hanna 497bcbcbb7 Recent changes to the build system make the build system complain loudly about ... pieces of core that depend on playground. Most of these have been eliminated by (temporarily) promoting Aaron's report system to core in this checkin. I'll follow up with other changes in separately. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4350 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-24 22:09:12 +00:00
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arguments	Adding the --sample-metadata (-SM) command line argument and associated functionality. This is something Matt and I have been working on for a while. Basically, it allows you to integrate sample metadata into an analysis, by including a sample file. More detailed documentation is on the wiki: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Sample_data_to_an_analysis	2010-09-15 11:50:22 +00:00
contexts	Support for --assume-single-sample in UG, better malformated bam exceptions, and ignoring out of order contigs in seqdictutils. All for the CG bam file	2010-09-21 20:33:34 +00:00
datasources	Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts.	2010-09-23 23:28:55 +00:00
examples	Enhancements to build external projects for walker sharing.	2010-09-24 21:17:16 +00:00
executive	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
filters	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
io	Tried to do a bit of pre-commit refactoring and screwed it up. Fixed.	2010-09-23 18:17:29 +00:00
iterators	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
phonehome	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
refdata	Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts.	2010-09-23 23:28:55 +00:00
report	Recent changes to the build system make the build system complain loudly about	2010-09-24 22:09:12 +00:00
traversals	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
walkers	Recent changes to the build system make the build system complain loudly about	2010-09-24 22:09:12 +00:00
AbstractGenomeAnalysisEngine.java	Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts.	2010-09-23 23:28:55 +00:00
CommandLineExecutable.java	Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts.	2010-09-23 23:28:55 +00:00
CommandLineGATK.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
DownsampleType.java	Eliminated -mrl option.	2010-08-26 21:38:03 +00:00
DownsamplingMethod.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
GenomeAnalysisEngine.java	Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts.	2010-09-23 23:28:55 +00:00
ReadMetrics.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
ReadProperties.java	Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts.	2010-09-23 23:28:55 +00:00
WalkerManager.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
package-info.java	Put a major.minor version into the GATK Javadoc for reading. Also,	2010-01-15 21:48:30 +00:00