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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Eric Banks 4fa439d89e Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now 2013-01-09 11:06:10 -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 NanoScheduler optimizations and simplification 2012-12-24 13:35:57 -05:00
pileup GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
progressmeter Make multi-threaded progress meter daemon unit test more robust 2013-01-05 12:59:18 -05:00
recalibration Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now 2013-01-09 11:06:10 -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