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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Mark DePristo 04cc75aaec Minor cleanup and expansion of the RecalDatum unit tests 2012-12-24 13:35:58 -05:00
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R Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. 2012-04-17 14:22:48 -04:00
activeregion Add ActiveRegionReadState handling 2012-11-28 13:59:57 -05:00
analysis Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
baq Minor cleanup of BAQ calculation (final variables, etc) 2012-12-17 16:47:27 -05:00
classloader Scala classes were only returning direct subclasses (confirmed when inspected in debugger) so changed PluginManager to allow specifying the explicit subclass. 2012-11-14 10:33:20 -05:00
clipping fixing typo 2012-09-05 10:41:03 -04:00
codecs Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
collections NanoScheduler optimization: don't use a PriorityBlockingQueue for the MapResultsQueue 2012-12-24 13:35:56 -05:00
crypt Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
duplicates Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
exceptions Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
fasta Work on GSA-508 / CachingIndexedFastaReader should internally upper case bases loading data 2012-11-01 15:34:03 -04:00
file Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
fragments Fixing bug from when FragmentUtils merging function moved over to the soft clipped start instead of the unclipped start 2012-08-30 10:10:43 -04:00
genotyper Merge branch 'master' of github.com:broadinstitute/gsa-unstable 2012-12-19 11:31:40 -05:00
help introduce a level of indirection for the forum URLs - this new function will allow me a place to morph the URL into something that is supported by Confluence 2012-12-03 22:33:02 -05:00
instrumentation Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
interval Quick pass of FindBugs 'inefficient use of keySet iterator instead of entrySet iterator' fixes for core tools. 2012-08-08 14:29:41 -04:00
io One less Queue command line requirement: -tempDir now defaults to .queue/tmp. 2012-08-27 12:04:50 -04:00
nanoScheduler NanoScheduler optimizations and simplification 2012-12-24 13:35:57 -05:00
pairhmm Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore. 2012-10-20 16:38:18 -04:00
pileup Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
progressmeter ProgressMeter optimization: don't do genome loc formatting, but instead create an object that only formats when printing is actually needed 2012-12-17 16:47:27 -05:00
recalibration Minor cleanup and expansion of the RecalDatum unit tests 2012-12-24 13:35:58 -05:00
runtime No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path. 2011-10-27 14:17:07 -04:00
sam Handle case where the ReadGroup is null in GATKSAMRecord 2012-12-24 13:35:57 -05:00
text Refactoring/fixing up UG HMM code: a) Make code use PairHMM class instead of having duplicated code. That way UG and HaplotypeCaller now use same core code. Changes to be able to do this: 1. Compute context-dependent GOP as a function of read, not of haplotype, b) Extracted code to initialize HMM arrays into separate method, c) Move PairHMM class and unit test to public, d) Reenable banded code in PairHMM, inverted sense of flag (true=enable feature) but leave off in HaplotypeCaller. 2012-04-17 14:22:48 -04:00
threading BQSR: use more granular locking for concurrency control 2012-10-24 15:22:50 -04:00
variant Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
wiggle Optimize imports run on the whole project, public and private. I just got too tired of all of the unused imports floating around. Confirmed that the system builds after the changes. 2011-07-17 20:29:58 -04:00
AminoAcid.java Removing the Genomic Annotator and its supporting classes 2011-07-25 15:10:25 -04:00
AminoAcidTable.java Removing the Genomic Annotator and its supporting classes 2011-07-25 15:10:25 -04:00
AutoFormattingTime.java Add GATK-wide command line argument to control the maximum runtime allowed for the GATK 2012-10-26 13:18:34 -04:00
BitSetUtils.java Refactoring of BQSRv2 to use longs (and standard bit fiddling techniques) instead of Java BitSets for performance improvements. 2012-06-12 09:19:36 -04:00
ContigComparator.java Documented following the new gatkdoc framework 2011-07-25 00:25:08 -04:00
GenomeLoc.java Major performance improvement to the GATK engine 2012-12-05 14:49:22 -05:00
GenomeLocComparator.java Optimized interval iteration 2011-09-28 16:07:34 -04:00
GenomeLocParser.java Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
GenomeLocSortedSet.java Minor efficiency: use >= instead of > in test 2012-11-27 01:11:23 -05:00
Haplotype.java Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
HasGenomeLocation.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
HeapSizeMonitor.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
IndelUtils.java Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
LRUCache.java Optimizations for applying BQSR table with PrintReads 2012-12-17 16:47:27 -05:00
LegacyReservoirDownsampler.java Use the new downsampling implementation by default 2012-12-10 09:44:50 -05:00
MannWhitneyU.java A couple of minor things. 2012-09-20 12:48:13 -04:00
MathUtils.java Merge AFCalcResultTracker into StateTracker, cleanup 2012-10-21 12:42:31 -04:00
Median.java ReadGroupProperties walker and associated infrastructure 2012-03-01 15:01:11 -05:00
MendelianViolation.java Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
MultiThreadedErrorTracker.java Proper error handling in NanoScheduler 2012-09-19 17:03:13 -04:00
NGSPlatform.java The GATK engine now ensures that incoming GATKSAMRecords have GATKSAMReadGroupRecord objects in their header 2012-12-24 13:35:09 -05:00
PathUtils.java GATKPerformanceOverTime script update 2012-01-02 09:58:46 -05:00
QualityUtils.java Added checking in the GATK for mis-encoded quality scores. 2012-12-03 11:18:41 -05:00
SWPairwiseAlignment.java FindBugs 'Efficiency' fixes 2012-08-16 15:40:52 -04:00
SampleUtils.java Move VCF/BCF2/VariantContext to new standalone org.broadinstitute.variant package 2012-12-19 10:25:22 -05:00
SequenceDictionaryUtils.java Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes. 2012-08-08 14:34:16 -04:00
SimpleTimer.java Fixes GSA-515 Nanoscheduler GSA-560 / Fix display of NanoScheduler and MonitoringEfficiency 2012-09-11 07:38:34 -04:00
Utils.java Merging latest CMI updates with UNSTABLE 2012-11-27 09:08:00 -05:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00