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arguments
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GSA-491: Add hidden tag to GATK that propagates to the GATK logs
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2012-08-21 14:44:18 -04:00 |
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contexts
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Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.
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2012-06-15 15:55:03 -04:00 |
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datasources
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Fixed GSA-434: GATK should generate error when gzipped FASTA is passed in.
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2012-08-17 11:49:02 -04:00 |
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downsampling
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Make downsampler classes themselves generic (instead of just the Downsampler interface)
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2012-06-13 16:43:39 -04:00 |
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examples
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Adding categories for the remaining uncategorized walkers
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2012-07-30 11:35:08 -04:00 |
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executive
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Killing off some FindBugs 'Realiability' issues
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2012-08-16 14:00:48 -04:00 |
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filters
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Updated and more thorough version of the BadCigar read filter
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2012-08-17 17:05:27 -04:00 |
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io
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Make sure the storage writer is closed before running mergeInfo in multi-threaded output management
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2012-08-16 13:03:13 -04:00 |
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iterators
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WTF - why is support for whole-read insertions all messed up in LIBS? I've pushed a temporary patch for now (the right solution should certainly not be implemented in stable; LIBS needs to be better thought out). Added another unit test.
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2012-08-22 00:24:01 -04:00 |
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phonehome
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GSA-491: Add hidden tag to GATK that propagates to the GATK logs
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2012-08-21 14:44:18 -04:00 |
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refdata
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GSA-485: Remove repairVCFHeader from GATK codebase
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2012-08-16 13:03:13 -04:00 |
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report
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Ready for full-scale evaluation adaptive BQSR contexts
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2012-08-03 16:02:53 -04:00 |
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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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Added function to get founders IDs in SampleDB
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2012-04-25 12:49:36 -04:00 |
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traversals
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Another round of FindBugs fixes. Class implements its own compareTo() but uses base Object.equals() which can lead to unpredictable behavior.
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2012-08-20 16:55:00 -04:00 |
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walkers
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Expanding the HaplotypeCaller integration tests to cover a wider range of data
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2012-08-22 14:18:44 -04:00 |
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CommandLineExecutable.java
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Update URL for phone home / GATK key documentation output by the GATK upon error
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2012-08-08 09:29:54 -04:00 |
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CommandLineGATK.java
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Quick fix to user error catching
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2012-07-31 15:50:32 -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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Removing SlowGenotype object from GATK
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2012-08-16 15:23:06 -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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Officially removing all code associated with extended events. Note that I still have a longer term project on my plate to refactor the ReadBackedPileup, but that's a much larger effort.
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2012-06-15 15:55:03 -04:00 |
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WalkerManager.java
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Removed support for walkers ending with "Walker" from the engine.
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2012-07-20 17:27:11 -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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