rpoplin 255cc246a2 Change in Methods development pipeline: dbsnp130 can't be used for anything, changed it to dbsnp129. Optimization for HaplotypeScore and the to-be-committed ReadRosRankSumTest in AlignmentUtils ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5301 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-24 16:09:03 +00:00
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arguments	Inserted a dangerous (but hidden) command-line argument for use by the Picard team.	2011-01-31 22:10:06 +00:00
contexts	After discussing with Mark, revert to "Master merging" of phase information from VCFs. This has the advantage of creating minimal phased VCFs from RBP, from which phase info is merged into the original "master VCF". Also, updated Genotype.sameGenotype() to be simpler and NOT REVERSE the ignorePhase flag in comparing Allele lists/sets	2011-02-01 19:50:15 +00:00
datasources	A few more unit tests plus some extra	2011-02-09 01:51:34 +00:00
examples	Fare thee well, UGv1. Here come the days UGv2.	2010-11-29 21:51:19 +00:00
executive	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +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	Additional logging of the temp file creation, management, and merging process	2011-02-11 22:07:25 +00:00
iterators	Missorted BAMs are User Exceptions	2011-01-26 14:09:39 +00:00
phonehome	ReplaceReadGroups. Fixes BAM files without read group info. MissingReadGroup points people to this tool now. Please point users on the forum to this tool now. Will migrate to Picard.	2011-02-21 14:02:41 +00:00
refdata	Another change in variant classification values	2011-02-14 17:47:58 +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	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +00:00
walkers	Change in Methods development pipeline: dbsnp130 can't be used for anything, changed it to dbsnp129. Optimization for HaplotypeScore and the to-be-committed ReadRosRankSumTest in AlignmentUtils	2011-02-24 16:09:03 +00:00
CommandLineExecutable.java	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +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	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +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	A few minor modifications masquerading as significant changes according to	2011-02-03 17:59:19 +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