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String formatting for bio_types::annot::contig::Contig #36

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fedxa opened this issue Apr 9, 2022 · 0 comments
Open

String formatting for bio_types::annot::contig::Contig #36

fedxa opened this issue Apr 9, 2022 · 0 comments

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@fedxa
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fedxa commented Apr 9, 2022

What is the reason for the choice of string formatting for contigs to be

The display format for a Contig is chr:start-end(+/-/.). The boundaries are given as a half-open 0-based interval, like the Rust Range and BED format.

I would thing that the convention is that if the coordinate is written as 'chr:start-end' then it is 1-based-end-inclusive, while 'chr start end' would be 0-based-end-exclusive. AT least this is the convention that is followed by UCSC and plethora of utilities.

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