depristo 40e6179911 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. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4258 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-12 14:02:43 +00:00
..
annotator	Moving supported tools to core	2010-08-26 13:56:19 +00:00
beagle	Moving supported tools to core	2010-08-26 13:56:19 +00:00
coverage	Updated tribble BED parsing code to use the official UCSC spec, and updated tests to match expected results.	2010-09-01 21:49:06 +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	Fix busted performance test (-outputBam has been deprecated in the BQ recalibrator in favor of -o)	2010-09-03 12:51:53 +00:00
sequenom	Office-mate courtesy: fixing Andrey's busted integration test	2010-08-26 02:00:06 +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	Truncate the floating point numbers coming out of the variant recalibration walkers. Integration tests now work with both 1.6.0_16-b01 and 1.6.0_21-b06	2010-09-10 18:37:49 +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	Removed hard-coded pointers to references	2010-08-04 17:59:37 +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