Mark DePristo ccac77d888 Bugfix for incorrect allele counting in IndelSummary ... -- Previous version would count all alt alleles as present in a sample, even if only 1 were present, because of the way VariantEval subsetted VCs -- Updated code for subsetting VCs by sample to be clearer about how it handles rederiving alleles -- Update a few pieces of code to get previous correct behavior -- Updated a few MD5s as now ref calls at sites in dbSNP are counted as having a comp sites, and therefore show up in known sites when Novelty strat is on (which I think is correct) -- Walkers that used old subsetting function with true are now using clearer version that does rederive alleles by default		2012-08-01 15:45:12 -04:00
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R	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
activeregion	ActiveRegionWalker's isActive function returns a results object now instead of just a double.	2012-07-27 11:01:39 -04:00
baq	Putative fix for BAQ array out of bounds	2011-09-21 11:25:08 -04:00
clipping	Fixing unit test	2012-07-06 12:08:09 -04:00
codecs	Adding an integration test for another feature that I snuck in during a previous commit: we now allow lower-case bases in the REF/ALT alleles of a VCF and upper-case them (this had been turned off because the previous version used Strings to do the uppercasing whereas we stick with byte operations now).	2012-07-29 22:19:49 -04:00
collections	…
crypt	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
fasta	A few misc. residual errors in last commit	2012-06-21 16:04:25 -04:00
fragments	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
interval	Refactored parsing of Rod/IntervalBinding. Queue S/G now uses all interval arguments passed to CommandLineGATK QFunctions including support for BED/tribble types, XL, ISR, and padding.	2012-06-27 01:15:22 -04:00
io	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
pileup	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
recalibration	Cleanup BQSR classes	2012-07-31 08:11:03 -04:00
report	…
runtime	No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.	2011-10-27 14:17:07 -04:00
sam	Bug fix for: https://getsatisfaction.com/gsa/topics/problem_with_indelrealigner_and_l_unmapped	2012-04-27 09:58:38 -04:00
text	Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller.	2012-04-17 14:22:48 -04:00
threading	Removed GATK use of distributed parallelism framework.	2011-07-20 16:26:09 -04:00
variantcontext	Bugfix for incorrect allele counting in IndelSummary	2012-08-01 15:45:12 -04:00
BaseUtilsUnitTest.java	…
BitSetUtilsUnitTest.java	NestedHashMap-based implementation of BQSRv2 along with a few minor optimizations. Not a huge runtime upgrade over the long bitset approach, but it allows us to implement further optimizations going forward. Integration test change because the original version had a bug in the quantized qual table creation.	2012-06-27 16:55:49 -04:00
GenomeLocParserUnitTest.java	During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.	2011-11-17 13:56:42 -05:00
GenomeLocSortedSetUnitTest.java	…
GenomeLocUnitTest.java	Support for list of known CNVs in VariantEval	2011-11-30 17:05:16 -05:00
HaplotypeUnitTest.java	With the new Allele representation we can finally handle complex events (because they aren't so complex anymore). One place this manifests itself is with the strict VCF validation (ValidateVariants used to skip these events but doesn't anymore) so I've added a new test with complex events to the VV integration test.	2012-07-29 19:22:02 -04:00
MWUnitTest.java	…
MathUtilsUnitTest.java	minor misc optimizations to PairHMM	2012-04-18 15:02:26 -04:00
MedianUnitTest.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
PairHMMUnitTest.java	Resolve merge conflicts	2012-04-18 16:25:03 -04:00
PathUtilsUnitTest.java	…
QualityUtilsUnitTest.java	Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests.	2012-03-21 08:45:42 -04:00
ReservoirDownsamplerUnitTest.java	Moving reduced read functionality into GATKSAMRecord	2011-10-21 13:28:05 -04:00
SimpleTimerUnitTest.java	The right fix for this test is just to delete it.	2011-11-15 14:53:27 -05:00
UtilsUnitTest.java	…