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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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depristo 6204e6ccc9 Merge pull request #76 from broadinstitute/md_kb_bugfix_GSA-795 
Bug fixes and optimizations for NA12878 KB
 		2013-03-01 10:52:16 -08:00
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R R issue in Queue fixed. 2013-01-28 14:42:20 -05:00
activeregion Replace Smith-Waterman alignment with the bubble traversal. 2013-02-22 15:42:16 -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 Added verbose error message to the PluginManager 2013-02-19 16:00:35 -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 Replace uses of NestedHashMap with NestedIntegerArray. 2013-02-27 14:03:39 -05:00
crypt Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
duplicates Cleanup and unit tests for QualityUtils 2013-02-16 07:31:37 -08:00
exceptions Added better error message for BAMs with bad read groups. 2013-02-27 16:02:56 -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 Fixed non-determinism in HaplotypeCaller and some UG calls - 2013-02-12 15:43:29 -05:00
help Added several more info types / annotations to GATKDocs 2013-02-21 03:12:40 -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 Vast improvements to AssessNA12878 code and functionality 2013-02-21 20:43:12 -05:00
nanoScheduler Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
pairhmm Refactored PairHMM.initialize to first take haplotype max length and then the read max length so that it is consistent with other PairHMM methods. 2013-02-25 15:04:23 -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 Resolves Genome Sequence Analysis GSA-750 Don't print an endless series of starting messages from the ProgressMeter 2013-02-04 15:47:30 -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 The maximum kmer length is derived from the reads. 2013-02-25 14:40:25 -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 Bugfixes for AssessNA12878 2013-02-28 10:35:06 -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 - Added more comprehensive tests for consensus creation to RR. Still need to add tests for I/D ops. 2013-02-01 15:37:19 -05:00
BitSetUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
ContigComparator.java Generalize and fixup ContigComparator 2013-02-09 09:52:13 -05:00
GenomeLoc.java Added distance across contigs calculation to GenomeLocs 2013-02-07 16:31:41 -05:00
GenomeLocParser.java Refactoring and unit testing GenomeLocParser 2013-01-30 09:47:47 -05:00
GenomeLocSortedSet.java Fixed the add functionality of GenomeLocSortedSet. 2013-02-28 23:31:00 -05:00
Haplotype.java Replace Smith-Waterman alignment with the bubble traversal. 2013-02-22 15:42:16 -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 Final edge case bug fixes to QualityUtil routines 2013-02-16 07:31:38 -08:00
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 Expand NGSPlatform to meet SAM 1.4 spec, with full unit tests 2013-02-09 11:16:21 -05:00
PathUtils.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
QualityUtils.java Relax bounds checking in QualityUtils.boundQual 2013-02-22 08:46:59 -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 Sequence dictionary validation: detect problematic contig indexing differences 2013-02-25 11:14:22 -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 Final version of PairHMMs with correct edge conditions 2013-02-09 19:19:22 -05:00
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00