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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo 810e2da1d4 Cleanup and unit tests for EventType and ReadRecalibrationInfo in BQSR 
-- Added unit tests for EventType and ReadRecalibrationInfo
-- Simplified interface of EventType.  Previously this enum carried an index with it, but this is redundant with the enum.ordinal function.  Now just using that function instead.
 		2013-01-04 11:39:25 -05:00
..
R AggregateMetrics: 2012-04-17 11:45:32 -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 NanoScheduler optimizations and simplification 2012-12-24 13:35:57 -05:00
pileup GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
progressmeter Unit tests for ProgressMeterDaemon 2013-01-04 11:39:24 -05:00
recalibration Cleanup and unit tests for EventType and ReadRecalibrationInfo in BQSR 2013-01-04 11:39:25 -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 AggregateMetrics: 2012-04-17 11:45:32 -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