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gatk-3.8/public/java/src/org/broadinstitute/sting/commandline
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Mark DePristo 80a4ce0edf Bugfix for incorrect error messages for missing BAMs and VCFs 
-- Missing BAMs were appearing as StingExceptions
-- Missing VCFs were showing up as CommandLineErrors, but it's clearer for them to be CouldNotReadInputFile exceptions
-- Added integration tests to ensure missing BAMs, VCFs, and -L files are properly thrown as CouldNotReadInputFile exceptions
-- Added path to standard b37 BAM to BaseTest
-- Cleaned up code in SAMDataSource, removing my parallel loading code as this just didn't prove to be useful.
 		2012-01-23 09:52:07 -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 Reorganized the codebase beneath top-level public and private directories, 2011-06-28 06:55:19 -04:00
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 A toString() method for IntervalBindings 2011-11-23 11:56:12 -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