Eric Banks e199562c25 I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever).		2012-11-27 10:26:17 -05:00
..
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	I have pulled out all of the documentation URLs and put them into the HelpUtils class as static variables; this way, Appistry can change links as needed to point commercial users to their own internal forum without having to muck things up all over our source. Added some TODOs for Geraldine to update links in the GATK docs that still point to the old wiki. Sorry that I am pushing into stable, but that's what Appistry is pulling from for their release next week (and unstable has been failing forever).	2012-11-27 10:26:17 -05:00
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