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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Eric Banks 937ac7290f Lots more GGA fixes for the HC now that I understand what's going on internally. Integration tests pass except for the GGA test which I believe now produces better results. 2012-11-20 16:13:29 -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 Initial testing of the Active Region Traversal contract 2012-11-15 10:08:00 -05:00
analysis Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
baq Revert "Separated out the DoC calculations from the XHMM pipeline, so that CalcDepthOfCoverage can be used for calculating joint coverage on a per-base accounting over multiple samples (e.g., family samples)" 2012-09-10 15:52:39 -04:00
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 Critical bugfix for GSA-652 / Multi-threaded VCF -> BCF writing produces invalid intermediate file that fails on merging 2012-11-02 09:09:59 -04:00
collections NestedIntegerArray: Pre-allocate only the first two dimensions 2012-10-25 15:17:42 -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 'Bug' fix: fix the error message from the vcf validator so people realize that the file fails strict validation but still adheres to the spec. 2012-10-29 16:29:27 -04:00
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 Added allele biased down-sampling capabilities to the PerReadAlleleLikelihoodMap object, which means that both the UG and HC can use this functionality. Note that it's only available in protected, so GATK-lite users won't be allowed to enable it. Needs more testing. 2012-10-24 22:52:25 -04:00
help Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -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 Fix thread name: should be master executor not input 2012-09-24 14:15:35 -04:00
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 Downsampling: experimental engine integration 2012-09-06 15:03:27 -04:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
progressmeter Add GATK-wide command line argument to control the maximum runtime allowed for the GATK 2012-10-26 13:18:34 -04:00
recalibration Fixed nasty bug in BQSR csv file creation: 2012-11-09 08:33:55 -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 Merging CMI-0.5.0 and GATK-2.2 together. 2012-11-14 10:42:03 -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
variantcontext Critical bugfix for GSA-652 / Multi-threaded VCF -> BCF writing produces invalid intermediate file that fails on merging 2012-11-02 09:09:59 -04:00
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
BaseUtils.java Work on GSA-508 / CachingIndexedFastaReader should internally upper case bases loading data 2012-11-01 15:34:03 -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 Bugfix to compareTo and equals in GenomeLoc 2012-08-30 19:41:49 -04:00
GenomeLocComparator.java Optimized interval iteration 2011-09-28 16:07:34 -04:00
GenomeLocParser.java Fixes GSA-515 Nanoscheduler GSA-577 -nt and -nct together appear to not close resources properly 2012-09-24 14:15:35 -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 Lots more GGA fixes for the HC now that I understand what's going on internally. Integration tests pass except for the GGA test which I believe now produces better results. 2012-11-20 16:13:29 -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 Improvements to indel analysis capabilities of VariantEval 2012-04-06 16:07:46 -04:00
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 Efficient Genotype object Intermediate commit 2012-06-14 16:42:24 -04:00
MultiThreadedErrorTracker.java Proper error handling in NanoScheduler 2012-09-19 17:03:13 -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
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 Fixes GSA-515 Nanoscheduler GSA-560 / Fix display of NanoScheduler and MonitoringEfficiency 2012-09-11 07:38:34 -04:00
Utils.java Breaking the utility to write @PG tags for SAMFileWriters and StingSAMFileWriters 2012-11-14 10:33:22 -05:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00