Mark DePristo 097ed4ecc4 Memory usage optimizations and safety improvements to StratNode and StratificationManager ... -- Added memory and safety optimizations to StratNode and StratificationManager. Fresh, immutable Hashmaps are allocated for final data structures, so they exactly the correct size and cannot be changed by users. -- Added ability of a stratification to specify incompatible evaluation. The two strats using this are AC and Sample with VariantSummary, as this computes per-sample averages and so combining these results in an O(n^2) memory requirement. Added integration test to cover incompatible strats and evals		2012-03-30 15:31:55 -04:00
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CNV	Updating md5 because the file changed	2011-09-23 07:33:20 -04:00
activeregionqc	CountReadsInActiveRegions now emits a detailed GATK report	2012-03-14 17:26:37 -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	fixed estimated Q reported calculation in the gatherer	2012-03-29 12:28:43 -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	UG integration tests updated. A handful of sites are lost because there are only 5 indels and one starts at the beginning of the read so it no longer passes our min threshold (now consistent with GGA), but mostly the depth changes ever so slightly once in a while between extended and normal pileups (I think the normal pileups are correct). I have looked thoroughly in IGV at ALL differences and am happy with the new results. As an aside, the AD is now calculated more accurately for indels.	2012-03-30 01:35:49 -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	Memory usage optimizations and safety improvements to StratNode and StratificationManager	2012-03-30 15:31:55 -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	Merged bug fix from Stable into Unstable	2012-03-21 12:44:43 -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
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