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gatk-3.8/java/src/org/broadinstitute/sting/gatk
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depristo d081b9b352 Improvements to error messages about @Requires and @Allows 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4334 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-23 12:08:27 +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 Fix for GATK run report ids: 2010-09-22 19:49:25 +00:00
examples Finishing up the playground cleanup (for now) 2010-08-27 01:19:37 +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 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
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 The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder. 2010-09-21 18:21:22 +00:00
traversals The battle is over. Picard is revved. 2010-09-03 05:28:01 +00:00
walkers Updated Phasing algorithm + evaluation module to properly implement haplotypes [including homozygous genotypes]; Implemented dynamic window phasing model for LARGE increase in efficiency 2010-09-22 21:29:58 +00:00
CommandLineExecutable.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
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 Improvements to error messages about @Requires and @Allows 2010-09-23 12:08:27 +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 Eliminated -mrl option. 2010-08-26 21:38:03 +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