Slice Header updates for 370 #372
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Added some text to 12 Indexing about multi-ref and unmapped slices. |
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I don't have any issue with the additions, but as we're fixing things we may as well go belt-and-braces and add a few more bits to make it as unambiguous as possible.
I also noted that the RI data series has a comment "only present in multi-ref slices" for section 10.2, but not in the primary table in section 8.4. We should add a similar comment there too.
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Thank you for the comments @jkbonfield and @jmarshall . Back to you. |
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I approve what we have here. There are additional things listed in #370 so this is a big step forward but not a complete fix of that. We can either squash and merge this and produce a new PR for the container updates, or continue with adding things to this. I'm easy either way. |
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Thanks! I'll remove the table and squash. |
- MAPPED_SLICE_HEADER -> SLICE_HEADER - remove "unsorted" - clarify unmapped-placed and unmapped-unplaced distinction - add -2 multi-ref flag - multi-ref may have unmapped-placed but must only be external-ref - add multi-ref and unmapped text to index section threeparttable note for SLICE_HEADER clarify "unmapped-but-placed" Add RI data series text rm "unmapped-unplaced", add CIGAR comment and bold Set indexing Aln Start + Span to 0 for unmapped unmapped footnote rm idea that unmapped unplaced can't go into slices with other reads - some wording and formatting changes rm "Multiple-reference slices have index entries for each of their constituent reference sequences." not required -> not present Add MD5 clarification text, per JKB rm "as is possible in BAM" and clarify unmapped BAM bit flag
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I'll need someone with write access to merge. |
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Merged as 5d9fc52 I removed some trailing white space from some of the lines, to be tidy. I think @jmarshall initially gave me the hints to make these appear in diffs, using .gitconfig: We'll need to get one of the samtools maintainers to grant you and @cmnbroad commit access here. |
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Done — I've added @cmnbroad and @jmthibault79 to Specification authors, so you should now be able to push to hts-specs. Use this power wisely 😄 |
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Thanks @jmarshall |
jmarshall
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Great - thx @jmarshall ! |
Renamed
MAPPED_SLICE_HEADERBlock Content Type toSLICE_HEADERUpdated slice header text and table: