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gatk-3.8/public/java/test/org/broadinstitute/sting/gatk/walkers
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Mauricio Carneiro f0c81b59b0 Implementation of the new BQSR plotting infrastructure 
* removed low quality bases from the recalibration report.
   * refactored the Datum (Recal and Accuracy) class structure
   * created a new plotting csv table for optimized performance with the R script
   * added a datum object that carries the accuracy information (AccuracyDatum) for plotting
   * added mean reported quality score to all covariates
   * added QualityScore as a covariate for plotting purposes
   * added unit test to the key manager to operate with one required covariate and multiple optional covariates
   * integrated the plotting into BQSR (automatically generates the pdf with the recalibration tearsheet)
 		2012-04-17 19:23:55 -04:00
..
CNV Updating md5 because the file changed 2011-09-23 07:33:20 -04:00
activeregionqc There are now three triggering options in the HaplotypeCaller. The default (mismatches, insertions, deletions, high quality soft clips), an external alleles file (from the UG for example), or extended triggers which include low quality soft clips, bad mates and unmapped mates. Added better algorithm for band pass filtering an ActivityProfile and breaking them apart when they get too big. Greatly increased the specificity of the caller by battening down the hatches on things like base quality and mapping quality thresholds for both the assembler and the likelihood function. 2012-04-10 14:48:23 -04:00
annotator Updating integration tests now that standard annotations support multiple alleles 2012-02-27 11:32:26 -05:00
beagle Minor tweaks to T2D-related qscripts. Replacing old md5s from the BeagleIntegrationTest. All differences boiled down either to the accounting of genotypes changed (./. --> 0/0 is no longer a "changed" genotype, and original genotypes that were ./. are represented as OG=. rather than OG=./. .) 2012-01-23 08:25:34 -05:00
bqsr Implementation of the new BQSR plotting infrastructure 2012-04-17 19:23:55 -04:00
coverage DoC now properly handles reference N bases + misc. additional cleanups 2012-02-25 11:32:50 -05:00
diagnostics GATKReport v1.0 2012-03-12 23:09:19 -04:00
diffengine Fixing MD5's (new GATKReport header was missing from old md5's) 2012-03-19 15:28:45 -04:00
fasta Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
filters Again, fixing the add call when we really mean replace 2011-11-21 19:15:56 -05:00
genotyper Added unit test to ensure that we genotype correctly cases with really large GLs 2012-04-12 15:43:14 -04:00
indels Removing dependence on extended events from the RealignerTargetCreator. Did some minor refactoring while I was in there. 2012-03-30 10:33:30 -04:00
phasing Added respectPhaseInInput flag to RBP and integration tests 2012-03-22 17:40:21 -04:00
qc First version of VariantContextBuilder 2011-11-18 11:06:15 -05:00
recalibration Patching special case in the adaptor clipping 2012-01-11 17:47:44 -05:00
validation Added integration test for ValidationSiteSelector, correct MD5's 2012-03-26 16:39:55 -04:00
varianteval Update VE IT to reflect new fields and bugfixes 2012-04-13 17:00:37 -04:00
variantrecalibration Changing the VQSR command line syntax back to the parsed tags approach. This cleans up the code and makes sure we won't be parsing the same rod file multiple times. I've tried to update the appropriate qscripts. 2011-09-12 12:17:43 -04:00
variantutils Final update for VE. VCFStreaming wasn't yet updated 2012-03-30 21:52:01 -04:00
BAQIntegrationTest.java merge master 2011-10-25 16:08:39 -04:00
ClipReadsWalkersIntegrationTest.java Updating MD5s for updated BAM with read groups 2011-10-06 12:15:48 -07:00
FlagStatIntegrationTest.java Adding integration test for Flag Stat 2012-04-10 22:40:38 -04:00
PileupWalkerIntegrationTest.java Had some free time, so I unplugged extended events from the walkers. Now they exist only in LocusIteratorByState, but ReadProperties.generateExtendedEvents() always returns false so that block is never actually executed anymore. I don't want to touch LIBS because I think David is in there right now. 2012-04-02 14:27:36 -04:00
PrintReadsIntegrationTest.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
PrintReadsUnitTest.java Better location for the downsampling of reads in PrintReads 2012-01-14 14:06:09 -05:00