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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Mark DePristo 972be8b4a4 Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers 
-- ReadMetaDataTracker is dead!  Long live the RefMetaDataTracker.  Read walkers will soon just take RefMetaDataTracker objects.  In this commit they take a class that trivially extends them
-- Rewrote ReadBasedReferenceOrderedView to produce RefMetaDataTrackers not the old class.
    -- This new implementation produces thread-safe objects (i.e., holds no points to shared state).  Suitable for use (to be tested) with nano scheduling
    -- Simplified interfaces to use the simplest data structures (PeekableIterator) not the LocusAwareSeekableIterator, since I both hate those classes and this is on the long term trajectory to remove those from the GATK entirely.
-- Massively expanded DataProvider unit tests for ReadBasedReferenceOrderedView
-- Note that the old implementation of offset -> ROD in ReadRefMetaDataTracker was broken for any read not completely matching the reference.  Rather than provide broken code the ReadMetaDataTracker only provides a "bag of RODs" interface.  If you want to work with the relationship between the read and the RODs in your tool you need to manage the CIGAR element itself.
    -- This commit breaks the new read walker BQSR, but Ryan knows this is coming
-- Subsequent commit will be retiring / fixing ValidateRODForReads
 		2012-08-30 10:15:10 -04:00
..
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 Merged bug fix from Stable into Unstable 2012-08-22 14:40:34 -04:00
analysis Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
baq Should've run 'ant clean' instead of just 'ant'. In any event, these are 2 cases where we are setting a class's internal static variable directly. Very dangerous. 2012-08-16 15:07:32 -04:00
classloader Usability cleanup for BQSR 2012-08-25 14:53:00 -04:00
clipping ReadClipper won't modify the original read 2012-08-29 11:33:19 -04:00
codecs Print "Parsing data stream with BCF version BCFx.y" in BCF2 codec as .debug not .info 2012-08-19 10:32:55 -04:00
collections Refactored/renamed the nested integer array; cleaned up code a bit. 2012-07-03 00:12:33 -04:00
crypt Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
duplicates GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
exceptions Fixed GSA-434: GATK should generate error when gzipped FASTA is passed in. 2012-08-17 11:49:02 -04:00
fasta Ensure thread-safety of CachingIndexedFastaSequenceFile 2012-08-27 12:11:54 -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
help GSA-483: Bug in GATKdocs for Enums 2012-08-16 16:24:17 -04:00
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 Optimizations for parallel read walkers 2012-08-25 17:21:12 -04:00
pileup Killing off some FindBugs 'Realiability' issues 2012-08-16 14:00:48 -04:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
recalibration Changing the commenting style in the BQSR 2012-08-29 11:27:45 -04:00
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 This along with Mauricio's previous commit (thanks!) fixes GSA-522. There are no longer any modifications to reads in the map calls of ActiveRegion walkers. Added the bam which identified this error as a new integration test. 2012-08-30 09:07:36 -04:00
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 Limited version of parallel read walkers 2012-08-25 17:21:12 -04:00
variantcontext Fix for badIndelLength() throwing NPE at non-indel sites. Added integration test. 2012-08-25 12:38:23 -07:00
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 Clean, documented implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates 2012-08-15 21:13:15 -04:00
BaseUtils.java Just noticed that the efficient conversion to uppercase method is redundant since it's already implemented efficiently in Picard; let's just have a single implementation. 2012-08-22 11:26:08 -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 Part I of GSA-462: Consistent RODBinding access across Ref and Read trackers 2012-08-30 10:15:10 -04:00
GenomeLocComparator.java Optimized interval iteration 2011-09-28 16:07:34 -04:00
GenomeLocParser.java Removing parallelism bottleneck in the GATK 2012-08-15 21:13:15 -04:00
GenomeLocSortedSet.java Active region walkers can now see the reads in a buffer around thier active reigons. This buffer size is specified as a walker annotation. Intervals are internally extended by this buffer size so that the extra reads make their way through the traversal engine but the walker author only needs to see the original interval. Also, several corner case bug fixes in active region traversal. 2012-01-19 22:05:08 -05:00
Haplotype.java Another round of FindBugs fixes. Object returns its internal reference to an externally mutable array. Very dangerous. 2012-08-21 09:35:55 -04:00
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 Improvements to indel analysis capabilities of VariantEval 2012-04-06 16:07:46 -04:00
MannWhitneyU.java Another round of FindBugs fixes. Comparator doesn't implement Serializable. 2012-08-21 09:20:55 -04:00
MathUtils.java Fix merge conflicts 2012-08-16 20:45:52 -04:00
Median.java ReadGroupProperties walker and associated infrastructure 2012-03-01 15:01:11 -05:00
MendelianViolation.java Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
NGSPlatform.java Stabilized NGSPlatform code: don't assume all reads have read groups (e.g. artificial SAM records) 2012-06-06 15:17:30 -04:00
PairHMM.java A few quick, minor findbugs fixes. 2012-08-09 16:30:58 -04:00
PathUtils.java GATKPerformanceOverTime script update 2012-01-02 09:58:46 -05:00
QualityUtils.java Extensive unit tests, contacts, and documentation for RecalDatum 2012-07-31 08:11:03 -04:00
ReservoirDownsampler.java 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
SWPairwiseAlignment.java FindBugs 'Efficiency' fixes 2012-08-16 15:40:52 -04:00
SampleUtils.java Phase I commit to get shadowBCFs passing tests 2012-06-21 15:16:26 -04:00
SequenceDictionaryUtils.java Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes. 2012-08-08 14:34:16 -04:00
SimpleTimer.java Removing contracts for the SimpleTimer 2011-11-06 22:22:49 -05:00
Utils.java Working (efficient?) implementation of NanoScheduler 2012-08-24 15:34:23 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00