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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Mark DePristo 206eab80e3 Expanded unit tests for AlignmentUtils 
-- Added JIRA entries for the remaining capabilities to be fixed up and unit tested
 		2013-02-01 13:51:31 -05:00
..
R R issue in Queue fixed. 2013-01-28 14:42:20 -05:00
activeregion Use base List and Map types in the HaplotypeCaller when possible. 2013-01-30 17:09:27 -05:00
analysis Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
baq Fixing BQSR/BAQ bug: 2013-01-31 11:03:17 -05:00
classloader Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
clipping Use base List and Map types in the HaplotypeCaller when possible. 2013-01-30 17:09:27 -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 BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -05:00
exceptions Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
fasta Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -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 Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -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 Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs 2013-01-30 16:42:23 -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 Move BaseUtils back to the GATK by request, along with associated utility methods 2013-01-30 13:09:44 -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 Expanded unit tests for AlignmentUtils 2013-02-01 13:51:31 -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 additional VariantContext utility methods back to the GATK 2013-01-30 13:58:17 -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
BaseUtils.java More aggressive checking of AWS key quality upon startup in the GATK 2013-01-31 09:08:38 -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 Refactoring the SimpleGenomeLoc into the now public utility UnvalidatingGenomeLoc and the RR-specific FinishedGenomeLoc. 2013-01-30 10:45:29 -05:00
GenomeLocParser.java Refactoring and unit testing GenomeLocParser 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 Use base List and Map types in the HaplotypeCaller when possible. 2013-01-30 17:09:27 -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
MRUCachingSAMSequenceDictionary.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -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
UnvalidatingGenomeLoc.java Refactoring the SimpleGenomeLoc into the now public utility UnvalidatingGenomeLoc and the RR-specific FinishedGenomeLoc. 2013-01-30 10:45:29 -05:00
Utils.java Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs 2013-01-30 16:42:23 -05:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00