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gatk-3.8/java/test/org/broadinstitute/sting/gatk/datasources/providers
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depristo e234589240 Contracts for GenomeLocParser and GenomeLoc are now fully implemented. 
GenomeLocs can officially have any start/stop values from -Inf - +Inf.  Bounds w.r.t. the reference are enforced, optionally, by GenomeLocParser.  General code cleanup throughout the subsystem.

All validation code for GLs is now centralized, and all I/O systems now validate their inputs.  Because of this, the Picard interval processing code has been changed to examine whether an interval is valid, and only keep the valid intervals.  Note that the scatter/gather test was changed, because the original hg18 chr20 interval files as actually malformed (all records for some reason where on chr20).  

Many interval processing routines were moved to IntervalUtils, as this is their natural home.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5830 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-05-21 02:01:59 +00:00
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AllLocusViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
CoveredLocusViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
LocusReferenceViewUnitTest.java A few minor modifications masquerading as significant changes according to 2011-02-03 17:59:19 +00:00
LocusViewTemplate.java Contracts for GenomeLocParser and GenomeLoc are now fully implemented. 2011-05-21 02:01:59 +00:00
ReadBasedReferenceOrderedViewUnitTest.java Oops...forgot to commit the changes that allow primitive VCF streaming. 2011-01-12 21:54:51 +00:00
ReadReferenceViewUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
ReferenceOrderedViewUnitTest.java Under guidance from Matt added ability to use key-value tags with ROD binding command line arguments, so now one can say -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmap.vcf and get the tags in a walker. Look at ContrastiveRecalibrator for an example of how to use the new ReferenceOrderedDataSource.getTags(). Removed references to FDR in tranches since we are only using truth sensitivity. Finally fixed long standing bug where tranche filters weren't set appropriately. 2011-03-29 21:04:09 +00:00
ReferenceViewTemplate.java Improved BAQ implementation. Now supports adding BAQ tags to reads on the fly with ADD_TAG_ONLY option. Caching fasta reader implementation, and changes throughout the system to enable this. Many performance improvements throughout the system due to better reference access patterns. 2010-12-05 18:29:39 +00:00
ShardDataProviderUnitTest.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00