This is *NOT* an ideal implementation. One day when we have lots of free time (or a greater desire), we will implement this correctly and sophisticatedly using all the power of JEXL. For now, though, this will have to do.
Docs coming tonight.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3060 348d0f76-0448-11de-a6fe-93d51630548a
1. emit AA,AB,BB likelihoods in the FORMAT field for Mark
2. remove constraint that genotype alleles (in the GT field) need to be lexigraphically sorted.
3. Add bam file(s) used by genotyper to header for Kiran
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2963 348d0f76-0448-11de-a6fe-93d51630548a
Removing obsolete genotyping classes.
First stage of removing dependence on old Genotype class.
More changes to come.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2960 348d0f76-0448-11de-a6fe-93d51630548a
We almost completely support indels. Not yet done with plink stuff.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2926 348d0f76-0448-11de-a6fe-93d51630548a
2. Significant refactoring of Plink code to work in the rods and use VariantContext. More coming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2913 348d0f76-0448-11de-a6fe-93d51630548a
when you want to protect your VCF header from being infected by the samples in a bound hapmap VCF. Changes are as follows:
VCFRecord - minor change to adapt isNovel() to the case where the dbsnp ID field is empty, but the info field has DB=1
HapmapVCFRod - introduced for the reason at the top
RODRecordIterator - was: catch ( Exception e ) { throw new StingException("long ass message") }
is now: catch ( Exception e ) { throw new StingException("long ass message",e) }
to permit full stack ejaculation.
RodVCF - Now with more brackets!
ReferenceOrderedData - registering HapmapVCF as a bindable string
VariantAnnotator - There's an extra space on a line. And some new brackets.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2733 348d0f76-0448-11de-a6fe-93d51630548a
1) Changed VCF/RodVCF to allow for inquiries to whether or not the site is novel; isNovel() looks at the ID field, and those members of the info field that indicate membership in dbsnp, hapmap2, or hapmap3; and if none can be found, returns true.
2) Changed VariantAnnotator to annotate hapmap2 and hapmap3, if you bind rods to it with those names. Works in the same way as DBSNP does -- if you give it a rod named "hapmap2" it'll annotate membership in it. -- Passes integration tests
3) Changed UnifiedGenotyper to do the same thing (since it uses Annotations as a subroutine) -- Passes integration tests
4) Changed MultiSampleConcordanceWalker to take a flag --ignoreKnownSites (or -novels) to examine concordance only on sites that are not marked as in dbSNP or in Hapmap in the variant VCF
5) Changed VCFConcordanceCalculator (the object MultiSampleConcordanceWalker runs on) to output Concordant_Het_Calls and Concordant_Hom_Calls separately, rather than combined as Concordant_Calls
6) AlleleBalanceHistogramWalker -- I don't know what i did to this thing. I've been jerry rigging System.outs to do stuff it was never really intended to do; so there's probably some dumb System.out.print("HI I AM AT LOCUS:"+loc) stuck somewhere. It compiles at any rate.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2724 348d0f76-0448-11de-a6fe-93d51630548a
Since binary files do not need encoded locus information in the SNP names there's no need to suggest that it is so in the name of the rod
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2671 348d0f76-0448-11de-a6fe-93d51630548a
Upcoming: Test that the instantiation is correct, do it for indel-containing files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2668 348d0f76-0448-11de-a6fe-93d51630548a
There is now a DELETION_REFERENCE allele type to allow for the storage of multi-base references rather than point-mutation references.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2667 348d0f76-0448-11de-a6fe-93d51630548a
- Annotations return null when given pileups with no second-base information
- SequenomRodWithGenomeLoc -- beter handling of indels
Eric; I made two small changes to the new Genotype interface that we should talk about (they basically have to do with allele/genotype representation):
Allele - added a new UNKNOWN_POINT_MUTATION to AlleleType. If I see a sequenom genotype AG; one's got to be ref, one's got to be SNP, but until I have
an actual reference base in hand, I don't know which is which. That's what this entry is for.
Genotype - added an enum class StandardAttributes for dealing with things like deletion/inversion length. This is probably not the way we want to
represent indels, so we should talk about this. Plus now that there's a direct link between my ROD and the genotype; when we do decide
how to deal with indels, we'll be forced to alter the SequenomRodWithGenomeLoc accordingly.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2642 348d0f76-0448-11de-a6fe-93d51630548a
aaron
ebanks
depristo
chartl
asivache