@jbrowse/plugin-alignments 2.1.7 → 2.2.1

package/src/AlignmentsFeatureDetail/index.test.js

@@ -11,14 +11,16 @@ test('open up a widget', () => {
   const pluginManager = new PluginManager([])
 
   const Session = types.model({
-    pluginManager: types.optional(types.frozen(), {}),
     rpcManager: types.optional(types.frozen(), {}),
     configuration: ConfigurationSchema('test', {}),
     widget: stateModelFactory(pluginManager),
   })
-  const session = Session.create({
-    widget: { type: 'AlignmentsFeatureWidget' },
-  })
+  const session = Session.create(
+    {
+      widget: { type: 'AlignmentsFeatureWidget' },
+    },
+    { pluginManager },
+  )
   session.widget.setFeatureData({
     seq: 'TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG',
     start: 2,

package/src/AlignmentsTrack/index.ts

@@ -5,28 +5,34 @@ import {
   createBaseTrackConfig,
   createBaseTrackModel,
 } from '@jbrowse/core/pluggableElementTypes/models'
+
+/**
+ * #config AlignmentsTrack
+ * has very little config; most config and state logic is on the display
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 function configSchemaFactory(pluginManager: PluginManager) {
   return ConfigurationSchema(
     'AlignmentsTrack',
     {},
-    { baseConfiguration: createBaseTrackConfig(pluginManager) },
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: createBaseTrackConfig(pluginManager),
+    },
   )
 }
-export default function register(pluginManager: PluginManager) {
-  pluginManager.addTrackType(() => {
-    const configSchema = configSchemaFactory(pluginManager)
+export default function register(pm: PluginManager) {
+  pm.addTrackType(() => {
+    const configSchema = configSchemaFactory(pm)
     const track = new TrackType({
       name: 'AlignmentsTrack',
       configSchema,
-      stateModel: createBaseTrackModel(
-        pluginManager,
-        'AlignmentsTrack',
-        configSchema,
-      ),
+      stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
     })
-    const linearAlignmentsDisplay = pluginManager.getDisplayType(
-      'LinearAlignmentsDisplay',
-    )
+    const linearAlignmentsDisplay = pm.getDisplayType('LinearAlignmentsDisplay')
     // Add LinearAlignmentsDisplay here so that it has priority over the other
     // linear displays (defaults to order the displays are added, but we have
     // to add the Pileup and SNPCoverage displays first).

package/src/BamAdapter/BamAdapter.ts

@@ -4,12 +4,12 @@ import {
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { Region } from '@jbrowse/core/util/types'
-import { bytesForRegions, updateStatus } from '@jbrowse/core/util'
+import { bytesForRegions, updateStatus, Feature } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
 import { toArray } from 'rxjs/operators'
-import { readConfObject } from '@jbrowse/core/configuration'
+
+// locals
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature'
 
 interface Header {
@@ -21,51 +21,52 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
   private samHeader?: Header
 
   private setupP?: Promise<Header>
-
-  protected configured?: Promise<{
+  private configureP?: Promise<{
     bam: BamFile
     sequenceAdapter?: BaseFeatureDataAdapter
   }>
 
   // derived classes may not use the same configuration so a custom
   // configure method allows derived classes to override this behavior
-  protected async configure() {
-    if (!this.configured) {
-      const bamLocation = readConfObject(this.config, 'bamLocation')
-      const location = readConfObject(this.config, ['index', 'location'])
-      const indexType = readConfObject(this.config, ['index', 'indexType'])
-      const bam = new BamFile({
-        bamFilehandle: openLocation(bamLocation, this.pluginManager),
-        csiFilehandle:
-          indexType === 'CSI'
-            ? openLocation(location, this.pluginManager)
-            : undefined,
-        baiFilehandle:
-          indexType !== 'CSI'
-            ? openLocation(location, this.pluginManager)
-            : undefined,
-
-        // chunkSizeLimit and fetchSizeLimit are more troublesome than
-        // helpful, and have given overly large values on the ultra long
-        // nanopore reads even with 500MB limits, so disabled with infinity
-        chunkSizeLimit: Infinity,
-        fetchSizeLimit: Infinity,
-        yieldThreadTime: Infinity,
-      })
+  protected async configurePre() {
+    const bamLocation = this.getConf('bamLocation')
+    const location = this.getConf(['index', 'location'])
+    const indexType = this.getConf(['index', 'indexType'])
+    const pm = this.pluginManager
+    const csi = indexType === 'CSI'
+    const bam = new BamFile({
+      bamFilehandle: openLocation(bamLocation, pm),
+      csiFilehandle: csi ? openLocation(location, pm) : undefined,
+      baiFilehandle: !csi ? openLocation(location, pm) : undefined,
+
+      // chunkSizeLimit and fetchSizeLimit are more troublesome than
+      // helpful, and have given overly large values on the ultra long
+      // nanopore reads even with 500MB limits, so disabled with infinity
+      chunkSizeLimit: Infinity,
+      fetchSizeLimit: Infinity,
+      yieldThreadTime: Infinity,
+    })
 
-      const adapterConfig = readConfObject(this.config, 'sequenceAdapter')
-      if (adapterConfig && this.getSubAdapter) {
-        this.configured = this.getSubAdapter(adapterConfig).then(
-          ({ dataAdapter }) => ({
-            bam,
-            sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,
-          }),
-        )
-      } else {
-        this.configured = Promise.resolve({ bam })
+    const adapterConfig = this.getConf('sequenceAdapter')
+    if (adapterConfig && this.getSubAdapter) {
+      const { dataAdapter } = await this.getSubAdapter(adapterConfig)
+      return {
+        bam,
+        sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,
       }
+    } else {
+      return { bam }
+    }
+  }
+
+  protected async configure() {
+    if (!this.configureP) {
+      this.configureP = this.configurePre().catch(e => {
+        this.configureP = undefined
+        throw e
+      })
     }
-    return this.configured
+    return this.configureP
   }
 
   async getHeader(opts?: BaseOptions) {
@@ -231,7 +232,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     // @ts-ignore
     if (bam.index.filehandle !== '?') {
       const bytes = await bytesForRegions(regions, bam)
-      const fetchSizeLimit = readConfObject(this.config, 'fetchSizeLimit')
+      const fetchSizeLimit = this.getConf('fetchSizeLimit')
       return { bytes, fetchSizeLimit }
     } else {
       return super.estimateRegionsStats(regions, opts)
@@ -241,7 +242,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
   freeResources(/* { region } */): void {}
 
   // depends on setup being called before the BAM constructor
-  refIdToName(refId: number): string | undefined {
+  refIdToName(refId: number) {
     return this.samHeader?.idToName[refId]
   }
 }

package/src/BamAdapter/BamSlightlyLazyFeature.ts

@@ -4,8 +4,9 @@ import {
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
 import { BamRecord } from '@gmod/bam'
-import { getMismatches } from './MismatchParser'
 
+// locals
+import { getMismatches } from './MismatchParser'
 import BamAdapter from './BamAdapter'
 
 export default class BamSlightlyLazyFeature implements Feature {

package/src/BamAdapter/MismatchParser.test.ts

@@ -139,79 +139,88 @@ test('more skip', () => {
       (a, b) => a.start - b.start,
     ),
   ).toMatchInlineSnapshot(`
-    Array [
-      Object {
+    [
+      {
         "altbase": "G",
         "base": "A",
         "length": 1,
+        "qual": undefined,
         "start": 6,
         "type": "mismatch",
       },
-      Object {
+      {
         "altbase": "C",
         "base": "A",
         "length": 1,
+        "qual": undefined,
         "start": 11,
         "type": "mismatch",
       },
-      Object {
+      {
         "base": "1",
         "length": 0,
         "start": 31,
         "type": "insertion",
       },
-      Object {
+      {
         "altbase": "G",
         "base": "C",
         "length": 1,
+        "qual": undefined,
         "start": 32,
         "type": "mismatch",
       },
-      Object {
+      {
         "altbase": "A",
         "base": "C",
         "length": 1,
+        "qual": undefined,
         "start": 34,
         "type": "mismatch",
       },
-      Object {
+      {
         "altbase": "C",
         "base": "C",
         "length": 1,
+        "qual": undefined,
         "start": 40,
         "type": "mismatch",
       },
-      Object {
+      {
         "altbase": "A",
         "base": "C",
         "length": 1,
+        "qual": undefined,
         "start": 46,
         "type": "mismatch",
       },
-      Object {
+      {
         "base": "*",
         "length": 1,
         "start": 48,
         "type": "deletion",
       },
-      Object {
+      {
         "altbase": "A",
         "base": "G",
         "length": 1,
+        "qual": undefined,
         "start": 52,
         "type": "mismatch",
       },
-      Object {
+      {
         "altbase": "G",
         "base": "G",
         "length": 1,
+        "qual": undefined,
         "start": 68,
         "type": "mismatch",
       },
-      Object {
+      {
         "altbase": "G",
         "base": "G",
         "length": 1,
+        "qual": undefined,
         "start": 70,
         "type": "mismatch",
       },

package/src/BamAdapter/MismatchParser.ts

@@ -16,7 +16,7 @@ export function parseCigar(cigar = '') {
 }
 export function cigarToMismatches(
   ops: string[],
-  seq: string,
+  seq?: string,
   ref?: string,
   qual?: Buffer,
 ): Mismatch[] {
@@ -70,7 +70,7 @@ export function cigarToMismatches(
         length: len,
       })
     } else if (op === 'X') {
-      const r = seq.slice(soffset, soffset + len)
+      const r = seq?.slice(soffset, soffset + len) || []
       const q = qual?.slice(soffset, soffset + len) || []
 
       for (let j = 0; j < len; j++) {
@@ -195,10 +195,7 @@ export function mdToMismatches(
         }
         const s = getTemplateCoordLocal(curr.start)
         curr.base = seq[s] || 'X'
-        const qualScore = qual?.[s]
-        if (qualScore) {
-          curr.qual = qualScore
-        }
+        curr.qual = qual?.[s]
         curr.altbase = token
         nextRecord()
       }
@@ -209,8 +206,8 @@ export function mdToMismatches(
 
 export function getMismatches(
   cigar: string,
-  md: string,
-  seq: string,
+  md?: string,
+  seq?: string,
   ref?: string,
   qual?: Buffer,
 ): Mismatch[] {
@@ -223,7 +220,7 @@ export function getMismatches(
   }
 
   // now let's look for CRAM or MD mismatches
-  if (md) {
+  if (md && seq) {
     mismatches = mismatches.concat(
       mdToMismatches(md, ops, mismatches, seq, qual),
     )
@@ -332,7 +329,7 @@ export function getModificationTypes(mm: string) {
 
       const matches = basemod.match(modificationRegex)
       if (!matches) {
-        throw new Error('bad format for MM tag')
+        throw new Error(`bad format for MM tag: ${mm}`)
       }
       const [, , , typestr] = matches