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sam: Quality score ambiguity when sequence is a single base #715

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zaeleus opened this issue Apr 13, 2023 · 2 comments · May be fixed by #724
Open

sam: Quality score ambiguity when sequence is a single base #715

zaeleus opened this issue Apr 13, 2023 · 2 comments · May be fixed by #724
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@zaeleus
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zaeleus commented Apr 13, 2023

This in regard to Sequence Alignment/Map Format Specification (2022-08-22) § 1.4 "The alignment section: mandatory fields".

In the following SAM record, the quality scores field (QUAL) is ambiguous.

*	4	*	0	255	*	*	0	0	A	*

Since there is a singe base in the sequence, the quality scores field can either be unavailable (*) or represent [9].
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jkbonfield commented Apr 14, 2023 •
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This has been a known issue for a long time, although probably not tracked here. I don't think there's anything we can do about it really. Fortunately, it also means a length 1 sequence which doesn't generally happen in the wild, so it's a moot point. Most implementations just take the most probable view which is to interpret is as unknown and attempting to remove ambiguity would turn a harmless issue into a potentially more serious one.

Edit: as an aside, I note you're also using MAPQ of 255 for "unavailable". Commendable, but my experience is that everyone just uses 0 with unmapped data. I think this is because when FLAG 4 is set the specification states no assumption can be made about MAPQ, so it just feels cleaner to zero it out as all other fields have been.

@jkbonfield jkbonfield added the sam label Apr 24, 2023
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TODO: Add footnote to say a single "*" for length 1 is still "unavailable"

@jkbonfield jkbonfield self-assigned this Apr 25, 2023
jkbonfield added a commit to jkbonfield/hts-specs that referenced this issue May 2, 2023
@jkbonfield
Document the ambiguity of 1-base long seq with QUAL *
cca15e8 
This is an extreme edge case likely to never occur, but nevertheless
tool implementors still need to know how to handle it.  Given it *may*
be QUAL 9 or it *may* be QUAL "unknown", we treat it as always unknown.

Fixes samtools#715
@jkbonfield jkbonfield linked a pull request May 2, 2023 that will close this issue
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@zaeleus zaeleus mentioned this issue Jun 8, 2023
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@jmarshall jmarshall mentioned this issue Aug 20, 2023
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jkbonfield added a commit to jkbonfield/hts-specs that referenced this issue Jan 29, 2024
@jkbonfield
Document SAM ambiguity of 1bp long seq with QUAL "*".
a8550ef 
"*" 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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Document the ambiguity of 1-base long seq with QUAL * jkbonfield/hts-specs
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