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R
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When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.
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2011-12-16 18:09:25 -05:00 |
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activeregion
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HaplotypeCaller is now an ActiveRegionWalker.
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2012-01-22 14:31:01 -05:00 |
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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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Active Region Traversal should use GATKSAMRecords everywhere instead of SAMRecords. misc cleanup.
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2012-02-03 17:13:52 -05:00 |
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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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clipping
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Add support for reads starting with insertion
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2012-01-03 09:29:45 -05:00 |
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codecs
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Catch exception for bad type and throw as a TribbleException
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2012-01-25 12:15:51 -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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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.
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2011-12-14 10:43:52 -05:00 |
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fasta
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Fix for ref 0 bases for Chris
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2012-01-24 10:55:09 -05:00 |
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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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HaplotypeCaller is now an ActiveRegionWalker.
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2012-01-22 14:31:01 -05:00 |
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gcf
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Vastly better way of doing on-demand genotyping loading
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2011-11-20 08:23:09 -05:00 |
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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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make the size of a GenomeLoc int instead of long
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2012-02-03 17:12:42 -05:00 |
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io
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Device files like /dev/null are now tracked as special by Queue and are not used to generate .out file paths, scattered into a temporary directory, gathered, deleted, etc.
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2012-01-23 16:17:04 -05:00 |
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pileup
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Initial version of on-the-fly, lazy loading base quality score recalibration. It isn't completely hooked up yet but I'm committing so Mauricio and Mark can see how I envision it will fit together. Look it over and give any feedback. With the exception of the Solid specific code we are very very close to being able to remove TableRecalibrationWalker from the code base and just replace it with PrintReads -BQSR recal.csv
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2012-02-05 13:09:03 -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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recalibration
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Initial version of on-the-fly, lazy loading base quality score recalibration. It isn't completely hooked up yet but I'm committing so Mauricio and Mark can see how I envision it will fit together. Look it over and give any feedback. With the exception of the Solid specific code we are very very close to being able to remove TableRecalibrationWalker from the code base and just replace it with PrintReads -BQSR recal.csv
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2012-02-05 13:09:03 -05:00 |
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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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Initial version of on-the-fly, lazy loading base quality score recalibration. It isn't completely hooked up yet but I'm committing so Mauricio and Mark can see how I envision it will fit together. Look it over and give any feedback. With the exception of the Solid specific code we are very very close to being able to remove TableRecalibrationWalker from the code base and just replace it with PrintReads -BQSR recal.csv
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2012-02-05 13:09:03 -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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Initial version of multi-allelic summary module in VariantEval
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2012-01-25 19:42:55 -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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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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GenomeLoc.java
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make the size of a GenomeLoc int instead of long
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2012-02-03 17:12:42 -05:00 |
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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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Merged bug fix from Stable into Unstable
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2011-12-08 13:11:39 -05:00 |
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GenomeLocSortedSet.java
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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.
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2012-01-19 22:05:08 -05:00 |
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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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First implementation of DiagnoseTargets
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2012-02-03 17:12:43 -05:00 |
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MendelianViolation.java
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Cleaned up unused import statements
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2011-11-30 15:30:30 +01:00 |
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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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GATKPerformanceOverTime script update
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2012-01-02 09:58:46 -05:00 |
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QualityUtils.java
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Initial version of on-the-fly, lazy loading base quality score recalibration. It isn't completely hooked up yet but I'm committing so Mauricio and Mark can see how I envision it will fit together. Look it over and give any feedback. With the exception of the Solid specific code we are very very close to being able to remove TableRecalibrationWalker from the code base and just replace it with PrintReads -BQSR recal.csv
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2012-02-05 13:09:03 -05:00 |
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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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Refactor of ReadClipper unit tests
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2011-12-15 19:05:43 -05:00 |
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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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