Recommend 1bp SEQ with QUAL="*" as quality-unavailable. #752
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The use of \textsc{cr\>lf} breaks pdfTeX 3.14159265-2.6-1.40.18.
Switching to \textsc{cr\,lf} cures it. Visually they're almost
identical and it's only a footnote anyway.
"*" is either QUAL 9, or QUAL unavailable. Made a recommendation in a footnote, mainly as an indication that the ambiguity exists. In practice it's vanishingly unlikely to matter. Fixes samtools#715
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IMHO PR #724 has the footnote in the better position, so I'll close this PR, cherry-pick the non-breaking space commit, and coalesce the best of both footnote texts over there. |
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The change is simply a footnote indicating the presence of the ambiguity and a mild recommendation, however it's not likely to make any practical difference in real-world data where even if 1bp reads exist their quality values aren't likely to be a deciding factor over their validity.
Also in attempting to build the SAM spec my latex blew up. This turns out to be due to #670 which added use of
\>for non-breaking space. Our systems here are pretty old, and latex couldn't cope with that. However in the interests of keeping the spec as easy to build as possible, I did a trivial replacement in its own commit.