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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Mark DePristo a648b5e65e First step towards an efficient Genotype object 
-- Created new clean FastGenotype and GenotypeBuilder classes with contracts to enforce expected behavior and correctness.  Tested utility of this approach by rewritting -- and then commenting out -- a path in BCF2Codec that could use this new code.  Much cleaner interface now, but not yet hooked up to anything
-- Disabled SHADOW_BCF generation and generating contigs in the output VCFs automatically to ensure that the current code bases integration tests, before switching the code to new Genotype class
-- Code cleanup.  Moved "AD" to VCFConstants under GENOTYPE_ALLELIC_DEPTHS.  Uses in code replaced with constant
 		2012-06-14 16:42:23 -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 Fixing the previous fix related to clipping. Adding extra reference padding in the HaplotypeCaller to get those larger alleles during GGA. 2012-06-04 12:49:36 -04:00
analysis Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
baq On the fly base quality score recalibration now happens up front in a SAMIterator on input instead of in a lazy-loading fashion if the BQSR table is provided as an engine argument. On the fly recalibration is now completely hooked up and live. 2012-02-13 12:35:09 -05:00
classloader Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths. 2011-09-27 14:33:57 -04:00
clipping New ReduceReads v2 with unclipped variant regions and soft-clipped bases 2012-06-08 14:58:31 -04:00
codecs First step towards an efficient Genotype object 2012-06-14 16:42:23 -04:00
collections Standalone common Pair HMM utility class with associated unit tests. 2012-03-01 22:41:13 -05:00
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 When an underlying exception occurs because of the user error, if the exception instance does not include a message instead of telling the user "because null", tell them "because <exception class name>". 2012-05-30 16:39:06 -04:00
fasta Fix for ref 0 bases for Chris 2012-01-24 10:55:09 -05:00
file Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
fragments Bug fix in fragment utils: the read name wasn't being set in the merged read. Misc minor updates to the HaplotypeCaller. 2012-06-11 10:38:35 -04:00
help Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -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 make the size of a GenomeLoc int instead of long 2012-02-03 17:12:42 -05:00
io Public-key authorization scheme to restrict use of NO_ET 2012-03-06 00:09:43 -05:00
pileup DiagnoseTargets with working Q1,Median,Q3 2012-05-29 10:16:45 -04:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
recalibration Long -> long conversions in BQSR 2012-06-14 09:07:02 -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 First step towards indel qualities in RR 2012-06-14 15:37:39 -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 Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
variantcontext First step towards an efficient Genotype object 2012-06-14 16:42:23 -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
BaseUtils.java BQSR optimization: String manipulation is extremely expensive in Java (accounts for 8% of BQSR runtime). Instead use byte[] and StringBuilder when possible. 2012-06-08 10:42:42 -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 make the size of a GenomeLoc int instead of long 2012-02-03 17:12:42 -05:00
GenomeLocComparator.java Optimized interval iteration 2011-09-28 16:07:34 -04:00
GenomeLocParser.java -- BCF2 is now a reference dependent codec so it can initialize the contigs in the case where the file doesn't have contigs in it 2012-05-24 10:57:06 -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 Bug fix in clipping function in ReadUtils for when the read ends at exactly the clipping boundary. Bug fixes in HaplotypeCaller GGA mode for when Smith-Waterman produces a different allele than what was given in the input alleles VCF. GGA mode now works with multiallelic records. Adding min pruning factor argument which is combined with the pruning factor that is determined dynamically by the coverage. 2012-06-04 10:55:36 -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 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtils.java Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000. 2012-05-29 11:18:22 -04:00
Median.java ReadGroupProperties walker and associated infrastructure 2012-03-01 15:01:11 -05:00
MendelianViolation.java Cleaned up unused import statements 2011-11-30 15:30:30 +01:00
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 Revert some bad merge changes 2012-04-18 16:35:09 -04:00
PathUtils.java GATKPerformanceOverTime script update 2012-01-02 09:58:46 -05:00
QualityUtils.java BQSR triage #4 2012-04-24 17:19:54 -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 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
SampleUtils.java 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
SequenceDictionaryUtils.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
SimpleTimer.java Removing contracts for the SimpleTimer 2011-11-06 22:22:49 -05:00
Utils.java 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
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00