File tree Expand file tree Collapse file tree 1 file changed +5
-2
lines changed
Expand file tree Collapse file tree 1 file changed +5
-2
lines changed Original file line number Diff line number Diff line change @@ -77,6 +77,7 @@ \section{The SAM Format Specification}
7777For example, floating-point values in SAM always use `{\tt .}' for the decimal-point character.
7878
7979The regular expressions in this specification are written using the POSIX\, /\, IEEE Std 1003.1 extended syntax.
80+ For brevity, named character classes are written as~{\tt [\cclass {class}]} without an additional pair of brackets.
8081
8182\subsection {An example }\label {sec:example }
8283Suppose we have the following alignment with bases in lowercase
@@ -223,8 +224,10 @@ \subsection{The header section}
223224each data field follows a format `{\tt TAG:VALUE}' where {\tt TAG}
224225is a two-character string that defines the format and content of {\tt VALUE}.
225226Thus header lines match {\tt
226- /\char 94@(HD|SQ|RG|PG)(\char 92t[A-Za-z][A-Za-z0-9]:[
227- -\char 126]+)+\$ /} or {\tt /\char 94@CO\char 92t.*/}.
227+ /\char 94@(HD|SQ|RG|PG)(\char 92t[A-Za-z][A-Za-z0-9]:[\cclass {print}]+)+\$ /}
228+ or {\tt /\char 94@CO\char 92t.*/}.%
229+ \footnote {{\tt [\cclass {print}]} indicates that header field values contain printable characters, i.e.,~non-control characters.
230+ For fields limited to~ASCII, which is the majority, this is equivalent to~{\tt [ -\char 126]}.}
228231Within each (non-{\tt @CO}) header line, no field tag may appear more than
229232once and the order in which the fields appear is not significant.
230233
You can’t perform that action at this time.
0 commit comments