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This is better phrased in terms of original strand/orientation produced by sequencing instrument, and "other strand" meaning the opposite to the one it called. This avoids trying to define what "top" means and any ambiguity that causes in relation to the template orientation (for example).

Fixes #639

This is better phrased in terms of original strand/orientation
produced by sequencing instrument, and "other strand" meaning the
opposite to the one it called.  This avoids trying to define what
"top" means and any ambiguity that causes in relation to the template
orientation (for example).

Fixes samtools#639
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Changed PDFs as of 6333a2c: SAMtags (diff). This link will expire in 30 days

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Base modifications section uses undefined term “top strand”

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