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Add CIGAR =/X entry to version history appendix #743

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merged 1 commit into from
Nov 16, 2023

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jmarshall
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The = and X CIGAR operations were added to SAM in 07dc1c6 in July 2010, which was the initial addition of the TeX specification; they were not present in the previous Pages document. It's so long ago as to be barely relevant now, but it's worth adding them to the history appendix and identifying them as requiring VN:1.3 rather than VN:1.0.

See the comments on this biostars posting for the motivating context.

In the SAM regexp in §1.4, write the operations in the familiar canonical order (though it doesn't affect the meaning of the regexp). Define \cigarops{...} to improve the formatting of lists of CIGAR operations like "M/I/D" by making the slashes non-\tt, and also use this in SAMtags.tex.

These CIGAR operations were added in 07dc1c6 in July 2010,
which was the initial addition of the TeX specification; they
were not present in the previous Pages document. It's so long ago
as to be barely relevant now, but it's worth mentioning them as
requiring VN:1.3 rather than VN:1.0.

In the SAM regexp in §1.4, write the operations in the familiar
canonical order (though it doesn't affect the meaning of the regexp).
Define \cigarops{...} to improve the formatting of lists of CIGAR
operations like "M/I/D" by making the slashes non-\tt, and also use
this in SAMtags.tex.
@jmarshall jmarshall added the sam label Oct 19, 2023
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Changed PDFs as of 575fb47: SAMtags (diff), SAMv1 (diff).

@jkbonfield jkbonfield self-assigned this Nov 14, 2023
@zaeleus
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zaeleus commented Nov 15, 2023

Alternatively, \cigarops{MIS=X} can be referred to as "query consuming operations"; and \cigarops{M=XDN}, "reference consuming operations". This would remove the need for a new command and might make it more natural to read.

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jmarshall commented Nov 15, 2023

My preference would be to keep it explicit.

It's obvious what “reference-consuming” etc mean if you read the CIGAR section. But one of the first things we learn from editing specs or maintaining software like samtools is that People Don't Read…

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Thanks. Looks good to go.

@jmarshall jmarshall merged commit 346a94a into samtools:master Nov 16, 2023
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@jmarshall jmarshall deleted the cigar=X branch November 16, 2023 09:54
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3 participants