Rollback of Variant-related changes of r1585, additional PGC code
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1586 348d0f76-0448-11de-a6fe-93d51630548a
@VariantEvalWalker - added a command line option to input a file path to a pooled call file for pooled genotype concordance checking. This string is to be passed to the PooledGenotypeConcordance object.
@AllelicVariant - added a method isPooled() to distinguish pooled AllelicVariants from unpooled ones.
@ all the rest - implemented isPooled(); for everything other than PooledEMSNProd it simply returns false, for PooledEMSNProd it returns true.
Added:
@PooledGenotypeConcordance - takes in a filepath to a pool file with the names of hapmap individuals for concordance checking with pooled calls
and does said concordance checking over all pools. Commented out as all the methods are as yet unwritten.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1585 348d0f76-0448-11de-a6fe-93d51630548a
After consulting our resident expert (Aaron), we're going to (temporarily) remove the date from the vcf output until we can come up with a better solution. However, this shouldn't cause any short-term problems because the data truly is optional.
VF test's MD5s are updated.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1580 348d0f76-0448-11de-a6fe-93d51630548a
1. VariantsToVCF can now be called statically to output VCF for a single ROD instance; this is temporary until we have a VCF ROD.
2. VariantFiltration now outputs only 2 files, both mandatory: all variants that pass filters in geli text, and all variants in VCF.
If there are any problems, go find Aaron.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1569 348d0f76-0448-11de-a6fe-93d51630548a
2) when reads with deletions are requested, adds to the pile just those: reads with 'D' over the current reference base, but not 'N'
3) next() now implements a loop: recursive forward iteration calls to next() until ref. position with non-zero coverage is encountered were OK for (short) deletions, but with long stretches of N's they end up with stack overflow
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1568 348d0f76-0448-11de-a6fe-93d51630548a
@CoverageAndPowerWalker - removed a hanging colon that was being printed after the reference position
@VariantEvalWalker - added a command line argument for pool size for eventual use in doing pooled caller evaluations. As now, the variable is unused.
@AlignmentContext - altered the scope of class variables from private to protected in order that child objects might have access to them
New Additions:
Filtered Contexts
Sometimes we want to filter or partition reads by some aspect (quality score, read direction, current base, whatever) and use only those reads as
part of the alignment context. Prior to this I've been doing the split externally and creating a new AlignmentContext object. This new approach makes
it a bit easier, as each of these objects are children of AlignmentContext, and can be instantiated from a "raw" AlignmentContext.
@FilteredAlignmentContext is an abstract class that defines the behavior. The abstract method 'filter' is called on the input AlignmentContext, filtering
those reads and offsets by whatever you can think of. The filtered reads/offsets are then maintained in the reads and offsets fields. These classes can
be passed around as AlignmentContexts themselves. Writing a new kind of read-filtered alignment context boils down to implementing the filter method.
@ReverseReadsContext - a FilteredAlignmentContext that takes only reads in the reverse direction
@ForwardReadsContext - a FilteredAlignmentContext that takes only reads in the forward direction
@QualityScoreThresholdContext - a FilteredAlignmentContext that takes only reads above a given quality score threshold (defaults to 22 if none provided).
A unit test bamfile and associated unit tests for these are in the works.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1559 348d0f76-0448-11de-a6fe-93d51630548a
-Bamboo will now run the integration tests once a day, and the normal units tests on each check-in.
-Also added a bunch of unit tests for VariantEval walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1555 348d0f76-0448-11de-a6fe-93d51630548a
-I also uncovered a corner case in the cleaner that for some reason was commented out but shouldn't have been. Hooray for unit tests!
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1553 348d0f76-0448-11de-a6fe-93d51630548a
Also fixed the case where MD5 sums had leading zero's clipped off
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1551 348d0f76-0448-11de-a6fe-93d51630548a
Note to self: never give project status in an svn log.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1550 348d0f76-0448-11de-a6fe-93d51630548a
depristo
hanna
andrewk
chartl
ebanks
aaron
asivache
kiran
sjia