responding to review comments

Author: yfarjoun

SAMtags.pdf

@@ -83,10 +83,10 @@ \section{Standard tags}
   {\tt MQ} & i & Mapping quality of the mate/next segment \\
   {\tt NH} & i & Number of reported alignments that contains the query in the current record\\
   {\tt NM} & i & Edit distance to the reference \\
-  {\tt OC} & Z & Original CIGAR \\
-  {\tt OP} & i & Original mapping position \\
+  {\tt OA} & Z & Original Alignment \\
+  {\tt OC} & Z & (Deprecated in favor of {\tt OA}.) Original CIGAR \\
+  {\tt OP} & i & (Deprecated in favor of {\tt OA}.) Original mapping position \\
   {\tt OQ} & Z & Original base quality \\
-  {\tt PA} & Z & Previous Alignment \\
   {\tt PG} & Z & Program \\
   {\tt PQ} & i & Phred likelihood of the template \\
   {\tt PT} & Z & Read annotations for parts of the padded read sequence \\
@@ -178,10 +178,6 @@ \subsection{Additional Template and Mapping data}
 \item[NM:i:\tagvalue{}]
 Edit distance to the reference, including ambiguous bases but excluding clipping.
 
-\item[PA:Z:\tagregex{{\tt}\emph{rname}{\tt,}\emph{pos}{\tt,}\emph{strand}{\tt,}\emph{CIGAR}{\tt,}\emph{mapQ}{\tt,}\emph{NM}{\tt;}}]
-Previous aligment of template prior to realignment/unalignment by subsequent tool. 
-\emph{NM} can be dropped if unknown, but both commas should remain for parsing. 
-
 \item[PQ:i:\tagvalue{}]
 Phred likelihood of the template, conditional on both the mapping being correct.
 
@@ -249,13 +245,17 @@ \subsection{Barcodes}
 \end{description}
 
 \subsection{Original data}
-
 \begin{description}
+\item[OA:Z:\tagregex{({\tt}\emph{rname}{\tt,}\emph{pos}{\tt,}\emph{strand}{\tt,}\emph{CIGAR}{\tt,}\emph{mapQ}{\tt,}\emph{NM}{\tt;})+}]
+Original alignment of template prior to realignment/unalignment by subsequent tool. 
+Unknown values may be dropped, but commas should remain for parsing. 
+In the presence of an {\tt OA} tag, a subsequent tool should append the current information after the semicolon, not replace its content.
+
 \item[OC:Z:\tagvalue{cigar}]
-Original CIGAR, usually before realignment.
+Deprecated, use {\tt OA instead}. Original CIGAR, usually before realignment.
 
 \item[OP:i:\tagvalue{pos}]
-Original mapping position, usually before realignment.
+Deprecated, use {\tt OA instead}. Original mapping position, usually before realignment.
 
 \item[OQ:Z:\tagvalue{qualities}]
 Original base quality, usually before recalibration.