@jbrowse/plugin-alignments 2.2.0 → 2.2.1

package/src/CramAdapter/util.test.ts

@@ -0,0 +1,26 @@
+import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util'
+
+test('cram read features mismatches', () => {
+  expect(
+    // from ctgA_15140_15565_0:0:1_1:0:0_2e8 in volvox-sorted.cram
+    readFeaturesToMismatches(
+      [{ code: 'i', data: 'C', pos: 25, refPos: 15164 }],
+      15139,
+    ),
+  ).toMatchSnapshot()
+})
+
+test('cram read features to CIGAR', () => {
+  expect(
+    // from ctgA_15140_15565_0:0:1_1:0:0_2e8 in volvox-sorted.cram
+    readFeaturesToCIGAR(
+      [{ code: 'i', data: 'C', pos: 25, refPos: 15164 }],
+      15140,
+      100,
+      {
+        start: 14998,
+        seq: 'agaccacattcagctctcggtaacatgggaggcttgtggttgcaccgtaaaagggggatagcccatccatcctgtaaacctacaatcgcgcgtagcttaatacgctcacattagacattcgatcgagagacctggtttcaagagccttcccttttgctttagtgggccaaatcgcaaccctgctcccctcccttacgccttatacacttcagtgcaaattcatgcgttcagcgaacaactggacttctgttgtacgtagtccacgggggcttattcattatagaaagccccctactgtcaccgttatatggttcacacatgagctgatcacctagagagtcgtcatgcacattcgcctaacaaggacatatgagtaaccg',
+      },
+    ),
+  ).toMatchSnapshot()
+})

package/src/CramAdapter/util.ts

@@ -0,0 +1,251 @@
+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: `${insLen}`,
+      length: 0,
+    }
+    insLen = 0
+  }
+
+  return mismatches.slice(0, j)
+}
+
+export function readFeaturesToCIGAR(
+  readFeatures: ReadFeatures,
+  alignmentStart: number,
+  readLen: number,
+  refRegion?: { seq: string; start: number },
+) {
+  let seq = ''
+  let cigar = ''
+  let op = 'M'
+  let oplen = 0
+  if (!refRegion) {
+    return ''
+  }
+
+  // not sure I should access these, but...
+  const ref = refRegion.seq
+  const refStart = refRegion.start
+  let lastPos = alignmentStart
+  let sublen = 0
+  let insLen = 0
+  if (readFeatures !== undefined) {
+    for (let i = 0; i < readFeatures.length; i++) {
+      const { code, refPos, sub, data } = readFeatures[i]
+      sublen = refPos - lastPos
+      seq += ref.substring(lastPos - refStart, refPos - refStart)
+      lastPos = refPos
+
+      if (insLen > 0 && sublen) {
+        cigar += `${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.substring(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/LinearAlignmentsDisplay/components/AlignmentsDisplay.tsx

@@ -1,8 +1,10 @@
 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'
-import { makeStyles } from 'tss-react/mui'
+
+// locals
 import { AlignmentsDisplayModel } from '../models/model'
 
 const useStyles = makeStyles()(() => ({

package/src/LinearAlignmentsDisplay/models/model.tsx

@@ -203,27 +203,28 @@ function stateModelFactory(
       /**
        * #action
        */
-      setSNPCoverageDisplay(displayConfig: AnyConfigurationModel) {
+      setSNPCoverageDisplay(configuration: AnyConfigurationModel) {
         self.SNPCoverageDisplay = {
           type: 'LinearSNPCoverageDisplay',
-          configuration: displayConfig,
+          configuration,
           height: self.snpCovHeight,
         }
       },
       /**
        * #action
        */
-      setUserFeatureScreenDensity(limit: number) {
-        self.PileupDisplay.setUserFeatureScreenDensity(limit)
-        self.SNPCoverageDisplay.setUserFeatureScreenDensity(limit)
+      updateStatsLimit(stats: unknown) {
+        self.PileupDisplay.updateStatsLimit(stats)
+        self.SNPCoverageDisplay.updateStatsLimit(stats)
       },
+
       /**
        * #action
        */
-      setPileupDisplay(displayConfig: AnyConfigurationModel) {
+      setPileupDisplay(configuration: AnyConfigurationModel) {
         self.PileupDisplay = {
           type: 'LinearPileupDisplay',
-          configuration: displayConfig,
+          configuration,
         }
       },
       /**

package/src/LinearPileupDisplay/configSchema.ts

@@ -8,7 +8,7 @@ import PluginManager from '@jbrowse/core/PluginManager'
  */
 function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
 
-function PileupConfigFactory(pluginManager: PluginManager) {
+function configSchemaF(pluginManager: PluginManager) {
   // modify config schema to take in a sub coverage display
   return ConfigurationSchema(
     'LinearPileupDisplay',
@@ -64,8 +64,6 @@ function PileupConfigFactory(pluginManager: PluginManager) {
   )
 }
 
-export type LinearPileupDisplayConfigModel = ReturnType<
-  typeof PileupConfigFactory
->
+export type LinearPileupDisplayConfigModel = ReturnType<typeof configSchemaF>
 export type LinearPileupDisplayConfig = Instance<LinearPileupDisplayConfigModel>
-export default PileupConfigFactory
+export default configSchemaF

package/src/LinearPileupDisplay/index.ts

@@ -17,3 +17,8 @@ export default function register(pluginManager: PluginManager) {
     })
   })
 }
+
+export {
+  modelFactory as linearPileupDisplayStateModelFactory,
+  configSchemaFactory as linearPileupDisplayConfigSchemaFactory,
+}

package/src/LinearPileupDisplay/model.ts

@@ -55,6 +55,7 @@ type LGV = LinearGenomeViewModel
 
 /**
  * #stateModel LinearPileupDisplay
+ * extends `BaseLinearDisplay`
  */
 function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
   return types
@@ -117,6 +118,10 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
             extra: types.frozen(),
           }),
         ),
+
+        /**
+         * #property
+         */
         filterBy: types.optional(
           types.model({
             flagInclude: types.optional(types.number, 0),
@@ -134,6 +139,7 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
       colorTagMap: observable.map<string, string>({}),
       modificationTagMap: observable.map<string, string>({}),
       featureUnderMouseVolatile: undefined as undefined | Feature,
+      currSortBpPerPx: 0,
       ready: false,
     }))
     .actions(self => ({
@@ -143,6 +149,12 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
       setReady(flag: boolean) {
         self.ready = flag
       },
+      /**
+       * #action
+       */
+      setCurrSortBpPerPx(n: number) {
+        self.currSortBpPerPx = n
+      },
       /**
        * #action
        */
@@ -288,7 +300,7 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
                     ...self.renderProps(),
                   })
                   self.setReady(true)
-                  self.setCurrBpPerPx(bpPerPx)
+                  self.setCurrSortBpPerPx(bpPerPx)
                 } else {
                   self.setReady(true)
                 }
@@ -302,6 +314,8 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
         )
 
         // autorun synchronizes featureUnderMouse with featureIdUnderMouse
+        // asynchronously. this is needed due to how we do not serialize all
+        // features from the BAM/CRAM over the rpc
         addDisposer(
           self,
           autorun(async () => {
@@ -567,7 +581,7 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
             colorBy,
             filterBy,
             rpcDriverName,
-            currBpPerPx,
+            currSortBpPerPx,
             ready,
           } = self
 
@@ -578,7 +592,7 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
             notReady:
               superProps.notReady ||
               !ready ||
-              (sortedBy && currBpPerPx !== view.bpPerPx),
+              (sortedBy && currSortBpPerPx !== view.bpPerPx),
             rpcDriverName,
             displayModel: self,
             sortedBy,
@@ -707,39 +721,31 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
               subMenu: [
                 {
                   label: 'Normal',
-                  onClick: () => {
-                    self.setColorScheme({ type: 'normal' })
-                  },
+                  onClick: () => self.setColorScheme({ type: 'normal' }),
                 },
                 {
                   label: 'Mapping quality',
-                  onClick: () => {
-                    self.setColorScheme({ type: 'mappingQuality' })
-                  },
+                  onClick: () =>
+                    self.setColorScheme({ type: 'mappingQuality' }),
                 },
                 {
                   label: 'Strand',
-                  onClick: () => {
-                    self.setColorScheme({ type: 'strand' })
-                  },
+                  onClick: () => self.setColorScheme({ type: 'strand' }),
                 },
                 {
                   label: 'Pair orientation',
-                  onClick: () => {
-                    self.setColorScheme({ type: 'pairOrientation' })
-                  },
+                  onClick: () =>
+                    self.setColorScheme({ type: 'pairOrientation' }),
                 },
                 {
                   label: 'Per-base quality',
-                  onClick: () => {
-                    self.setColorScheme({ type: 'perBaseQuality' })
-                  },
+                  onClick: () =>
+                    self.setColorScheme({ type: 'perBaseQuality' }),
                 },
                 {
                   label: 'Per-base lettering',
-                  onClick: () => {
-                    self.setColorScheme({ type: 'perBaseLettering' })
-                  },
+                  onClick: () =>
+                    self.setColorScheme({ type: 'perBaseLettering' }),
                 },
                 {
                   label: 'Modifications or methylation',
@@ -752,15 +758,12 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
                 },
                 {
                   label: 'Insert size',
-                  onClick: () => {
-                    self.setColorScheme({ type: 'insertSize' })
-                  },
+                  onClick: () => self.setColorScheme({ type: 'insertSize' }),
                 },
                 {
                   label: 'Stranded paired-end',
-                  onClick: () => {
-                    self.setColorScheme({ type: 'reverseTemplate' })
-                  },
+                  onClick: () =>
+                    self.setColorScheme({ type: 'reverseTemplate' }),
                 },
                 {
                   label: 'Color by tag...',
@@ -805,9 +808,7 @@ function stateModelFactory(configSchema: LinearPileupDisplayConfigModel) {
               label: 'Fade mismatches by quality',
               type: 'checkbox',
               checked: self.mismatchAlphaSetting,
-              onClick: () => {
-                self.toggleMismatchAlpha()
-              },
+              onClick: () => self.toggleMismatchAlpha(),
             },
           ]
         },

package/src/PileupRPC/rpcMethods.ts

@@ -1,11 +1,12 @@
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
 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 { renameRegionsIfNeeded } from '@jbrowse/core/util'
-import { Region } from '@jbrowse/core/util/types'
 import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals'
-import { toArray } from 'rxjs/operators'
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
+import { toArray } from 'rxjs/operators'
+
+// locals
 import { getTagAlt } from '../util'
 import { getModificationTypes } from '../BamAdapter/MismatchParser'
 
@@ -41,14 +42,11 @@ export class PileupGetGlobalValueForTag extends RpcMethodType {
     },
     rpcDriverClassName: string,
   ) {
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { adapterConfig, sessionId, regions, tag } = deserializedArgs
-    const dataAdapter = (
-      await getAdapter(this.pluginManager, sessionId, adapterConfig)
-    ).dataAdapter as BaseFeatureDataAdapter
+    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()
@@ -96,14 +94,11 @@ export class PileupGetVisibleModifications extends RpcMethodType {
     },
     rpcDriverClassName: string,
   ) {
-    const deserializedArgs = await this.deserializeArguments(
-      args,
-      rpcDriverClassName,
-    )
-    const { adapterConfig, sessionId, regions } = deserializedArgs
-    const dataAdapter = (
-      await getAdapter(this.pluginManager, sessionId, adapterConfig)
-    ).dataAdapter as BaseFeatureDataAdapter
+    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()