depristo 41c8552d0a Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5031 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-20 12:54:03 +00:00
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features	small fix for the table codec; if you see a header line, you know you've finished parsing the header. Also also some changes to return the ref ordered data pool test to using MappedStreamSegment instead of EntireStream	2011-01-05 21:20:26 +00:00
indexer	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
tracks	Fix concurrency issue that periodically kills VariantEvalIntegrationTest --	2011-01-14 18:52:21 +00:00
utils	Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.	2011-01-20 12:54:03 +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	Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.	2011-01-20 12:54:03 +00:00
ReadMetaDataTracker.java	add convenience methods for RODs-for-reads: the ability to get all the RODs covering the read, regardless of their type or position on the read.	2010-12-29 20:46:03 +00:00
RefMetaDataTracker.java	Useful profiling tool that reads in a single rod and evalutes the time it takes to read the file by byte, by line, into pieces, just the sites of the vcf, and finally the full vcf. Emits a useful table for plotting with the associated R script that can be run like Rscript R/analyzeRodProfile.R table.txt table.pdf titleString	2010-11-24 14:59:16 +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	Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.	2011-01-20 12:54:03 +00:00
SeekableRODIterator.java	Oops...forgot to commit the changes that allow primitive VCF streaming.	2011-01-12 21:54:51 +00:00
Transcript.java	Added implements HasGenomeLocation to all revelant classes. It's not possible to write generic code for working with objects that support the getLocation() function in HasGenomeLocation. Please, if you have an object that has a location, implement this interface and start using / writing generic functions to sort, compare, etc. these objects.	2011-01-20 12:54:03 +00:00
VariantContextAdaptors.java	Support for indels in hapmap. This was non-trivial because not only does hapmap not tell you whether the allele is an insertion or deletion, but it also has a completely different positioning strategy (rightmost base). I'll send out an email tomorrow when the new HapMap3.3 VCF is ready.	2010-12-27 07:37:46 +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