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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Mark DePristo 8562bfaae1 Optimize GenomeLocParser.createGenomeLoc 
-- The new version is roughly 2x faster than the previous version.  The key here was to cleanup the workflow for validateGenomeLoc and remove the now unnecessary synchronization blocks from the CachingSequencingDictionary, since these are now thread local variables
-- #resolves https://jira.broadinstitute.org/browse/GSA-724
 		2013-01-30 09:47:47 -05:00
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R R issue in Queue fixed. 2013-01-28 14:42:20 -05:00
activeregion Cleanup, document, and unit test ActiveRegion 2013-01-30 09:47:12 -05:00
analysis Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
baq Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
classloader Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
clipping getAdaptorBoundary returns an int, not an Integer, as this was taking 30% of the allocation effort for LIBS 2013-01-14 16:30:15 -05:00
codecs Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
collections Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
crypt Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
duplicates Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
exceptions Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fasta Added tests for changing IUPAC bases to Ns, for failing on bad ref bases, and for the HaplotypeCaller not failing when running over a region with an IUPAC base. 2013-01-16 14:55:33 -05:00
file Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fragments Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
genotyper Updating licenses of latest moved files 2013-01-26 13:46:52 -05:00
help Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
instrumentation Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
interval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
io Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
locusiterator LIBS optimization for adapter clipping 2013-01-25 16:05:17 -05:00
nanoScheduler Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
pairhmm Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
pileup The CachingIndexedFastaSequenceFile now automatically converts IUPAC bases to Ns and errors out on other non-standard bases. 2013-01-16 10:22:43 -05:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
progressmeter Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
recalibration The Bayesian calculation of Qemp in the BQSR is now hierarchical. This fixes issues in which the covariate bins were very sparse and the prior estimate being used was the original quality score. This resulted in large correction factors for each covariate which breaks the equation. There is also now a new option, qlobalQScorePrior, which can be used to ignore the given (very high) quality scores and instead use this value as the prior. 2013-01-28 15:56:33 -05:00
runtime Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
sam Cleanup, document, and unit test ActiveRegion 2013-01-30 09:47:12 -05:00
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 Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
wiggle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
AutoFormattingTime.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
BitSetUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ContigComparator.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLoc.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocComparator.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
GenomeLocParser.java Optimize GenomeLocParser.createGenomeLoc 2013-01-30 09:47:47 -05:00
GenomeLocSortedSet.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Haplotype.java I finally gave up on trying to get the Haplotype/Allele merging to work in the HaplotypeCaller. 2013-01-18 01:21:08 -05:00
HasGenomeLocation.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
HeapSizeMonitor.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
IndelUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
LRUCache.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MannWhitneyU.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
MathUtils.java Making band pass filter size, sigma, active region max size and extension all accessible from the command line 2013-01-24 13:47:59 -05:00
Median.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MendelianViolation.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
MultiThreadedErrorTracker.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
NGSPlatform.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
PathUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
SWPairwiseAlignment.java Updating licenses manually 2013-01-29 17:27:53 -05:00
SampleUtils.java Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
SequenceDictionaryUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
SimpleTimer.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
Utils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00