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Make the BED parser not interpret general tab delimited data as BED12 #2199

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merged 1 commit into from
Aug 21, 2021

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@cmdcolin cmdcolin commented Aug 9, 2021

The current @gmod/bed parser makes I think too assumptions about what a BED file is if no info is specified e.g. as with BED tabix files.

For example, currently the inversion BED tabix files in #2198 are displayed incorrectly (it thinks it is an intron because it thinks it's like a BED12 file)

This proposes using an "unassuming" BED parser that will use the strand/score fields if it makes sense to, otherwise it just stores the fieldnames, and only tries to use @gmod/bed if the code is actually a BED12 file or has autoSql attached

With this change added, the BED tabix files in #2198 display properly e.g. just as boxes indicating the region of the inversion, and some fields that don't have any description are called field5,field6,field7... in the feature details panel

@github-actions github-actions bot added the needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) label Aug 9, 2021
@cmdcolin cmdcolin added enhancement New feature or request and removed needs label triage Needs a label to show in changelog (breaking, enhancement, bug, documentation, or internal) labels Aug 9, 2021
@cmdcolin cmdcolin marked this pull request as draft August 9, 2021 19:18
@cmdcolin cmdcolin marked this pull request as ready for review August 21, 2021 02:49
@cmdcolin cmdcolin changed the title Make an unassuming version of the BED parser Make the BED parser not interpret general tab delimited data as BED12 Aug 21, 2021
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Change added to @gmod/bed

@cmdcolin cmdcolin merged commit 9a170c8 into main Aug 21, 2021
@cmdcolin cmdcolin deleted the bed_parser_unassuming branch August 21, 2021 02:52
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