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Advanced.java
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Usability improvements to GATKDocs
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2011-08-18 21:39:11 -04:00 |
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Argument.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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ArgumentCollection.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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ArgumentDefinition.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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ArgumentDefinitionGroup.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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ArgumentDefinitions.java
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Fix improper detection of command-line arguments with missing values.
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2011-07-25 13:20:00 -04:00 |
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ArgumentException.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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ArgumentIOType.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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ArgumentMatch.java
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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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ArgumentMatchSite.java
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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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ArgumentMatchSource.java
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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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ArgumentMatchSourceType.java
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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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ArgumentMatches.java
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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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ArgumentSource.java
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ArgumentSource no longer comparable. Arguments sorted by GATKDoclet
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2011-08-18 22:20:14 -04:00 |
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ArgumentTypeDescriptor.java
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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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ClassType.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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CommandLineProgram.java
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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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CommandLineUtils.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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EnumerationArgumentDefault.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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Gather.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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Gatherer.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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Hidden.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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Input.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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IntervalBinding.java
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Go around the ROD system for now so that we can just call decodeLoc() for efficiency. Noted that we should go through the ROD system once it gets cleaned up. This means that currently gzipped files are not supported with -L.
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2011-10-26 15:42:53 -04:00 |
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MissingArgumentValueException.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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Output.java
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Minor doc fixes
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2011-08-16 12:55:45 -04:00 |
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ParsingEngine.java
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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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ParsingMethod.java
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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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RodBinding.java
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makeUnbound now package protected
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2011-08-10 22:29:32 -04:00 |
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Tags.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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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 |
b39fcb1bea