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R
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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.
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2012-04-17 14:22:48 -04:00 |
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activeregion
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Another round of FindBugs fixes. Class implements its own compareTo() but uses base Object.equals() which can lead to unpredictable behavior.
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2012-08-20 16:55:00 -04:00 |
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analysis
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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baq
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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.
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2012-08-16 15:07:32 -04:00 |
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classloader
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Cleanup BQSR classes
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2012-07-31 08:11:03 -04:00 |
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clipping
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Quick pass of FindBugs 'should be static inner class' fixes.
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2012-08-08 14:42:06 -04:00 |
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codecs
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Print "Parsing data stream with BCF version BCFx.y" in BCF2 codec as .debug not .info
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2012-08-19 10:32:55 -04:00 |
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collections
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Refactored/renamed the nested integer array; cleaned up code a bit.
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2012-07-03 00:12:33 -04:00 |
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crypt
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Public-key authorization scheme to restrict use of NO_ET
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2012-03-06 00:09:43 -05:00 |
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duplicates
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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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exceptions
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Fixed GSA-434: GATK should generate error when gzipped FASTA is passed in.
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2012-08-17 11:49:02 -04:00 |
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fasta
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Print to logger not to System.out in CachingIndexFastaSequenceFile when profiling cache performance
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2012-08-17 11:49:02 -04:00 |
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file
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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fragments
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First pass of implementation of Reduced Reads with HaplotypeCaller. Main changes: a) Active region: scale PL's by representative count to determine whether region is active. b) Scale per-read, per-haplotype likelihoods by read representative counts. A read representative count is (temporarily) defined as the average representative count over all bases in read, TBD whether this is good enough to avoid biases in GL's. c) DeBruijn assembler inserts kmers N times in graph, where N is min representative count of read over kmer span - TBD again whether this is the best approach. d) Bug fixes in FragmentUtils: logic to merge fragments was wrong in cases where there is discrepancy of overlaps between unclipped/soft clipped bases. Didn't affect things before but RR makes prevalence of hard-clipped bases in CIGARs more prevalent so this was exposed. e) Cache read representative counts along with read likelihoods associated with a Haplotype. Code can/should be cleaned up and unified with PairHMMIndelErrorModelCode, as well as refactored to support arbitrary ploidy in HaplotypeCaller
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2012-08-03 12:24:23 -04:00 |
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help
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GSA-483: Bug in GATKdocs for Enums
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2012-08-16 16:24:17 -04:00 |
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instrumentation
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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.
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2011-07-17 20:29:58 -04:00 |
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interval
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Quick pass of FindBugs 'inefficient use of keySet iterator instead of entrySet iterator' fixes for core tools.
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2012-08-08 14:29:41 -04:00 |
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io
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Public-key authorization scheme to restrict use of NO_ET
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2012-03-06 00:09:43 -05:00 |
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pileup
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Killing off some FindBugs 'Realiability' issues
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2012-08-16 14:00:48 -04:00 |
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pileup2
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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recalibration
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Killing off some FindBugs 'Realiability' issues
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2012-08-16 14:00:48 -04:00 |
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runtime
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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2011-10-27 14:17:07 -04:00 |
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sam
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Killing off some FindBugs 'Realiability' issues
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2012-08-16 14:00:48 -04:00 |
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text
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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.
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2012-04-17 14:22:48 -04:00 |
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threading
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Clean, documented implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates
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2012-08-15 21:13:15 -04:00 |
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variantcontext
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number of stashed changes are lurking in here. In order of importance:
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2012-08-21 07:08:58 -04:00 |
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wiggle
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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.
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2011-07-17 20:29:58 -04:00 |
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AminoAcid.java
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Removing the Genomic Annotator and its supporting classes
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2011-07-25 15:10:25 -04:00 |
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AminoAcidTable.java
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Removing the Genomic Annotator and its supporting classes
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2011-07-25 15:10:25 -04:00 |
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AutoFormattingTime.java
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Clean, documented implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates
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2012-08-15 21:13:15 -04:00 |
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BaseUtils.java
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Bug fix in HaplotypeCaller for non-regular bases in the reference or reads. Those events don't get created any more. Bug fix for advanced GenotypeFullActiveRegion mode: custom variant annotations created by the HC don't make sense when in this mode so don't try to calculate them.
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2012-08-20 13:41:08 -04:00 |
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BitSetUtils.java
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Refactoring of BQSRv2 to use longs (and standard bit fiddling techniques) instead of Java BitSets for performance improvements.
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2012-06-12 09:19:36 -04:00 |
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ContigComparator.java
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Documented following the new gatkdoc framework
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2011-07-25 00:25:08 -04:00 |
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GenomeLoc.java
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make the size of a GenomeLoc int instead of long
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2012-02-03 17:12:42 -05:00 |
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GenomeLocComparator.java
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Optimized interval iteration
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2011-09-28 16:07:34 -04:00 |
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GenomeLocParser.java
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Removing parallelism bottleneck in the GATK
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2012-08-15 21:13:15 -04:00 |
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GenomeLocSortedSet.java
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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.
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2012-01-19 22:05:08 -05:00 |
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Haplotype.java
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Another round of FindBugs fixes. Object returns its internal reference to an externally mutable array. Very dangerous.
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2012-08-21 09:35:55 -04:00 |
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HasGenomeLocation.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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HeapSizeMonitor.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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IndelUtils.java
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Improvements to indel analysis capabilities of VariantEval
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2012-04-06 16:07:46 -04:00 |
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MannWhitneyU.java
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Another round of FindBugs fixes. Comparator doesn't implement Serializable.
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2012-08-21 09:20:55 -04:00 |
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MathUtils.java
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Killing off some FindBugs 'Usability' issues
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2012-08-16 13:32:44 -04:00 |
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Median.java
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ReadGroupProperties walker and associated infrastructure
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2012-03-01 15:01:11 -05:00 |
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MendelianViolation.java
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Efficient Genotype object Intermediate commit
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2012-06-14 16:42:24 -04:00 |
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NGSPlatform.java
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Stabilized NGSPlatform code: don't assume all reads have read groups (e.g. artificial SAM records)
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2012-06-06 15:17:30 -04:00 |
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PairHMM.java
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A few quick, minor findbugs fixes.
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2012-08-09 16:30:58 -04:00 |
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PathUtils.java
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GATKPerformanceOverTime script update
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2012-01-02 09:58:46 -05:00 |
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QualityUtils.java
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Extensive unit tests, contacts, and documentation for RecalDatum
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2012-07-31 08:11:03 -04:00 |
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ReservoirDownsampler.java
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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.
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2011-07-17 20:29:58 -04:00 |
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SWPairwiseAlignment.java
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FindBugs 'Efficiency' fixes
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2012-08-16 15:40:52 -04:00 |
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SampleUtils.java
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Phase I commit to get shadowBCFs passing tests
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2012-06-21 15:16:26 -04:00 |
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SequenceDictionaryUtils.java
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Quick pass of FindBugs 'method invokes inefficient Number constructor' fixes.
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2012-08-08 14:34:16 -04:00 |
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SimpleTimer.java
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Removing contracts for the SimpleTimer
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2011-11-06 22:22:49 -05:00 |
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Utils.java
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Killing off some FindBugs 'Usability' issues
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2012-08-16 13:32:44 -04:00 |
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package-info.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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