Mark DePristo 4e42988c66 GSA-485: Remove repairVCFHeader from GATK codebase ... -- Removed half-a*ssed attempt to automatically repair VCF files with bad headers, which allowed users to provide a replacement header overwriting the file's actually header on the fly. Not a good idea, really. Eric has promised to create a utility that walks through a VCF file and creates a meaningful header field based on the file's contents (if this ever becomes a priority)		2012-08-16 13:03:13 -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	GSA-485: Remove repairVCFHeader from GATK codebase	2012-08-16 13:03:13 -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	Fix missing argument in unittest	2012-08-12 13:58:14 -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	Temporarily disable StateMonitoringThreadTests while I get them reliably working across platforms	2012-08-15 21:13:16 -04:00
variantcontext	BCF2 optimizations; parallel CombineVariants	2012-08-15 21:13:16 -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	Bug fixes related to the changes in allele padding. If a haplotype started with an insertion it led to array index out of bounds. Haplotype allele insert function is now very simple because all alleles are treated the same way. HaplotypeUnitTest now uses a variant context instead of creating Allele objects directly.	2012-08-05 12:29:10 -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	…