1-indexed should be replaced with inter-residue when describing coordinates

[jarbesfeld]

Describe the bug

For Transcript Segment objects, when choosing genomic coordinates and transcript, the UI indicates that coordinates should be 1-indexed. However, it looks like it is taking in inter-residue coordinates.

Steps to reproduce

1. Choose Transcript Segment, genomic coordinates and transcript
2. For transcript, enter NM_152263.3
3. For chromosome, enter NC_000001.11
4. For ending position, enter 154191901

Expected behavior

N/A

Current behavior

The Transcript Segment object reported exon 1 with an offset of 0. This is correct since the coordinate corresponds to the alt_start_i value for exon 1, and the transcript is on the negative strand, so this Transcript Segment includes all of exon 1. If the coordinate was 1-indexed, there would be a nonzero offset.

Possible reason(s)

No response

Suggested fix

Indicate that supplied coordinates should be inter-residue. This will also ensure compatibility with cool-seq-tool as its methods expect inter-residue coordinates by default.

Branch, commit, and/or version

Was looking at http://fusion-curation-dev-eb.us-east-2.elasticbeanstalk.com/assayed-fusion

Screenshots

No response

Environment details

Mac M1

Additional details

No response

Contribution

None

[jsstevenson]

I mean, they should be 0-indexed inter-residue, right?

[jarbesfeld]

@jsstevenson Yes, but currently the UI reports that it is expects 1-indexed coordinates.

[github-actions]

Closed by #332.