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arguments
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First draft of a test script for I/O performance with the new asynchronous I/O processing.
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2011-11-30 13:13:16 -05:00 |
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contexts
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Get rid of support for bams without sample information in the read groups. This hidden option wasn't being used anyways because it wasn't hooked up properly in the AlignmentContext.
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2011-11-05 23:54:28 -04:00 |
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datasources
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Fix for chartl's stale null representation issue.
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2011-12-06 18:05:17 -05:00 |
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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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First pass of the asynchronous block loader.
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2011-11-18 15:02:59 -05:00 |
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filters
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It wouldn't harm integrationtests if we had our logic right... :-)
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2011-11-10 14:03:22 -05:00 |
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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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Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup.
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2011-12-06 10:10:38 -05:00 |
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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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Tribble v42 changes the Codec.canDecode method to take in a String instead of a File; this is something that Jim was adamant about (because Tribble can handle streams other than files). I didn't want the next person who needed to rev Tribble to deal with this change additionally, so I took care of updating the GATK now.
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2011-11-28 14:18:28 -05:00 |
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report
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Right aligning GATKReport numeric columns and updated MD5s in tests.
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2011-12-05 23:22:15 -05:00 |
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resourcemanagement
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First pass of the asynchronous block loader.
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2011-11-18 15:02:59 -05:00 |
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samples
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Corrected bug causing getChildrenWithParents() to not take the last family member into consideration.
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2011-12-09 14:51:34 +01:00 |
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traversals
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GATKSAMRecord refactor
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2011-11-03 15:43:26 -04:00 |
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walkers
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Merge branch 'master' of ssh://copper.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
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2011-12-09 15:57:24 +01:00 |
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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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Check for null comment
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2011-11-23 10:47:21 -05:00 |
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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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Fixed issue with RODWalker parallelization.
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2011-12-07 11:55:42 -05:00 |
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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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Better file count / buffering variation in test suite. Parameterized read shard buffering. Misc cleanup.
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2011-12-06 10:10:38 -05:00 |
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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 |
a79144f7db