Create annotation from alignment read (#345)

* tmp commit

* tmp commit

* 1st version ready

* Factor annotation from pileup into a separate file

---------

Co-authored-by: Garrett Stevens <stevens.garrett.j@gmail.com>

packages/jbrowse-plugin-apollo/src/extensions/annotationFromPileup.ts

@@ -0,0 +1,208 @@
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { DisplayType } from '@jbrowse/core/pluggableElementTypes'
+import PluggableElementBase from '@jbrowse/core/pluggableElementTypes/PluggableElementBase'
+import { getContainingView, getSession } from '@jbrowse/core/util'
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
+import AddIcon from '@mui/icons-material/Add'
+import { AnnotationFeatureSnapshot } from 'apollo-mst'
+import { AddFeatureChange } from 'apollo-shared'
+import ObjectID from 'bson-objectid'
+
+import { ApolloSessionModel } from '../session'
+
+function parseCigar(cigar: string): [string | undefined, number][] {
+  return (cigar.toUpperCase().match(/\d+\D/g) ?? []).map((op) => {
+    return [(op.match(/\D/) ?? [])[0], Number.parseInt(op, 10)]
+  })
+}
+
+export function annotationFromPileup(pluggableElement: PluggableElementBase) {
+  if (pluggableElement.name !== 'LinearPileupDisplay') {
+    return pluggableElement
+  }
+  const { stateModel } = pluggableElement as DisplayType
+  const newStateModel = stateModel
+    .views((self) => ({
+      getFirstRegion() {
+        const lgv = getContainingView(self) as unknown as LinearGenomeViewModel
+        return lgv.dynamicBlocks.contentBlocks[0]
+      },
+      getAssembly() {
+        const firstRegion = self.getFirstRegion()
+        const session = getSession(self)
+        const { assemblyManager } = session
+        const { assemblyName } = firstRegion
+        const assembly = assemblyManager.get(assemblyName)
+        if (!assembly) {
+          throw new Error(`Could not find assembly named ${assemblyName}`)
+        }
+        return assembly
+      },
+      getRefSeqId(assembly: Assembly) {
+        const firstRegion = self.getFirstRegion()
+        const { refName } = firstRegion
+        const { refNameAliases } = assembly
+        if (!refNameAliases) {
+          throw new Error(`Could not find aliases for ${assembly.name}`)
+        }
+        const newRefNames = [...Object.entries(refNameAliases)]
+          .filter(([id, refName]) => id !== refName)
+          .map(([id, refName]) => ({
+            _id: id,
+            name: refName ?? '',
+          }))
+        const refSeqId = newRefNames.find((item) => item.name === refName)?._id
+        if (!refSeqId) {
+          throw new Error(`Could not find refSeqId named ${refName}`)
+        }
+        return refSeqId
+      },
+      createFeature() {
+        const feature = self.contextMenuFeature
+        const assembly = self.getAssembly()
+        const refSeqId = self.getRefSeqId(assembly)
+        const cigarData: string = feature.get('CIGAR')
+        const ops = parseCigar(cigarData)
+        let currOffset = 0
+        const start: number = feature.get('start')
+        let openStart: number | undefined
+        const exons: {
+          start: number
+          end: number
+        }[] = []
+        for (const [op, len] of ops) {
+          // open or continue open
+          if (op === 'M' || op === '=') {
+            // if it was closed, then open with start, strand, type
+            if (openStart === undefined) {
+              // add subfeature
+              openStart = currOffset + start
+            }
+          } else if (op === 'N' && openStart !== undefined) {
+            // if it was open, then close and add the subfeature
+            exons.push({
+              start: openStart,
+              end: currOffset + openStart,
+            })
+            openStart = undefined
+          }
+          if (op !== 'I') {
+            // we ignore insertions when calculating potential exon length
+            currOffset += len
+          }
+        }
+        // if we are still open, then close with the final length and add subfeature
+        if (openStart !== undefined) {
+          exons.push({
+            start: openStart,
+            end: currOffset + start,
+          })
+        }
+
+        const newFeature: AnnotationFeatureSnapshot = {
+          _id: ObjectID().toHexString(),
+          gffId: '',
+          refSeq: refSeqId,
+          start: feature.get('start'),
+          end: feature.get('end'),
+          type: 'mRNA',
+          strand: feature.get('strand'),
+        }
+        if (exons.length === 0) {
+          return newFeature
+        }
+
+        const children: Record<string, AnnotationFeatureSnapshot> = {}
+        newFeature.children = children
+        const [firstExon] = exons
+        const cdsFeature: AnnotationFeatureSnapshot = {
+          _id: ObjectID().toHexString(),
+          gffId: '',
+          refSeq: refSeqId,
+          start: firstExon.start,
+          end: firstExon.end,
+          type: 'CDS',
+          strand: feature.get('strand'),
+          phase: 0,
+        }
+        newFeature.children[cdsFeature._id] = cdsFeature
+        if (exons.length === 1) {
+          const exon: AnnotationFeatureSnapshot = {
+            _id: ObjectID().toHexString(),
+            gffId: '',
+            refSeq: refSeqId,
+            start: firstExon.start,
+            end: firstExon.end,
+            type: 'exon',
+            strand: feature.get('strand'),
+          }
+          newFeature.children[exon._id] = exon
+          return newFeature
+        }
+
+        const discontinuousLocations: {
+          start: number
+          end: number
+          phase: 0 | 1 | 2
+        }[] = []
+        let phase: 0 | 1 | 2 = 0
+        for (const exon of exons) {
+          cdsFeature.start = Math.min(cdsFeature.start, exon.start)
+          cdsFeature.end = Math.max(cdsFeature.end, exon.end)
+          const { end, start } = exon
+          discontinuousLocations?.push({ start, end, phase })
+          const localPhase = (end - start) % 3
+          phase = ((phase + localPhase) % 3) as 0 | 1 | 2
+          const newExon: AnnotationFeatureSnapshot = {
+            _id: ObjectID().toHexString(),
+            gffId: '',
+            refSeq: refSeqId,
+            start,
+            end,
+            type: 'exon',
+            strand: feature.get('strand'),
+          }
+          newFeature.children[newExon._id] = newExon
+        }
+        cdsFeature.discontinuousLocations = discontinuousLocations
+        return newFeature
+      },
+      async onPileupFeatureContext() {
+        const newFeature = self.createFeature()
+        const assembly = self.getAssembly()
+        const assemblyId = assembly.name
+        const change = new AddFeatureChange({
+          changedIds: [newFeature._id],
+          typeName: 'AddFeatureChange',
+          assembly: assemblyId,
+          addedFeature: newFeature,
+        })
+        const session = getSession(self)
+        await (
+          session as unknown as ApolloSessionModel
+        ).apolloDataStore.changeManager.submit?.(change)
+        session.notify('Annotation added successfully', 'success')
+      },
+    }))
+    .views((self) => {
+      const superContextMenuItems = self.contextMenuItems
+      return {
+        contextMenuItems() {
+          const feature = self.contextMenuFeature
+          if (!feature) {
+            return superContextMenuItems()
+          }
+          return [
+            ...superContextMenuItems(),
+            {
+              label: 'Create Apollo annotation',
+              icon: AddIcon,
+              onClick: self.onPileupFeatureContext,
+            },
+          ]
+        },
+      }
+    })
+  ;(pluggableElement as DisplayType).stateModel = newStateModel
+  return pluggableElement
+}

packages/jbrowse-plugin-apollo/src/extensions/index.ts

@@ -0,0 +1 @@
+export * from './annotationFromPileup'

packages/jbrowse-plugin-apollo/src/index.ts

@@ -49,6 +49,7 @@ import {
 import { AddFeature } from './components/AddFeature'
 import { ViewCheckResults } from './components/ViewCheckResults'
 import ApolloPluginConfigurationSchema from './config'
+import { annotationFromPileup } from './extensions'
 import {
   stateModelFactory as LinearApolloDisplayStateModelFactory,
   configSchemaFactory as linearApolloDisplayConfigSchemaFactory,
@@ -94,7 +95,6 @@ for (const [changeName, change] of Object.entries(changes)) {
 
 const cdsCheck = new CDSCheck()
 checkRegistry.registerCheck(cdsCheck.name, cdsCheck)
-
 validationRegistry.registerValidation(new CoreValidation())
 validationRegistry.registerValidation(new ParentChildValidation())
 
@@ -228,12 +228,16 @@ export default class ApolloPlugin extends Plugin {
               },
             }
           })
-
           ;(pluggableElement as ViewType).stateModel = newStateModel
         }
         return pluggableElement
       },
     )
+
+    pluginManager.addToExtensionPoint(
+      'Core-extendPluggableElement',
+      annotationFromPileup,
+    )
     if (!inWebWorker) {
       pluginManager.addToExtensionPoint(
         'Core-extendWorker',