Committee has decided not to elide excess brackets in character classes

This affects the existing [[:rname:^*=]]... and the new [[:print:]].

Author: jmarshall

SAMv1.tex

@@ -33,7 +33,8 @@
 \newcommand*{\firstbytebox}[2]{\byteboxAux{#1}{#2}{\put(0,0){\line(0,1){\bytetotalheight}}}}
 \newcommand*{\bytebox}[2]{\byteboxAux{#1}{#2}{}}
 
-\newcommand*{\cclass}[1]{{\rm\sf :#1:}}
+\newcommand*{\cclass}[1]{[{\rm\sf :#1:}]}
+\newcommand*{\cclassexcept}[2]{[{\rm\sf :#1:}\caret #2]}
 \newcommand*{\caret}{\textsuperscript{$\wedge$}}
 
 \newcommand*{\memlimited}{\textcolor{gray}{\footnotesize\it limited}}
@@ -77,7 +78,6 @@ \section{The SAM Format Specification}
 For example, floating-point values in SAM always use `{\tt .}' for the decimal-point character.
 
 The regular expressions in this specification are written using the POSIX\,/\,IEEE Std 1003.1 extended syntax.
-For brevity, named character classes are written as~{\tt [\cclass{class}]} without an additional pair of brackets.
 
 \subsection{An example}\label{sec:example}
 Suppose we have the following alignment with bases in lowercase
@@ -209,9 +209,7 @@ \subsubsection{Character set restrictions}\label{sec:charset}
 {\tt [\verb"0-9A-Za-z!#$%&+./:;?@^_|~-"][\verb"0-9A-Za-z!#$%&*+./:;=?@^_|~-"]*}
 \end{center}
 
-% Pedantically this should be [[:rname:]^*=][[:rname:]]*, but we take advantage
-% of POSIX (Issue 7) section 9.3.5/8 to elide the excess brackets for clarity.
-\newcommand*{\rnameRegexp}{[\cclass{rname}\caret*=][\cclass{rname}]*}
+\newcommand*{\rnameRegexp}{[\cclassexcept{rname}{*=}][\cclass{rname}]*}
 
 \noindent
 For clarity, elsewhere in this specification we write this set of allowed characters as a character class~{\tt [\cclass{rname}]} and extend the POSIX regular expression notation to use {\tt\caret *=} to indicate the omission of `{\tt *}' and `{\tt =}' from the character class.
@@ -301,6 +299,7 @@ \subsection{The header section}
 These alternative names are not used elsewhere within the SAM file;
 in particular, they must not appear in alignment records' {\sf RNAME}
 or~{\sf RNEXT} fields.
+\newline
 \emph{Regular expression}: \emph{name}{\tt (,}\emph{name}{\tt )*}
 where \emph{name} is {\tt\rnameRegexp}\\\cline{2-3}
   & {\tt AS} & Genome assembly identifier. \\\cline{2-3}