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Removed "intended to be" and don't touch PDF
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lh3 committed Nov 9, 2017
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10 changes: 5 additions & 5 deletions SAMtags.tex
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Expand Up @@ -60,7 +60,7 @@ \section{Standard tags}
{\tt BQ} & Z & Offset to base alignment quality (BAQ) \\
{\tt BZ} & Z & Phred quality of the unique molecular barcode bases in the {\tt OX} tag \\
{\tt CC} & Z & Reference name of the next hit \\
{\tt CG} & B,I & {\sf CIGAR} in BAM's binary encoding (see also the {\sf cigar} field in the BAM spec); intended to be a BAM-only tag and restricted to CIGARs with $>$65535 operators \\
{\tt CG} & B,I & BAM only: {\sf CIGAR} in BAM's binary encoding if it consists of $>$65535 operators \\
{\tt CM} & i & Edit distance between the color sequence and the color reference (see also {\tt NM})\\
{\tt CO} & Z & Free-text comments \\
{\tt CP} & i & Leftmost coordinate of the next hit \\
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\item[CG:B:I,\tagvalue{encodedCigar}]
Real CIGAR in its binary form if it contains $>$65535 operations. This is
intended to be a BAM file only tag as a workaround of BAM's incapability to
store long CIGARs in the standard way. SAM and CRAM files created with updated
tools aware of the workaround are not expected to contain this tag. See also
the footnote in Section 4.2 of the SAM spec for details.
a BAM file only tag as a workaround of BAM's incapability to store long CIGARs
in the standard way. SAM and CRAM files created with updated tools aware of the
workaround are not expected to contain this tag. See also the footnote in
Section 4.2 of the SAM spec for details.

\item[CP:i:\tagvalue{pos}]
Leftmost coordinate of the next hit.
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