@jbrowse/plugin-alignments 2.6.1 → 2.6.2

package/src/PileupRenderer/renderModifications.ts

@@ -1,74 +0,0 @@
-import { bpSpanPx, Region } from '@jbrowse/core/util'
-import {
-  getModificationPositions,
-  getModificationProbabilities,
-  getNextRefPos,
-  parseCigar,
-} from '../MismatchParser'
-import { getTagAlt } from '../util'
-import { fillRect, LayoutFeature } from './util'
-import { RenderArgsWithColor } from './makeImageData'
-
-// render modifications stored in MM tag in BAM
-//
-// ML stores probabilities as array of numerics and MP is scaled phred scores
-// https://github.com/samtools/hts-specs/pull/418/files#diff-e765c6479316309f56b636f88189cdde8c40b854c7bdcce9ee7fe87a4e76febcR596
-//
-// if we have ML or Ml, it is an 8bit probability, divide by 255
-//
-// if we have MP or Mp it is phred scaled ASCII, which can go up to 90 but
-// has very high likelihood basecalls at that point, we really only care
-// about low qual calls <20 approx
-export function renderModifications({
-  ctx,
-  feat,
-  region,
-  bpPerPx,
-  renderArgs,
-  canvasWidth,
-}: {
-  ctx: CanvasRenderingContext2D
-  feat: LayoutFeature
-  region: Region
-  bpPerPx: number
-  renderArgs: RenderArgsWithColor
-  canvasWidth: number
-}) {
-  const { feature, topPx, heightPx } = feat
-  const { Color, modificationTagMap = {} } = renderArgs
-
-  const seq = feature.get('seq') as string | undefined
-
-  if (!seq) {
-    return
-  }
-  const mm = (getTagAlt(feature, 'MM', 'Mm') as string) || ''
-  const cigar = feature.get('CIGAR')
-  const start = feature.get('start')
-  const strand = feature.get('strand')
-  const cigarOps = parseCigar(cigar)
-  const probabilities = getModificationProbabilities(feature)
-  const modifications = getModificationPositions(mm, seq, strand)
-
-  // probIndex applies across multiple modifications e.g.
-  let probIndex = 0
-  for (const { type, positions } of modifications) {
-    const col = modificationTagMap[type] || 'black'
-    const base = Color(col)
-    for (const readPos of getNextRefPos(cigarOps, positions)) {
-      const r = start + readPos
-      const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx)
-      const prob = probabilities?.[probIndex] || 0
-      const c =
-        prob !== 1
-          ? base
-              .alpha(prob + 0.1)
-              .hsl()
-              .string()
-          : col
-      const w = rightPx - leftPx + 0.5
-      fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c)
-      probIndex++
-    }
-  }
-}

package/src/PileupRenderer/renderPerBaseLettering.ts

@@ -1,67 +0,0 @@
-import { bpSpanPx, Region } from '@jbrowse/core/util'
-import { parseCigar } from '../MismatchParser'
-import { fillRect, LayoutFeature } from './util'
-
-export function renderPerBaseLettering({
-  ctx,
-  feat,
-  region,
-  bpPerPx,
-  colorForBase,
-  contrastForBase,
-  charWidth,
-  charHeight,
-  canvasWidth,
-}: {
-  ctx: CanvasRenderingContext2D
-  feat: LayoutFeature
-  region: Region
-  bpPerPx: number
-  colorForBase: Record<string, string>
-  contrastForBase: Record<string, string>
-  charWidth: number
-  charHeight: number
-  canvasWidth: number
-}) {
-  const heightLim = charHeight - 2
-  const { feature, topPx, heightPx } = feat
-  const seq = feature.get('seq') as string | undefined
-  const cigarOps = parseCigar(feature.get('CIGAR'))
-  const w = 1 / bpPerPx
-  const start = feature.get('start')
-  let soffset = 0
-  let roffset = 0
-
-  if (!seq) {
-    return
-  }
-  for (let i = 0; i < cigarOps.length; i += 2) {
-    const len = +cigarOps[i]
-    const op = cigarOps[i + 1]
-    if (op === 'S' || op === 'I') {
-      soffset += len
-    } else if (op === 'D' || op === 'N') {
-      roffset += len
-    } else if (op === 'M' || op === 'X' || op === '=') {
-      for (let m = 0; m < len; m++) {
-        const letter = seq[soffset + m]
-        const r = start + roffset + m
-        const [leftPx] = bpSpanPx(r, r + 1, region, bpPerPx)
-        const c = colorForBase[letter]
-        fillRect(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c)
-
-        if (w >= charWidth && heightPx >= heightLim) {
-          // normal SNP coloring
-          ctx.fillStyle = contrastForBase[letter]
-          ctx.fillText(
-            letter,
-            leftPx + (w - charWidth) / 2 + 1,
-            topPx + heightPx,
-          )
-        }
-      }
-      soffset += len
-      roffset += len
-    }
-  }
-}

package/src/PileupRenderer/renderPerBaseQuality.ts

@@ -1,46 +0,0 @@
-import { bpSpanPx, Region } from '@jbrowse/core/util'
-import { parseCigar } from '../MismatchParser'
-import { fillRect, LayoutFeature } from './util'
-
-export function renderPerBaseQuality({
-  ctx,
-  feat,
-  region,
-  bpPerPx,
-  canvasWidth,
-}: {
-  ctx: CanvasRenderingContext2D
-  feat: LayoutFeature
-  region: Region
-  bpPerPx: number
-  canvasWidth: number
-}) {
-  const { feature, topPx, heightPx } = feat
-  const qual: string = feature.get('qual') || ''
-  const scores = qual.split(' ').map(val => +val)
-  const cigarOps = parseCigar(feature.get('CIGAR'))
-  const w = 1 / bpPerPx
-  const start = feature.get('start')
-  let soffset = 0 // sequence offset
-  let roffset = 0 // reference offset
-
-  for (let i = 0; i < cigarOps.length; i += 2) {
-    const len = +cigarOps[i]
-    const op = cigarOps[i + 1]
-    if (op === 'S' || op === 'I') {
-      soffset += len
-    } else if (op === 'D' || op === 'N') {
-      roffset += len
-    } else if (op === 'M' || op === 'X' || op === '=') {
-      for (let m = 0; m < len; m++) {
-        const score = scores[soffset + m]
-        const start0 = start + roffset + m
-        const leftPx = bpSpanPx(start0, start0 + 1, region, bpPerPx)[0]
-        const c = `hsl(${score === 255 ? 150 : score * 1.5},55%,50%)`
-        fillRect(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c)
-      }
-      soffset += len
-      roffset += len
-    }
-  }
-}

package/src/PileupRenderer/renderSoftClipping.ts

@@ -1,78 +0,0 @@
-import {
-  AnyConfigurationModel,
-  readConfObject,
-} from '@jbrowse/core/configuration'
-import { bpSpanPx } from '@jbrowse/core/util'
-import { Theme } from '@mui/material'
-
-// locals
-import { Mismatch } from '../MismatchParser'
-import { RenderArgsDeserializedWithFeaturesAndLayout } from './PileupRenderer'
-import { fillRect, getCharWidthHeight, LayoutFeature } from './util'
-
-export function renderSoftClipping({
-  ctx,
-  feat,
-  renderArgs,
-  config,
-  theme,
-  colorForBase,
-  canvasWidth,
-}: {
-  ctx: CanvasRenderingContext2D
-  feat: LayoutFeature
-  renderArgs: RenderArgsDeserializedWithFeaturesAndLayout
-  config: AnyConfigurationModel
-  colorForBase: Record<string, string>
-  theme: Theme
-  canvasWidth: number
-}) {
-  const { feature, topPx, heightPx } = feat
-  const { regions, bpPerPx } = renderArgs
-  const [region] = regions
-  const minFeatWidth = readConfObject(config, 'minSubfeatureWidth')
-  const mismatches = feature.get('mismatches') as Mismatch[] | undefined
-  const seq = feature.get('seq') as string | undefined
-  const { charWidth, charHeight } = getCharWidthHeight()
-
-  // Display all bases softclipped off in lightened colors
-  if (!(seq && mismatches)) {
-    return
-  }
-  mismatches
-    .filter(mismatch => mismatch.type === 'softclip')
-    .forEach(mismatch => {
-      const len = mismatch.cliplen || 0
-      const s = feature.get('start')
-      const start = mismatch.start === 0 ? s - len : s + mismatch.start
-
-      for (let k = 0; k < len; k += 1) {
-        const base = seq.charAt(k + mismatch.start)
-
-        // If softclip length+start is longer than sequence, no need to
-        // continue showing base
-        if (!base) {
-          return
-        }
-
-        const s0 = start + k
-        const [leftPx, rightPx] = bpSpanPx(s0, s0 + 1, region, bpPerPx)
-        const widthPx = Math.max(minFeatWidth, rightPx - leftPx)
-
-        // Black accounts for IUPAC ambiguity code bases such as N that
-        // show in soft clipping
-        const baseColor = colorForBase[base] || '#000000'
-        ctx.fillStyle = baseColor
-        fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth)
-
-        if (widthPx >= charWidth && heightPx >= charHeight - 5) {
-          ctx.fillStyle = theme.palette.getContrastText(baseColor)
-          ctx.fillText(
-            base,
-            leftPx + (widthPx - charWidth) / 2 + 1,
-            topPx + heightPx,
-          )
-        }
-      }
-    })
-}

package/src/PileupRenderer/sortUtil.ts

@@ -1,107 +0,0 @@
-import { doesIntersect2, Feature } from '@jbrowse/core/util'
-import { Mismatch } from '../MismatchParser'
-
-interface SortObject {
-  pos: number
-  type: string
-  tag?: string
-}
-export const sortFeature = (
-  features: Map<string, Feature>,
-  sortedBy: SortObject,
-) => {
-  const featureArray = Array.from(features.values())
-  const featuresInCenterLine: Feature[] = []
-  const featuresOutsideCenter: Feature[] = []
-  const { pos, type } = sortedBy
-
-  // only sort on features that intersect center line, append those outside post-sort
-  featureArray.forEach(innerArray => {
-    const feature = innerArray
-    const start = feature.get('start')
-    const end = feature.get('end')
-    if (doesIntersect2(pos - 1, pos, start, end)) {
-      featuresInCenterLine.push(innerArray)
-    } else {
-      featuresOutsideCenter.push(innerArray)
-    }
-  })
-
-  const isCram = featureArray.length ? featureArray[0].get('tags') : false
-  switch (type) {
-    case 'Start location': {
-      featuresInCenterLine.sort((a, b) => a.get('start') - b.get('start'))
-      break
-    }
-
-    case 'tag': {
-      const tag = sortedBy.tag as string
-      const getTag = (f: Feature, t: string) => {
-        return isCram ? f.get('tags')[t] : f.get(t)
-      }
-      const isString =
-        featuresInCenterLine[0] &&
-        typeof getTag(featuresInCenterLine[0], tag) === 'string'
-      if (isString) {
-        featuresInCenterLine.sort((a, b) =>
-          getTag(b, tag).localeCompare(getTag(a, tag)),
-        )
-      } else {
-        featuresInCenterLine.sort(
-          (a, b) => (getTag(b, tag) || 0) - (getTag(a, tag) || 0),
-        )
-      }
-      break
-    }
-
-    // first sort all mismatches, then all reference bases at the end
-    case 'Base pair': {
-      const baseSortArray: [string, Mismatch][] = []
-      featuresInCenterLine.forEach(feature => {
-        const mismatches: Mismatch[] = feature.get('mismatches')
-        mismatches.forEach(mismatch => {
-          const start = feature.get('start')
-          const offset = start + mismatch.start + 1
-          const consuming =
-            mismatch.type === 'insertion' || mismatch.type === 'softclip'
-          const len = consuming ? 0 : mismatch.length
-          if (pos >= offset && pos < offset + len) {
-            baseSortArray.push([feature.id(), mismatch])
-          }
-        })
-      })
-
-      const baseMap = new Map(baseSortArray)
-      featuresInCenterLine.sort((a, b) => {
-        const aMismatch = baseMap.get(a.id())
-        const bMismatch = baseMap.get(b.id())
-        const acode = bMismatch && bMismatch.base.toUpperCase()
-        const bcode = aMismatch && aMismatch.base.toUpperCase()
-        if (acode === bcode && acode === '*') {
-          // @ts-expect-error
-          return aMismatch.length - bMismatch.length
-        }
-        return (
-          (acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0)
-        )
-      })
-
-      break
-    }
-
-    // sorts positive strands then negative strands
-    case 'Read strand': {
-      featuresInCenterLine.sort((a, b) =>
-        a.get('strand') <= b.get('strand') ? 1 : -1,
-      )
-      break
-    }
-  }
-
-  return new Map(
-    [...featuresInCenterLine, ...featuresOutsideCenter].map(feature => [
-      feature.id(),
-      feature,
-    ]),
-  )
-}

package/src/PileupRenderer/util.ts

@@ -1,63 +0,0 @@
-import { Feature, measureText } from '@jbrowse/core/util'
-import { Theme } from '@mui/material'
-
-export function fillRect(
-  ctx: CanvasRenderingContext2D,
-  l: number,
-  t: number,
-  w: number,
-  h: number,
-  cw: number,
-  color?: string,
-) {
-  if (l + w < 0 || l > cw) {
-    return
-  } else {
-    if (color) {
-      ctx.fillStyle = color
-    }
-    ctx.fillRect(l, t, w, h)
-  }
-}
-
-export function getColorBaseMap(theme: Theme) {
-  const { bases } = theme.palette
-  return {
-    A: bases.A.main,
-    C: bases.C.main,
-    G: bases.G.main,
-    T: bases.T.main,
-    deletion: '#808080', // gray
-  }
-}
-
-export function getContrastBaseMap(theme: Theme) {
-  return Object.fromEntries(
-    Object.entries(getColorBaseMap(theme)).map(([key, value]) => [
-      key,
-      theme.palette.getContrastText(value),
-    ]),
-  )
-}
-
-export function shouldDrawSNPsMuted(type?: string) {
-  return ['methylation', 'modifications'].includes(type || '')
-}
-
-export function shouldDrawIndels() {
-  return true
-}
-
-export interface LayoutFeature {
-  heightPx: number
-  topPx: number
-  feature: Feature
-}
-
-// get width and height of chars the height is an approximation: width letter M
-// is approximately the height
-export function getCharWidthHeight() {
-  const charWidth = measureText('A')
-  const charHeight = measureText('M') - 2
-  return { charWidth, charHeight }
-}

package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts

@@ -1,111 +0,0 @@
-import {
-  BaseFeatureDataAdapter,
-  BaseOptions,
-} from '@jbrowse/core/data_adapters/BaseAdapter'
-import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-
-// locals
-import generateCoverageBins from './generateCoverageBins'
-import { fetchSequence } from '../util'
-
-export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
-  protected async configure() {
-    const subadapterConfig = this.getConf('subadapter')
-    const sequenceConf = subadapterConfig.sequenceAdapter
-    const dataAdapter = await this.getSubAdapter?.(subadapterConfig)
-
-    const sequenceAdapter = sequenceConf
-      ? await this.getSubAdapter?.(sequenceConf)
-      : undefined
-
-    if (!dataAdapter) {
-      throw new Error('Failed to get subadapter')
-    }
-
-    return {
-      subadapter: dataAdapter.dataAdapter as BaseFeatureDataAdapter,
-      sequenceAdapter: sequenceAdapter?.dataAdapter as
-        | BaseFeatureDataAdapter
-        | undefined,
-    }
-  }
-
-  async fetchSequence(region: Region) {
-    const { sequenceAdapter } = await this.configure()
-    if (!sequenceAdapter) {
-      return undefined
-    }
-
-    return fetchSequence(region, sequenceAdapter)
-  }
-
-  getFeatures(region: Region, opts: BaseOptions = {}) {
-    return ObservableCreate<Feature>(async observer => {
-      const { subadapter } = await this.configure()
-      const feats = await firstValueFrom(
-        subadapter.getFeatures(region, opts).pipe(toArray()),
-      )
-
-      const { bins, skipmap } = await generateCoverageBins(
-        feats,
-        region,
-        opts,
-        arg => this.fetchSequence(arg),
-      )
-
-      bins.forEach((bin, index) => {
-        const start = region.start + index
-        observer.next(
-          new SimpleFeature({
-            id: `${this.id}-${start}`,
-            data: {
-              score: bin.total,
-              snpinfo: bin,
-              start,
-              end: start + 1,
-              refName: region.refName,
-            },
-          }),
-        )
-      })
-
-      // make fake features from the coverage
-      Object.entries(skipmap).forEach(([key, skip]) => {
-        observer.next(
-          new SimpleFeature({
-            id: key,
-            data: {
-              type: 'skip',
-              start: skip.start,
-              end: skip.end,
-              strand: skip.strand,
-              score: skip.score,
-              xs: skip.xs,
-            },
-          }),
-        )
-      })
-
-      observer.complete()
-    }, opts.signal)
-  }
-
-  async getMultiRegionFeatureDensityStats(
-    regions: Region[],
-    opts?: BaseOptions,
-  ) {
-    const { subadapter } = await this.configure()
-    return subadapter.getMultiRegionFeatureDensityStats(regions, opts)
-  }
-
-  async getRefNames(opts: BaseOptions = {}) {
-    const { subadapter } = await this.configure()
-    return subadapter.getRefNames(opts)
-  }
-
-  freeResources(/* { region } */): void {}
-}

package/src/SNPCoverageAdapter/configSchema.ts

@@ -1,23 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config SNPCoverageAdapter
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const configSchema = ConfigurationSchema(
-  'SNPCoverageAdapter',
-  {
-    /**
-     * #slot
-     * normally refers to a BAM or CRAM adapter
-     */
-    subadapter: {
-      type: 'frozen',
-      defaultValue: null,
-    },
-  },
-  { explicitlyTyped: true },
-)
-
-export default configSchema