Mark DePristo aff508e091 ReadGroupProperties walker and associated infrastructure ... -- ReadGroupProperties: Emits a GATKReport containing read group, sample, library, platform, center, median insert size and median read length for each read group in every BAM file. -- Median tool that collects up to a given maximum number of elements and returns the median of the elements. -- Unit and integration tests for everything. -- Making name of TestProvider protected so subclasses and override name more easily		2012-03-01 15:01:11 -05:00
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CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -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
coverage	DoC now properly handles reference N bases + misc. additional cleanups	2012-02-25 11:32:50 -05:00
diagnostics	ReadGroupProperties walker and associated infrastructure	2012-03-01 15:01:11 -05:00
diffengine	Right aligning GATKReport numeric columns and updated MD5s in tests.	2011-12-05 23:22:15 -05:00
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	Updating integration tests now that standard annotations support multiple alleles	2012-02-27 11:32:26 -05:00
indels	Rename *PerformanceTest test classes to *LargeScaleTest	2011-12-22 10:38:49 -05:00
phasing	Merge with master	2011-11-19 09:56:06 -05:00
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	Removing all instances of -BTI (in tests and in GATKdocs) and replacing them with the appropriate alternative.	2011-10-27 23:55:11 -04:00
varianteval	Bug fix for VariantSummary	2012-01-05 21:51:06 -05:00
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	Another test where we no longer print out 'NaN' for the AF.	2012-02-27 15:19:08 -05:00
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
PileupWalkerIntegrationTest.java	Updated integration tests for the new adaptor clipping fix.	2011-12-30 18:47:14 -05:00
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