More refactors

plugins/alignments/src/CramAdapter/CramSlightlyLazyFeature.ts

@@ -1,12 +1,10 @@
-import {
-  Feature,
-  SimpleFeatureSerialized,
-} from '@jbrowse/core/util/simpleFeature'
+import { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'
 import { CramRecord } from '@gmod/cram'
 
 // locals
 import CramAdapter from './CramAdapter'
 import { readFeaturesToCIGAR, readFeaturesToMismatches } from './util'
+import { mdToMismatches, parseCigar } from '../MismatchParser'
 
 export default class CramSlightlyLazyFeature implements Feature {
   // uses parameter properties to automatically create fields on the class
@@ -28,10 +26,6 @@ export default class CramSlightlyLazyFeature implements Feature {
     return this.start + (this.record.lengthOnRef ?? 1)
   }
 
-  get type() {
-    return 'match'
-  }
-
   get score() {
     return this.record.mappingQuality
   }
@@ -122,11 +116,22 @@ export default class CramSlightlyLazyFeature implements Feature {
   }
 
   get mismatches() {
-    return readFeaturesToMismatches(
+    const mismatches = readFeaturesToMismatches(
       this.record.readFeatures,
       this.start,
       this.qualRaw,
     )
+    return this.tags.MD && this.seq
+      ? mismatches.concat(
+          mdToMismatches(
+            this.tags.MD,
+            parseCigar(this.CIGAR),
+            mismatches,
+            this.seq,
+            this.qualRaw,
+          ),
+        )
+      : mismatches
   }
 
   get fields(): SimpleFeatureSerialized {

plugins/alignments/src/CramAdapter/util.ts

@@ -1,18 +1,8 @@
 import { CramRecord } from '@gmod/cram'
+import { Mismatch } from '../shared/types'
 
 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,
@@ -48,7 +38,7 @@ export function readFeaturesToMismatches(
       mismatches[j++] = {
         start: refPos,
         length: 1,
-        base: sub,
+        base: sub!,
         qual: qual?.[pos - 1],
         altbase: ref?.toUpperCase(),
         type: 'mismatch',

plugins/alignments/src/MismatchParser/index.ts

@@ -1,16 +1,7 @@
 import { Feature } from '@jbrowse/core/util'
 import type { Buffer } from 'buffer'
+import { Mismatch } from '../shared/types'
 
-export interface Mismatch {
-  qual?: number
-  start: number
-  length: number
-  type: string
-  base: string
-  altbase?: string
-  seq?: string
-  cliplen?: number
-}
 const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi)
 const cigarRegex = new RegExp(/([MIDNSHPX=])/)
 const startClip = new RegExp(/(\d+)[SH]$/)
@@ -125,7 +116,7 @@ export function mdToMismatches(
   ops: string[],
   cigarMismatches: Mismatch[],
   seq: string,
-  qual?: Buffer,
+  qual?: Buffer | number[] | null,
 ) {
   let curr: Mismatch = { start: 0, base: '', length: 0, type: 'mismatch' }
   let lastCigar = 0

plugins/alignments/src/PileupRenderer/layoutFeature.ts

@@ -1,7 +1,7 @@
 import { bpSpanPx, Feature, Region } from '@jbrowse/core/util'
 import { BaseLayout } from '@jbrowse/core/util/layouts'
+import { Mismatch } from '../shared/types'
 // locals
-import { Mismatch } from '../MismatchParser'
 
 export interface LayoutRecord {
   feature: Feature

plugins/alignments/src/PileupRenderer/renderMismatches.ts

@@ -1,8 +1,8 @@
 import { bpSpanPx, measureText } from '@jbrowse/core/util'
-import { Mismatch } from '../MismatchParser'
 import { fillRect, LayoutFeature } from './util'
 import { RenderArgsWithColor } from './makeImageData'
 import { colord } from '@jbrowse/core/util/colord'
+import { Mismatch } from '../shared/types'
 
 export function renderMismatches({
   ctx,

plugins/alignments/src/PileupRenderer/renderSoftClipping.ts

@@ -6,9 +6,9 @@ import { bpSpanPx } from '@jbrowse/core/util'
 import { Theme } from '@mui/material'
 
 // locals
-import { Mismatch } from '../MismatchParser'
 import { RenderArgsDeserializedWithFeaturesAndLayout } from './PileupRenderer'
 import { fillRect, getCharWidthHeight, LayoutFeature } from './util'
+import { Mismatch } from '../shared/types'
 
 export function renderSoftClipping({
   ctx,

plugins/alignments/src/PileupRenderer/sortUtil.ts

@@ -1,6 +1,5 @@
 import { doesIntersect2, Feature } from '@jbrowse/core/util'
-import { Mismatch } from '../MismatchParser'
-import { SortedBy } from '../shared/types'
+import { Mismatch, SortedBy } from '../shared/types'
 
 export const sortFeature = (
   features: Map<string, Feature>,
@@ -53,33 +52,30 @@ export const sortFeature = (
     // first sort all mismatches, then all reference bases at the end
     case 'Base pair': {
       const baseSortArray: [string, Mismatch][] = []
-      featuresInCenterLine.forEach(feature => {
+      for (const feature of featuresInCenterLine) {
         const mismatches: Mismatch[] = feature.get('mismatches')
-        mismatches.forEach(mismatch => {
+        for (const m of mismatches) {
           const start = feature.get('start')
-          const offset = start + mismatch.start + 1
-          const consuming =
-            mismatch.type === 'insertion' || mismatch.type === 'softclip'
-          const len = consuming ? 0 : mismatch.length
+          const offset = start + m.start + 1
+          const consuming = m.type === 'insertion' || m.type === 'softclip'
+          const len = consuming ? 0 : m.length
           if (pos >= offset && pos < offset + len) {
-            baseSortArray.push([feature.id(), mismatch])
+            baseSortArray.push([feature.id(), m])
           }
-        })
-      })
+        }
+      }
 
       const baseMap = new Map(baseSortArray)
       featuresInCenterLine.sort((a, b) => {
         const aMismatch = baseMap.get(a.id())
         const bMismatch = baseMap.get(b.id())
         const acode = bMismatch?.base.toUpperCase()
         const bcode = aMismatch?.base.toUpperCase()
-        if (acode === bcode && acode === '*') {
-          // @ts-expect-error
-          return aMismatch.length - bMismatch.length
-        }
-        return (
-          (acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0)
-        )
+        return acode === bcode && acode === '*'
+          ? // @ts-expect-error
+            aMismatch.length - bMismatch.length
+          : (acode ? acode.charCodeAt(0) : 0) -
+              (bcode ? bcode.charCodeAt(0) : 0)
       })
 
       break

plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts

@@ -2,10 +2,11 @@ import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
 import { doesIntersect2, Feature, max, sum } from '@jbrowse/core/util'
 
 // locals
-import { parseCigar, Mismatch } from '../MismatchParser'
+import { parseCigar } from '../MismatchParser'
 import { getMethBins } from '../ModificationParser'
 import {
   ColorBy,
+  Mismatch,
   PreBaseCoverageBin,
   PreBaseCoverageBinSubtypes,
   SkipMap,

plugins/alignments/src/shared/types.ts

@@ -106,3 +106,14 @@ export interface SortedBy {
   assemblyName: string
   tag?: string
 }
+
+export interface Mismatch {
+  qual?: number
+  start: number
+  length: number
+  type: string
+  base: string
+  altbase?: string
+  seq?: string
+  cliplen?: number
+}

test_data/volvox/config.json

@@ -2217,19 +2217,20 @@
       },
       "assemblyNames": ["volvox"]
     },
+
     {
       "type": "AlignmentsTrack",
-      "trackId": "out_noref",
-      "name": "out_noref",
+      "trackId": "volvox-sorted.noref.cram",
+      "name": "volvox-sorted.cram (noref)",
       "category": ["Integration test"],
       "adapter": {
         "type": "CramAdapter",
         "cramLocation": {
-          "uri": "out_noref.cram",
+          "uri": "volvox-sorted.noref.cram",
           "locationType": "UriLocation"
         },
         "craiLocation": {
-          "uri": "out_noref.cram.crai",
+          "uri": "volvox-sorted.noref.cram.crai",
           "locationType": "UriLocation"
         },
         "sequenceAdapter": {

website/docs/user_guides/alignments_track.md

@@ -90,8 +90,9 @@ If you have data that marks DNA/RNA modifications using the MM tag in BAM/CRAM
 format, then the alignments track can use these tags to color modifications. It
 uses two modes:
 
-1. Modifications mode - draws the modifications as they are
-2. Methylation mode - draws both unmodified and modified CpGs (unmodified
+1. All modifications - draws the modifications as they are
+1. modifications - draws the modifications as they are
+1. Methylation mode - draws both unmodified and modified CpGs (unmodified
    positions are not indicated by the MM tag and this mode considers the
    sequence context)