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gatk-3.8/public/java/src/org/broadinstitute/sting/commandline
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Mark DePristo fa9b2a91d0 Bugfix for GSA-552 
-- https://jira.broadinstitute.org/browse/GSA-552
-- User reports a null exception while using VariantsToVCF:
   http://gatkforums.broadinstitute.org/discussion/1461/nullpointerexception-converting-vcf3-to-vcf-using-variantstovcf
   The problem is that he left out an input VCF file for the --variant argument and the command-line argument parsing code didn't catch this, so we NPE out later on.
 		2012-10-26 16:34:16 -04:00
..
Advanced.java Usability improvements to GATKDocs 2011-08-18 21:39:11 -04:00
Argument.java Added explicit @ClassType annotations to @Argument for Option[Int] or Option[Double] since scala seems to change the reflected type to Option[Object] on some systems. 2012-10-19 13:20:29 -04:00
ArgumentCollection.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ArgumentDefinition.java Fixed: GSA-392 @arguments with just a short name get the wrong argument bindings 2012-08-17 11:49:01 -04:00
ArgumentDefinitionGroup.java Killing off some FindBugs 'Usability' issues 2012-08-16 13:32:44 -04:00
ArgumentDefinitions.java Fix improper detection of command-line arguments with missing values. 2011-07-25 13:20:00 -04:00
ArgumentException.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ArgumentIOType.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ArgumentMatch.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ArgumentMatchFileValue.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ArgumentMatchSite.java Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
ArgumentMatchSource.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ArgumentMatchSourceType.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ArgumentMatchStringValue.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ArgumentMatchValue.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ArgumentMatches.java Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
ArgumentSource.java ArgumentSource no longer comparable. Arguments sorted by GATKDoclet 2011-08-18 22:20:14 -04:00
ArgumentTypeDescriptor.java Bugfix for GSA-552 2012-10-26 16:34:16 -04:00
ClassType.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
CommandLineProgram.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
CommandLineUtils.java 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. 2011-07-17 20:29:58 -04:00
EnumerationArgumentDefault.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
Gather.java No more "Q-<pid>@<host>". Generated log file names now use the first output + ".out" (ex. my.vcf.out) or the name of the first QScript plus the order the function was added (ex. MyScript-1.out). The same function added twice with the same outputs will now have the same default logs, meaning the 2nd instance of the function won't be added to the graph twice. 2012-01-08 12:11:55 -05:00
Gatherer.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
Hidden.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
Input.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
IntervalBinding.java Feature request from Tim that could be useful to all: there's now an --interval_padding argument that specifies how many basepairs to add to each of the intervals provided with -L (on both ends). This is particularly useful when trying to run over the exome plus flanks and don't want to have to pre-compute the flanks (just use e.g. --interval_padding 50). Added integration test to cover this feature. 2012-06-18 21:36:27 -04:00
MissingArgumentValueException.java 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. 2011-07-17 20:29:58 -04:00
Output.java Minor doc fixes 2011-08-16 12:55:45 -04:00
ParsedArgs.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ParsedListArgs.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ParsingEngine.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ParsingEngineArgumentFiles.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ParsingEngineArgumentProvider.java Refactored argument matching to support other plugins in addition to file lists. 2012-10-15 15:10:45 -04:00
ParsingMethod.java Killing off some FindBugs 'Realiability' issues 2012-08-16 14:00:48 -04:00
RodBinding.java Cleanup RefMetaDataTracker before refactoring ReadMetaDataTracker 2012-08-30 10:13:06 -04:00
Tags.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
package-info.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00