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	…
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	…
codecs/hapmap	Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package	2012-12-19 10:25:22 -05:00
collections	…
crypt	…
fasta	Work on GSA-508 / CachingIndexedFastaReader should internally upper case bases loading data	2012-11-01 15:34:03 -04:00
fragments	…
interval	…
io	…
nanoScheduler	Fundamentally better model for the NanoScheduler	2012-12-19 09:31:31 -05:00
pileup	…
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	…
runtime	…
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	…
threading	Disable EfficiencyMonitoringThreadFactoryUnitTest	2012-10-21 12:43:46 -04:00
BitSetUtilsUnitTest.java	…
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	…
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	…
PathUtilsUnitTest.java	…
QualityUtilsUnitTest.java	…
SimpleTimerUnitTest.java	Done GSA-539: SimpleTimer should use System.nanoTime for nanoSecond resolution	2012-09-05 15:45:23 -04:00
UtilsUnitTest.java	…