Added basic ambiguity codes to base modification tags

Author: jkbonfield

SAMtags.tex

@@ -503,6 +503,10 @@ \subsection{Base modifications}
 below, taken from \emph{Modeling methyl-sensitive transcription factor
 motifs with an expanded epigenetic alphabet}, Coby Viner
 et.al. \url{https://www.biorxiv.org/content/10.1101/043794v1}.
+Additionally ambiguity codes {\tt A}, {\tt C}, {\tt G} and {\tt T}
+exist to represent unspecified modifications bases of their respective
+canonical base types, plus code {\tt N} to represent an unspecified
+modification of any base type.
 
 \begin{center}
 \begin{tabular}{lllll}
@@ -512,16 +516,21 @@ \subsection{Base modifications}
 C & h & 5hmC  & 5-Hydroxymethylcytosine & 76792 \\
 C & f & 5fC   & 5-Formylcytosine        & 76794 \\
 C & c & 5caC  & 5-Carboxylcytosine      & 76793 \\
+C & C &       & Ambiguity code; any C mod & \\
 \hline
 T & g & 5hmU  & 5-Hydroxymethyluracil   & 16964 \\
 T & e & 5fU   & 5-Formyluracil          & 80961 \\
 T & b & 5caU  & 5-Carboxyluracil        & 17477 \\
+T & T &       & Ambiguity code; any T mod & \\
 \hline
 A & a & 6mA   & 6-Methyladenine         & 28871 \\
+A & A &       & Ambiguity code; any A mod & \\
 \hline
 G & o & 8oxoG & 8-Oxoguanine            & 44605 \\
+G & G &       & Ambiguity code; any G mod & \\
 \hline
 N & n & Xao   & Xanthosine              & 18107 \\
+N & N &       & Ambiguity code; any mod & \\
 \end{tabular}
 \end{center}
 
@@ -536,6 +545,13 @@ \subsection{Base modifications}
 For example {\tt MM:Z:C+m,5,12,3;C+h,57;} may have an associated
 quality tag of {\tt MP:Z:5EB/}.
 
+Quality values for ambiguity codes give the likelihood that the
+modification is one of the possible codes compatible with that
+ambiguity code.  For example {\tt MM:Z:C+C,10 MP:Z:+} indicates a C
+call with an unspecified modification and the phred score of 10 (ASCII
+value {\tt +}).  This corresponds to a 90\% chance of the base being
+modified.
+
 
 \end{description}
 
@@ -560,6 +576,9 @@ \section{Tag History}
 \setlength{\parindent}{0pt}
 \newcommand*{\gap}{\vspace*{2ex}}
 
+\subsubsection*{June 2019}
+Added the MM and MP tags describing base modifications.
+
 \subsubsection*{January 2019}
 Added the OA tag for recording original/previous alignment information.