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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Guillermo del Angel e0ab4e4b30 Refactoring so that ConsensusAlleleCounter can use regular pileups and can operate correctly. This involved adding utility functions to ReadBackedPileup to count # of insertions/deletions right after current position. Added unit test for IndelGenotypeLikelihoods, esp. ConsensusAlleleCounter logic 2012-03-28 21:01:31 -04:00
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R When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter. 2011-12-16 18:09:25 -05:00
activeregion Fixing a bug identified by the ActivityProfile unit tests 2012-03-15 14:24:30 -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 BitSet implementation of the on-the-fly recalibration using the CSV format file. 2012-03-16 13:02:15 -04:00
codecs Since we allow any generic header types, there's no longer any reason to check for supported types 2012-03-20 00:12:17 -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 BAMScheduler: detect contigs from the interval list that are not in the merged BAM header's sequence dictionary 2012-03-09 15:20:16 -05:00
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 BitSet implementation of the on-the-fly recalibration using the CSV format file. 2012-03-16 13:02:15 -04:00
gcf Vastly better way of doing on-demand genotyping loading 2011-11-20 08:23:09 -05:00
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 Refactoring so that ConsensusAlleleCounter can use regular pileups and can operate correctly. This involved adding utility functions to ReadBackedPileup to count # of insertions/deletions right after current position. Added unit test for IndelGenotypeLikelihoods, esp. ConsensusAlleleCounter logic 2012-03-28 21:01:31 -04:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
recalibration BQSR Gatherer implementation and integration tests 2012-03-27 13:50:22 -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 BQSR with GATKReport implementation 2012-03-23 15:42:32 -04:00
text Reorganization of Sample 2011-09-30 15:50:54 -04:00
threading Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
variantcontext Merged bug fix from Stable into Unstable 2012-03-27 22:43:00 -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 laying groundwork to have insertions and deletions going through the system. 2012-02-07 18:11:53 -05:00
BitSetUtils.java BitSets keys to lower BQSR's memory footprint 2012-03-16 13:01:48 -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 Merged bug fix from Stable into Unstable 2011-12-08 13:11:39 -05:00
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 Initial algorithm for choosing best alternate haplotypes to genotype based on the likelihoods from all samples instead of choosing for each sample independently. Simple tradeoff of penalty for increasing model complexity and likelihood of the data. 2012-03-27 13:38:52 -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 Fixing up and refactoring usage of indel categories. On a variant context, isInsertion() and isDeletion() are now removed because behavior before was wrong in case of multiallelic sites. Now, methods isSimpleInsertion() and isSimpleDeletion() will return true only if sites are biallelic. For multiallelic sites, isComplex() will return true in all cases. 2011-08-18 16:17:38 -04:00
MannWhitneyU.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtils.java First Pool Caller exact model: silly straightforward math implementation of biallelic pool caller exact likelihood model, no attempt and any smartness or optimization, no support yet for generalized multiallelic form, just hooking up for testing 2012-03-27 20:59:44 -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 BQSR with indels integrated! 2012-02-09 18:46:45 -05:00
PathUtils.java GATKPerformanceOverTime script update 2012-01-02 09:58:46 -05:00
QualityUtils.java Caching log calculations cut the non-Map runtime of HaplotypeCaller in half. Moved the qual log cache used in HC and PairHMM into a common place and added unit tests. 2012-03-21 08:45:42 -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 Cleanup for new SampleUtils function 2011-11-10 13:27:13 -05:00
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 Simple utility function for converting an Iterable<T> to Collection<T> 2012-03-27 11:54:58 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00