@jbrowse/plugin-alignments 2.1.7 → 2.2.0

package/src/CramAdapter/CramAdapter.ts

@@ -1,7 +1,8 @@
-import { CraiIndex, IndexedCramFile } from '@gmod/cram'
+import { CraiIndex, IndexedCramFile, CramRecord } from '@gmod/cram'
 import {
   BaseFeatureDataAdapter,
   BaseOptions,
+  BaseSequenceAdapter,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { checkAbortSignal, Region, Feature } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
@@ -9,15 +10,10 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { toArray } from 'rxjs/operators'
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature'
 
-interface HeaderLine {
-  tag: string
-  value: any // eslint-disable-line @typescript-eslint/no-explicit-any
-  data: HeaderLine[]
-}
 interface Header {
   idToName?: string[]
   nameToId?: Record<string, number>
-  readGroups?: number[]
+  readGroups?: (string | undefined)[]
 }
 
 interface FilterBy {
@@ -32,8 +28,13 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
 
   private setupP?: Promise<{
     samHeader: Header
-    cram: any // eslint-disable-line @typescript-eslint/no-explicit-any
-    sequenceAdapter: any // eslint-disable-line @typescript-eslint/no-explicit-any
+    cram: IndexedCramFile
+    sequenceAdapter: BaseSequenceAdapter
+  }>
+
+  private configureP?: Promise<{
+    cram: IndexedCramFile
+    sequenceAdapter: BaseSequenceAdapter
   }>
 
   // maps a refname to an id
@@ -42,7 +43,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
   // maps a seqId to original refname, passed specially to render args, to a seqid
   private seqIdToOriginalRefName: string[] = []
 
-  public async configure() {
+  public async configurePre() {
     const cramLocation = this.getConf('cramLocation')
     const craiLocation = this.getConf('craiLocation')
     if (!cramLocation) {
@@ -51,48 +52,55 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     if (!craiLocation) {
       throw new Error('missing craiLocation argument')
     }
+    const pm = this.pluginManager
 
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const cram: any = new IndexedCramFile({
-      cramFilehandle: openLocation(cramLocation, this.pluginManager),
-      index: new CraiIndex({
-        filehandle: openLocation(craiLocation, this.pluginManager),
-      }),
-      seqFetch: this.seqFetch.bind(this),
+    const cram = new IndexedCramFile({
+      cramFilehandle: openLocation(cramLocation, pm),
+      index: new CraiIndex({ filehandle: openLocation(craiLocation, pm) }),
+      seqFetch: (...args) => this.seqFetch(...args),
       checkSequenceMD5: false,
       fetchSizeLimit: 200_000_000, // just make this a large size to avoid hitting it
     })
-    // instantiate the sequence adapter
-    const sequenceAdapterType = this.getConf(['sequenceAdapter', 'type'])
 
     if (!this.getSubAdapter) {
       throw new Error('Error getting subadapter')
     }
 
     const seqConf = this.getConf('sequenceAdapter')
-    const { dataAdapter: sequenceAdapter } = await this.getSubAdapter(seqConf)
+    const subadapter = await this.getSubAdapter(seqConf)
 
-    if (!(sequenceAdapter instanceof BaseFeatureDataAdapter)) {
-      throw new Error(
-        `CRAM feature adapters cannot use sequence adapters of type '${sequenceAdapterType}'`,
-      )
+    return {
+      cram,
+      sequenceAdapter: subadapter.dataAdapter as BaseSequenceAdapter,
     }
+  }
 
-    return { cram, sequenceAdapter }
+  public async configure() {
+    if (!this.configureP) {
+      this.configureP = this.configurePre().catch(e => {
+        this.configureP = undefined
+        throw e
+      })
+    }
+    return this.configureP
   }
 
   async getHeader(opts?: BaseOptions) {
     const { cram } = await this.configure()
-    return cram.cram.getHeaderText(opts)
+    return cram.cram.getHeaderText()
   }
 
-  private async seqFetch(seqId: number, start: number, end: number) {
+  private async seqFetch(
+    seqId: number,
+    start: number,
+    end: number,
+  ): Promise<string> {
     start -= 1 // convert from 1-based closed to interbase
 
     const { sequenceAdapter } = await this.configure()
     const refName = this.refIdToOriginalName(seqId) || this.refIdToName(seqId)
     if (!refName) {
-      return undefined
+      throw new Error('unknown')
     }
 
     const seqChunks = await sequenceAdapter
@@ -132,10 +140,10 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
 
   private async setupPre(opts?: BaseOptions) {
     const { statusCallback = () => {} } = opts || {}
-    const configured = await this.configure()
+    const conf = await this.configure()
     statusCallback('Downloading index')
-    const { cram } = configured
-    const samHeader: HeaderLine[] = await cram.cram.getSamHeader(opts?.signal)
+    const { cram } = conf
+    const samHeader = await cram.cram.getSamHeader()
 
     // use the @SQ lines in the header to figure out the
     // mapping between ref ID numbers and names
@@ -161,7 +169,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     const data = { idToName, nameToId, readGroups }
     statusCallback('')
     this.samHeader = data
-    return { samHeader: data, ...configured }
+    return { samHeader: data, ...conf }
   }
 
   private async setup(opts?: BaseOptions) {
@@ -197,13 +205,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
   // use info from the SAM header if possible, but fall back to using
   // the ref seq order from when the browser's refseqs were loaded
   refIdToName(refId: number) {
-    if (this.samHeader.idToName) {
-      return this.samHeader.idToName[refId]
-    }
-    if (this.seqIdToRefName) {
-      return this.seqIdToRefName[refId]
-    }
-    return undefined
+    return this.samHeader.idToName?.[refId] || this.seqIdToRefName?.[refId]
   }
 
   refIdToOriginalName(refId: number) {
@@ -220,53 +222,48 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     const { refName, start, end, originalRefName } = region
 
     return ObservableCreate<Feature>(async observer => {
-      const { cram, sequenceAdapter } = await this.setup(opts)
-      statusCallback('Downloading alignments')
-      if (!this.seqIdToRefName) {
-        this.seqIdToRefName = await sequenceAdapter.getRefNames(opts)
-      }
+      const { cram } = await this.setup(opts)
+
       const refId = this.refNameToId(refName)
-      if (refId !== undefined) {
-        if (originalRefName) {
-          this.seqIdToOriginalRefName[refId] = originalRefName
-        }
-        const records = await cram.getRecordsForRange(refId, start, end, opts)
-        checkAbortSignal(signal)
-        const {
-          flagInclude = 0,
-          flagExclude = 0,
-          tagFilter,
-          readName,
-        } = filterBy || {}
-
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        let filtered = records.filter((record: any) => {
-          const flags = record.flags
-          return (flags & flagInclude) === flagInclude && !(flags & flagExclude)
-        })
+      if (refId === undefined) {
+        console.warn('Unknown refName', refName)
+        observer.complete()
+        return
+      }
+
+      if (originalRefName) {
+        this.seqIdToOriginalRefName[refId] = originalRefName
+      }
+      statusCallback('Downloading alignments')
+      const records = await cram.getRecordsForRange(refId, start, end)
+      checkAbortSignal(signal)
+      const {
+        flagInclude = 0,
+        flagExclude = 0,
+        tagFilter,
+        readName,
+      } = filterBy || {}
+
+      let filtered = records.filter(record => {
+        const flags = record.flags
+        return (flags & flagInclude) === flagInclude && !(flags & flagExclude)
+      })
 
-        if (tagFilter) {
-          // eslint-disable-next-line @typescript-eslint/no-explicit-any
-          filtered = filtered.filter((record: any) => {
-            const val = record[tagFilter.tag]
-            return val === '*' ? val !== undefined : val === tagFilter.value
-          })
-        }
-
-        if (readName) {
-          filtered = filtered.filter(
-            // eslint-disable-next-line @typescript-eslint/no-explicit-any
-            (record: any) => record.readName === readName,
-          )
-        }
-
-        // eslint-disable-next-line @typescript-eslint/no-explicit-any
-        filtered.forEach((record: any) => {
-          observer.next(this.cramRecordToFeature(record))
+      if (tagFilter) {
+        filtered = filtered.filter(record => {
+          // @ts-ignore
+          const val = record[tagFilter.tag]
+          return val === '*' ? val !== undefined : val === tagFilter.value
         })
-      } else {
-        console.warn('Unknown refName', refName)
       }
+
+      if (readName) {
+        filtered = filtered.filter(record => record.readName === readName)
+      }
+
+      filtered.forEach(record => {
+        observer.next(this.cramRecordToFeature(record))
+      })
       statusCallback('')
       observer.complete()
     }, signal)
@@ -274,7 +271,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
 
   freeResources(/* { region } */): void {}
 
-  cramRecordToFeature(record: unknown) {
+  cramRecordToFeature(record: CramRecord) {
     return new CramSlightlyLazyFeature(record, this)
   }
 
@@ -299,7 +296,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
       regions.map(region => {
         const { refName, start, end } = region
         const chrId = this.refNameToId(refName)
-        return cram.index.getEntriesForRange(chrId, start, end)
+        return chrId !== undefined
+          ? cram.index.getEntriesForRange(chrId, start, end)
+          : [{ sliceBytes: 0 }]
       }),
     )
 

package/src/CramAdapter/CramSlightlyLazyFeature.ts

@@ -3,7 +3,7 @@ import {
   Feature,
   SimpleFeatureSerialized,
 } from '@jbrowse/core/util/simpleFeature'
-
+import { CramRecord } from '@gmod/cram'
 import CramAdapter from './CramAdapter'
 
 export interface Mismatch {
@@ -20,8 +20,8 @@ export interface Mismatch {
 export default class CramSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class
   // https://www.typescriptlang.org/docs/handbook/classes.html#parameter-properties
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  constructor(private record: any, private _store: CramAdapter) {}
+
+  constructor(private record: CramRecord, private _store: CramAdapter) {}
 
   _get_name() {
     return this.record.readName
@@ -32,7 +32,7 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   _get_end() {
-    return this.record.alignmentStart + this.record.lengthOnRef - 1
+    return this.record.alignmentStart + (this.record.lengthOnRef ?? 1) - 1
   }
 
   _get_cram_read_features() {
@@ -123,6 +123,9 @@ export default class CramSlightlyLazyFeature implements Feature {
     let cigar = ''
     let op = 'M'
     let oplen = 0
+    if (!this.record._refRegion) {
+      return ''
+    }
 
     // not sure I should access these, but...
     const ref = this.record._refRegion.seq
@@ -130,6 +133,7 @@ export default class CramSlightlyLazyFeature implements Feature {
     let last_pos = this.record.alignmentStart
     let sublen = 0
     if (typeof this.record.readFeatures !== 'undefined') {
+      let insLen = 0
       // @ts-ignore
       for (let i = 0; i < this.record.readFeatures.length; i++) {
         const { code, refPos, sub, data } = this.record.readFeatures[i]
@@ -145,6 +149,10 @@ export default class CramSlightlyLazyFeature implements Feature {
           op = 'M'
           oplen += sublen
         }
+        if (insLen > 0 && code !== 'i') {
+          cigar += `${insLen}I`
+          insLen = 0
+        }
 
         if (code === 'b') {
           // An array of bases stored verbatim
@@ -181,11 +189,11 @@ export default class CramSlightlyLazyFeature implements Feature {
           oplen = 0
         } else if (code === 'i') {
           // Single base insertion
-          seq += data
+          // seq += data
           if (oplen) {
             cigar += oplen + op
           }
-          cigar += `${1}I`
+          insLen++
           oplen = 0
         } else if (code === 'P') {
           // Padding
@@ -280,19 +288,12 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   toJSON(): SimpleFeatureSerialized {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    const tags: Record<string, any> = {}
-    this.tags().forEach((t: string) => {
-      const val = this.get(t)
-      if (val !== undefined) {
-        tags[t] = val
-      }
-    })
-
     return {
-      ...tags,
-      name: this.get('name'),
-      type: this.get('type'),
+      ...Object.fromEntries(
+        this.tags()
+          .map(t => [t, this.get(t)])
+          .filter(elt => elt[1] !== undefined),
+      ),
       uniqueId: this.id(),
     }
   }
@@ -306,10 +307,23 @@ export default class CramSlightlyLazyFeature implements Feature {
     const start = this.get('start')
     const mismatches: Mismatch[] = new Array(readFeatures.length)
     let j = 0
+    let insLen = 0
+
+    let refPos = 0
     for (let i = 0; i < readFeatures.length; i++) {
       const f = readFeatures[i]
       const { code, pos, data, sub, ref } = f
-      const refPos = f.refPos - 1 - start
+      if (insLen > 0 && code !== 'i') {
+        mismatches[j++] = {
+          start: refPos,
+          type: 'insertion',
+          base: `${insLen}`,
+          length: 0,
+        }
+        insLen = 0
+      }
+      refPos = f.refPos - 1 - start
+
       if (code === 'X') {
         // substitution
         mismatches[j++] = {
@@ -375,12 +389,7 @@ export default class CramSlightlyLazyFeature implements Feature {
       } else if (code === 'i') {
         // single-base insertion
         // insertion
-        mismatches[j++] = {
-          start: refPos,
-          type: 'insertion',
-          base: data,
-          length: 1,
-        }
+        insLen++
       } else if (code === 'Q') {
         // single quality value
       }

package/src/CramAdapter/configSchema.ts

@@ -1,33 +1,58 @@
-import PluginManager from '@jbrowse/core/PluginManager'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
 
-export default (pluginManager: PluginManager) => {
-  return types.late(() =>
-    ConfigurationSchema(
-      'CramAdapter',
-      {
-        fetchSizeLimit: {
-          type: 'number',
-          defaultValue: 3_000_000,
-        },
-        cramLocation: {
-          type: 'fileLocation',
-          defaultValue: {
-            uri: '/path/to/my.cram',
-            locationType: 'UriLocation',
-          },
-        },
-        craiLocation: {
-          type: 'fileLocation',
-          defaultValue: {
-            uri: '/path/to/my.cram.crai',
-            locationType: 'UriLocation',
-          },
-        },
-        sequenceAdapter: pluginManager.pluggableConfigSchemaType('adapter'),
+/**
+ * #config CramAdapter
+ * used to configure CRAM adapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = ConfigurationSchema(
+  'CramAdapter',
+  {
+    /**
+     * #slot fetchSizeLimit
+     */
+    fetchSizeLimit: {
+      type: 'number',
+      description:
+        'used to determine when to display a warning to the user that too much data will be fetched',
+      defaultValue: 3_000_000,
+    },
+
+    /**
+     * #slot cramLocation
+     */
+    cramLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.cram',
+        locationType: 'UriLocation',
       },
-      { explicitlyTyped: true },
-    ),
-  )
-}
+    },
+
+    /**
+     * #slot craiLocation
+     */
+    craiLocation: {
+      type: 'fileLocation',
+      defaultValue: {
+        uri: '/path/to/my.cram.crai',
+        locationType: 'UriLocation',
+      },
+    },
+
+    /**
+     * #slot sequenceAdapter
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+      type: 'frozen',
+      description:
+        'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
+      defaultValue: null,
+    },
+  },
+  { explicitlyTyped: true },
+)
+export default configSchema

package/src/CramAdapter/index.ts

@@ -2,14 +2,14 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
 
 // locals
-import configSchemaF from './configSchema'
+import configSchema from './configSchema'
 
 export default (pluginManager: PluginManager) => {
   pluginManager.addAdapterType(
     () =>
       new AdapterType({
         name: 'CramAdapter',
-        configSchema: pluginManager.load(configSchemaF),
+        configSchema,
         getAdapterClass: () => import('./CramAdapter').then(r => r.default),
       }),
   )

package/src/HtsgetBamAdapter/HtsgetBamAdapter.ts

@@ -1,31 +1,24 @@
 import { BamFile, HtsgetFile } from '@gmod/bam'
-import { readConfObject } from '@jbrowse/core/configuration'
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import BamAdapter from '../BamAdapter/BamAdapter'
 
 export default class HtsgetBamAdapter extends BamAdapter {
-  protected async configure() {
-    if (!this.configured) {
-      const htsgetBase = readConfObject(this.config, 'htsgetBase')
-      const htsgetTrackId = readConfObject(this.config, 'htsgetTrackId')
-      const bam = new HtsgetFile({
-        baseUrl: htsgetBase,
-        trackId: htsgetTrackId,
-      }) as unknown as BamFile
+  protected async configurePre() {
+    const htsgetBase = this.getConf('htsgetBase')
+    const htsgetTrackId = this.getConf('htsgetTrackId')
+    const bam = new HtsgetFile({
+      baseUrl: htsgetBase,
+      trackId: htsgetTrackId,
+    }) as unknown as BamFile
 
-      const adapterConfig = readConfObject(this.config, 'sequenceAdapter')
-      if (adapterConfig && this.getSubAdapter) {
-        this.configured = this.getSubAdapter(adapterConfig).then(
-          ({ dataAdapter }) => {
-            return {
-              bam,
-              sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,
-            }
-          },
-        )
+    const adapterConfig = this.getConf('sequenceAdapter')
+    if (adapterConfig && this.getSubAdapter) {
+      const adapter = await this.getSubAdapter(adapterConfig)
+      return {
+        bam,
+        sequenceAdapter: adapter.dataAdapter as BaseFeatureDataAdapter,
       }
-      this.configured = Promise.resolve({ bam })
     }
-    return this.configured
+    return { bam }
   }
 }

package/src/HtsgetBamAdapter/configSchema.ts

@@ -1,23 +1,40 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { types } from 'mobx-state-tree'
+/**
+ * #config HtsgetBamAdapter
+ * Used to fetch data from Htsget endpoints in BAM format, using the gmod/bam library
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
-export default types.late(() =>
-  ConfigurationSchema(
-    'HtsgetBamAdapter',
-    {
-      htsgetBase: {
-        type: 'string',
-        defaultValue: '',
-      },
-      htsgetTrackId: {
-        type: 'string',
-        defaultValue: '',
-      },
-      sequenceAdapter: {
-        type: 'frozen',
-        defaultValue: null,
-      },
+const HtsgetBamAdapter = ConfigurationSchema(
+  'HtsgetBamAdapter',
+  {
+    /**
+     * #slot
+     */
+    htsgetBase: {
+      type: 'string',
+      description: 'the base URL to fetch from',
+      defaultValue: '',
     },
-    { explicitlyTyped: true },
-  ),
+    /**
+     * #slot
+     */
+    htsgetTrackId: {
+      type: 'string',
+      description: 'the trackId, which is appended to the base URL',
+      defaultValue: '',
+    },
+    /**
+     * #slot
+     */
+    sequenceAdapter: {
+      type: 'frozen',
+      description:
+        'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
+      defaultValue: null,
+    },
+  },
+  { explicitlyTyped: true },
 )
+
+export default HtsgetBamAdapter

package/src/LinearAlignmentsDisplay/models/configSchema.ts

@@ -2,21 +2,34 @@ import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
 import PluginManager from '@jbrowse/core/PluginManager'
 
-const configModelFactory = (pluginManager: PluginManager) => {
-  const PileupDisplayConfigSchema = pluginManager.getDisplayType(
-    'LinearPileupDisplay',
-  ).configSchema
-  const SNPCoverageDisplayConfigSchema = pluginManager.getDisplayType(
-    'LinearSNPCoverageDisplay',
-  ).configSchema
+/**
+ * #config LinearAlignmentsDisplay
+ * has a "pileup" sub-display, where you can see individual reads and a
+ * quantitative "snpcoverage" sub-display track showing SNP frequencies
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
+const configModelFactory = (pm: PluginManager) => {
   return ConfigurationSchema(
     'LinearAlignmentsDisplay',
     {
-      pileupDisplay: PileupDisplayConfigSchema,
-      snpCoverageDisplay: SNPCoverageDisplayConfigSchema,
+      /**
+       * #slot
+       */
+      pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema,
+      /**
+       * #slot
+       */
+      snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')
+        .configSchema,
+    },
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: baseLinearDisplayConfigSchema,
+      explicitlyTyped: true,
     },
-    { baseConfiguration: baseLinearDisplayConfigSchema, explicitlyTyped: true },
   )
 }