diff --git a/SAMv1.tex b/SAMv1.tex index 7b0b4c7a..6987501f 100644 --- a/SAMv1.tex +++ b/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}} @@ -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. @@ -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. @@ -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}