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arguments
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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contexts
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Lazy reference loading; the engine doesn't fetch the reference bases until you actually call ref.getBases(). With the new hidden --dontUpdateUG to table recalibrator this is 2-3x faster than before. Enabled for locus, read, and rod walkers.
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2010-08-16 13:46:22 +00:00 |
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datasources
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Lazy reference loading; the engine doesn't fetch the reference bases until you actually call ref.getBases(). With the new hidden --dontUpdateUG to table recalibrator this is 2-3x faster than before. Enabled for locus, read, and rod walkers.
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2010-08-16 13:46:22 +00:00 |
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examples
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Add deprecated command-line arguments, and switched over UG to output to
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2010-08-22 21:01:44 +00:00 |
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executive
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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filters
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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io
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Okay, finally done with VCF compression. Now:
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2010-08-24 16:36:54 +00:00 |
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iterators
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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refdata
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adding the ability in Tribble to create indexes from a stream of features, so that we can create multiple indexes from one pass of the file. In the GATK we now create multiple indexes, and choose the
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2010-08-23 06:54:59 +00:00 |
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traversals
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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walkers
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Fixing stray comments.
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2010-08-24 20:19:39 +00:00 |
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CommandLineExecutable.java
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allow other objects access to the static method that resolves bam lists, and some renaming and improved documentation for the function.
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2010-08-23 18:52:00 +00:00 |
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CommandLineGATK.java
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Changed logging level to default at INFO instead of WARN.
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2010-08-09 16:42:48 +00:00 |
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DownsampleType.java
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We're unable to make the naive deduper more worldly, so we're killing it instead.
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2010-06-18 13:54:27 +00:00 |
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DownsamplingMethod.java
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We're unable to make the naive deduper more worldly, so we're killing it instead.
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2010-06-18 13:54:27 +00:00 |
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GATKErrorReport.java
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The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
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2010-04-20 15:26:32 +00:00 |
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GenomeAnalysisEngine.java
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Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.
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2010-08-22 14:27:05 +00:00 |
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ReadMetrics.java
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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ReadProperties.java
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Massive cleanup of read filtering.
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2010-08-11 20:17:11 +00:00 |
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WalkerManager.java
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Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).
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2010-08-11 21:58:26 +00:00 |
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package-info.java
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Put a major.minor version into the GATK Javadoc for reading. Also,
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2010-01-15 21:48:30 +00:00 |
7bbd67f3c4