+1 for nextMatePosition from Heng for the reasons given by David Glazer

On 27 May 2014, at 20:19, David Glazer <notifications@github.com> wrote:

> In src/main/resources/avro/reads.avdl:
> 
> > +
> > +    // By convention, each read has one and only one alignment with both of the
> > +    // two following flags being flase. The full read sequence and quality
> > +    // should be present in this alignment.
> > +    union { null, boolean } secondaryAlignment = false;  // SAM flag 0x100
> > +    union { null, boolean } supplementAlignment = false; // SAM flag 0x800
> > +
> > +    // The portion of the read sequence and quality in the alignment. In a
> > +    // supplementary or seconday alignment, alignedSequence and alignedQuality
> > +    // may be shorter than the read sequence and quality, or even absent.
> > +    union { null, string } alignedSequence = null;
> > +    array<int> alignedQuality = [];
> > +
> > +    // The mapping of the primary alignment of the (readNumber+1)%numberReads
> > +    // read in the fragment. It replaces mate position and mate strand in SAM.
> > +    union { null, GAMappingPosition } nextMatePosition = null;
> IIUC, in today's world the way you find mates is you look for reads that share a qname and contig, and match the specified position. Not very elegant from first principles, but changing it adds a bunch of burden to repository implementors that I'm very leery of doing in v0.5. (Since they'd have to build a whole new index.)
> 
> I'm inclined to leave it as proposed for now, and know we'll be changing it (e.g. by adding alternate options for specifying mate pairs) down the road. I'm open to other suggestions, but every time we tried it got hairy; this approach by @lh3 feels like a nice balance between the past and the future.
> 
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