Ignore trailing semicolons in GFF3 attributes column

[heavywatal]

jbrowse text-index (and FeatureTrack display sometimes?) fails to parse GFF3 file with trailing semicolons at attributes (9th) column.

Sorry I haven't tested this thoroughly with minimal data, but it is recovered by applying sed -e 's/;$//' to GFF3.

Expected behavior

GFF3 parser should (be able to) ignore trailing semicolons although it may be input files' fault. The current GFF3 spec is not clear enough about this.

Screenshots

Version:

@jbrowse/cli/1.6.4 darwin-x64 node-v16.13.21
Google Chrome Version 97.0.4692.99
macOS 12.2 Monterey

Additional context

I have submitted an issue The-Sequence-Ontology/Specifications#28 to clarify this, and another lawremi/rtracklayer#58 to avoid writing trailing semicolons.

[cmdcolin]

what behavior do you see when it 'fails to parse'? in basic testing on our volvox sample data i'm not sure i see any issue

[heavywatal]

The output is like this:

Indexing assembly Oryza_sativa.IRGSP-1.0.dna_sm.genome...                                                       
░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░░ renamed.gff3 0% | ETA: 0s/node_modules/@jb1
                        .split(';')                                                                             
                         ^                                                                                      
                                                                                                                
TypeError: Cannot read properties of undefined (reading 'split')                                                
    at indexGff3_1 (/node_modules/@jbrowse/cli/lib/types/gff3Adapter.js:61:26)
    at indexGff3_1.next (<anonymous>)
    at resume (/node_modules/tslib/tslib.js:225:48)
    at fulfill (/node_modules/tslib/tslib.js:227:35)
    at processTicksAndRejections (node:internal/process/task_queues:96:5)

The cause may be not semicolons, but filenames. This file, renamed.gff3.bgz, can be jbrowse text-indexed successfully after just renaming to renamed.gff3.gz without removing semicolons. A file without trailing semicolons causes the same error if it is named *.gff3.bgz.

[cmdcolin]

@heavywatal ah I see, indeed the code does explicitly check for .gz file extension and doesn't handle .bgz extension. we can fix that!