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gatk-3.8/public/java/src/org/broadinstitute/sting/utils
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Eric Banks 9497e9492c Bug fix for complex records: do not ever reverse clip out a complete allele. 2011-12-14 11:21:28 -05:00
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R 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
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
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 returning read instead of GATKSAMRecord 2011-11-18 16:49:59 -05:00
codecs Bug fix for complex records: do not ever reverse clip out a complete allele. 2011-12-14 11:21:28 -05:00
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 GATKSAMRecord refactor 2011-11-03 15:43:26 -04:00
exceptions Don't update lineNo for decodeLoc - only for decode (otherwise they get double-counted). Even still, because of the way the GATK currently utilizes Tribble we can parse the same line multiple times, which knocks the line counter out of sync. For now, I've added a TODO in the code to remind us and the error messages note that it's an approximate line number. 2011-12-14 10:43:52 -05:00
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
fragments GATKSAMRecord refactor 2011-11-03 15:43:26 -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 Removing the legacy -L "interval1;interval2" syntax 2011-11-21 13:18:53 -05:00
io Right aligning GATKReport numeric columns and updated MD5s in tests. 2011-12-05 23:22:15 -05:00
pileup Fix to deal with reduced reads containing a deletion 2011-11-14 12:23:46 -05:00
pileup2 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -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 isEmpty now checks if mReadBases is null 2011-11-18 18:34:05 -05:00
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 Final performance optimization for GenotypesContext 2011-11-22 17:19:30 -05:00
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 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
GenomeLoc.java Support for list of known CNVs in VariantEval 2011-11-30 17:05:16 -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 IntervalUtils for completely balanced locus-based scatter/gather 2011-11-02 10:49:40 -04:00
Haplotype.java Now properly extending candidate haplotypes with bases from the reference context instead of filling with padding bases. Functionality in the private Haplotype class is no longer necessary so removing it. No need to have four different Haplotype classes in the GATK. 2011-11-05 12:18:56 -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 The log10cache needs to be larger if we want to handle 10K samples in the UG. 2011-12-13 23:36:10 -05:00
MendelianViolation.java Cleaned up unused import statements 2011-11-30 15:30:30 +01:00
NGSPlatform.java Renamed GATKSamRecord -> GATKSAMRecord for consistency. Better docs. 2011-10-21 09:59:24 -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 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 IntervalUtils for completely balanced locus-based scatter/gather 2011-11-02 10:49:40 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00