Address issue #504

[dariober]

Some imporvements probably needed

[shashankbrgowda]

@dariober Changes looks good to me and works fine.

If you don't want to use const xfeature = JSON.parse(JSON.stringify(feature)) we could consider using SimpleFeatureSerializedNoId instead of Feature as it provides getters for some of the fields.

or we can access properties like this start: "start" in feature ? feature.start as number + 1 : null

We might have to add source: gff_source and score: gff_score reserved key mapping in gffToInternal here apollo-shared/src/GFF3/gffReservedKeys.ts to avoid duplicates when we save it.

after adding mapping make necessary change in convertFeatureAttributes of gff3ToAnnotationFeature.ts.

if (existingVal) {
  if (existingVal === val) {
    continue
  }
  const valSet = new Set([...existingVal, ...val])
  convertedAttributes[newKey] = [...valSet]
}

[shashankbrgowda]

Add condition to filter attributes with undefined/null values

[dariober]

Unless I'm missing something, it seems enough to add source and score here:

Apollo3/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.ts

Lines 60 to 71 in 572e33b

	const defaultFields = new Set([
	'start',
	'end',
	'type',
	'strand',
	'refName',
	'subfeatures',
	'derived_features',
	'phase',
	'source',
	'score',
	])

[shashankbrgowda]

Makes sense. Better to filter source and score here as they're getting added again in gff3ToAnnotationFeature.ts.

Do we also need to filter attributes with undefined/null values ?

[dariober]

If score or source are missing, they will not be included as attribute at all. There's a test here

Apollo3/packages/jbrowse-plugin-apollo/src/extensions/annotationFromJBrowseFeature.test.ts

Lines 96 to 97 in 572e33b

	expect(af.attributes?.score).toBeUndefined()
	expect(af.attributes?.gff_score).toBeUndefined()

If I'm not mistaken, we should not end up with attributes with null/undefined values.

[shashankbrgowda]

Sorry, tested your recent changes and its working fine. Thanks

[shashankbrgowda]

remove comment