Commits on Jan 15, 2019

1. Disallow commas and other punctuation in RNAME etc (PR samtools#333) …

   Disallow \ , "`' ()[]{}<> punctuation characters in reference sequence
   names. Commas and angle brackets are used to delimit refnames in other
   SAM fields (e.g. SA) and in VCF files, and restricting these other
   characters facilitates future delimiter and quoting syntax.
   
   Statistics gathered from various reference sequence archives suggest
   that these characters appear vanishingly infrequently in refnames in
   existing files in the wild.
   
   Fixes the SAM aspects of samtools#124, samtools#167, samtools#258, and samtools#291.
   
   Add appendix describing parsing `name:beg-end` when name allows colons:
   pseudocode description of algorithm to detect ambiguous input, as proposed
   in a comment on samtools#124; suggest also accepting an alternative `{name}:beg-end`
   delimited notation.
   
   Add previously omitted SQ-AN history note.

   

   jmarshall committed Jan 15, 2019
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