samtools/hts-specs — pull request #23 by jrandall (2014-03-17 13:25:32+00:00)
Title: TLEN clarification to SAM spec

States clearly that TLEN should be length (i.e. pos.right-pos.left+1) rather than subtraction
(i.e. pos.right-pos.left) -- this was somewhat ambiguous before.

Makes it clear that the sign character is prepended to the

States that TLEN may be set to 0 whenever the information is unavailable,
and gives examples as to when this would be the case.

Adds explicit statement that soft-clipped bases don't count as mapped bases.