[Samtools-help] definitions of template, segment, and read

[Josep I. L. L. <jos...@in...>]

Hello.

While writing a paper about sequencing strategies with paired-ends, I
face the dilema of how to refer to the sequenced ends of a pair (reads
or segments?). Should I reserve the term "read" for the whole pair? I
personally enjoy the definitions given in the SAM specifications.
However, I don't see the SAM definitions widely adopted in the
literature (yet?). For example, people keep talking about the "insert
size distribution", instead of "template length distribution"; and the
term "read" is widely used to refer to a single segment.

I want to ask if the definitions given by the SAM format have ever been
intended to become a standard in the literature (beyond the sam files
environment). To put it another way: would I have the blessing of the
samtools developers if I didn't follow their definitions when talking
about sequencing strategies in a paper?