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gatk-3.8/java/src/org/broadinstitute/sting/gatk/refdata
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aaron 53672361cc capture more details when something IO-related goes wrong in writing a Tribble index 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4720 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-23 17:06:28 +00:00
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features Putting my changes from earlier in the day back in after someone (rhymes with 'Dark') trounced on them with his last commit... 2010-11-16 01:55:50 +00:00
indexer Change the interface for RMDTrackBuilder, therefore always mandating the specification 2010-11-17 19:00:17 +00:00
tracks capture more details when something IO-related goes wrong in writing a Tribble index 2010-11-23 17:06:28 +00:00
utils Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
RODRecordIterator.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
RODRecordListImpl.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
ReadMetaDataTracker.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
RefMetaDataTracker.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
ReferenceDependentFeatureCodec.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
ReferenceOrderedData.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
ReferenceOrderedDatum.java Better interface to the tabular ROD, now makes writing files easier. Also has corresponding test files 2009-05-14 23:20:11 +00:00
SeekableRODIterator.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
Transcript.java Transcript is now simply an interface 2009-09-23 18:13:31 +00:00
VariantContextAdaptors.java Convert GenomeLocParser into an instance variable. This change is required 2010-11-10 17:59:50 +00:00
package-info.java Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file 2009-12-04 20:08:41 +00:00