Mark DePristo 567dba0f76 Cleanup of VCF header lines and constants, BCF2 bugfixes ... -- Created public static UnifiedGenotyper.getHeaderInfo that loads UG standard header lines, and use this in tools like PoolCaller -- Created VCFStandardHeaderLines class that keeps standard header lines in the GATK in a single place. Provides convenient methods to add these to a header, as well as functionality to repair standard lines in incoming VCF headers -- VCF parsers now automatically repair standard VCF header lines when reading the header -- Updating integration tests to reflect header changes -- Created private and public testdata directories (public/testdata and private/testdata). Updated tests to use test -- SelectHeaders now always updates the header to include the contig lines -- SelectVariants add UG header lines when in regenotype mode -- Renamed PHRED_GENOTYPE_LIKELIHOODS_KEY to GENOTYPE_PL_KEY -- Bugfix in BCF2 to handle lists of null elements (can happen in genotype field values from VCFs) -- Throw error when VCF has unbounded non-flag values that don't have = value bindings -- By default we no longer allow writing of BCF2 files without contig lines in the header		2012-06-21 15:16:31 -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	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
baq	Putative fix for BAQ array out of bounds	2011-09-21 11:25:08 -04:00
clipping	Refactor on how RR treats soft clips	2012-06-21 14:02:03 -04:00
codecs	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
collections	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
crypt	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
fasta	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
fragments	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
interval	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -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	The next round of BQSR optimizations: no more Long[] array creation	2012-06-14 00:05:42 -04:00
report	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
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	Cleanup of VCF header lines and constants, BCF2 bugfixes	2012-06-21 15:16:31 -04:00
BaseUtilsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
BitSetUtilsUnitTest.java	Oops, forgot to push the unit tests	2012-06-12 11:38:30 -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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
GenomeLocUnitTest.java	Support for list of known CNVs in VariantEval	2011-11-30 17:05:16 -05:00
HaplotypeUnitTest.java	Adding genotype given alleles mode to the HaplotypeCaller.	2012-05-30 15:07:01 -04:00
MWUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
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	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00