Explicitly permit eg N+m in MM tag (PR#799)

The text already states that an unmodified base of N means we count
any base type, but base N code N in the table is a little misleading
as to the intention.  It was intended to mean any unspecified
modification, in the same way C+C is any unspecified C mod, but in
this case it's against all bases rather than a specific base type.

However that doesn't solve the issue of whether we can record specific
mods against any "fundamental" source base.  Clarified this by adding
an extra line to the table and some text.  (However note this doesn't
necessarily imply downstream processing tools will not do any
compatibility assessment and reject N+m when the SEQ base is a T.)

Fixes samtools#785

Author: jkbonfield

Diff for: SAMtags.tex

@@ -530,8 +530,9 @@ \subsection{Base modifications}
 If the modification is not one of the standard common types (listed below) it can be specified as a numeric ChEBI code.
 For example `{\tt C+76792,57;}' is the same as `{\tt C+h,57;}'.
 
-An unmodified base of `{\tt N}' means count any base in {\sf SEQ}, not only those of `{\tt N}'.
+A fundamental base of `{\tt N}' means count any base in {\sf SEQ}, not only those of `{\tt N}'.
 Thus `{\tt N+n,100;}' means the 101st base is Xanthosine (n), irrespective of the sequence composition.
+A fundamental base of `{\tt N}' may also be used with a base-specific modification code to force the counting to be applied per base rather than per base-type.
 
 The standard code types and their associated ChEBI values are listed
 below, taken from Viner {\it et al.}%
@@ -567,6 +568,7 @@ \subsection{Base modifications}
 \hline
 N & n & Xao   & Xanthosine              & 18107 \\
 N & N &       & Ambiguity code; any mod & \\
+N & any &     & Mod applied to any base & \\
 \end{tabular}
 \end{center}