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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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7 changes: 5 additions & 2 deletions SAMv1.tex
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Expand Up @@ -77,6 +77,7 @@ \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
Expand Down Expand Up @@ -223,8 +224,10 @@ \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.

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