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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Eric Banks 2f5ef6db44 New faster Smith-Waterman implementation that is edge greedy and assumes that ref and haplotype have same global start/end points. 
* This version inherits from the original SW implementation so it can use the same matrix creation method.
   * A bunch of refactoring was done to the original version to clean it up a bit and to have it do the
     right thing for indels at the edges of the alignments.
     * Enum added for the overhang strategy to use; added implementation for the INDEL version of this strategy.
   * Lots of systematic testing added for this implementation.
   * NOT HOOKED UP TO HAPLOTYPE CALLER YET. Committing so that people can play around with this for now.
 		2013-05-13 09:36:39 -04:00
..
R R issue in Queue fixed. 2013-01-28 14:42:20 -05:00
activeregion Major improvements to HC that trims down active regions before genotyping 2013-04-08 12:47:49 -04:00
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 Enable convenient display of diff engine output in Bamboo, plus misc. minor test-related improvements 2013-05-10 19:00:33 -04:00
clipping Setting the reduce reads count tag was all wrong in a previous commit; fixing. 2013-04-30 13:45:42 -04:00
codecs Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
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 Detect stuck lock-acquisition calls, and disable file locking for tests 2013-04-24 22:49:02 -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
genotyper Extended the allele-biased down-sampling functionality to handle reduced reads. 2013-04-26 11:23:17 -04:00
haplotype Fix residual merge conflicts 2013-04-08 12:47:50 -04:00
help Created ListAnnotations utility (extends CommandLineProgram) 2013-03-20 06:15:27 -04:00
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 Performance optimizations and caliper benchmarking code for consolidateCigar 2013-04-24 11:36:43 -04:00
nanoScheduler Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
pairhmm Fix another caching issue with the PairHMM 2013-04-12 14:52:45 -04:00
pileup Setting the reduce reads count tag was all wrong in a previous commit; fixing. 2013-04-30 13:45:42 -04:00
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 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 System to merge multiple nearby alleles into block substitutions 2013-04-08 12:47:47 -04:00
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
DeprecatedToolChecks.java Created new DeprecatedToolChecks class 2013-03-20 06:46:02 -04:00
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
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 Setting the reduce reads count tag was all wrong in a previous commit; fixing. 2013-04-30 13:45:42 -04:00
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 Trivial BQSR bug fixes and improvement 2013-04-11 17:08:35 -04:00
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
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 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
package-info.java Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00