Update to cache modifications

plugins/alignments/src/BamAdapter/BamAdapter.ts

@@ -189,6 +189,8 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
           readName,
         } = filterBy || {}
 
+        let hits = 0
+        let nohits = 0
         for (const record of records) {
           let ref: string | undefined
           if (!record.tags.MD) {
@@ -224,14 +226,18 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
           // features in the cache have pre-computed mismatches objects that
           // can be re-used across blocks
           const ret = this.featureCache.get(`${record.id}`)
+
           if (!ret) {
+            nohits++
             const elt = new BamSlightlyLazyFeature(record, this, ref)
             this.featureCache.set(`${record.id}`, elt)
             observer.next(elt)
           } else {
+            hits++
             observer.next(ret)
           }
         }
+        console.log({ hits, nohits })
         observer.complete()
       })
     }, signal)

plugins/alignments/src/BamAdapter/BamSlightlyLazyFeature.ts

@@ -5,9 +5,12 @@ import {
 import { BamRecord } from '@gmod/bam'
 
 // locals
-import { getMismatches } from '../MismatchParser'
+import { getMismatches, parseCigar } from '../MismatchParser'
 import BamAdapter from './BamAdapter'
 import { cacheGetter } from '../shared/util'
+import { getTagAlt } from '../util'
+import { getModPositions, getModProbabilities } from '../ModificationParser'
+import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition'
 
 export default class BamSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class
@@ -31,6 +34,10 @@ export default class BamSlightlyLazyFeature implements Feature {
     )
   }
 
+  get modifications() {
+    return getMaxProbModAtEachPosition(this)
+  }
+
   get qual() {
     return this.record.qual?.join(' ')
   }
@@ -40,7 +47,9 @@ export default class BamSlightlyLazyFeature implements Feature {
       ? this.mismatches
       : field === 'qual'
         ? this.qual
-        : this.fields[field]
+        : field === 'modifications'
+          ? this.modifications
+          : this.fields[field]
   }
 
   parent() {
@@ -88,3 +97,4 @@ export default class BamSlightlyLazyFeature implements Feature {
 
 cacheGetter(BamSlightlyLazyFeature, 'fields')
 cacheGetter(BamSlightlyLazyFeature, 'mismatches')
+cacheGetter(BamSlightlyLazyFeature, 'modifications')

plugins/alignments/src/CramAdapter/CramAdapter.ts

@@ -245,7 +245,8 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
           tagFilter,
           readName,
         } = filterBy || {}
-
+        let hits = 0
+        let nohits = 0
         for (const record of records) {
           const flags = record.flags
           if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
@@ -275,13 +276,16 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
           // can be re-used across blocks
           const ret = this.featureCache.get(`${record.uniqueId}`)
           if (!ret) {
+            nohits++
             const elt = this.cramRecordToFeature(record)
             this.featureCache.set(`${record.uniqueId}`, elt)
             observer.next(elt)
           } else {
+            hits++
             observer.next(ret)
           }
         }
+        console.log({ nohits, hits })
 
         observer.complete()
       })

plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts

@@ -7,6 +7,7 @@ import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util'
 import { parseCigar } from '../MismatchParser'
 import { mdToMismatches } from '../MismatchParser/mdToMismatches'
 import { cacheGetter } from '../shared/util'
+import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition'
 
 export default class CramSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class
@@ -112,7 +113,9 @@ export default class CramSlightlyLazyFeature implements Feature {
         ? this.qual
         : field === 'CIGAR'
           ? this.CIGAR
-          : this.fields[field]
+          : field === 'modifications'
+            ? this.modifications
+            : this.fields[field]
   }
 
   parent() {
@@ -142,6 +145,11 @@ export default class CramSlightlyLazyFeature implements Feature {
       : mismatches
   }
 
+  get modifications() {
+    console.log('here')
+    return getMaxProbModAtEachPosition(this)
+  }
+
   get fields(): SimpleFeatureSerialized {
     return {
       start: this.start,
@@ -177,3 +185,4 @@ export default class CramSlightlyLazyFeature implements Feature {
 cacheGetter(CramSlightlyLazyFeature, 'fields')
 cacheGetter(CramSlightlyLazyFeature, 'CIGAR')
 cacheGetter(CramSlightlyLazyFeature, 'mismatches')
+cacheGetter(CramSlightlyLazyFeature, 'modifications')

plugins/alignments/src/PileupRenderer/renderAlignment.ts

@@ -88,7 +88,6 @@ export function renderAlignment({
         bpPerPx,
         renderArgs,
         canvasWidth,
-        cigarOps,
       })
       break
     }

plugins/alignments/src/PileupRenderer/renderModifications.ts

@@ -5,7 +5,7 @@ import { bpSpanPx, max, sum } from '@jbrowse/core/util'
 import { fillRect, LayoutFeature } from './util'
 import { RenderArgsWithColor } from './makeImageData'
 import { alphaColor } from '../shared/util'
-import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition'
+import { MaximumProbabilityMod } from '../shared/getMaximumModificationAtEachPosition'
 
 // render modifications stored in MM tag in BAM
 export function renderModifications({
@@ -15,15 +15,13 @@ export function renderModifications({
   bpPerPx,
   renderArgs,
   canvasWidth,
-  cigarOps,
 }: {
   ctx: CanvasRenderingContext2D
   feat: LayoutFeature
   region: Region
   bpPerPx: number
   renderArgs: RenderArgsWithColor
   canvasWidth: number
-  cigarOps: string[]
 }) {
   const { feature, topPx, heightPx } = feat
   const { colorBy, visibleModifications = {} } = renderArgs
@@ -37,7 +35,7 @@ export function renderModifications({
   const isolatedModification = colorBy?.modifications?.isolatedModification
   const twoColor = colorBy?.modifications?.twoColor
 
-  getMaxProbModAtEachPosition(feature, cigarOps)?.forEach(
+  ;(feature.get('modifications') as MaximumProbabilityMod[])?.forEach(
     ({ allProbs, prob, type }, pos) => {
       const r = start + pos
       const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx)

plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts

@@ -11,7 +11,7 @@ import {
   PreBaseCoverageBinSubtypes,
   SkipMap,
 } from '../shared/types'
-import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition'
+import { MaximumProbabilityMod } from '../shared/getMaxProbModAtEachPosition'
 
 function mismatchLen(mismatch: Mismatch) {
   return !isInterbase(mismatch.type) ? mismatch.length : 1
@@ -282,7 +282,8 @@ function processModification({
   const fend = feature.get('end')
   const twoColor = colorBy?.modifications?.twoColor
   const isolatedModification = colorBy?.modifications?.isolatedModification
-  getMaxProbModAtEachPosition(feature)?.forEach(
+
+  ;(feature.get('modifications') as MaximumProbabilityMod[])?.forEach(
     ({ type, prob, allProbs }, pos) => {
       if (isolatedModification && type !== isolatedModification) {
         return

plugins/alignments/src/shared/getMaximumModificationAtEachPosition.ts

@@ -4,7 +4,7 @@ import { getModPositions, getModProbabilities } from '../ModificationParser'
 import { getNextRefPos, parseCigar } from '../MismatchParser'
 import { getTagAlt } from '../util'
 
-interface MaximumProbabilityMod {
+export interface MaximumProbabilityMod {
   type: string
   prob: number
   allProbs: number[]