VCFRecord - "." dbsnp-ID entries now taken into account (thought these were represented as null; but I guess not)
VCFGenotypeRecord - added a replaceFormat option; since intersecting Broad/BC call sets required genotype formats also be intersected (no changing on-the-fly)
VCFCombine - altered doc to instruct user to give complete priority list (was throwing exception if not)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2760 348d0f76-0448-11de-a6fe-93d51630548a
This completely separates the genotyper walker from other walkers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2758 348d0f76-0448-11de-a6fe-93d51630548a
2. Set the default confidence cutoff to 50 (instead of 0).
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2752 348d0f76-0448-11de-a6fe-93d51630548a
1) Now cares about Genotype filtering. If it is flagged as filtered, it can count as a FP/FN/TP; but goes into a "non-confident genotype" bin, rather than het/hom.
2) Can give it a Genotype Confidence flag (-GC) which will automatically filter genotypes in the way above for quality > Q for "-GC Q"
3) Can give it an -assumeRef flag. For sites only in the truth VCF (that don't even appear in the variant VCF), that locus will be treated as confident
ref calls for all individuals in the variant VCF; and the calculators updated accordingly.
*** Important: Default behavior is that sites unique to the truth VCF are considered no-call sites for the variant. This flag can help get aroudn that;
however the safest way to run this is to have a variant VCF with calls at each and every locus, if that is possible.
VCFGenotypeRecord -- added an isFiltered() call to automate looking up the FILTERED flag for VCF v3.3
SimpleVCFIntersectWalker - basic outline for a walker I'm working on tonight.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2747 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
After adding some more minor changes to the new realigner it now gets the same exact results as the original version - except that sometimes it doesn't clean when it shouldn't!
More testing coming.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2731 348d0f76-0448-11de-a6fe-93d51630548a
support batched intervals in a single shard, but intervals are not yet compressed into a single
shard.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2730 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
Cleaned up SW code and started moving over everything to use byte[] instead of String or char[].
Added a wrapper class for SAMFileWriter that allows for adding reads out of order.
Not even close to done, but I need to commit now to sync up with Andrey.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2712 348d0f76-0448-11de-a6fe-93d51630548a
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