zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
gatk-3.8/public/java/src/org/broadinstitute/sting/utils
History
Mauricio Carneiro ff2f4df043 Fixed hardclipping inside indel (right tail) 
when hard clipping the right tail of a read falls inside a deletion, clipping should fall back to the last base before the deletion to follow the ReadClipper's contract.
 		2011-09-28 16:07:34 -04:00
..
R Updating Rscript path doc text for Broad users 2011-09-21 15:22:26 -04:00
analysis Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
baq Putative fix for BAQ array out of bounds 2011-09-21 11:25:08 -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 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
clipreads clipping both ends of the reads was modifying the original read 2011-09-28 16:07:34 -04:00
codecs My interpretation of the VCF spec is that the FORMAT field should only be present if there is genotype/sample data. So the VCFCodec now throws an exception when it encounters such a case. I had to fix one of the integration test VCFs. 2011-09-21 22:23:28 -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 My interpretation of the VCF spec is that the FORMAT field should only be present if there is genotype/sample data. So the VCFCodec now throws an exception when it encounters such a case. I had to fix one of the integration test VCFs. 2011-09-21 22:23:28 -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
gcf Fixed long-standing bug in tribble index creation 2011-09-20 10:53:18 -04:00
help Shows "" not empty space when default string value is "" 2011-09-28 11:35:52 -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 Final intervals cleanup 2011-09-19 10:19:10 -04:00
pileup Refactored reduced read utilities 2011-09-26 12:58:31 -04:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
sam Fixed hardclipping inside indel (right tail) 2011-09-28 16:07:34 -04:00
text Add longhand form to the error message. 2011-09-27 20:29:31 -04:00
threading Removed GATK use of distributed parallelism framework. 2011-07-20 16:26:09 -04:00
variantcontext Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-09-24 21:20:11 -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 Performance bugfix for GenomeLoc.hashcode 2011-09-09 14:25:37 -04:00
GenomeLocComparator.java Optimized interval iteration 2011-09-28 16:07:34 -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
Haplotype.java Moved Haplotype into Utils root 2011-09-24 09:14:05 -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 Minor refactoring: add ability to MathUtils.normalizeFromLog10 to not go to linear domain but just substract max value from log values and return. Use this function in snp and indel GL computation. 2011-09-25 21:18:56 -04:00
MendelianViolation.java Adding in likelihood calculations for mendelian violations. Also fixing a minor and rare bug in SelectVariants when specifying family structure on the command line. 2011-09-21 16:40:29 -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 Bugfix for cached quals 2011-09-02 21:13:28 -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 Support for sample sets in AssignSomaticStatus 2011-09-19 11:40:45 -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 Intermediate commit of bugfixes to CombineVariants 2011-09-21 10:15:05 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00