Eric Banks 75d5b88a3d Enabling the Recal Report unit test (which looks like it was never ever enabled)		2012-12-26 15:35:50 -05:00
..
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	NanoScheduler optimizations and simplification	2012-12-24 13:35:57 -05:00
pileup	…
recalibration	Enabling the Recal Report unit test (which looks like it was never ever enabled)	2012-12-26 15:35:50 -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	…