varianteval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variantrecalibration Update MD5s for VQSR header change 2013-04-16 11:45:45 -04:00
variantutils CombineVariants no longer adds PASS to unfiltered records 2013-05-20 16:53:51 -04:00