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gatk-3.8/java/src/org/broadinstitute/sting/gatk
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delangel e80742e72f Use -o as argument for output file in ProduceBeagleInputWalker, to be consistent with other walkers (you're welcome, chartl :)). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4386 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-29 22:46:39 +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 Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 2010-09-28 02:16:25 +00:00
examples Enhancements to build external projects for walker sharing. 2010-09-24 21:17:16 +00:00
executive Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +00:00
filters Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +00:00
io Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +00:00
iterators Chris found a bug in the downsampler where, if the number of reads entering 2010-09-29 11:18:12 +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 first pass of well-formatted tribble exceptions 2010-09-25 03:29:33 +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 Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +00:00
walkers Use -o as argument for output file in ProduceBeagleInputWalker, to be consistent with other walkers (you're welcome, chartl :)). 2010-09-29 22:46:39 +00:00
AbstractGenomeAnalysisEngine.java Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 2010-09-28 02:16:25 +00:00
CommandLineExecutable.java Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +00:00
CommandLineGATK.java Every Sting app from now on will be forced into the US English locale. 2010-09-29 21:55:21 +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 Adding a few helper methods for accessing sample metadata, and associated unit tests. These are motivated by discussion with Ryan about how he'll use sample metadata in VariantEvalwalker - hopefully will make it easier for him. Methods are: 2010-09-28 02:16:25 +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 Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance. 2010-09-25 02:49:30 +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