Allow single coodinate bedgraph files

GMOD · Dec 7, 2024 · 55d3c6b · 55d3c6b
1 parent 1409060
commit 55d3c6b
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Showing 2 changed files with 47 additions and 27 deletions.
diff --git a/plugins/bed/src/BedGraphTabixAdapter/BedGraphTabixAdapter.ts b/plugins/bed/src/BedGraphTabixAdapter/BedGraphTabixAdapter.ts
@@ -76,36 +76,48 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
 
   public getFeatures(query: Region, opts: BaseOptions = {}) {
     return ObservableCreate<Feature>(async observer => {
-      const { refName, start, end } = query
       const { bedGraph } = await this.configure()
-      const names = (await this.getNames())?.slice(3) || []
-      await bedGraph.getLines(refName, start, end, {
-        lineCallback: (line, fileOffset) => {
-          const [refName, s, e, ...rest] = line.split('\t')
-          for (let j = 0; j < rest.length; j++) {
-            const uniqueId = `${this.id}-${fileOffset}-${j}`
-            const start = +s!
-            const end = +e!
-            const score = +rest[j]!
-            const source = names[j] || `col${j}`
-            if (score) {
-              observer.next(
-                new SimpleFeature({
-                  id: uniqueId,
-                  data: {
-                    refName,
-                    start,
-                    end,
-                    score,
-                    source,
-                  },
-                }),
-              )
+      const meta = await bedGraph.getMetadata()
+      const { columnNumbers } = meta
+      const colRef = columnNumbers.ref - 1
+      const colStart = columnNumbers.start - 1
+      const colEnd = columnNumbers.end - 1
+      const same = colStart === colEnd
+      const names = (await this.getNames())?.slice(same ? 2 : 3) || []
+      await bedGraph.getLines(
+        query.refName,
+        query.start + (same ? -1 : 0),
+        query.end,
+        {
+          lineCallback: (line, fileOffset) => {
+            const cols = line.split('\t')
+            const refName = cols[colRef]!
+            const start = +cols[colStart]!
+            const end = +(same ? start + 1 : cols[colEnd]!)
+            const rest = cols.slice(colEnd + 1)
+            for (let j = 0; j < rest.length; j++) {
+              const uniqueId = `${this.id}-${fileOffset}-${j}`
+              const score = Math.abs(+rest[j]!)
+              const source = names[j] || `col${j}`
+              if (score) {
+                observer.next(
+                  new SimpleFeature({
+                    id: uniqueId,
+                    data: {
+                      refName,
+                      start,
+                      end,
+                      score,
+                      source,
+                    },
+                  }),
+                )
+              }
             }
-          }
+          },
+          ...opts,
         },
-        ...opts,
-      })
+      )
       observer.complete()
     })
   }

diff --git a/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts b/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts
@@ -4,6 +4,7 @@ import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { SimpleFeature } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
+import { checkStopToken } from '@jbrowse/core/util/stopToken'
 
 import { featureData } from '../util'
 
@@ -71,15 +72,22 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
   }
 
   public getFeatures(query: Region, opts: BaseOptions = {}) {
+    const { stopToken } = opts
     return ObservableCreate<Feature>(async observer => {
       const meta = await this.bed.getMetadata()
       const { columnNumbers } = meta
       const colRef = columnNumbers.ref - 1
       const colStart = columnNumbers.start - 1
       const colEnd = columnNumbers.end - 1
       const names = await this.getNames()
+      let start = performance.now()
+      checkStopToken(stopToken)
       await this.bed.getLines(query.refName, query.start, query.end, {
         lineCallback: (line, fileOffset) => {
+          if (performance.now() - start > 200) {
+            checkStopToken(stopToken)
+            start = performance.now()
+          }
           observer.next(
             new SimpleFeature(
               featureData({