Fix RNA-seq stranded arc coloring, change the color of RNA-seq intron…

…s, and improve compact rendering (#4639)
GMOD · Nov 7, 2024 · 46ca580 · 46ca580
1 parent 32ad1a6
commit 46ca580
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Showing 30 changed files with 1,449 additions and 1,218 deletions.
diff --git a/packages/core/util/simpleFeature.ts b/packages/core/util/simpleFeature.ts
@@ -11,18 +11,6 @@ export interface Feature {
   get(name: 'subfeatures'): Feature[] | undefined
 
   get(name: string): any
-
-  /**
-   * Set an item of data.
-   */
-
-  set(name: string, val: any): void
-
-  /**
-   * Get an array listing which data keys are present in this feature.
-   */
-  tags(): string[]
-
   /**
    * Get the unique ID of this feature.
    */

diff --git a/plugins/alignments/package.json b/plugins/alignments/package.json
@@ -36,7 +36,7 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@gmod/bam": "^2.0.0",
+    "@gmod/bam": "^3.0.0",
     "@gmod/cram": "^3.0.3",
     "@jbrowse/sv-core": "^2.16.1",
     "@mui/icons-material": "^6.0.0",

diff --git a/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx b/plugins/alignments/src/AlignmentsFeatureDetail/AlignmentsFeatureDetail.tsx
@@ -18,8 +18,6 @@ import Formatter from './Formatter'
 const SupplementaryAlignments = lazy(() => import('./SupplementaryAlignments'))
 const LinkedPairedAlignments = lazy(() => import('./LinkedPairedAlignments'))
 
-const omit = ['clipPos', 'flags']
-
 const AlignmentsFeatureDetails = observer(function (props: {
   model: AlignmentFeatureWidgetModel
 }) {
@@ -32,7 +30,6 @@ const AlignmentsFeatureDetails = observer(function (props: {
     <Paper data-testid="alignment-side-drawer">
       <FeatureDetails
         {...props}
-        omit={omit}
         // @ts-expect-error
         descriptions={{ ...tags, tags: tags }}
         feature={feat}

diff --git a/plugins/alignments/src/BamAdapter/BamAdapter.ts b/plugins/alignments/src/BamAdapter/BamAdapter.ts
@@ -186,11 +186,11 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
 
         for (const record of records) {
           let ref: string | undefined
-          if (!record.get('MD')) {
+          if (!record.tags.MD) {
             ref = await this.seqFetch(
               originalRefName || refName,
-              record.get('start'),
-              record.get('end'),
+              record.start,
+              record.end,
             )
           }
 
@@ -200,7 +200,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
           }
 
           if (tagFilter) {
-            const readVal = record.get(tagFilter.tag)
+            const readVal = record.tags[tagFilter.tag]
             const filterVal = tagFilter.value
             if (
               filterVal === '*'
@@ -211,7 +211,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             }
           }
 
-          if (readName && record.get('name') !== readName) {
+          if (readName && record.name !== readName) {
             continue
           }
 

diff --git a/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts b/plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts
@@ -5,7 +5,7 @@ import {
 import { BamRecord } from '@gmod/bam'
 
 // locals
-import { getClip, getMismatches } from '../MismatchParser'
+import { getMismatches, parseCigar } from '../MismatchParser'
 import BamAdapter from './BamAdapter'
 
 export default class BamSlightlyLazyFeature implements Feature {
@@ -17,94 +17,20 @@ export default class BamSlightlyLazyFeature implements Feature {
     private ref?: string,
   ) {}
 
-  _get_name() {
-    return this.record.get('name')
-  }
-
-  _get_type(): string {
-    return 'match'
-  }
-
-  _get_score(): number {
-    return this.record.get('mq')
-  }
-
-  _get_flags(): string {
-    return this.record.flags
-  }
-
-  _get_strand(): number {
-    return this.record.isReverseComplemented() ? -1 : 1
-  }
-
-  _get_pair_orientation() {
-    return this.record.isPaired() ? this.record.getPairOrientation() : undefined
-  }
-
-  _get_next_ref() {
-    return this.record.isPaired()
-      ? this.adapter.refIdToName(this.record._next_refid())
-      : undefined
-  }
-
-  _get_next_pos() {
-    return this.record.isPaired() ? this.record._next_pos() : undefined
-  }
-
-  _get_next_segment_position() {
-    return this.record.isPaired()
-      ? `${this.adapter.refIdToName(this.record._next_refid())}:${
-          this.record._next_pos() + 1
-        }`
-      : undefined
-  }
-
-  _get_seq() {
-    return this.record.getReadBases()
-  }
-
-  qualRaw() {
-    return this.record.qualRaw()
-  }
-
-  set() {}
-
-  tags() {
-    const properties = Object.getOwnPropertyNames(
-      BamSlightlyLazyFeature.prototype,
-    )
-
-    return [
-      ...new Set(
-        properties
-          .filter(
-            prop =>
-              prop.startsWith('_get_') &&
-              prop !== '_get_mismatches' &&
-              prop !== '_get_tags',
-          )
-          .map(methodName => methodName.replace('_get_', ''))
-          .concat(this.record._tags()),
-      ),
-    ]
-  }
-
   id() {
-    return `${this.adapter.id}-${this.record.id()}`
+    return `${this.adapter.id}-${this.record.id}`
   }
 
   get(field: string): any {
-    const methodName = `_get_${field}`
-    // @ts-expect-error
-    if (this[methodName]) {
-      // @ts-expect-error
-      return this[methodName]()
-    }
-    return this.record.get(field)
-  }
-
-  _get_refName() {
-    return this.adapter.refIdToName(this.record.seq_id())
+    return field === 'mismatches'
+      ? getMismatches(
+          this.record.CIGAR,
+          this.record.tags.MD as string | undefined,
+          this.record.seq,
+          this.ref,
+          this.record.qualRaw,
+        )
+      : this.fields[field]
   }
 
   parent() {
@@ -115,33 +41,62 @@ export default class BamSlightlyLazyFeature implements Feature {
     return undefined
   }
 
-  pairedFeature() {
-    return false
+  get parsedCigar() {
+    return parseCigar(this.record.CIGAR)
   }
 
-  toJSON(): SimpleFeatureSerialized {
+  get fields(): SimpleFeatureSerialized {
+    const r = this.record
+    const a = this.adapter
+    const p = r.isPaired()
     return {
-      ...Object.fromEntries(
-        this.tags()
-          .map(t => [t, this.get(t)])
-          .filter(elt => elt[1] !== undefined),
-      ),
+      id: this.id(),
+      start: r.start,
+      name: r.name,
+      end: r.end,
+      score: r.score,
+      qual: r.qual,
+      strand: r.strand,
+      template_length: r.template_length,
+      flags: r.flags,
+      tags: r.tags,
+      refName: a.refIdToName(r.ref_id)!,
+      CIGAR: r.CIGAR,
+      seq: r.seq,
+      type: 'match',
+      pair_orientation: r.pair_orientation,
+      next_ref: p ? a.refIdToName(r.next_refid) : undefined,
+      next_pos: p ? r.next_pos : undefined,
+      next_segment_position: p
+        ? `${a.refIdToName(r.next_refid)}:${r.next_pos + 1}`
+        : undefined,
       uniqueId: this.id(),
     }
   }
 
-  _get_mismatches() {
-    return getMismatches(
-      this.get('CIGAR'),
-      this.get('MD'),
-      this.get('seq'),
-      this.ref,
-      this.qualRaw(),
-    )
+  toJSON(): SimpleFeatureSerialized {
+    return this.fields
+  }
+}
+
+function cacheGetter<T>(ctor: { prototype: T }, prop: keyof T): void {
+  const desc = Object.getOwnPropertyDescriptor(ctor.prototype, prop)
+  if (!desc) {
+    throw new Error('t1')
   }
 
-  _get_clipPos() {
-    const cigar = this.get('CIGAR') || ''
-    return getClip(cigar, this.get('strand'))
+  const getter = desc.get
+  if (!getter) {
+    throw new Error('t2')
   }
+  Object.defineProperty(ctor.prototype, prop, {
+    get() {
+      const ret = getter.call(this)
+      Object.defineProperty(this, prop, { value: ret })
+      return ret
+    },
+  })
 }
+
+cacheGetter(BamSlightlyLazyFeature, 'fields')
+cacheGetter(BamSlightlyLazyFeature, 'parsedCigar')