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Allow for UTF-8 field values in header regular expression #726

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Allow for UTF-8 field values in header regular expression #726

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4560a37
Allow for UTF-8 field values in header regular expression
jmarshall May 4, 2023
3692643
Committee has decided not to elide excess brackets in character classes
jmarshall Jan 28, 2025
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14 changes: 8 additions & 6 deletions SAMv1.tex
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Original file line number Diff line number Diff line change
Expand Up @@ -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}}
Expand Down Expand Up @@ -212,9 +213,7 @@ \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.
Expand All @@ -227,8 +226,10 @@ \subsection{The header section}
each data field follows a format `{\tt TAG:VALUE}' where {\tt TAG}
is a two-character string that defines the format and content of {\tt VALUE}.
Thus header lines match {\tt
/\char94@(HD|SQ|RG|PG)(\char92t[A-Za-z][A-Za-z0-9]:[
-\char126]+)+\$/} or {\tt /\char94@CO\char92t.*/}.
/\char94@(HD|SQ|RG|PG)(\char92t[A-Za-z][A-Za-z0-9]:[\cclass{print}]+)+\$/}
or {\tt /\char94@CO\char92t.*/}.%
\footnote{{\tt [\cclass{print}]} indicates that header field values contain printable characters, i.e.,~non-control characters.
For fields limited to~ASCII, which is the majority, this is equivalent to~{\tt [ -\char126]}.}
Within each (non-{\tt @CO}) header line, no field tag may appear more than
once and the order in which the fields appear is not significant.

Expand Down Expand Up @@ -302,6 +303,7 @@ \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}
Expand Down