Add SAM recommendation of MAPQ=0 for unmapped reads #753
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We already have a recommendation that MAPQ of 255 should not be used. Expand on this to recommend zero is used when unmapped. This is purely a recommendation, made for maximum compatibility, and not a specification requirement. Fixes samtools#727
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Should this be further constrained to unmapped records with missing mapping qualities? That is, recommend using 0 instead of 255. Otherwise, is this recommending that all unmapped records have their mapping qualities reset to 0? |
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Is there any value in another mapping quality? By definition, if it's not mapped, the mapping quality doesn't make sense. |
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We already have a recommendation that MAPQ of 255 should not be used. Expand on this to recommend zero is used when unmapped.
This is purely a recommendation, made for maximum compatibility, and not a specification requirement.
Fixes #727