hanna 0d7cca169e Sigh. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5645 348d0f76-0448-11de-a6fe-93d51630548a		2011-04-15 14:37:24 +00:00
..
arguments	Sigh.	2011-04-15 14:37:24 +00:00
contexts	UnifiedGenotyper now BAQs via ADD_TAG to facilitate using BAQed quals for GL calculations but unBAQed quals for annotation calculations. UnifiedGenotyper now produces SNP and indel calls simultaneously. 40 base mismatch intrinsic filter removed from UG to greatly simplify the code. RankSumTests are now standard annotations but the integration tests are commented out pending changes that will allow random annotations to work.	2011-04-06 19:06:24 +00:00
datasources	Low-memory sharding is now enabled by default.	2011-04-15 14:22:07 +00:00
examples	Fare thee well, UGv1. Here come the days UGv2.	2010-11-29 21:51:19 +00:00
executive	Removed the completely unused generic but extremely expensive infrastructure for dynamic LocusIteratorFilters. Now the one, and probably only useful one, is called directly in the LocusIteratorByState itself to filter adaptor bases from reads. This shaves 10% off the runtime of all walkers, apparently. Has the additional benefit of eliminating a lot of complex infrastructure that resulted ultimately in only a single function call.	2011-03-27 20:48:24 +00:00
filters	Remove the adaptor sequence clipping read filter because it is dangerous (it breaks LocusIteratorByState). We'll bring it back to life when ReadTransformers are created. Instead, have the utility code return a new clipped SAMRecord (necessary so that we don't break SNP calling in UG when the indel caller tries to hard-clip the reads).	2011-04-13 18:47:47 +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	IntelliJ complains that @Override is not allowed when implementing interface methods. Whatever.	2011-04-05 16:57:59 +00:00
report	Fixed an issue where an eval module with TableType objects would get an extra, empty table in the output, screwing up the parse in R.	2011-02-17 23:03:46 +00:00
traversals	Traversal now says 'done with mapped reads' instead of 'done' so we don't confuse users when there are a lot of unmapped reads left to process.	2011-04-05 15:11:28 +00:00
walkers	UG can still return null in certain nasty cases	2011-04-14 20:11:17 +00:00
CommandLineExecutable.java	Fix for bug GSA-441: BAM file list with blank lines gives a confusing error	2011-04-01 15:04:35 +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	Low-memory sharding is now enabled by default.	2011-04-15 14:22:07 +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	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +00:00
WalkerManager.java	Allow walkers to enforce the ordering in which ReadFilters are applied (so that they're now done in the order specified in the walker). Useful if you have a computationally expensive filter (like adaptor clipping) that should only be applied to reads passing all other filters.	2011-04-08 03:34:50 +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