David Roazen 07b369ca7e Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package ... This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move.		2012-12-19 10:25:22 -05:00
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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	Bugfix for GSA-647 HaplotypeCaller misses good variant because the active region doesn't trigger for an exome	2012-11-01 15:34:04 -04:00
baq	Added checking in the GATK for mis-encoded quality scores.	2012-12-03 11:18:41 -05:00
clipping	Updated and more thorough version of the BadCigar read filter	2012-08-17 17:05:27 -04:00
codecs/hapmap	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
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	Work on GSA-508 / CachingIndexedFastaReader should internally upper case bases loading data	2012-11-01 15:34:03 -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
nanoScheduler	Fundamentally better model for the NanoScheduler	2012-12-19 09:31:31 -05:00
pileup	GATKSAMRecord refactor	2011-11-03 15:43:26 -04:00
recalibration	The user can now set the maximum allowable cycle on the command-line with --maximum_cycle_value. This value is (now) enforced in the Cycle covariate and a User Error is thrown if the maximum value is passed (with a helpful error message). Added unit tests to cover this new functionality.	2012-11-20 22:41:57 -05:00
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	Quick fix: base qual array in the GATKSAMRecord stores the actual phred values (-33) and not the original bytes (duh).	2012-12-03 12:18:20 -05:00
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	Disable EfficiencyMonitoringThreadFactoryUnitTest	2012-10-21 12:43:46 -04:00
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	Fixing parsing of genomelocs that contain colons in the contig names (which is allowed by the spec) as reported on the forum. Added unit test for this case.	2012-11-27 11:00:33 -05:00
GenomeLocSortedSetUnitTest.java	Fix for GSA-649: GenomeLocSortedSet.overlaps is crazy slow. Also improved GenomeLocSortedSet.sizeBeforeLoc.	2012-11-27 01:07:00 -05:00
GenomeLocUnitTest.java	Bugfix to compareTo and equals in GenomeLoc	2012-08-30 19:41:49 -04:00
HaplotypeUnitTest.java	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
LegacyReservoirDownsamplerUnitTest.java	Use the new downsampling implementation by default	2012-12-10 09:44:50 -05:00
MWUnitTest.java	A couple of minor things.	2012-09-20 12:48:13 -04:00
MathUtilsUnitTest.java	Increasing the precision of MathUtils.approximateLog10SumLog10 from 1E-3 to 1E-4. Genotyper integration tests change as a result. Expanding the unit tests of MathUtils.log10sumLog10.	2012-10-15 13:24:32 -04:00
MedianUnitTest.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -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
SimpleTimerUnitTest.java	Done GSA-539: SimpleTimer should use System.nanoTime for nanoSecond resolution	2012-09-05 15:45:23 -04:00
UtilsUnitTest.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00