Yeah, that's fair enough.  And actually, if there are 2+ neighbors, you
have to make a decision about which to send to, for which you need to look
at the read anyway.

--
Jake Biesinger
Graduate Student
Xie Lab, UC Irvine


On Tue, Jan 21, 2014 at 9:06 AM, 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(),
>
> This one should work in the unmerged graph, directly after the graph
> building.
>
> My assumption here is that if the offset come from the unflippedset, then
> the offset should always <=0. Because the direction is the same, and the
> only shift sequence allowed should be -1 --> -2 --> -3 --> .... And the
> correspond flippedset should always be >= kmerlength-1.
>
> I was using the neighborlist before, then I found it really tedious to
> play with FF, FR ..., and also I need to compare the dest with every info
> inside the ReadHeadSet to get the proper ones. Then I decide to change to
> directly loop through the ReadHeadSet which is more deterministic.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/uci-cbcl/genomix/pull/129/files#r9044414>
> .
>