Clarify when VCF meta entries are mandatory about hts-specs HOT 6 CLOSED

My vote is that they be treated just like any other header lines: they are optional but if present must be well-formed.
Note that tools may still choose to require them (and will exit with a friendly error saying "sorry, but we won't process your VCF until it has them included"). But the spec doesn't need to enforce that.

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@eitanbanks +1 from me.

However, to make it clear that we do not encourage undefined tags, I included the following sentence in the draft:

Note that BCF, the binary counterpart of VCF, requires that all entries are
present, therefore the use of undefined tags is strongly discouraged.

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Thank you both for your answers, I agree with the "optional but well-formed if present" idea. The BCF note is also adequate, but I still find the previous paragraph confusing.

If I can make a suggestion, I would write something like the following. The order is somewhat changed to refer first to meta-information lines in general, then recommendations for specific tags.

File meta-information is included after the ## string and must be key=value
pairs. Meta-information lines are optional, but if they are present then
they must be completely well-formed {\color{red} and their ID must be
unique within their type. Note that BCF, the binary counterpart of VCF, requires
that all entries are present.

It is strongly encouraged to include meta-information lines describing the \texttt{INFO},
\texttt{FILTER}, \texttt{FORMAT} and {\color{red}\texttt{contig}} entries used
in the body of the VCF file.

Meta-information lines can be in any order with the exception of fileformat
which must come first.

Please let me know your opinions, and if I should make a PR for this.

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I think that reads better, thank you. There was a proposal discussed at length offline to make the ID attribute mandatory for all structured values. With this addition, the section would read like this:

File meta-information is included after the ## string and must be key=value
pairs. Meta-information lines are optional, but if they are present then
they must be completely well-formed. {\color{red} Note that BCF, the binary
counterpart of VCF, requires that all entries are present. It is strongly
encouraged to include meta-information lines describing the entries used in the
body of the VCF file.

All structured lines that have their value enclosed within "$<>$" require an ID
which must be unique within their type.

Meta-information lines can be in any order with the exception of fileformat
which must come first.}

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Looks good to me :)

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Since there were no further comments, I am closing the issue as solved.

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