rpoplin fe4b40ac2c Adding new InbreedingCoeff and PercentNBases annotations for Guillermo to use. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5823 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-19 19:50:39 +00:00
..
arguments	Making the GATK unpredictably random...	2011-04-29 19:29:08 +00:00
contexts	Added splitContextByReadGroup() and fixed bug in getPileupForReadGroup() that resulted in a NPE when no reads where present for a read group.	2011-05-15 17:36:07 +00:00
datasources	Locus iterators were implemented in a peekable style, which meant that a locus	2011-05-18 21:40:40 +00:00
examples	Fare thee well, UGv1. Here come the days UGv2.	2010-11-29 21:51:19 +00:00
executive	Locus iterators were implemented in a peekable style, which meant that a locus	2011-05-18 21:40:40 +00:00
filters	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +00:00
io	Marked boolean SAMFileWriterATD arguments as flags so scala generator maps them to Boolean instead of Option[Boolean].	2011-04-08 18:44:32 +00:00
iterators	As I threatened yesterday, I've moved the various and disparate randomization code out of the walkers. Now they all (except VQSRv1, whose days are numbered anyways) use a static generator available in the engine itself. Please use this from now on. The seed is reset before every individual integration test is run. I think there may still be an issue with the IndelRealigner but I need to confirm with the commit to see what testNG does. Integration tests are already broken anyways, so no big deal.	2011-04-07 17:03:48 +00:00
phonehome	Now that logging is so standard, only prints messages about logging to DEBUG. Also, found a way to silence the mime.types warning, that doesn't matter at all to us.	2011-03-31 16:49:39 +00:00
refdata	Added splitContextByReadGroup() and fixed bug in getPileupForReadGroup() that resulted in a NPE when no reads where present for a read group.	2011-05-15 17:36:07 +00:00
report	Added a utility method to retrieve the contig lengths for WG chunking.	2011-04-20 19:22:21 +00:00
traversals	Two optimizations. Even more aggressive printProgress meter optimization to only even consider doing work once every 1000 cycles through the engine. Second, GenomeLocParser now uses a single indirection around the contigInfo variable. This class uses a last used cache to retrieve efficiently contig information instead of always returning to the underlying SAMSequenceDictionary hashmap to make genome locs.	2011-04-21 01:31:26 +00:00
walkers	Adding new InbreedingCoeff and PercentNBases annotations for Guillermo to use.	2011-05-19 19:50:39 +00:00
CommandLineExecutable.java	A 'fat shard' finder. Cranks through the indices of a BAM file or list of	2011-05-10 12:56:47 +00:00
CommandLineGATK.java	Catch samtools exceptions and make them 'BAM Exceptions' asking the user to run Picard's validator and re-index the file before posting anything to the forum. Let's see whether this helps or not.	2011-04-18 03:52:43 +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	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +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	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +00:00
WalkerManager.java	Some refactoring that Mauricio and I worked through together. Changed filters	2011-05-04 19:29:08 +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