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CRAM: Need to improve feature positions description #747

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daviesrob opened this issue Nov 30, 2023 · 1 comment · Fixed by #754
Closed

CRAM: Need to improve feature positions description #747

daviesrob opened this issue Nov 30, 2023 · 1 comment · Fixed by #754
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@daviesrob
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The CRAM FP data series is described as "position of the read feature" in the CRAMv3 spec. here and here. This seems to imply an absolute position, but in fact it's relative to the previous feature, as can be seen in the encoders for htslib, htsjdk and noodles. To make this clear without having to read existing implementations, the "Read feature records" section could do with a line or two explaining how the FP data series works.

@daviesrob daviesrob added the cram label Nov 30, 2023
@jkbonfield
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I thought I'd documented this in CRAM 4, even if it was just the pseudocode bit, but apparently not. (I was probably misremembering AP.)

Good spot.

@jkbonfield jkbonfield self-assigned this Jan 2, 2024
jkbonfield added a commit to jkbonfield/hts-specs that referenced this issue Jan 29, 2024
jkbonfield added a commit to jkbonfield/hts-specs that referenced this issue Jan 29, 2024
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