@jbrowse/plugin-alignments 2.2.2 → 2.3.1

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/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

package/src/SNPCoverageAdapter/generateCoverageBins.ts

@@ -6,7 +6,7 @@ import {
   getNextRefPos,
   getModificationPositions,
   Mismatch,
-} from '../BamAdapter/MismatchParser'
+} from '../MismatchParser'
 
 function mismatchLen(mismatch: Mismatch) {
   return !isInterbase(mismatch.type) ? mismatch.length : 1

package/src/SNPCoverageAdapter/index.ts

@@ -7,11 +7,9 @@ export default function (pluginManager: PluginManager) {
   pluginManager.addAdapterType(() => {
     return new AdapterType({
       name: 'SNPCoverageAdapter',
+      displayName: 'SNPCoverage adapter',
       adapterMetadata: {
-        category: null,
-        displayName: null,
         hiddenFromGUI: true,
-        description: null,
       },
       getAdapterClass: () =>
         import('./SNPCoverageAdapter').then(r => r.default),

package/src/index.ts

@@ -1,9 +1,5 @@
-import { FileLocation } from '@jbrowse/core/util/types'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import * as MismatchParser from './BamAdapter/MismatchParser'
-import { LinearPileupDisplayModel } from './LinearPileupDisplay/model'
-
 import BamAdapterF from './CramAdapter'
 import CramAdapterF from './BamAdapter'
 import HtsgetBamAdapterF from './HtsgetBamAdapter'
@@ -12,24 +8,18 @@ import SNPCoverageRendererF from './SNPCoverageRenderer'
 import PileupRendererF from './PileupRenderer'
 import LinearAlignmentsDisplayF from './LinearAlignmentsDisplay'
 import LinearSNPCoverageDisplayF from './LinearSNPCoverageDisplay'
+import LinearReadArcsDisplayF from './LinearReadArcsDisplay'
+import LinearReadCloudDisplayF from './LinearReadCloudDisplay'
+import AlignmentsTrackF from './AlignmentsTrack'
+import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail'
+import PileupRPCMethodsF from './PileupRPC'
+import GuessAlignmentsTypesF from './GuessAlignmentsTypes'
 import LinearPileupDisplayF, {
   linearPileupDisplayStateModelFactory,
   linearPileupDisplayConfigSchemaFactory,
 } from './LinearPileupDisplay'
-import AlignmentsTrackF from './AlignmentsTrack'
-import AlignmentsFeatureWidgetF from './AlignmentsFeatureDetail'
-
-import {
-  PileupGetGlobalValueForTag,
-  PileupGetVisibleModifications,
-} from './PileupRPC/rpcMethods'
-import {
-  makeIndex,
-  makeIndexType,
-  getFileName,
-  AdapterGuesser,
-  TrackTypeGuesser,
-} from '@jbrowse/core/util/tracks'
+import { LinearPileupDisplayModel } from './LinearPileupDisplay/model'
+import * as MismatchParser from './MismatchParser'
 
 export default class AlignmentsPlugin extends Plugin {
   name = 'AlignmentsPlugin'
@@ -44,85 +34,14 @@ export default class AlignmentsPlugin extends Plugin {
       SNPCoverageAdapterF,
       HtsgetBamAdapterF,
       PileupRendererF,
+      PileupRPCMethodsF,
       SNPCoverageRendererF,
+      LinearReadArcsDisplayF,
+      LinearReadCloudDisplayF,
       LinearAlignmentsDisplayF,
       AlignmentsFeatureWidgetF,
+      GuessAlignmentsTypesF,
     ].map(f => f(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)
-        }
-      },
-    )
-
-    pluginManager.addRpcMethod(
-      () => new PileupGetGlobalValueForTag(pluginManager),
-    )
-    pluginManager.addRpcMethod(
-      () => new PileupGetVisibleModifications(pluginManager),
-    )
   }
 }
 

package/src/{LinearPileupDisplay/components → shared}/FilterByTag.tsx

@@ -123,9 +123,7 @@ function FilterByTagDlg(props: {
           <TextField
             className={classes.field}
             value={tag}
-            onChange={event => {
-              setTag(event.target.value)
-            }}
+            onChange={event => setTag(event.target.value)}
             placeholder="Enter tag name"
             inputProps={{
               maxLength: 2,
@@ -138,9 +136,7 @@ function FilterByTagDlg(props: {
           <TextField
             className={classes.field}
             value={tagValue}
-            onChange={event => {
-              setTagValue(event.target.value)
-            }}
+            onChange={event => setTagValue(event.target.value)}
             placeholder="Enter tag value"
             inputProps={{
               'data-testid': 'color-tag-name-input',
@@ -153,9 +149,7 @@ function FilterByTagDlg(props: {
           <TextField
             className={classes.field}
             value={readName}
-            onChange={event => {
-              setReadName(event.target.value)
-            }}
+            onChange={event => setReadName(event.target.value)}
             placeholder="Enter read name"
             inputProps={{
               'data-testid': 'color-tag-readname-input',

package/src/shared/color.ts

@@ -0,0 +1,47 @@
+import { orientationTypes } from '../util'
+import { ChainStats } from './fetchChains'
+
+const alignmentColoring: { [key: string]: string } = {
+  color_pair_lr: '#c8c8c8',
+  color_pair_rr: 'navy',
+  color_pair_rl: 'teal',
+  color_pair_ll: 'green',
+}
+
+export function getInsertSizeColor(
+  f1: { refName: string; tlen?: number },
+  f2: { refName: string },
+  stats?: ChainStats,
+) {
+  const sameRef = f1.refName === f2.refName
+  const tlen = Math.abs(f1.tlen || 0)
+  if (sameRef && tlen > (stats?.upper || 0)) {
+    return 'red'
+  } else if (sameRef && tlen < (stats?.lower || 0)) {
+    return '#f0f'
+  } else if (!sameRef) {
+    return 'purple'
+  }
+  return ''
+}
+
+export function getInsertSizeAndOrientationColor(
+  f1: { refName: string; pair_orientation?: string; tlen?: number },
+  f2: { refName: string },
+  stats?: ChainStats,
+) {
+  return getInsertSizeColor(f1, f2, stats) || getOrientationColor(f1)
+}
+
+export function getOrientationColor(f: { pair_orientation?: string }) {
+  const type = orientationTypes['fr']
+  const orientation = type[f.pair_orientation || '']
+  const map = {
+    LR: 'color_pair_lr',
+    RR: 'color_pair_rr',
+    RL: 'color_pair_rl',
+    LL: 'color_pair_ll',
+  }
+  const val = map[orientation as keyof typeof map]
+  return alignmentColoring[val] || 'grey'
+}

package/src/shared/fetchChains.ts

@@ -0,0 +1,63 @@
+import {
+  getContainingTrack,
+  getContainingView,
+  getSession,
+} from '@jbrowse/core/util'
+import { getSnapshot, IAnyStateTreeNode } from 'mobx-state-tree'
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+
+type LGV = LinearGenomeViewModel
+
+export interface ReducedFeature {
+  name: string
+  strand: number
+  refName: string
+  start: number
+  end: number
+  id: string
+  flags: number
+  tlen: number
+  pair_orientation: string
+  next_ref?: string
+  next_pos?: number
+  clipPos: number
+  SA?: string
+}
+
+export interface ChainStats {
+  max: number
+  min: number
+  upper: number
+  lower: number
+}
+
+export interface ChainData {
+  chains: ReducedFeature[][]
+  stats?: ChainStats
+}
+
+export async function fetchChains(self: IAnyStateTreeNode) {
+  try {
+    const { rpcSessionId: sessionId } = getContainingTrack(self)
+    const { rpcManager } = getSession(self)
+    const view = getContainingView(self) as LGV
+
+    if (!view.initialized || self.error) {
+      return
+    }
+    self.setLoading(true)
+
+    const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
+      sessionId,
+      regions: view.staticBlocks.contentBlocks,
+      filterBy: getSnapshot(self.filterBy),
+      adapterConfig: self.adapterConfig,
+    })) as ChainData
+
+    self.setChainData(ret)
+    self.setLoading(false)
+  } catch (e) {
+    console.error(e)
+    self.setError(e)
+  }
+}

package/src/{shared.ts → shared/index.ts}

@@ -1,9 +1,8 @@
+import { types, IAnyStateTreeNode } from 'mobx-state-tree'
 import { BlockSet } from '@jbrowse/core/util/blockTypes'
-
 import { getSession } from '@jbrowse/core/util'
 import { getRpcSessionId } from '@jbrowse/core/util/tracks'
-import { IAnyStateTreeNode } from 'mobx-state-tree'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration'
 
 export async function getUniqueTagValues(
   self: IAnyStateTreeNode & { adapterConfig: AnyConfigurationModel },
@@ -32,9 +31,11 @@ export async function getUniqueTagValues(
   return values as string[]
 }
 
+type Track = IAnyStateTreeNode & { configuration: AnyConfigurationModel }
+
 export async function getUniqueModificationValues(
   self: IAnyStateTreeNode & {
-    parentTrack: IAnyStateTreeNode & { configuration: AnyConfigurationModel }
+    parentTrack: Track
   },
   adapterConfig: AnyConfigurationModel,
   colorScheme: { type: string; tag?: string },
@@ -60,3 +61,15 @@ export async function getUniqueModificationValues(
   )
   return values as string[]
 }
+
+export const FilterModel = types.model({
+  flagInclude: types.optional(types.number, 0),
+  flagExclude: types.optional(types.number, 1540),
+  readName: types.maybe(types.string),
+  tagFilter: types.maybe(
+    types.model({
+      tag: types.string,
+      value: types.string,
+    }),
+  ),
+})

package/dist/BamAdapter/MismatchParser.js.map

@@ -1 +0,0 @@
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package/dist/LinearPileupDisplay/components/FilterByTag.js.map

@@ -1 +0,0 @@
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package/dist/shared.d.ts

@@ -1,25 +0,0 @@
-import { BlockSet } from '@jbrowse/core/util/blockTypes';
-import { IAnyStateTreeNode } from 'mobx-state-tree';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
-export declare function getUniqueTagValues(self: IAnyStateTreeNode & {
-    adapterConfig: AnyConfigurationModel;
-}, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;
-export declare function getUniqueModificationValues(self: IAnyStateTreeNode & {
-    parentTrack: IAnyStateTreeNode & {
-        configuration: AnyConfigurationModel;
-    };
-}, adapterConfig: AnyConfigurationModel, colorScheme: {
-    type: string;
-    tag?: string;
-}, blocks: BlockSet, opts?: {
-    headers?: Record<string, string>;
-    signal?: AbortSignal;
-    filters?: string[];
-}): Promise<string[]>;

package/dist/shared.js.map

@@ -1 +0,0 @@
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