Updates

plugins/alignments/src/BamAdapter/BamAdapter.ts

@@ -189,8 +189,6 @@ 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) {
@@ -228,16 +226,13 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
           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

@@ -5,12 +5,10 @@ import {
 import { BamRecord } from '@gmod/bam'
 
 // locals
-import { getMismatches, parseCigar } from '../MismatchParser'
+import { getMismatches } 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'
+import { getMaxProbModAtEachPosition } from '../shared/getMaxProbModAtEachPosition'
 
 export default class BamSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class

plugins/alignments/src/CramAdapter/CramAdapter.ts

@@ -245,8 +245,6 @@ 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)) {
@@ -276,16 +274,13 @@ 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

@@ -7,7 +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'
+import { getMaxProbModAtEachPosition } from '../shared/getMaxProbModAtEachPosition'
 
 export default class CramSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class
@@ -146,7 +146,6 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   get modifications() {
-    console.log('here')
     return getMaxProbModAtEachPosition(this)
   }
 

plugins/alignments/src/PileupRenderer/renderAlignment.ts

@@ -80,7 +80,6 @@ export function renderAlignment({
     }
 
     case 'modifications': {
-      const cigarOps = parseCigar(feature.get('CIGAR'))
       renderModifications({
         ctx,
         feat,

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 { MaximumProbabilityMod } from '../shared/getMaximumModificationAtEachPosition'
+import { MaxProbMod } from '../shared/getMaxProbModAtEachPosition'
 
 // render modifications stored in MM tag in BAM
 export function renderModifications({
@@ -35,7 +35,7 @@ export function renderModifications({
   const isolatedModification = colorBy?.modifications?.isolatedModification
   const twoColor = colorBy?.modifications?.twoColor
 
-  ;(feature.get('modifications') as MaximumProbabilityMod[])?.forEach(
+  ;(feature.get('modifications') as MaxProbMod[] | undefined)?.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 { MaximumProbabilityMod } from '../shared/getMaxProbModAtEachPosition'
+import { MaxProbMod } from '../shared/getMaxProbModAtEachPosition'
 
 function mismatchLen(mismatch: Mismatch) {
   return !isInterbase(mismatch.type) ? mismatch.length : 1
@@ -283,7 +283,7 @@ function processModification({
   const twoColor = colorBy?.modifications?.twoColor
   const isolatedModification = colorBy?.modifications?.isolatedModification
 
-  ;(feature.get('modifications') as MaximumProbabilityMod[])?.forEach(
+  ;(feature.get('modifications') as MaxProbMod[] | undefined)?.forEach(
     ({ type, prob, allProbs }, pos) => {
       if (isolatedModification && type !== isolatedModification) {
         return

plugins/alignments/src/shared/getMaximumModificationAtEachPosition.ts → plugins/alignments/src/shared/getMaxProbModAtEachPosition.ts

@@ -4,7 +4,7 @@ import { getModPositions, getModProbabilities } from '../ModificationParser'
 import { getNextRefPos, parseCigar } from '../MismatchParser'
 import { getTagAlt } from '../util'
 
-export interface MaximumProbabilityMod {
+export interface MaxProbMod {
   type: string
   prob: number
   allProbs: number[]
@@ -21,7 +21,7 @@ export function getMaxProbModAtEachPosition(
   if (seq) {
     const modifications = getModPositions(mm, seq, fstrand)
     const probabilities = getModProbabilities(feature)
-    const maxProbModForPosition = [] as MaximumProbabilityMod[]
+    const maxProbModForPosition = [] as MaxProbMod[]
 
     let probIndex = 0
     for (const { type, positions } of modifications) {