I haven't thought through what the negative offsets will mean for scoring.
 I recently tried to run the pipeline and found some negative offsets
(which caused errors!).  Actually, there shouldn't be any negative offsets
in the main branch, right?  I'll have to spend a bit more time debugging.

But anyway, yes I think this can merge but maybe make it an option to
include this behavior?

--
Jake Biesinger
Graduate Student
Xie Lab, UC Irvine


On Wed, Jan 22, 2014 at 1:28 PM, Jianfeng Jia <notifications@github.com>wrote:

> In
> genomix/genomix-pregelix/src/main/java/edu/uci/ics/genomix/pregelix/operator/removelowcoverage/ShiftLowCoverageReadSetVertex.java:
>
> > +            shiftReadSetToNeighors();
> > +            clearupMyReadSet();
> > +        }
> > +        super.voteToHalt();
> > +    }
> > +
> > +    private void clearupMyReadSet() {
> > +        getVertexValue().getUnflippedReadIds().reset();
> > +        getVertexValue().getFlippedReadIds().reset();
> > +    }
> > +
> > +    private void shiftReadSetToNeighors() {
> > +        ReadHeadSet unflippedSet = getVertexValue().getUnflippedReadIds();
> > +        KmerFactory kmerFactory = new KmerFactory(Kmer.getKmerLength());
> > +        for (ReadHeadInfo info : unflippedSet) {
> > +            VKmer destForward = kmerFactory.getSubKmerFromChain(-info.getOffset() + 1, Kmer.getKmerLength(),
>
> So we can merge this branch now ?
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/uci-cbcl/genomix/pull/129/files#r9092953>
> .
>