[DRAFT] Disallow commas and other punctuation in RNAME etc

Add previously omitted SQ-AN history note.

SAMv1.tex

@@ -32,6 +32,9 @@
 \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*{\caret}{\textsuperscript{$\wedge$}}
+
 \makeindex
 
 \begin{document}
@@ -178,6 +181,20 @@ \subsection{Terminologies and Concepts}
 mapping, all the other mappings get mapping quality $<$Q3
 and are ignored by most SNP/INDEL callers.}
 
+\subsubsection{Query and reference sequence names}\label{sec:qrnames}
+
+Reference sequence names may contain any printable ASCII characters in the range {\tt [!-\verb:~:]} apart from backslashs, commas, quotation marks, and brackets---i.e., apart from `{\tt \verb:\:\,,\,"`'\,()\,[]\,\verb:{}:\,<>}'---and may not start with `{\tt *}' or `{\tt =}'.
+Thus they match the following regular expression:
+\begin{center}
+{\tt [\verb"0-9A-Za-z!#$%&+./:;?@^_|~-"][\verb"0-9A-Za-z!#$%&*+./:;=?@^_|~-"]*}
+\end{center}
+
+\newcommand*{\rnameRegexp}{[\cclass{rname}\caret*=][\cclass{rname}]*}
+
+\noindent
+For clarity, elsewhere in this specification we write this set of 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.
+Thus this regular expression can be written more clearly as {\tt\rnameRegexp}.
+
 \subsection{The header section}
 Each header line begins with the character `{\tt @}' followed by
 one of the two-letter header record type codes defined in this section.
@@ -229,7 +246,7 @@ \subsection{The header section}
 The {\tt SN} tags and all individual {\tt AN} names in all {\tt @SQ} lines
 must be distinct.
   The value of this field is used in the
-  alignment records in {\sf RNAME} and {\sf RNEXT} fields. Regular expression: {\tt [!-)+-\char60\char62-\char126][!-\char126]*}\\\cline{2-3}
+  alignment records in {\sf RNAME} and {\sf RNEXT} fields. Regular expression: {\tt\rnameRegexp}\\\cline{2-3}
   & {\tt LN}* & Reference sequence length. \emph{Range}: $[1,\,2^{31}-1]$\\\cline{2-3}
   & {\tt AH} & Indicates that this sequence is an alternate locus.%
 \footnote{See \url{https://www.ncbi.nlm.nih.gov/grc/help/definitions} for descriptions of \emph{alternate locus} and \emph{primary assembly}.}
@@ -240,13 +257,12 @@ \subsection{The header section}
 to this reference sequence.%
 \footnote{For example, given `{\tt @SQ SN:MT AN:chrMT,M,chrM LN:16569}',
 tools can ensure that a user's request for any of `MT', `chrMT', `M',
-or~`chrM' succeeds and refers to the same sequence.
-Note the restricted set of characters allowed in an alternative name.}
+or~`chrM' succeeds and refers to the same sequence.}
 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.
 \emph{Regular expression}: \emph{name}{\tt (,}\emph{name}{\tt )*}
-where \emph{name} is {\tt [0-9A-Za-z][0-9A-Za-z*+.@\_|-]*}\\\cline{2-3}
+where \emph{name} is {\tt\rnameRegexp}\\\cline{2-3}
   & {\tt AS} & Genome assembly identifier. \\\cline{2-3}
   & {\tt DS} & Description.  UTF-8 encoding may be used.\\\cline{2-3}
   & {\tt M5} & MD5 checksum of the sequence.  See Section~\ref{sec:ref-md5}\\\cline{2-3}
@@ -348,11 +364,11 @@ \subsection{The alignment section: mandatory fields}\label{sec:alnrecord}
   \hline
   1 & {\sf QNAME} & String & \verb:[!-?A-~]{1,254}: & Query template NAME\\
   2 & {\sf FLAG} & Int & $[0,\,2^{16}-1]$ & bitwise FLAG \\
-  3 & {\sf RNAME} & String & {\tt \char92*|[!-()+-\char60\char62-\char126][!-\char126]*} & Reference sequence NAME\\
+  3 & {\sf RNAME} & String & {\tt \verb"\*"|\rnameRegexp} & Reference sequence NAME\footnotemark \\
   4 & {\sf POS} & Int & $[0,\,2^{31}-1]$ & 1-based leftmost mapping POSition \\
   5 & {\sf MAPQ} & Int & $[0,\,2^8-1]$ & MAPping Quality \\
   6 & {\sf CIGAR} & String & {\tt \char92*|([0-9]+[MIDNSHPX=])+} & CIGAR string \\
-  7 & {\sf RNEXT} & String & {\tt \char92*|=|[!-()+-\char60\char62-\char126][!-\char126]*} & Ref. name of the mate/next read\\
+  7 & {\sf RNEXT} & String & {\tt \verb"\*"|=|\rnameRegexp} & Reference name of the mate/next read \\
   8 & {\sf PNEXT} & Int & $[0,\,2^{31}-1]$ & Position of the mate/next read \\
   9 & {\sf TLEN} & Int & $[-2^{31}+1,\,2^{31}-1]$ & observed Template LENgth \\
   10 & {\sf SEQ} & String & {\tt \char92*|[A-Za-z=.]+} & segment SEQuence\\
@@ -361,6 +377,9 @@ \subsection{The alignment section: mandatory fields}\label{sec:alnrecord}
 \end{tabular}
 \end{center}
 
+\footnotetext{Reference sequence names may contain any printable ASCII characters with the exception of certain punctuation characters, and may not start with `{\tt *}' or `{\tt =}'.
+See Section~\ref{sec:qrnames} for details and an explanation of the {\tt [\cclass{rname}]} notation.}
+
 \begin{enumerate}
 \item {\sf QNAME}: Query template NAME. Reads/segments having identical {\sf QNAME}
 	are regarded to come from the same template. A {\sf QNAME} `{\tt *}'
@@ -1233,6 +1252,9 @@ \section{SAM Version History}\label{sec:history}
 \subsection*{1.6: 28 November 2017 to current}
 
 \begin{itemize}
+\item Restricted the allowable punctuation characters in RNAME and similar fields.
+The sets of characters allowed in {\tt @SQ SN} and {\tt @SQ AN} are now identical, which slightly enlarges the previous {\tt AN} set.
+(Sep 2018)
 \item B array optional fields may have no entries---this was already representable in BAM, clarified that empty arrays are permitted in SAM too. (Jul 2018)
 \item Add {\tt @SQ DS} header tag. (Jul 2018)
 \item Add {\tt @RG BC} header tag. (Apr 2018)
@@ -1243,6 +1265,7 @@ \subsection*{1.6: 28 November 2017 to current}
 \subsection*{1.5: 23 May 2013 to November 2017}
 
 \begin{itemize}
+\item Add {\tt @SQ AN} header tag, allowing only alphanumeric and `\verb"*+-.@_|"' characters in its names. (Jul 2017)
 \item Add {\tt @SQ AH} header tag. (Mar 2017)
 \item Auxiliary tags migrated to SAMtags document. (Sep 2016)
 \item Z and H auxiliary tags are permitted to be zero length. (Jun 2016)