aaron 782e0018e4 removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come. ... *** Three integration tests had to change: *** RecalibarationWalkersIntegrationTest: One of the tests was using the interval as the snp track, and wasn't supplying a DbSNP track (for CountCovariates) SequenomValidationConverterIntegrationTest: relies on Plink ROD which we've removed. PileupWalkerIntegrationTest: we no longer have implicit interval tracks, so there isn't a rod name over the specified region. Otherwise the same result. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4292 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-15 22:54:49 +00:00
..
annotator	Added iterator for tribble, fixing GS bug report. Removed unnecessary tabix double wrapping. Intergation tests to ensure the BTI works with both vcfs and vcf.gz	2010-09-15 16:38:04 +00:00
beagle	Oops, ran integration tests before Guillermo committed his change to the Beagle code	2010-09-15 01:41:02 +00:00
coverage	Improvements to the error display code to print out the SVN number in all messages. Fixes to CallableLoci and tests to check for that case	2010-09-13 18:36:45 +00:00
fasta	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
filters	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
genotyper	Remove the check in the Unified Genotyper for hitting the max reads at locus value. Instead, simply add a flag to the INFO field if any of the samples has been downsampled. 95% hooked up.	2010-08-26 05:50:47 +00:00
indels	Damnit. Enabling the Picard code to recalculate all of the relevant SAMRecord attribute tags means that I need to have reference bases over all read bases even after realignment (and there are some big indels in dbsnp). Fortunately, I have my trusty IndexedFastaSequenceFile reader handy! Re-enabling the previously broken performance test.	2010-09-12 05:06:37 +00:00
qc	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
recalibration	removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come.	2010-09-15 22:54:49 +00:00
sequenom	removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come.	2010-09-15 22:54:49 +00:00
varianteval	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +00:00
variantrecalibration	Adding header lines to output of VR walkers to settle validator warnings. Command lines are added to the VCF header. GATK version numbers will be added to the header lines by Matt.	2010-09-15 16:45:03 +00:00
variantutils	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00
ClipReadsWalkersIntegrationTest.java	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
PileupWalkerIntegrationTest.java	removal of most of the old GATK ROD system; also a fix for -Dsingle so we can again run just a single unit or integration test (single tests in tribble can be run with the -DsingleTest option now). More to come.	2010-09-15 22:54:49 +00:00
PrintReadsWalkerUnitTest.java	Modifications to the output system for better interaction with @Output. Multiplexed arguments. More details in the Monday meeting.	2010-08-22 14:27:05 +00:00
VariantsToVCFIntegrationTest.java	Update integration tests to use the new ROD syntax.	2010-08-25 18:13:30 +00:00