ebanks 72c5b75460 Tribble exceptions can be generated outside of the normal codec parsing code because we now lazy load the VCF genotype fields. I'm not sure how else to account for this (to make sure they show up as user errors and not GATK system errors) besides catching them here. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4554 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-22 15:22:17 +00:00
..
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	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +00:00
ArgumentMatches.java	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
ArgumentSource.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
ArgumentTypeDescriptor.java	Bug fixes to allow us to generate GATKRunReports for very early errors that leave the engine in a corrupt state. Vastly better error handling of common command line problems. Analysis output now notes whether an exception is a a UserException or a StingException	2010-09-14 22:45:15 +00:00
ClassType.java	Workaround for scala trait erasing parameterized types:	2010-07-07 03:15:10 +00:00
CommandLineProgram.java	Tribble exceptions can be generated outside of the normal codec parsing code because we now lazy load the VCF genotype fields. I'm not sure how else to account for this (to make sure they show up as user errors and not GATK system errors) besides catching them here.	2010-10-22 15:22:17 +00:00
CommandLineUtils.java	The engine now automatically adds the command-line arguments to the header of every VCF, unless -NO_HEADER is specified.	2010-09-22 15:27:58 +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
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	Changed parsing engine to store the order the argument bindings based on their definition in the class, moving "-T" to the front of Queue command lines.	2010-10-20 21:43:52 +00:00
ParsingMethod.java	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +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