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R
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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2011-10-27 14:17:07 -04:00 |
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analysis
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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baq
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Putative fix for BAQ array out of bounds
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2011-09-21 11:25:08 -04:00 |
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classloader
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Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.
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2011-09-27 14:33:57 -04:00 |
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clipreads
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Fixing no cigar bug
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2011-11-09 14:39:20 -05:00 |
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codecs
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Cleanup for new SampleUtils function
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2011-11-10 13:27:13 -05:00 |
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collections
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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.
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2011-07-17 20:29:58 -04:00 |
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duplicates
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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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exceptions
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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2011-10-27 14:17:07 -04:00 |
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fasta
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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.
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2011-07-17 20:29:58 -04:00 |
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file
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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fragments
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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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gcf
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Fixed long-standing bug in tribble index creation
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2011-09-20 10:53:18 -04:00 |
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help
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Added ability to specify arguments in files via -args/--arg_file
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2011-10-24 15:58:34 -04:00 |
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instrumentation
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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.
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2011-07-17 20:29:58 -04:00 |
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interval
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During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.
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2011-11-17 13:56:42 -05:00 |
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io
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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2011-10-27 14:17:07 -04:00 |
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pileup
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Fix to deal with reduced reads containing a deletion
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2011-11-14 12:23:46 -05:00 |
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pileup2
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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runtime
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No more hunting down R "resources". As a tradeoff Rscript cannot be specified on the commandline and will be found in the environment path.
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2011-10-27 14:17:07 -04:00 |
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sam
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compress Reduce Read counts bytes by offset
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2011-11-14 18:30:24 -05:00 |
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text
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Reorganization of Sample
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2011-09-30 15:50:54 -04:00 |
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threading
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Removed GATK use of distributed parallelism framework.
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2011-07-20 16:26:09 -04:00 |
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variantcontext
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Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-11-15 16:23:53 -05:00 |
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wiggle
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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.
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2011-07-17 20:29:58 -04:00 |
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yaml
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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AminoAcid.java
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Removing the Genomic Annotator and its supporting classes
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2011-07-25 15:10:25 -04:00 |
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AminoAcidTable.java
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Removing the Genomic Annotator and its supporting classes
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2011-07-25 15:10:25 -04:00 |
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BaseUtils.java
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Functional VCF output.
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2011-08-04 17:49:08 -04:00 |
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ContigComparator.java
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Documented following the new gatkdoc framework
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2011-07-25 00:25:08 -04:00 |
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DisjointSet.java
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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.
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2011-07-17 20:29:58 -04:00 |
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GenomeLoc.java
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IntervalUtils for completely balanced locus-based scatter/gather
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2011-11-02 10:49:40 -04:00 |
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GenomeLocComparator.java
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Optimized interval iteration
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2011-09-28 16:07:34 -04:00 |
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GenomeLocParser.java
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During flanking interval creation merging overlapping flanks so that on scatter the list doesn't accidentally genotype the same site twice.
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2011-11-17 13:56:42 -05:00 |
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GenomeLocSortedSet.java
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IntervalUtils for completely balanced locus-based scatter/gather
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2011-11-02 10:49:40 -04:00 |
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Haplotype.java
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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.
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2011-11-05 12:18:56 -04:00 |
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HasGenomeLocation.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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HeapSizeMonitor.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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IndelUtils.java
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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.
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2011-08-18 16:17:38 -04:00 |
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MannWhitneyU.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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MathUtils.java
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added MQ of low MQ/BQ to consensus RMS
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2011-11-01 17:46:12 -04:00 |
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MendelianViolation.java
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You know how the wiki has a big section on commiting local changes to BRANCHES of the repository you clone it from? Yeah. It sucks if you don't do that.
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2011-10-19 17:42:37 -04:00 |
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NGSPlatform.java
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Renamed GATKSamRecord -> GATKSAMRecord for consistency. Better docs.
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2011-10-21 09:59:24 -04:00 |
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PathUtils.java
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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.
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2011-07-17 20:29:58 -04:00 |
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QualityUtils.java
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Bugfix for cached quals
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2011-09-02 21:13:28 -04:00 |
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ReservoirDownsampler.java
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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.
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2011-07-17 20:29:58 -04:00 |
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SWPairwiseAlignment.java
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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.
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2011-07-17 20:29:58 -04:00 |
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SampleUtils.java
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Cleanup for new SampleUtils function
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2011-11-10 13:27:13 -05:00 |
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SequenceDictionaryUtils.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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SimpleTimer.java
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Removing contracts for the SimpleTimer
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2011-11-06 22:22:49 -05:00 |
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Utils.java
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IntervalUtils for completely balanced locus-based scatter/gather
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2011-11-02 10:49:40 -04:00 |
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package-info.java
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Reorganized the codebase beneath top-level public and private directories,
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2011-06-28 06:55:19 -04:00 |
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