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arguments
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Oops, working too quickly last time. This is the proper fix for the potential NPE in the equals() test.
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2011-10-27 15:32:08 -04:00 |
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contexts
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Renamed ReadBackedPileup getXSampleName() functions to getXSample
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2011-09-30 10:02:57 -04:00 |
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datasources
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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-10-26 15:44:25 -04:00 |
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examples
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@Hidden for DocumentationTest and GATKDocsExample
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2011-09-23 09:03:37 -04:00 |
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executive
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Merged bug fix from Stable into Unstable
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2011-10-27 11:31:17 -04:00 |
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filters
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Validation of GATKSamRecord in read filters
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2011-10-21 17:40:43 -04:00 |
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io
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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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iterators
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GATKSamRecord now produced by SAMFileReaders by default
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2011-10-19 13:15:27 -04:00 |
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phonehome
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Don't serialize the GATKArgumentCollection for the GATKRunReports (which would have meant dealing with the new IntervalBindings). Also, forgot to remove a test that's no longer relevant to BED parsing.
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2011-10-27 13:58:19 -04:00 |
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refdata
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Initial working version of new interval system in which the argument for -L (and -XL) is allowed to be a rod file (e.g. VCF). Old samtools-style intervals still behave as before. BTI is no longer supported. The merging (union or intersection) of intervals is now consistently applied to all -L (or -XL) intervals, which is nice. More testing needed.
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2011-10-26 14:11:49 -04:00 |
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report
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Failed to commit changes to the GATKReport required for more easy access when using the files as data sources (read: histograms) for walkers
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2011-09-21 18:15:23 -04:00 |
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samples
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Final PED documentation
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2011-10-05 15:17:41 -07:00 |
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traversals
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Counts of records failing filters are displayed sorted
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2011-10-06 18:42:26 -07:00 |
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walkers
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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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CommandLineExecutable.java
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Removed -B support. Now explodes with error if -B provided.
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2011-08-16 16:13:47 -04:00 |
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CommandLineGATK.java
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Only concrete classes are now documented
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2011-08-18 14:04:47 -04:00 |
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DownsampleType.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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DownsamplingMethod.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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GenomeAnalysisEngine.java
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Removed debugging output
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2011-10-26 15:50:20 -04:00 |
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ReadMetrics.java
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Counts of records failing filters are displayed sorted
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2011-10-06 18:42:26 -07:00 |
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ReadProperties.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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WalkerManager.java
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Removed support for RMD in @Requires and @Allows
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2011-08-03 15:36:55 -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 |
c2f343773e