updates following the discussion in #582

SAMtags.tex

@@ -498,28 +498,33 @@ \subsection{Base modifications}
 This potentially differs to the sequence stored in the main SAM {\sf SEQ} field if the latter has been reverse complemented, in which case SAM {\sf FLAG} 0x10 must be set.
 This means modification positions are also recorded against the original orientation (i.e. starting at the 5' end), and count the original base types.
 
-Each modified base listed also has a quality value associated with it.
+Each modified base prediction listed also has a quality value associated with it.
 Given the unmodified base already has a phred likelihood, this base modification quality should be interpreted as the likelihood of this modification being correct given an assumption the original call is correct.
 
 \begin{description}
-\item[Mm:Z:\tagregex{([ACGTUN][-+][.?]([a-z]+|[0-9]+)(,[0-9]+)*;)*}]
+\item[Mm:Z:\tagregex{([ACGTUN][-+]([a-z]+|[0-9]+)(,[0-9]+)*[.?]?;)*}]
 \hfill\\
 The first character is the unmodified ``fundamental'' base as reported
 by the sequencing instrument for the top strand.
 It must be one of {\tt A}, {\tt C}, {\tt G}, {\tt T}, {\tt U} (if RNA) or {\tt N} for anything else, including any IUPAC ambiguity codes in the reported SEQ field.
 Note {\tt N} may be used to match any base rather than specifically an {\tt N} call by the sequencing instrument.
 This may be used in situations where the base modification is not a derivation of a standard base type.
-This is followed by either plus or minus indicating the strand the modification was observed on (relative to the original sequenced strand of {\sf SEQ} with plus meaning same orientation),\footnote{Hence a tool that may reverse complement sequences does not need to understand how to manipulate the {\tt Mm} and {\tt Ml} tags.} and one or more base modification codes.
-This is followed by either {\tt .} or {\tt ?} describing how skipped seq bases of the stated base type should be interpreted by downstream tools. 
-When this flag is {\tt .} these bases should be assumed to be unmodified. When it is {\tt ?} there is no information about the modification status of these bases provided.
-This is then followed by a comma separated list of how many unmodified seq bases of the stated base type to skip, stored as a delta to the last and starting with 0 as the first (or next) base, starting from the uncomplemented 5' end of the {\sf SEQ} field.
+This is followed by either plus or minus indicating the strand the modification was analysed for (relative to the original sequenced strand of {\sf SEQ} with plus meaning same orientation),\footnote{Hence a tool that may reverse complement sequences does not need to understand how to manipulate the {\tt Mm} and {\tt Ml} tags.} and one or more base modification codes.
+Following the base modification codes is an optional {\tt .} or {\tt ?} describing how skipped seq bases of the stated base type should be interpreted by downstream tools. 
+When this flag is {\tt ?} there is no information about the modification status of the skipped bases provided.
+When this flag is not present, or it is {\tt .}, these bases should be assumed to have low probability of modification\footnote{The decision whether a base is assumed to be unmodified or has a probability explicitly provided is up to the modification calling program. Some programs will elide calls with modification probabilites below a threshold to provide a more compact modification tag.}.
+This is then followed by a comma separated list of how many seq bases of the stated base type to skip, stored as a delta to the last and starting with 0 as the first (or next) base, starting from the uncomplemented 5' end of the {\sf SEQ} field.
 This number series is comparable to the numbers in an {\tt MD} tag,
 albeit counting specific base types only and potentially reverse-complemented.
 
-For example {\tt C+.m,5,12,0;} tells us there are three
-5-Methylcytosine bases on the top strand of {\sf SEQ}.
-The first 5 {\tt C} bases are unmodified and the 6th is modified, as are the 19th (with 12 between the 6th and 19th) and 20th.
-Similarly {\tt G-.m,14;} indicates the 15th {\tt G} is a 5-Methylcytosine on the opposite strand (still counting using the top strand base calls from the 5' end).
+For example {\tt C+m,5,12,0;} tells us there are three
+potential 5-Methylcytosine bases on the top strand of {\sf SEQ}.
+The first 5 {\tt C} bases are unmodified and the 6th, 19th and 20th have modification status indicated by the corresponding probabilities in the {\tt Ml} tag. The 12 cytosines between the 6th and 19th cytosine are unmodified. Modification probabilities for the 17 skipped cytosines are not provided.
+
+When the {\tt ?} flag is present the tag {\tt C+.m?,5,12,0;} tells us the modification status of the first five 
+cytosine bases is unknown, the sixth cytosine is called, followed by 12 more unknown cytosines, and the 19th and 20th are called.
+
+Similarly {\tt G-m,14;} indicates the 15th {\tt G} there might be a 5-Methylcytosine on the opposite strand (still counting using the top strand base calls from the 5' end).
 When the alignment record is reverse complemented (SAM flag 0x10) these two examples do not change since the tag always refers to the as-sequenced orientation.
 See the test/SAMtags/MM-orient.sam file for examples.
 
@@ -529,16 +534,16 @@ \subsection{Base modifications}
 Note it is permitted for the coordinate list to be empty (for example {\tt Mm:Z:C+m;}), which may be used as an explicit indicator that this base modification is not present.
 It is not permitted for coordinates to be beyond the length of the sequence.
 
-When multiple modifications are listed, for example {\tt C+.mh,5,12,0;}, it indicates the modification may be any of the stated bases.
+When multiple modifications are listed, for example {\tt C+mh,5,12,0;}, it indicates the modification may be any of the stated bases.
 The associated confidence values in the {\tt Ml} tag may be used to determine the relative likelihoods between the options.
-The example above is equivalent to {\tt C+.m,5,12,0;C+.h,5,12,0;}, although this will have a different ordering of confidence values in {\tt Ml}.
+The example above is equivalent to {\tt C+m,5,12,0;C+h,5,12,0;}, although this will have a different ordering of confidence values in {\tt Ml}.
 Note ChEBI codes cannot be used in the multi-modification form (such as the {\tt C+.mh} example above).
 
 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;}.
+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}.
-Thus {\tt N+.n,100;} means the 101st base is Xanthosine (n), irrespective of the sequence composition.
+Thus {\tt N+n,100;} means the 101st base is Xanthosine (n), irrespective of the sequence composition.
 
 The standard code types and their associated ChEBI values are listed
 below, taken from Viner {\it et al.}%