..
Argument.java
New behavior for filling it output streams: if required==true for a field and the field
2010-08-23 23:39:13 +00:00
ArgumentCollection.java
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
2010-04-20 15:26:32 +00:00
ArgumentDefinition.java
Moving StingException
2010-09-12 14:34:15 +00:00
ArgumentDefinitionGroup.java
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
ArgumentDefinitions.java
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
ArgumentException.java
Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong.
2010-09-12 14:02:43 +00:00
ArgumentIOType.java
Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.
2010-09-12 15:07:38 +00:00
ArgumentMatch.java
<key>=<value> tagging support for command-line arguments. Unfortunately, still
2011-01-21 00:22:42 +00:00
ArgumentMatches.java
Get rid of the static cache of ArgumentTypeDescriptors by making them an integral part of the
2010-10-27 19:44:55 +00:00
ArgumentSource.java
Fixed recently introduced multiplexer issue where DoC couldn't be written
2010-12-14 19:35:15 +00:00
ArgumentTypeDescriptor.java
<key>=<value> tagging support for command-line arguments. Unfortunately, still
2011-01-21 00:22:42 +00:00
ClassType.java
Workaround for scala trait erasing parameterized types:
2010-07-07 03:15:10 +00:00
CommandLineProgram.java
Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.
2010-11-22 22:59:42 +00:00
CommandLineUtils.java
Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.
2010-11-22 22:59:42 +00:00
EnumerationArgumentDefault.java
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
2010-04-20 15:26:32 +00:00
Hidden.java
Exposed CommandLineFunction defaults to the Queue.jar command line (see -help).
2010-08-11 21:58:26 +00:00
Input.java
New behavior for filling it output streams: if required==true for a field and the field
2010-08-23 23:39:13 +00:00
MissingArgumentValueException.java
Fix issue where non-required file inputs can throw a NullPointerException
2010-11-22 01:49:17 +00:00
Output.java
New behavior for filling it output streams: if required==true for a field and the field
2010-08-23 23:39:13 +00:00
ParsingEngine.java
<key>=<value> tagging support for command-line arguments. Unfortunately, still
2011-01-21 00:22:42 +00:00
ParsingMethod.java
<key>=<value> tagging support for command-line arguments. Unfortunately, still
2011-01-21 00:22:42 +00:00
Tags.java
<key>=<value> tagging support for command-line arguments. Unfortunately, still
2011-01-21 00:22:42 +00:00
package-info.java
The copyright tag that I copied/pasted from a LaTeX document into IntelliJ had
2010-04-20 15:26:32 +00:00
aea121a9d5