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gatk-3.8/public/java/src/org/broadinstitute/sting/commandline
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Mark DePristo 24356f11b7 Merged bug fix from Stable into Unstable 
-- Resolved conflict

Conflicts:
	public/java/src/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSource.java
 		2012-02-27 17:13:17 -05:00
..
Advanced.java Usability improvements to GATKDocs 2011-08-18 21:39:11 -04:00
Argument.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
ArgumentCollection.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ArgumentDefinition.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
ArgumentDefinitionGroup.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
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 Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -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 Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
ArgumentMatchSourceType.java Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -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 incorrect error messages for missing BAMs and VCFs 2012-01-23 09:52:07 -05:00
ClassType.java Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
CommandLineProgram.java For BAM and Reviewed errors we now check the error message to see if it's actually a 'too many open files' problem and, if so, we generate a User Error instead. 2011-11-22 10:50:22 -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 More general catching of Exceptions in interval reading to throw MalformedFile exception in all cases 2012-02-27 14:02:26 -05:00
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
ParsingEngine.java Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable 2011-10-26 15:44:25 -04:00
ParsingMethod.java Added ability to specify arguments in files via -args/--arg_file 2011-10-24 15:58:34 -04:00
RodBinding.java makeUnbound now package protected 2011-08-10 22:29:32 -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