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