@jbrowse/plugin-alignments 2.6.1 → 2.6.2

package/src/CramAdapter/util.ts

@@ -1,251 +0,0 @@
-import { CramRecord } from '@gmod/cram'
-
-type ReadFeatures = CramRecord['readFeatures']
-
-export interface Mismatch {
-  qual?: number
-  start: number
-  length: number
-  type: string
-  base: string | undefined
-  altbase?: string
-  seq?: string
-  cliplen?: number
-}
-
-export function readFeaturesToMismatches(
-  readFeatures: ReadFeatures,
-  start: number,
-  qual?: number[] | null,
-) {
-  if (!readFeatures) {
-    return []
-  }
-  const mismatches: Mismatch[] = new Array(readFeatures.length)
-  let j = 0
-  let insLen = 0
-  let refPos = 0
-  let sublen = 0
-  let lastPos = start
-
-  for (let i = 0; i < readFeatures.length; i++) {
-    const f = readFeatures[i]
-    const { code, pos, data, sub, ref } = f
-    sublen = refPos - lastPos
-    lastPos = refPos
-
-    if (sublen && insLen > 0) {
-      mismatches[j++] = {
-        start: refPos,
-        type: 'insertion',
-        base: `${insLen}`,
-        length: 0,
-      }
-      insLen = 0
-    }
-    refPos = f.refPos - 1 - start
-
-    if (code === 'X') {
-      // substitution
-      mismatches[j++] = {
-        start: refPos,
-        length: 1,
-        base: sub,
-        qual: qual?.[pos - 1],
-        altbase: ref?.toUpperCase(),
-        type: 'mismatch',
-      }
-    } else if (code === 'I') {
-      // insertion
-      mismatches[j++] = {
-        start: refPos,
-        type: 'insertion',
-        base: `${data.length}`,
-        length: 0,
-      }
-    } else if (code === 'N') {
-      // reference skip
-      mismatches[j++] = {
-        type: 'skip',
-        length: data,
-        start: refPos,
-        base: 'N',
-      }
-    } else if (code === 'S') {
-      // soft clip
-      const len = data.length
-      mismatches[j++] = {
-        start: refPos,
-        type: 'softclip',
-        base: `S${len}`,
-        cliplen: len,
-        length: 1,
-      }
-    } else if (code === 'P') {
-      // padding
-    } else if (code === 'H') {
-      // hard clip
-      const len = data
-      mismatches[j++] = {
-        start: refPos,
-        type: 'hardclip',
-        base: `H${len}`,
-        cliplen: len,
-        length: 1,
-      }
-    } else if (code === 'D') {
-      // deletion
-      mismatches[j++] = {
-        type: 'deletion',
-        length: data,
-        start: refPos,
-        base: '*',
-      }
-    } else if (code === 'b') {
-      // stretch of bases
-    } else if (code === 'q') {
-      // stretch of qual scores
-    } else if (code === 'B') {
-      // a pair of [base, qual]
-    } else if (code === 'i') {
-      // single-base insertion, we collect these if there are multiple in a row
-      // into a single insertion entry
-      insLen++
-    } else if (code === 'Q') {
-      // single quality value
-    }
-  }
-
-  if (sublen && insLen > 0) {
-    mismatches[j++] = {
-      start: refPos,
-      type: 'insertion',
-      base: `${insLen}`,
-      length: 0,
-    }
-    insLen = 0
-  }
-
-  return mismatches.slice(0, j)
-}
-
-export function readFeaturesToCIGAR(
-  readFeatures: ReadFeatures,
-  alignmentStart: number,
-  readLen: number,
-  refRegion?: { seq: string; start: number },
-) {
-  let seq = ''
-  let cigar = ''
-  let op = 'M'
-  let oplen = 0
-  if (!refRegion) {
-    return ''
-  }
-
-  // not sure I should access these, but...
-  const ref = refRegion.seq
-  const refStart = refRegion.start
-  let lastPos = alignmentStart
-  let sublen = 0
-  let insLen = 0
-  if (readFeatures !== undefined) {
-    for (let i = 0; i < readFeatures.length; i++) {
-      const { code, refPos, sub, data } = readFeatures[i]
-      sublen = refPos - lastPos
-      seq += ref.slice(lastPos - refStart, refPos - refStart)
-      lastPos = refPos
-
-      if (insLen > 0 && sublen) {
-        cigar += `${insLen}I`
-        insLen = 0
-      }
-      if (oplen && op !== 'M') {
-        cigar += `${oplen}${op}`
-        oplen = 0
-      }
-      if (sublen) {
-        op = 'M'
-        oplen += sublen
-      }
-
-      if (code === 'b') {
-        // An array of bases stored verbatim
-        const ret = data.split(',')
-        const added = String.fromCharCode(...ret)
-        seq += added
-        lastPos += added.length
-        oplen += added.length
-      } else if (code === 'B') {
-        // Single base (+ qual score)
-        seq += sub
-        lastPos++
-        oplen++
-      } else if (code === 'X') {
-        // Substitution
-        seq += sub
-        lastPos++
-        oplen++
-      } else if (code === 'D' || code === 'N') {
-        // Deletion or Ref Skip
-        lastPos += data
-        if (oplen) {
-          cigar += `${oplen}${op}`
-        }
-        cigar += data + code
-        oplen = 0
-      } else if (code === 'I' || code === 'S') {
-        // Insertion or soft-clip
-        seq += data
-        if (oplen) {
-          cigar += `${oplen}${op}`
-        }
-        cigar += data.length + code
-        oplen = 0
-      } else if (code === 'i') {
-        // Single base insertion
-        // seq += data
-        if (oplen) {
-          cigar += `${oplen}${op}`
-        }
-        insLen++
-        seq += data
-        oplen = 0
-      } else if (code === 'P') {
-        // Padding
-        if (oplen) {
-          cigar += `${oplen}${op}`
-        }
-        cigar += `${data}P`
-      } else if (code === 'H') {
-        // Hard clip
-        if (oplen) {
-          cigar += `${oplen}${op}`
-        }
-        cigar += `${data}H`
-        oplen = 0
-      } // else q or Q
-    }
-  } else {
-    sublen = readLen - seq.length
-  }
-  if (seq.length !== readLen) {
-    sublen = readLen - seq.length
-    seq += ref.slice(lastPos - refStart, lastPos - refStart + sublen)
-
-    if (oplen && op !== 'M') {
-      cigar += `${oplen}${op}`
-      oplen = 0
-    }
-    op = 'M'
-    oplen += sublen
-  }
-  if (sublen && insLen > 0) {
-    cigar += `${insLen}I`
-  }
-  if (oplen) {
-    cigar += `${oplen}${op}`
-  }
-
-  return cigar
-}

package/src/GuessAlignmentsTypes/index.ts

@@ -1,79 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { FileLocation } from '@jbrowse/core/util/types'
-import {
-  makeIndex,
-  makeIndexType,
-  getFileName,
-  AdapterGuesser,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.cram$/i
-        const adapterName = 'CramAdapter'
-        const fileName = getFileName(file)
-        const obj = {
-          type: adapterName,
-          cramLocation: file,
-          craiLocation: index || makeIndex(file, '.crai'),
-        }
-        if (regexGuess.test(fileName) && !adapterHint) {
-          return obj
-        } else if (adapterHint === adapterName) {
-          return obj
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-
-  pluginManager.addToExtensionPoint(
-    'Core-guessAdapterForLocation',
-    (adapterGuesser: AdapterGuesser) => {
-      return (
-        file: FileLocation,
-        index?: FileLocation,
-        adapterHint?: string,
-      ) => {
-        const regexGuess = /\.bam$/i
-        const adapterName = 'BamAdapter'
-        const fileName = getFileName(file)
-        const indexName = index && getFileName(index)
-
-        const obj = {
-          type: adapterName,
-          bamLocation: file,
-          index: {
-            location: index || makeIndex(file, '.bai'),
-            indexType: makeIndexType(indexName, 'CSI', 'BAI'),
-          },
-        }
-        if (regexGuess.test(fileName) && !adapterHint) {
-          return obj
-        } else if (adapterHint === adapterName) {
-          return obj
-        }
-        return adapterGuesser(file, index, adapterHint)
-      }
-    },
-  )
-  pluginManager.addToExtensionPoint(
-    'Core-guessTrackTypeForLocation',
-    (trackTypeGuesser: TrackTypeGuesser) => {
-      return (adapterName: string) => {
-        if (adapterName === 'BamAdapter' || adapterName === 'CramAdapter') {
-          return 'AlignmentsTrack'
-        }
-        return trackTypeGuesser(adapterName)
-      }
-    },
-  )
-}

package/src/HtsgetBamAdapter/HtsgetBamAdapter.ts

@@ -1,24 +0,0 @@
-import { BamFile, HtsgetFile } from '@gmod/bam'
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import BamAdapter from '../BamAdapter/BamAdapter'
-
-export default class HtsgetBamAdapter extends BamAdapter {
-  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 = this.getConf('sequenceAdapter')
-    if (adapterConfig && this.getSubAdapter) {
-      const adapter = await this.getSubAdapter(adapterConfig)
-      return {
-        bam,
-        sequenceAdapter: adapter.dataAdapter as BaseFeatureDataAdapter,
-      }
-    }
-    return { bam }
-  }
-}

package/src/HtsgetBamAdapter/configSchema.ts

@@ -1,40 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-/**
- * #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
-
-const HtsgetBamAdapter = ConfigurationSchema(
-  'HtsgetBamAdapter',
-  {
-    /**
-     * #slot
-     */
-    htsgetBase: {
-      type: 'string',
-      description: 'the base URL to fetch from',
-      defaultValue: '',
-    },
-    /**
-     * #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/HtsgetBamAdapter/index.ts

@@ -1,17 +0,0 @@
-import configSchema from './configSchema'
-import PluginManager from '@jbrowse/core/PluginManager'
-import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addAdapterType(() => {
-    return new AdapterType({
-      name: 'HtsgetBamAdapter',
-      displayName: 'Htsget BAM adapter',
-      adapterMetadata: {
-        hiddenFromGUI: true,
-      },
-      configSchema,
-      getAdapterClass: () => import('./HtsgetBamAdapter').then(r => r.default),
-    })
-  })
-}

package/src/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx

@@ -1,52 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import { makeStyles } from 'tss-react/mui'
-import { getConf } from '@jbrowse/core/configuration'
-import { ResizeHandle } from '@jbrowse/core/ui'
-
-// locals
-import { AlignmentsDisplayModel } from '../models/model'
-
-const useStyles = makeStyles()({
-  resizeHandle: {
-    height: 5,
-    position: 'absolute',
-    zIndex: 2,
-  },
-})
-
-function AlignmentsDisplay({ model }: { model: AlignmentsDisplayModel }) {
-  const { PileupDisplay, SNPCoverageDisplay } = model
-  const { classes } = useStyles()
-  const top = SNPCoverageDisplay.height
-  return (
-    <div
-      data-testid={`display-${getConf(model, 'displayId')}`}
-      style={{ position: 'relative' }}
-    >
-      <div data-testid="Blockset-snpcoverage">
-        <SNPCoverageDisplay.RenderingComponent model={SNPCoverageDisplay} />
-      </div>
-      <ResizeHandle
-        onDrag={delta => {
-          SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta)
-          return delta
-        }}
-        className={classes.resizeHandle}
-        style={{ top: top - 4 }}
-      />
-
-      <div
-        data-testid="Blockset-pileup"
-        style={{
-          position: 'absolute',
-          top,
-        }}
-      >
-        <PileupDisplay.RenderingComponent model={PileupDisplay} />
-      </div>
-    </div>
-  )
-}
-
-export default observer(AlignmentsDisplay)

package/src/LinearAlignmentsDisplay/index.ts

@@ -1,21 +0,0 @@
-import DisplayType from '@jbrowse/core/pluggableElementTypes/DisplayType'
-import PluginManager from '@jbrowse/core/PluginManager'
-// locals
-import configSchemaFactory from './models/configSchema'
-import modelFactory from './models/model'
-import ReactComponent from './components/AlignmentsDisplay'
-
-export default function (pluginManager: PluginManager) {
-  pluginManager.addDisplayType(() => {
-    const configSchema = configSchemaFactory(pluginManager)
-    return new DisplayType({
-      name: 'LinearAlignmentsDisplay',
-      displayName: 'Alignments display (combination)',
-      configSchema,
-      stateModel: modelFactory(pluginManager, configSchema),
-      trackType: 'AlignmentsTrack',
-      viewType: 'LinearGenomeView',
-      ReactComponent,
-    })
-  })
-}

package/src/LinearAlignmentsDisplay/models/configSchema.test.ts

@@ -1,60 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'
-import {
-  svgFeatureRendererConfigSchema,
-  SvgFeatureRendererReactComponent,
-} from '@jbrowse/plugin-svg'
-
-// locals
-import PileupRenderer from '../../PileupRenderer'
-import SNPCoverageRenderer from '../../SNPCoverageRenderer'
-import LinearPileupDisplay from '../../LinearPileupDisplay'
-import LinearSNPCoverageDisplay from '../../LinearSNPCoverageDisplay'
-import configSchemaFactory from './configSchema'
-
-// mock warnings to avoid unnecessary outputs
-beforeEach(() => {
-  jest.spyOn(console, 'warn').mockImplementation(() => {})
-})
-
-afterEach(() => {
-  // @ts-expect-error
-  console.warn.mockRestore()
-})
-
-class AlignmentsPlugin extends Plugin {
-  name = 'AlignmentsPlugin'
-  install(pluginManager: PluginManager) {
-    PileupRenderer(pluginManager)
-
-    pluginManager.addRendererType(
-      () =>
-        new BoxRendererType({
-          name: 'SvgFeatureRenderer',
-          ReactComponent: SvgFeatureRendererReactComponent,
-          configSchema: svgFeatureRendererConfigSchema,
-          pluginManager,
-        }),
-    )
-
-    SNPCoverageRenderer(pluginManager)
-    LinearPileupDisplay(pluginManager)
-    LinearSNPCoverageDisplay(pluginManager)
-  }
-}
-
-test('has a type attr', () => {
-  const configSchema = configSchemaFactory(
-    new PluginManager([new AlignmentsPlugin()])
-      .createPluggableElements()
-      .configure(),
-  )
-  const config = configSchema.create({
-    type: 'LinearAlignmentsDisplay',
-    displayId: 'display0',
-    name: 'Zonker Display',
-  })
-
-  expect(config.type).toEqual('LinearAlignmentsDisplay')
-})

package/src/LinearAlignmentsDisplay/models/configSchema.ts

@@ -1,41 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { baseLinearDisplayConfigSchema } from '@jbrowse/plugin-linear-genome-view'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-/**
- * #config LinearAlignmentsDisplay
- * has a "pileup" sub-display, where you can see individual reads and a
- * quantitative "snpcoverage" sub-display track showing SNP frequencies
- */
-export default function configModelFactory(pm: PluginManager) {
-  return ConfigurationSchema(
-    'LinearAlignmentsDisplay',
-    {
-      /**
-       * #slot
-       */
-      pileupDisplay: pm.getDisplayType('LinearPileupDisplay').configSchema,
-
-      /**
-       * #slot
-       */
-      snpCoverageDisplay: pm.getDisplayType('LinearSNPCoverageDisplay')
-        .configSchema,
-
-      /**
-       * #slot
-       */
-      height: {
-        type: 'number',
-        defaultValue: 250,
-      },
-    },
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: baseLinearDisplayConfigSchema,
-      explicitlyTyped: true,
-    },
-  )
-}