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Segment name must not contain +, nor -, #40

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merged 1 commit into from
Sep 27, 2016

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@sjackman sjackman commented Sep 21, 2016

Commas are used to separate segment IDs in a path.

Closes #37.

This clarification is suggested by @lh3 in #37 (comment)

My recommendation is for GFA1, we test regex pattern /[+-],/ at an S-line. If we find a match, we throw an error, saying the current spec does not allow it. I think this treatment is working most of time in practice. I have seen commas in sequence names, but I am yet to see a /[+-],/ pattern – it is very rare.

Commas are used to separate segment IDs in a path.

Closes GFA-spec#37.
@sjackman sjackman self-assigned this Sep 21, 2016
@sjackman sjackman added the bug label Sep 21, 2016
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Great. Maybe we should also make clear that this requirement is not checked by the regular expression? (Because other limitations, such as that the name should not start with * or = are implied by it).

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sjackman commented Sep 22, 2016

As Heng Li @lh3 proposed this fix, we have three 👍. I'll merge on 2016-09-26.

@sjackman sjackman added this to the 1.0 milestone Sep 22, 2016
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sjackman commented Sep 22, 2016

Great. Maybe we should also make clear that this requirement is not checked by the regular expression? (Because other limitations, such as that the name should not start with * or = are implied by it).

I'm starting to find the regular expressions more trouble than help.

@sjackman sjackman merged commit e7576cd into GFA-spec:master Sep 27, 2016
@sjackman sjackman deleted the segment-comma branch September 27, 2016 00:11
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Merged.

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