[DRAFT] Disallow commas and other punctuation in RNAME etc

Author: jmarshall

SAMv1.tex

@@ -230,6 +230,7 @@ \subsection{The header section}
 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}
+% FIXME SQ-SN regexp
   & {\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}.}
@@ -247,6 +248,7 @@ \subsection{The header section}
 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}
+% FIXME SQ-AN regexp
   & {\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}
@@ -346,9 +348,18 @@ \subsection{The alignment section: mandatory fields}\label{sec:alnrecord}
   \hline
   {\bf Col} & {\bf Field} & {\bf Type} & {\bf Regexp/Range} & {\bf Brief description} \\
   \hline
+% !-?A-~  :: all punct except @
   1 & {\sf QNAME} & String & \verb:[!-?A-~]{1,254}: & Query template NAME\\
   2 & {\sf FLAG} & Int & $[0,\,2^{16}-1]$ & bitwise FLAG \\
+% !-()+-<>-~ -- all punct except * =   forbid comma change +-< to +.-<>-~-
+
+% [!-()+-<>-~][!-~]*	7e14ccee  Nov 2010  fixed a few bugs in regexp
+%  [!-)+-<>-~][!-~]*	e6ca3195  Jul 2010  remove implict rules; more descs
+%  [!-)+-<>-~]+		cdaf8624  Jul 2010  update based on MKTrost (ie [^*=])
+%  [!-~]+		07dc1c67  Jul 2010
   3 & {\sf RNAME} & String & {\tt \char92*|[!-()+-\char60\char62-\char126][!-\char126]*} & Reference sequence NAME\\
+  3 & {\sf RNAME} & String & {\tt \char92*|[0-9A-Za-z!\#\char36\%\&+./:;?@\char94\_|\char126-][0-9A-Za-z!\#\char36\%\&+./:;?@\char94\_|\char126*=-]*} & Reference sequence NAME\\
+  3 & {\sf RNAME} & String & {\tt \char92*|[\char94"'`,()<>[]\{\}\char92*=][\char94"'`,()<>[]\{\}\char92]*} & Reference sequence NAME\\
   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 \\
@@ -435,6 +446,9 @@ \subsection{The alignment section: mandatory fields}\label{sec:alnrecord}
   also have an ordinary coordinate such that it can be placed at a
   desired position after sorting. If {\sf RNAME} is `*', no assumptions
   can be made about {\sf POS} and {\sf CIGAR}.
+
+FIXME reference name details.
+
 \item {\sf POS}: 1-based leftmost mapping POSition of the first {\sf
     CIGAR} operation that ``consumes'' a reference base (see table below).
     The first base in a reference sequence has coordinate 1. {\sf
@@ -1233,6 +1247,7 @@ \section{SAM Version History}\label{sec:history}
 \subsection*{1.6: 28 November 2017 to current}
 
 \begin{itemize}
+\item Allowable punctuation in RNAME and similar fields restricted. (Aug 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)