Updatse

plugins/alignments/src/SNPCoverageAdapter/generateCoverageBins.ts

@@ -75,17 +75,18 @@ export async function generateCoverageBins({
     // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
     if (bin) {
       bin.mods = Object.fromEntries(
-        Object.entries(bin.mods).map(([key, val]) => {
-          return [
-            key,
-            {
-              ...val,
-              avgProbability: val.probabilities.length
-                ? sum(val.probabilities) / val.probabilities.length
-                : undefined,
-            },
-          ] as const
-        }),
+        Object.entries(bin.mods).map(
+          ([key, val]) =>
+            [
+              key,
+              {
+                ...val,
+                avgProbability: val.probabilities.length
+                  ? sum(val.probabilities) / val.probabilities.length
+                  : undefined,
+              },
+            ] as const,
+        ),
       )
       bin.nonmods = Object.fromEntries(
         Object.entries(bin.nonmods).map(([key, val]) => {

plugins/alignments/src/SNPCoverageAdapter/processModifications.ts

@@ -36,7 +36,6 @@ export function processModifications({
           bins[epos] = {
             depth: 0,
             readsCounted: 0,
-            refbase: regionSequence[epos],
             snps: {},
             ref: {
               probabilities: [],
@@ -54,6 +53,7 @@ export function processModifications({
 
         const s = 1 - sum(allProbs)
         const bin = bins[epos]
+        bin.refbase = regionSequence[epos]
         if (twoColor && s > max(allProbs)) {
           incWithProbabilities(bin, fstrand, 'nonmods', `nonmod_${type}`, s)
         } else {

plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts

@@ -5,6 +5,7 @@ import type { RenderArgsDeserializedWithFeatures } from './types'
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
   // note: the snps are drawn on linear scale even if the data is drawn in log
   // scape hence the two different scales being used
+  // @ts-expect-error
   async draw(
     ctx: CanvasRenderingContext2D,
     props: RenderArgsDeserializedWithFeatures,

plugins/alignments/src/SNPCoverageRenderer/makeImage.ts

@@ -130,13 +130,9 @@ export async function makeImage(
   // are located to the left when forward and right when reversed
   const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx : 0
 
-  // @ts-expect-error
   const drawingModifications = colorBy?.type === 'modifications'
-  // @ts-expect-error
   const drawingMethylation = colorBy?.type === 'methylation'
-  const isolatedModification =
-    // @ts-expect-error
-    colorBy?.modifications?.isolatedModification
+  const isolatedModification = colorBy?.modifications?.isolatedModification
 
   // Second pass: draw the SNP data, and add a minimum feature width of 1px
   // which can be wider than the actual bpPerPx This reduces overdrawing of

plugins/alignments/src/SNPCoverageRenderer/types.ts

@@ -1,4 +1,4 @@
-import type { ModificationTypeWithColor } from '../shared/types'
+import type { ColorBy, ModificationTypeWithColor } from '../shared/types'
 import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
 import type { Feature } from '@jbrowse/core/util'
 import type { ScaleOpts } from '@jbrowse/plugin-wiggle'
@@ -16,4 +16,5 @@ export interface RenderArgsDeserializedWithFeatures
   ticks: { values: number[] }
   displayCrossHatches: boolean
   visibleModifications?: Record<string, ModificationTypeWithColor>
+  colorBy: ColorBy
 }