flag for first line in example should be 99 not 163 about hts-specs HOT 3 CLOSED

In the SAM/BAM format spec, it's confusing to describe "TLEN" as a "signed length", because lengths are non-negative quantities. TLEN could be described more clearly as an "offset". It is the observed offset from one end of the template to the other. For the leftmost segment, the offset is positive. For the rightmost, it is negative. In other cases it is undefined or 0.

from hts-specs.

You are correct about the flags in the example, and I am in the process of fixing it.

IMHO it's barely reasonable to describe something as a signed length, to mean a length (which is of course unsigned) together with a sign attached to it denoting something related. However in any case, we've been reworking the description of TLEN to hopefully make it clearer -- please have a look at #23 and comment there on whether you think it's an improvement.

from hts-specs.

The same change to the flags needs to be made for the padded SAM version of the same example that is provided in section 3.2. That is, the flags 163 and 83 for the first and last reads of qname=r001 should be 99 and 147, respectively. Sorry for not mentioning this previously-- I hadn't finished working all the way through the spec.

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