Updates

GMOD · Nov 19, 2024 · a410a68 · a410a68
1 parent 1194a7c
commit a410a68
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Showing 3 changed files with 59 additions and 18 deletions.
diff --git a/plugins/bed/src/BedGraphAdapter/BedGraphAdapter.ts b/plugins/bed/src/BedGraphAdapter/BedGraphAdapter.ts
@@ -1,5 +1,10 @@
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature, fetchAndMaybeUnzip, SimpleFeature } from '@jbrowse/core/util'
+import {
+  Feature,
+  fetchAndMaybeUnzip,
+  Region,
+  SimpleFeature,
+} from '@jbrowse/core/util'
 import IntervalTree from '@flatten-js/interval-tree'
 import {
   BaseFeatureDataAdapter,
@@ -42,24 +47,29 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
     const names = (await this.getNames())?.slice(3) || []
     const intervalTree = new IntervalTree()
     for (let i = 0; i < lines.length; i++) {
-      const [refName, s, e, ...rest] = lines[i]!.split('\t')
+      const line = lines[i]!
+      const [refName, s, e, ...rest] = line.split('\t')
       for (let j = 0; j < rest.length; j++) {
-        const uniqueId = `${this.id}-${refName}-${i}`
+        const uniqueId = `${this.id}-${refName}-${i}-${j}`
         const start = +s!
         const end = +e!
-        intervalTree.insert(
-          [start, end],
-          new SimpleFeature({
-            id: uniqueId,
-            data: {
-              refName,
-              start,
-              end,
-              score: +rest[i]!,
-              source: names[i] || `col${i}`,
-            },
-          }),
-        )
+        const score = +rest[j]!
+        const source = names[j] || `col${j}`
+        if (score) {
+          intervalTree.insert(
+            [start, end],
+            new SimpleFeature({
+              id: uniqueId,
+              data: {
+                refName,
+                start,
+                end,
+                score,
+                source,
+              },
+            }),
+          )
+        }
       }
     }
 
@@ -132,7 +142,6 @@ export default class BedGraphAdapter extends BaseFeatureDataAdapter {
       const { start, end, refName } = query
       const intervalTree = await this.loadFeatureIntervalTree(refName)
       intervalTree?.search([start, end]).forEach(f => {
-        console.log({ f })
         observer.next(f)
       })
       observer.complete()

diff --git a/plugins/bed/src/BedGraphAdapter/configSchema.ts b/plugins/bed/src/BedGraphAdapter/configSchema.ts
@@ -0,0 +1,32 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+/**
+ * #config BedGraphAdapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const BedGraphAdapter = ConfigurationSchema(
+  'BedGraphAdapter',
+  {
+    /**
+     * #slot
+     */
+    bedGraphLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.bedgraph',
+        locationType: 'UriLocation',
+      },
+    },
+    /**
+     * #slot
+     */
+    columnNames: {
+      type: 'stringArray',
+      description: 'List of column names',
+      defaultValue: [],
+    },
+  },
+  { explicitlyTyped: true },
+)
+export default BedGraphAdapter
diff --git a/plugins/bed/src/BedGraphAdapter/index.ts b/plugins/bed/src/BedGraphAdapter/index.ts
@@ -1,7 +1,7 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
 
-import configSchema from '../BedAdapter/configSchema'
+import configSchema from './configSchema'
 
 export default function BedGraphAdapterF(pluginManager: PluginManager) {
   pluginManager.addAdapterType(