Handle case insensitive UTR

GMOD · Feb 20, 2025 · 11cb0d2 · 11cb0d2
1 parent b362a9f
commit 11cb0d2
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Showing 3 changed files with 4 additions and 10 deletions.
diff --git a/plugins/gtf/src/GtfAdapter/GtfAdapter.ts b/plugins/gtf/src/GtfAdapter/GtfAdapter.ts
@@ -212,7 +212,7 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
         }
       }
 
-      Object.entries(parentAggregation).map(([name, subfeatures]) => {
+      for (const [name, subfeatures] of Object.entries(parentAggregation)) {
         const s = min(subfeatures.map(f => f.start))
         const e = max(subfeatures.map(f => f.end))
         if (doesIntersect2(s, e, originalQuery.start, originalQuery.end)) {
@@ -232,7 +232,7 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
             }),
           )
         }
-      })
+      }
     }
     observer.complete()
   }

diff --git a/plugins/svg/src/SvgFeatureRenderer/components/ProcessedTranscript.tsx b/plugins/svg/src/SvgFeatureRenderer/components/ProcessedTranscript.tsx
@@ -3,7 +3,7 @@ import { SimpleFeature } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
 import Segments from './Segments'
-import { layOutFeature, layOutSubfeatures } from './util'
+import { isUTR, layOutFeature, layOutSubfeatures } from './util'
 
 import type { ExtraGlyphValidator } from './util'
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
@@ -29,12 +29,6 @@ function filterSubpart(feature: Feature, config: AnyConfigurationModel) {
   return makeSubpartsFilter('subParts', config)(feature)
 }
 
-function isUTR(feature: Feature) {
-  return /(\bUTR|_UTR|untranslated[_\s]region)\b/.test(
-    feature.get('type') || '',
-  )
-}
-
 function makeUTRs(parent: Feature, subs: Feature[]) {
   // based on Lincoln's UTR-making code in
   // Bio::Graphics::Glyph::processed_transcript

diff --git a/plugins/svg/src/SvgFeatureRenderer/components/util.ts b/plugins/svg/src/SvgFeatureRenderer/components/util.ts
@@ -172,7 +172,7 @@ export function layOutSubfeatures(args: SubfeatureLayOutArgs) {
 }
 
 export function isUTR(feature: Feature) {
-  return /(\bUTR|_UTR|untranslated[_\s]region)\b/.test(
+  return /(\bUTR|_UTR|untranslated[_\s]region)\b/i.test(
     feature.get('type') || '',
   )
 }