@jbrowse/plugin-alignments 2.6.1 → 2.6.3

package/src/MismatchParser/index.ts

@@ -1,508 +0,0 @@
-import { revcom, Feature } from '@jbrowse/core/util'
-import { getTagAlt } from '../util'
-
-export interface Mismatch {
-  qual?: number
-  start: number
-  length: number
-  type: string
-  base: string
-  altbase?: string
-  seq?: string
-  cliplen?: number
-}
-const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi)
-const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/)
-const cigarRegex = new RegExp(/([MIDNSHPX=])/)
-const startClip = new RegExp(/(\d+)[SH]$/)
-const endClip = new RegExp(/^(\d+)([SH])/)
-
-export function parseCigar(cigar = '') {
-  return cigar.split(cigarRegex).slice(0, -1)
-}
-
-export function cigarToMismatches(
-  ops: string[],
-  seq?: string,
-  ref?: string,
-  qual?: Buffer,
-) {
-  let roffset = 0 // reference offset
-  let soffset = 0 // seq offset
-  const mismatches: Mismatch[] = []
-  const hasRefAndSeq = ref && seq
-  for (let i = 0; i < ops.length; i += 2) {
-    const len = +ops[i]
-    const op = ops[i + 1]
-
-    if (op === 'M' || op === '=' || op === 'E') {
-      if (hasRefAndSeq) {
-        for (let j = 0; j < len; j++) {
-          if (
-            // @ts-ignore in the full yarn build of the repo, this says that object is possibly undefined for some reason, ignored
-            seq[soffset + j].toUpperCase() !== ref[roffset + j].toUpperCase()
-          ) {
-            mismatches.push({
-              start: roffset + j,
-              type: 'mismatch',
-              base: seq[soffset + j],
-              altbase: ref[roffset + j],
-              length: 1,
-            })
-          }
-        }
-      }
-      soffset += len
-    }
-    if (op === 'I') {
-      mismatches.push({
-        start: roffset,
-        type: 'insertion',
-        base: `${len}`,
-        length: 0,
-      })
-      soffset += len
-    } else if (op === 'D') {
-      mismatches.push({
-        start: roffset,
-        type: 'deletion',
-        base: '*',
-        length: len,
-      })
-    } else if (op === 'N') {
-      mismatches.push({
-        start: roffset,
-        type: 'skip',
-        base: 'N',
-        length: len,
-      })
-    } else if (op === 'X') {
-      const r = seq?.slice(soffset, soffset + len) || []
-      const q = qual?.slice(soffset, soffset + len) || []
-
-      for (let j = 0; j < len; j++) {
-        mismatches.push({
-          start: roffset + j,
-          type: 'mismatch',
-          base: r[j],
-          qual: q[j],
-          length: 1,
-        })
-      }
-      soffset += len
-    } else if (op === 'H') {
-      mismatches.push({
-        start: roffset,
-        type: 'hardclip',
-        base: `H${len}`,
-        cliplen: len,
-        length: 1,
-      })
-    } else if (op === 'S') {
-      mismatches.push({
-        start: roffset,
-        type: 'softclip',
-        base: `S${len}`,
-        cliplen: len,
-        length: 1,
-      })
-      soffset += len
-    }
-
-    if (op !== 'I' && op !== 'S' && op !== 'H') {
-      roffset += len
-    }
-  }
-  return mismatches
-}
-
-/**
- * parse a SAM MD tag to find mismatching bases of the template versus the
- * reference @returns array of mismatches and their positions
- */
-export function mdToMismatches(
-  mdstring: string,
-  ops: string[],
-  cigarMismatches: Mismatch[],
-  seq: string,
-  qual?: Buffer,
-) {
-  let curr: Mismatch = { start: 0, base: '', length: 0, type: 'mismatch' }
-  let lastCigar = 0
-  let lastTemplateOffset = 0
-  let lastRefOffset = 0
-  let lastSkipPos = 0
-  const mismatchRecords: Mismatch[] = []
-  const skips = cigarMismatches.filter(cigar => cigar.type === 'skip')
-
-  // convert a position on the reference sequence to a position
-  // on the template sequence, taking into account hard and soft
-  // clipping of reads
-
-  function nextRecord(): void {
-    mismatchRecords.push(curr)
-
-    // get a new mismatch record ready
-    curr = {
-      start: curr.start + curr.length,
-      length: 0,
-      base: '',
-      type: 'mismatch',
-    }
-  }
-
-  function getTemplateCoordLocal(refCoord: number): number {
-    let templateOffset = lastTemplateOffset
-    let refOffset = lastRefOffset
-    for (
-      let i = lastCigar;
-      i < ops.length && refOffset <= refCoord;
-      i += 2, lastCigar = i
-    ) {
-      const len = +ops[i]
-      const op = ops[i + 1]
-
-      if (op === 'S' || op === 'I') {
-        templateOffset += len
-      } else if (op === 'D' || op === 'P' || op === 'N') {
-        refOffset += len
-      } else if (op !== 'H') {
-        templateOffset += len
-        refOffset += len
-      }
-    }
-    lastTemplateOffset = templateOffset
-    lastRefOffset = refOffset
-
-    return templateOffset - (refOffset - refCoord)
-  }
-
-  // now actually parse the MD string
-  const md = mdstring.match(mdRegex) || []
-  for (let i = 0; i < md.length; i++) {
-    const token = md[i]
-    const num = +token
-    if (!Number.isNaN(num)) {
-      curr.start += num
-    } else if (token.startsWith('^')) {
-      curr.start += token.length - 1
-    } else {
-      // mismatch
-      for (let j = 0; j < token.length; j += 1) {
-        curr.length = 1
-
-        while (lastSkipPos < skips.length) {
-          const mismatch = skips[lastSkipPos]
-          if (curr.start >= mismatch.start) {
-            curr.start += mismatch.length
-            lastSkipPos++
-          } else {
-            break
-          }
-        }
-        const s = getTemplateCoordLocal(curr.start)
-        curr.base = seq[s] || 'X'
-        curr.qual = qual?.[s]
-        curr.altbase = token
-        nextRecord()
-      }
-    }
-  }
-  return mismatchRecords
-}
-
-export function getMismatches(
-  cigar: string,
-  md?: string,
-  seq?: string,
-  ref?: string,
-  qual?: Buffer,
-) {
-  let mismatches: Mismatch[] = []
-  const ops = parseCigar(cigar)
-
-  // parse the CIGAR tag if it has one
-  if (cigar) {
-    mismatches = mismatches.concat(cigarToMismatches(ops, seq, ref, qual))
-  }
-
-  // now let's look for CRAM or MD mismatches
-  if (md && seq) {
-    mismatches = mismatches.concat(
-      mdToMismatches(md, ops, mismatches, seq, qual),
-    )
-  }
-
-  return mismatches
-}
-// get relative reference sequence positions for positions given relative to
-// the read sequence
-export function* getNextRefPos(cigarOps: string[], positions: number[]) {
-  let readPos = 0
-  let refPos = 0
-  let currPos = 0
-
-  for (let i = 0; i < cigarOps.length && currPos < positions.length; i += 2) {
-    const len = +cigarOps[i]
-    const op = cigarOps[i + 1]
-    if (op === 'S' || op === 'I') {
-      for (let i = 0; i < len && currPos < positions.length; i++) {
-        if (positions[currPos] === readPos + i) {
-          currPos++
-        }
-      }
-      readPos += len
-    } else if (op === 'D' || op === 'N') {
-      refPos += len
-    } else if (op === 'M' || op === 'X' || op === '=') {
-      for (let i = 0; i < len && currPos < positions.length; i++) {
-        if (positions[currPos] === readPos + i) {
-          yield refPos + i
-          currPos++
-        }
-      }
-      readPos += len
-      refPos += len
-    }
-  }
-}
-
-export function getModificationProbabilities(feature: Feature) {
-  const m = (getTagAlt(feature, 'ML', 'Ml') as number[] | string) || []
-  return m
-    ? (typeof m === 'string' ? m.split(',').map(e => +e) : m).map(e => e / 255)
-    : (getTagAlt(feature, 'MP', 'Mp') as string | undefined)
-        ?.split('')
-        .map(s => s.charCodeAt(0) - 33)
-        .map(elt => Math.min(1, elt / 50))
-}
-
-export function getMethBins(feature: Feature) {
-  const fstart = feature.get('start')
-  const fend = feature.get('end')
-  const fstrand = feature.get('strand') as -1 | 0 | 1
-  const flen = fend - fstart
-  const mm = (getTagAlt(feature, 'MM', 'Mm') as string | undefined) || ''
-  const methBins = new Array<number>(flen)
-  const methProbs = new Array<number>(flen)
-  const seq = feature.get('seq') as string | undefined
-  if (seq) {
-    const ops = parseCigar(feature.get('CIGAR'))
-    const probabilities = getModificationProbabilities(feature)
-    const modifications = getModificationPositions(mm, seq, fstrand)
-    let probIndex = 0
-    for (const { type, positions } of modifications) {
-      if (type === 'm') {
-        for (const ref of getNextRefPos(ops, positions)) {
-          const prob = probabilities?.[probIndex] || 0
-          probIndex++
-          if (ref >= 0 && ref < flen) {
-            methBins[ref] = 1
-            methProbs[ref] = prob
-          }
-        }
-      }
-    }
-  }
-  return { methBins, methProbs }
-}
-
-export function getModificationPositions(
-  mm: string,
-  fseq: string,
-  fstrand: number,
-) {
-  const seq = fstrand === -1 ? revcom(fseq) : fseq
-  const mods = mm.split(';').filter(mod => !!mod)
-  const result = []
-  for (let i = 0; i < mods.length; i++) {
-    const mod = mods[i]
-    const [basemod, ...skips] = mod.split(',')
-
-    // regexes based on parse_mm.pl from hts-specs
-    const matches = basemod.match(modificationRegex)
-    if (!matches) {
-      throw new Error('bad format for MM tag')
-    }
-    const [, base, strand, typestr] = matches
-
-    // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
-    // split, and they can also be chemical codes (ChEBI) e.g. C+16061
-    const types = typestr.split(/(\d+|.)/).filter(f => !!f)
-
-    if (strand === '-') {
-      console.warn('unsupported negative strand modifications')
-      // make sure to return a somewhat matching type even in this case
-      result.push({ type: 'unsupported', positions: [] as number[] })
-    }
-
-    // this logic also based on parse_mm.pl from hts-specs is that in the
-    // sequence of the read, if we have a modification type e.g. C+m;2 and a
-    // sequence ACGTACGTAC we skip the two instances of C and go to the last
-    // C
-    for (let j = 0; j < types.length; j++) {
-      const type = types[j]
-      let i = 0
-      const positions = []
-      for (let k = 0; k < skips.length; k++) {
-        let delta = +skips[k]
-        do {
-          if (base === 'N' || base === seq[i]) {
-            delta--
-          }
-          i++
-        } while (delta >= 0 && i < seq.length)
-
-        const temp = i - 1
-        positions.push(fstrand === -1 ? seq.length - 1 - temp : temp)
-      }
-      if (fstrand === -1) {
-        positions.sort((a, b) => a - b)
-      }
-      result.push({
-        type,
-        positions,
-      })
-    }
-  }
-  return result
-}
-
-export function getModificationTypes(mm: string) {
-  return mm
-    .split(';')
-    .filter(mod => !!mod)
-    .flatMap(mod => {
-      const [basemod] = mod.split(',')
-
-      const matches = basemod.match(modificationRegex)
-      if (!matches) {
-        throw new Error(`bad format for MM tag: ${mm}`)
-      }
-      const typestr = matches[3]
-
-      // can be a multi e.g. C+mh for both meth (m) and hydroxymeth (h) so
-      // split, and they can also be chemical codes (ChEBI) e.g. C+16061
-      return typestr.split(/(\d+|.)/).filter(f => !!f)
-    })
-}
-
-export function getOrientedCigar(flip: boolean, cigar: string[]) {
-  if (flip) {
-    const ret = []
-    for (let i = 0; i < cigar.length; i += 2) {
-      const len = cigar[i]
-      let op = cigar[i + 1]
-      if (op === 'D') {
-        op = 'I'
-      } else if (op === 'I') {
-        op = 'D'
-      }
-      ret.push(len, op)
-    }
-    return ret
-  } else {
-    return cigar
-  }
-}
-
-export function getOrientedMismatches(flip: boolean, cigar: string) {
-  const p = parseCigar(cigar)
-  return cigarToMismatches(flip ? getOrientedCigar(flip, p) : p)
-}
-
-export function getLengthOnRef(cigar: string) {
-  const cigarOps = parseCigar(cigar)
-  let lengthOnRef = 0
-  for (let i = 0; i < cigarOps.length; i += 2) {
-    const len = +cigarOps[i]
-    const op = cigarOps[i + 1]
-    if (op !== 'H' && op !== 'S' && op !== 'I') {
-      lengthOnRef += len
-    }
-  }
-  return lengthOnRef
-}
-
-export function getLength(cigar: string) {
-  const cigarOps = parseCigar(cigar)
-  let length = 0
-  for (let i = 0; i < cigarOps.length; i += 2) {
-    const len = +cigarOps[i]
-    const op = cigarOps[i + 1]
-    if (op !== 'D' && op !== 'N') {
-      length += len
-    }
-  }
-  return length
-}
-
-export function getLengthSansClipping(cigar: string) {
-  const cigarOps = parseCigar(cigar)
-  let length = 0
-  for (let i = 0; i < cigarOps.length; i += 2) {
-    const len = +cigarOps[i]
-    const op = cigarOps[i + 1]
-    if (op !== 'H' && op !== 'S' && op !== 'D' && op !== 'N') {
-      length += len
-    }
-  }
-  return length
-}
-
-export function getClip(cigar: string, strand: number) {
-  return strand === -1
-    ? +(cigar.match(startClip) || [])[1] || 0
-    : +(cigar.match(endClip) || [])[1] || 0
-}
-
-export function getTag(f: Feature, tag: string) {
-  const tags = f.get('tags')
-  return tags ? tags[tag] : f.get(tag)
-}
-
-// produces a list of "feature-like" object from parsing supplementary
-// alignments in the SA tag
-//
-// @param normalize - used specifically in the linear-read-vs-ref context, it
-// flips features around relative to the original feature. other contexts of
-// usage can keep this false
-export function featurizeSA(
-  SA: string | undefined,
-  id: string,
-  strand: number,
-  readName: string,
-  normalize?: boolean,
-) {
-  return (
-    SA?.split(';')
-      .filter(aln => !!aln)
-      .map((aln, index) => {
-        const [saRef, saStart, saStrand, saCigar] = aln.split(',')
-        const saLengthOnRef = getLengthOnRef(saCigar)
-        const saLength = getLength(saCigar)
-        const saLengthSansClipping = getLengthSansClipping(saCigar)
-        const saStrandNormalized = saStrand === '-' ? -1 : 1
-        const saClipPos = getClip(
-          saCigar,
-          (normalize ? strand : 1) * saStrandNormalized,
-        )
-        const saRealStart = +saStart - 1
-        return {
-          refName: saRef,
-          start: saRealStart,
-          end: saRealStart + saLengthOnRef,
-          seqLength: saLength,
-          clipPos: saClipPos,
-          CIGAR: saCigar,
-          strand: (normalize ? strand : 1) * saStrandNormalized,
-          uniqueId: `${id}_SA${index}`,
-          mate: {
-            start: saClipPos,
-            end: saClipPos + saLengthSansClipping,
-            refName: readName,
-          },
-        }
-      }) || []
-  )
-}

package/src/PileupRPC/base.ts

@@ -1,24 +0,0 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
-import { renameRegionsIfNeeded } from '@jbrowse/core/util'
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
-
-// specialized get features to return limited data about alignments
-export default abstract class PileupBaseRPC extends RpcMethodType {
-  async serializeArguments(
-    args: RenderArgs & {
-      signal?: AbortSignal
-      statusCallback?: (arg: string) => void
-    },
-    rpcDriver: string,
-  ) {
-    const { rootModel } = this.pluginManager
-    const assemblyManager = rootModel?.session?.assemblyManager
-    if (!assemblyManager) {
-      throw new Error('no assembly manager available')
-    }
-
-    const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args)
-
-    return super.serializeArguments(renamedArgs, rpcDriver)
-  }
-}

package/src/PileupRPC/index.ts

@@ -1,12 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import {
-  PileupGetGlobalValueForTag,
-  PileupGetVisibleModifications,
-  PileupGetReducedFeatures,
-} from './rpcMethods'
-
-export default (pm: PluginManager) => {
-  pm.addRpcMethod(() => new PileupGetGlobalValueForTag(pm))
-  pm.addRpcMethod(() => new PileupGetVisibleModifications(pm))
-  pm.addRpcMethod(() => new PileupGetReducedFeatures(pm))
-}

package/src/PileupRPC/methods/GetGlobalValueForTag.ts

@@ -1,44 +0,0 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { Region } from '@jbrowse/core/util'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-
-// locals
-import PileupBaseRPC from '../base'
-import { getTag } from '../../util'
-
-export default class PileupGetGlobalValueForTag extends PileupBaseRPC {
-  name = 'PileupGetGlobalValueForTag'
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      headers?: Record<string, string>
-      regions: Region[]
-      sessionId: string
-      tag: string
-    },
-    rpcDriver: string,
-  ) {
-    const { adapterConfig, sessionId, regions, tag } =
-      await this.deserializeArguments(args, rpcDriver)
-
-    const dataAdapter = (
-      await getAdapter(this.pluginManager, sessionId, adapterConfig)
-    ).dataAdapter as BaseFeatureDataAdapter
-
-    const features = dataAdapter.getFeaturesInMultipleRegions(regions)
-    const featuresArray = await firstValueFrom(features.pipe(toArray()))
-    return [
-      ...new Set(
-        featuresArray
-          .map(feature => getTag(feature, tag))
-          .filter(f => f !== undefined)
-          .map(f => `${f}`),
-      ),
-    ]
-  }
-}

package/src/PileupRPC/methods/GetReducedFeatures.ts

@@ -1,67 +0,0 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { Region, dedupe, groupBy } from '@jbrowse/core/util'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-// locals
-import { filterForPairs, getInsertSizeStats } from '../util'
-import PileupBaseRPC from '../base'
-import { getTag } from '../../util'
-
-// specialized get features to return limited data about alignments
-export default class PileupGetReducedFeatures extends PileupBaseRPC {
-  name = 'PileupGetReducedFeatures'
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      headers?: Record<string, string>
-      regions: Region[]
-      sessionId: string
-      tag: string
-    },
-    rpcDriver: string,
-  ) {
-    const des = await this.deserializeArguments(args, rpcDriver)
-    const { adapterConfig, sessionId, regions } = des
-    const dataAdapter = (
-      await getAdapter(this.pluginManager, sessionId, adapterConfig)
-    ).dataAdapter as BaseFeatureDataAdapter
-
-    const featuresArray = await firstValueFrom(
-      dataAdapter.getFeaturesInMultipleRegions(regions, des).pipe(toArray()),
-    )
-
-    const reduced = dedupe(
-      featuresArray.map(f => ({
-        id: f.id(),
-        refName: f.get('refName'),
-        name: f.get('name'),
-        start: f.get('start'),
-        strand: f.get('strand'),
-        end: f.get('end'),
-        flags: f.get('flags'),
-        tlen: f.get('template_length'),
-        pair_orientation: f.get('pair_orientation'),
-        next_ref: f.get('next_ref'),
-        next_pos: f.get('next_pos'),
-        clipPos: f.get('clipPos'),
-        SA: getTag(f, 'SA'),
-      })),
-      f => f.id,
-    )
-
-    const filtered = filterForPairs(reduced)
-    const stats = filtered.length ? getInsertSizeStats(filtered) : undefined
-    const chains = groupBy(reduced, f => f.name)
-
-    return {
-      chains: Object.values(chains),
-      stats,
-      hasPaired: !!stats,
-      containsNoTransferables: true,
-    }
-  }
-}

package/src/PileupRPC/methods/GetVisibleModifications.ts

@@ -1,45 +0,0 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { Region } from '@jbrowse/core/util'
-import { toArray } from 'rxjs/operators'
-import { firstValueFrom } from 'rxjs'
-
-// locals
-import { getModificationTypes } from '../../MismatchParser'
-import PileupBaseRPC from '../base'
-import { getTagAlt } from '../../util'
-
-export default class PileupGetVisibleModifications extends PileupBaseRPC {
-  name = 'PileupGetVisibleModifications'
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      headers?: Record<string, string>
-      regions: Region[]
-      sessionId: string
-      tag: string
-    },
-    rpcDriver: string,
-  ) {
-    const { adapterConfig, sessionId, regions } =
-      await this.deserializeArguments(args, rpcDriver)
-    const dataAdapter = (
-      await getAdapter(this.pluginManager, sessionId, adapterConfig)
-    ).dataAdapter as BaseFeatureDataAdapter
-
-    const featuresArray = await firstValueFrom(
-      dataAdapter.getFeaturesInMultipleRegions(regions).pipe(toArray()),
-    )
-
-    const uniqueValues = new Set<string>()
-    featuresArray.forEach(f => {
-      getModificationTypes(getTagAlt(f, 'MM', 'Mm') || '').forEach(t =>
-        uniqueValues.add(t),
-      )
-    })
-    return [...uniqueValues]
-  }
-}

package/src/PileupRPC/rpcMethods.ts

@@ -1,3 +0,0 @@
-export { default as PileupGetReducedFeatures } from './methods/GetReducedFeatures'
-export { default as PileupGetVisibleModifications } from './methods/GetVisibleModifications'
-export { default as PileupGetGlobalValueForTag } from './methods/GetGlobalValueForTag'