@jbrowse/plugin-alignments 2.2.1 → 2.3.0

package/src/{BamAdapter/MismatchParser.ts → MismatchParser/index.ts}

@@ -1,4 +1,5 @@
-import { revcom } from '@jbrowse/core/util'
+import { revcom, Feature } from '@jbrowse/core/util'
+
 export interface Mismatch {
   qual?: number
   start: number
@@ -11,9 +12,14 @@ export interface Mismatch {
 }
 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(/([MIDNSHPX=])/).slice(0, -1)
+  return cigar.split(cigarRegex).slice(0, -1)
 }
+
 export function cigarToMismatches(
   ops: string[],
   seq?: string,
@@ -339,3 +345,124 @@ export function getModificationTypes(mm: string) {
     })
     .flat()
 }
+
+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)
+      ret.push(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

@@ -0,0 +1,24 @@
+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

@@ -0,0 +1,12 @@
+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

@@ -0,0 +1,41 @@
+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 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 features.pipe(toArray()).toPromise()
+    return [
+      ...new Set(
+        featuresArray
+          .map(feature => getTag(feature, tag))
+          .filter(f => f !== undefined)
+          .map(f => `${f}`),
+      ),
+    ]
+  }
+}

package/src/PileupRPC/methods/GetReducedFeatures.ts

@@ -0,0 +1,76 @@
+import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
+import { Region, dedupe } from '@jbrowse/core/util'
+import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
+import { toArray } from 'rxjs/operators'
+
+// locals
+import { filterForPairs, getInsertSizeStats } from '../util'
+import { ReducedFeature } from '../../shared/fetchChains'
+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 dataAdapter
+      .getFeaturesInMultipleRegions(regions, des)
+      .pipe(toArray())
+      .toPromise()
+
+    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 = {} as { [key: string]: ReducedFeature[] }
+
+    // pair features
+    reduced.forEach(f => {
+      if (!chains[f.name]) {
+        chains[f.name] = []
+      }
+      chains[f.name].push(f)
+    })
+    return {
+      chains: Object.values(chains),
+      stats,
+      hasPaired: !!stats,
+      containsNoTransferables: true,
+    }
+  }
+}

package/src/PileupRPC/methods/GetVisibleModifications.ts

@@ -0,0 +1,45 @@
+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'
+
+// 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 dataAdapter
+      .getFeaturesInMultipleRegions(regions)
+      .pipe(toArray())
+      .toPromise()
+
+    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

@@ -1,114 +1,9 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType'
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { renameRegionsIfNeeded, Region } from '@jbrowse/core/util'
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods'
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { toArray } from 'rxjs/operators'
-
-// locals
-import { getTagAlt } from '../util'
-import { getModificationTypes } from '../BamAdapter/MismatchParser'
-
-export class PileupGetGlobalValueForTag extends RpcMethodType {
-  name = 'PileupGetGlobalValueForTag'
-
-  async serializeArguments(
-    args: RenderArgs & {
-      signal?: AbortSignal
-      statusCallback?: (arg: string) => void
-    },
-    rpcDriverClassName: 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, rpcDriverClassName)
-  }
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      headers?: Record<string, string>
-      regions: Region[]
-      sessionId: string
-      tag: string
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const deArgs = await this.deserializeArguments(args, rpcDriverClassName)
-    const { adapterConfig, sessionId, regions, tag } = deArgs
-    const dataAdapter = (await getAdapter(pm, sessionId, adapterConfig))
-      .dataAdapter as BaseFeatureDataAdapter
-
-    const features = dataAdapter.getFeaturesInMultipleRegions(regions)
-    const featuresArray = await features.pipe(toArray()).toPromise()
-    const uniqueValues = new Set<string>()
-    featuresArray.forEach(feature => {
-      const tags = feature.get('tags')
-      const val = tags ? tags[tag] : feature.get(tag)
-      if (val !== undefined) {
-        uniqueValues.add(`${val}`)
-      }
-    })
-    return [...uniqueValues]
-  }
-}
-
-export class PileupGetVisibleModifications extends RpcMethodType {
-  name = 'PileupGetVisibleModifications'
-
-  async serializeArguments(
-    args: RenderArgs & {
-      signal?: AbortSignal
-      statusCallback?: (arg: string) => void
-    },
-    rpcDriverClassName: 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, rpcDriverClassName)
-  }
-
-  async execute(
-    args: {
-      adapterConfig: {}
-      signal?: RemoteAbortSignal
-      headers?: Record<string, string>
-      regions: Region[]
-      sessionId: string
-      tag: string
-    },
-    rpcDriverClassName: string,
-  ) {
-    const pm = this.pluginManager
-    const deArgs = await this.deserializeArguments(args, rpcDriverClassName)
-    const { adapterConfig, sessionId, regions } = deArgs
-    const dataAdapter = (await getAdapter(pm, sessionId, adapterConfig))
-      .dataAdapter as BaseFeatureDataAdapter
-
-    const features = dataAdapter.getFeaturesInMultipleRegions(regions)
-    const featuresArray = await features.pipe(toArray()).toPromise()
-    const uniqueValues = new Set<string>()
-    featuresArray.forEach(feature => {
-      const val = (getTagAlt(feature, 'MM', 'Mm') as string) || ''
-      if (val !== undefined) {
-        getModificationTypes(val).forEach(t => uniqueValues.add(t))
-      }
-    })
-    return [...uniqueValues]
-  }
+import PileupGetReducedFeatures from './methods/GetReducedFeatures'
+import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag'
+import PileupGetVisibleModifications from './methods/GetVisibleModifications'
+
+export {
+  PileupGetReducedFeatures,
+  PileupGetVisibleModifications,
+  PileupGetGlobalValueForTag,
 }

package/src/PileupRPC/util.ts

@@ -0,0 +1,19 @@
+import { ReducedFeature } from '../shared/fetchChains'
+
+export function getInsertSizeStats(features: ReducedFeature[]) {
+  const filtered = features.map(f => Math.abs(f.tlen))
+  const sum = filtered.reduce((a, b) => a + b, 0)
+  const sum2 = filtered.map(a => a * a).reduce((a, b) => a + b, 0)
+  const total = filtered.length
+  const avg = sum / total
+  const sd = Math.sqrt((total * sum2 - sum * sum) / (total * total))
+  const upper = avg + 4 * sd
+  const lower = avg - 3 * sd
+  return { upper, lower, avg, sd }
+}
+
+export function filterForPairs(features: ReducedFeature[]) {
+  return features.filter(
+    f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048),
+  )
+}

package/src/PileupRenderer/PileupRenderer.ts

@@ -29,7 +29,7 @@ import {
   parseCigar,
   getModificationPositions,
   getNextRefPos,
-} from '../BamAdapter/MismatchParser'
+} from '../MismatchParser'
 import { sortFeature } from './sortUtil'
 import {
   getTagAlt,
@@ -271,7 +271,7 @@ export default class PileupRenderer extends BoxRendererType {
 
   colorByInsertSize(feature: Feature, _config: AnyConfigurationModel) {
     return feature.get('is_paired') &&
-      feature.get('seq_id') !== feature.get('next_seq_id')
+      feature.get('refName') !== feature.get('next_ref')
       ? '#555'
       : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)`
   }
@@ -292,7 +292,7 @@ export default class PileupRenderer extends BoxRendererType {
           ? 'color_rev_missing_mate'
           : 'color_fwd_missing_mate'
       }
-      if (feature.get('seq_id') === feature.get('next_seq_id')) {
+      if (feature.get('refName') === feature.get('next_refName')) {
         return strand * flipper === 1
           ? 'color_rev_strand_not_proper'
           : 'color_fwd_strand_not_proper'
@@ -919,7 +919,7 @@ export default class PileupRenderer extends BoxRendererType {
           ctx,
           leftPx,
           topPx,
-          widthPx,
+          Math.abs(leftPx - rightPx),
           heightPx,
           canvasWidth,
           colorForBase.deletion,
@@ -938,10 +938,7 @@ export default class PileupRenderer extends BoxRendererType {
         ctx.fillStyle = 'purple'
         const pos = leftPx + extraHorizontallyFlippedOffset
         const len = +mismatch.base || mismatch.length
-        const insW = Math.max(
-          minSubfeatureWidth / 2,
-          Math.min(1.2, 1 / bpPerPx),
-        )
+        const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx))
         if (len < 10) {
           fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple')
           if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {

package/src/PileupRenderer/configSchema.ts

@@ -28,7 +28,7 @@ const PileupRenderer = ConfigurationSchema(
       model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),
       defaultValue: 'fr',
       description:
-        'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
+        'read sequencer orientation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
     },
     /**
      * #slot

package/src/PileupRenderer/index.ts

@@ -7,6 +7,7 @@ export default function register(pluginManager: PluginManager) {
   pluginManager.addRendererType(() => {
     return new PileupRenderer({
       name: 'PileupRenderer',
+      displayName: 'Pileup renderer',
       ReactComponent,
       configSchema,
       pluginManager,

package/src/PileupRenderer/sortUtil.ts

@@ -1,6 +1,5 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature'
-import { doesIntersect2 } from '@jbrowse/core/util/range'
-import { Mismatch } from '../BamAdapter/MismatchParser'
+import { doesIntersect2, Feature } from '@jbrowse/core/util'
+import { Mismatch } from '../MismatchParser'
 
 interface SortObject {
   pos: number