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gatk-3.8/public/java/test/org/broadinstitute/sting/utils
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Mark DePristo a1093ad230 Optimization for ActiveRegion.removeAll 
-- Previous version took a Collection<GATKSAMRecord> to remove, and called ArrayList.removeAll() on this collection to remove reads from the ActiveRegion.  This can be very slow when there are lots of reads, as ArrayList.removeAll ultimately calls indexOf() that searches through the list calling equals() on each element.   New version takes a set, and uses an iterator on the list to remove() from the iterator any read that is in the set.  Given that we were already iterating over the list of reads to update the read span, this algorithm is actually simpler and faster than the previous one.
-- Update HaplotypeCaller filterReadsInRegion to use a Set not a List.
-- Expanded the unit tests a bit for ActiveRegion.removeAll
 		2013-05-21 16:18:57 -04:00
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R Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
activeregion Optimization for ActiveRegion.removeAll 2013-05-21 16:18:57 -04:00
baq Fixing BQSR/BAQ bug: 2013-01-31 11:03:17 -05:00
classloader Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
clipping Replace DeBruijnAssembler with ReadThreadingAssembler 2013-05-08 21:41:42 -04:00
codecs/hapmap Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
collections Fixing license on Yossi's file 2013-02-05 11:14:43 -05:00
crypt Update expected test output for Java 7 2013-05-01 16:18:01 -04:00
fasta Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
file Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -04:00
fragments Bugfix for FragmentUtils.mergeOverlappingPairedFragments 2013-04-25 11:11:15 -04:00
haplotype Major improvements to HC that trims down active regions before genotyping 2013-04-08 12:47:49 -04:00
interval Intervals: fix bug where we could fail to find the intersection of unsorted/missorted interval lists 2013-04-02 14:01:52 -04:00
io Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
locusiterator LIBS unit test debugging should be false 2013-04-08 12:47:47 -04:00
nanoScheduler Further tweaking of test timeouts 2013-03-15 14:49:21 -04:00
pileup Last manual license update (hopefully) 2013-01-18 16:13:07 -05:00
progressmeter Subshard timeouts in the GATK 2013-05-15 07:00:39 -04:00
recalibration Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
report Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
runtime Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
sam e# This is a combination of 2 commits. 2013-05-03 11:19:14 -04:00
smithwaterman New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. 2013-05-13 09:36:39 -04:00
text Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
threading Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
variant AssessNA12878 bugfixes 2013-03-18 15:48:08 -04:00
AutoFormattingTimeUnitTest.java AutoFormattingTimeUnitTest should be in utils 2013-01-30 09:47:47 -05:00
BaseUtilsUnitTest.java More aggressive checking of AWS key quality upon startup in the GATK 2013-01-31 09:08:38 -05:00
BitSetUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocParserBenchmark.java Optimize GenomeLocParser.createGenomeLoc 2013-01-30 09:47:47 -05:00
GenomeLocParserUnitTest.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
GenomeLocSortedSetUnitTest.java Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
GenomeLocUnitTest.java Added distance across contigs calculation to GenomeLocs 2013-02-07 16:31:41 -05:00
MRUCachingSAMSequencingDictionaryUnitTest.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
MWUnitTest.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
MathUtilsUnitTest.java Refactored binomial probability code in MathUtils. 2013-04-16 18:19:07 -04:00
MedianUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
NGSPlatformUnitTest.java Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests 2013-02-09 11:16:21 -05:00
PathUtilsUnitTest.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtilsUnitTest.java Final edge case bug fixes to QualityUtil routines 2013-02-16 07:31:38 -08:00
SequenceDictionaryUtilsUnitTest.java Sequence dictionary validation: detect problematic contig indexing differences 2013-02-25 11:14:22 -05:00
SimpleTimerUnitTest.java Fix tests that were consistently or intermittently failing when run in parallel on the farm 2013-03-06 13:56:54 -05:00
UtilsUnitTest.java New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. 2013-05-13 09:36:39 -04:00