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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Ryan Poplin 2d5bbecd9e Merged bug fix from Stable into Unstable 2011-08-16 14:19:04 -04:00
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analysis Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
baq 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
bed 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
classloader Refactored a FeatureManager class from RMDTrackBuilder 2011-08-08 14:04:46 -04:00
clipreads Fixes to ReadClipper and added Reference Coordinate clipping. 2011-08-14 14:54:33 -04:00
codecs Renaming the HapMap codec and feature to RawHapMap so that we don't get esoteric errors when trying to bind a rod with the name 'hapmap' (since it was also a feature). 2011-08-12 11:11:56 -04:00
collections 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
duplicates 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
exceptions Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles 2011-08-12 12:23:44 -04:00
fasta 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
file Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
genotype 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
help Added docs to RTC 2011-08-16 12:46:48 -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 refdata directory cleanup 2011-07-25 13:21:52 -04:00
pileup 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
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
sam Merged bug fix from Stable into Unstable 2011-08-16 14:19:04 -04:00
text Better error message for name/type clashes. 2011-08-12 11:18:14 -04:00
threading Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
variantcontext Fixed bug that required symbolic alleles to be padded with reference base and added integration test to test parsing and output of symbolic alleles 2011-08-12 12:23:44 -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
yaml Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -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 Functional VCF output. 2011-08-04 17:49:08 -04:00
ContigComparator.java Documented following the new gatkdoc framework 2011-07-25 00:25:08 -04:00
DisjointSet.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
GenomeLoc.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
GenomeLocParser.java Removed getFeaturesAsGATKFeature and created createGenomeLoc(Feature) in genomeLocParser 2011-08-03 16:04:51 -04:00
GenomeLocSortedSet.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -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 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
MannWhitneyU.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
MathUtils.java Merge branches to get new RodBinding framework 2011-08-10 18:23:01 -04:00
MendelianViolation.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
PathUtils.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
QualityUtils.java This commit incorporates several different changes that each pretty much break all the VCF-based integration tests, so I bunched them all together. We now officially emit VCF4.1 files (woo hoo), which means that the VCF headers are now all different (header version is 4.1 plus counts for some of the annotations are 'A' or 'G'). Also, I've added a Read Filter for reads with MQ=255 ('unavailable' in the SAM spec) and have applied this to the UG and the RMS MQ annotation. 2011-07-12 14:11:53 -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 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
SequenceDictionaryUtils.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
SimpleTimer.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
Utils.java Added a simple utility method Utils.optimumHashSize() to calculate the optimum 2011-08-02 21:59:06 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00