Somewhat unclear references to types in SAMtags

[cmdcolin]

"Optional fields are usually displayed as TAG:TYPE:VALUE; the type may be one of A (character), B (general
array), f (real number), H (hexadecimal array), i (integer), or Z (string)."

however there is C,I,S, and the notion that B is combined with the types is not immediately obvious from the sentence. somewhat unclear what H is also.

digging deeper into cross references from BAM/CRAM might reveal more clarity, but perhaps even explicitly linking to those docs from SAMtags could help

[jkbonfield]

c, C, i, I and s, S are (or were) BAM encoding specific. So in SAM we could have AB:i:7 while in BAM it would be e.g. AB C \007.

Once "B" was added as a byte array, the internal C,I,S representation was exposed to the text format. Although arguably it's not needed and i could have sufficed, I am guessing this was to aid rapid conversion to BAM and to avoid the need for multiple passes through the data to work out the minimum and maximum values.

PS. I'm not sure I like "are usually displayed". For SAM it's mandatory, and there's really no "display" for CRAM or BAM. It's a bit of a woolly definition. We should probably copy the table from SAMv1.tex where it defines them more precisely using a regular expression.