samtools/hts-specs — pull request #53 by jkbonfield (2014-11-17 12:01:23+00:00)
Title: Changed rnext/pnext/tlen to operate per template alignment rather than for primary alignments only.

This for a discussion point at the next GA4GH conference call, rather than for acceptance immediately.

Also see discussions in issues #44 and #48.

Things still to resolve:

1) TLEN definition has not changed from left/right to 5'/3'. We need to come to a decision once and for all.

2) Should PNEXT/RNEXT/TLEN *always* be linking together to form circles per template alignment, or should we permit the old method of linking to next (aka "other end" in a 2-segment world) primary alignment for cases where it makes more sense to the aligner. Ie do we have to double up the other end in such cases?

3) There are no additional auxiliary tags defined here yet; specifically no SI (which secondary alignment number this is within), SC (count of secondary alignments) and AC (total count of all segment alignments in file for this template). Field names subject to discussion and change of course.

4) No commentary of CC/CP. These are already in use by novoalign, but do not form a circular linked list meaning that it is not possible to start at any point and do a full round-trip to find all segment alignments for all primary, secondary and supplementary alignment cases.