asivache 74779a9a78 First version of the tool that tries determining indel error rate (basically, counts indels that look like sequencing/alignment errors - such as a single observation at deeply covered locus, and reports the rate of their occurence) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2648 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-21 15:28:20 +00:00
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annotator	Changes:	2010-01-20 16:45:17 +00:00
AlignedReadsHistoWalker.java	Yet more walkers moved to oneoffprojects.	2009-12-01 21:29:12 +00:00
BaseTransitionTableCalculatorJavaWalker.java	Stage 1 of massive Variation/Genotype refactoring.	2009-12-06 03:12:41 +00:00
HapmapPoolAllelicInfoWalker.java	The previous commit broke the build, so this is a temporary patch to get it to compile. ConcordanceTruthTable should use enums (esp. now that all of the concordance variables need to be public), but VariantEval will need to be rewritten soon anyways so I'll just push it off until then.	2009-12-20 02:34:41 +00:00
IOCrusherWalker.java	Started transition to oneoffprojects.	2009-12-01 21:19:02 +00:00
IndelErrorRateWalker.java	First version of the tool that tries determining indel error rate (basically, counts indels that look like sequencing/alignment errors - such as a single observation at deeply covered locus, and reports the rate of their occurence)	2010-01-21 15:28:20 +00:00
MismatchCounterWalker.java	Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used.	2009-12-02 20:28:07 +00:00
MismatchHistoWalker.java	Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used.	2009-12-02 20:28:07 +00:00
NeighborhoodQualityWalker.java	Yet more walkers moved to oneoffprojects.	2009-12-01 21:29:12 +00:00
PairedQualityScoreCountsWalker.java	Added - PairedQualityScoreCountsWalker: counts quality scores (e.g. as a histogram) on first reads of a pair and second reads of a pair. Turns out there's a consistent difference in quality scores; even after recalibrating without the pair ordering as a covariate (there's a bit of averaging -- but not as much as I initially thought).	2009-12-18 15:01:01 +00:00
QualityScoreByStrandWalker.java	Modifications:	2010-01-06 19:18:07 +00:00
ReadErrorRateWalker.java	Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used.	2009-12-02 20:28:07 +00:00
ReadQualityScoreWalker.java	Yet more walkers moved to oneoffprojects.	2009-12-01 21:29:12 +00:00
ReplaceQuals.java	Moved some more walkers to oneoffprojects and killed an old indel-related walker that isn't being used.	2009-12-02 20:28:07 +00:00
TestReadFishingWalker.java	Misc bug fixes.	2010-01-05 14:48:19 +00:00
ValidateDbSNPConversion.java	two fixes in the new cached DbSNP code:	2010-01-13 00:27:34 +00:00