depristo 5d2c2bd280 Just refactoring into utils/baq directory ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4795 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-06 17:43:43 +00:00
..
arguments	Just refactoring into utils/baq directory	2010-12-06 17:43:43 +00:00
contexts	As per Eric and Mark's suggestions, separated the segregating MNP merger (MergeMNPs) from the more general merger employed for annotation purposes (MergeSegregatingAlternateAlleles). Both use the same core MergePhasedSegregatingAlternateAllelesVCFWriter	2010-12-01 16:42:08 +00:00
datasources	Just refactoring into utils/baq directory	2010-12-06 17:43:43 +00:00
examples	Fare thee well, UGv1. Here come the days UGv2.	2010-11-29 21:51:19 +00:00
executive	Updating the core LocusWalker tools to include the Sample infrastructure that I added last month. This commit touches a lot of files, but only significantly changes a few: LocusIteratorByState and ReadBackedPileup and associated classes.	2010-11-19 19:59:05 +00:00
filters	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00
io	Fix issue where non-required file inputs can throw a NullPointerException	2010-11-22 01:49:17 +00:00
iterators	Just refactoring into utils/baq directory	2010-12-06 17:43:43 +00:00
phonehome	No longer getting the inet, it seems to potentially hang the JVM	2010-11-11 23:49:42 +00:00
refdata	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
report	Recent changes to the build system make the build system complain loudly about	2010-09-24 22:09:12 +00:00
traversals	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +00:00
walkers	Just refactoring into utils/baq directory	2010-12-06 17:43:43 +00:00
AbstractGenomeAnalysisEngine.java	Engine-level BAQ calculation now available in the GATK [totally experimental right now]. -baq argument to disable (NONE), to only use the tags in the BAM (USE_TAG_ONLY), use the tag when present but calculate on the fly as necessary (CALCULATE_AS_NECESSARY), and to always recalculate (RECALCULATE_ALWAYS). BAQ.java contains the complete implementation, for those interested. ValidateBAQWalker is a useful QC tool for verifying the BAQ is correct. BAQSamIterator applies BAQ to reads, as needed, in the engine. Let me know if you encounter any problems. Before prime-time, needs a caching implementation of IndexedFastaReader to avoid loading *lots* of reference data all of the time	2010-12-04 20:23:06 +00:00
CommandLineExecutable.java	Cleanup for multithreading memory leak during integration tests...unregister MXBean at end	2010-10-28 18:37:42 +00:00
CommandLineGATK.java	Tribble exceptions can be generated outside of the normal codec parsing code because we now lazy load the VCF genotype fields. I'm not sure how else to account for this (to make sure they show up as user errors and not GATK system errors) besides catching them here.	2010-10-22 15:22:17 +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	Convert GenomeLocParser into an instance variable. This change is required	2010-11-10 17:59:50 +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	Just refactoring into utils/baq directory	2010-12-06 17:43:43 +00:00
WalkerManager.java	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +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