Color by base quality

Take into account CIGAR string when doing color by base quality

Avoid duplicate fill if possible in offscreenCanvasPolyfill

packages/core/util/offscreenCanvasPonyfill.js

@@ -26,11 +26,17 @@ class PonyfillOffscreenContext {
 
   // setters (no getters working)
   set strokeStyle(style) {
-    this.commands.push({ type: 'strokeStyle', style })
+    if (style !== this.currentStrokeStyle) {
+      this.commands.push({ type: 'strokeStyle', style })
+      this.currentStrokeStyle = style
+    }
   }
 
   set fillStyle(style) {
-    this.commands.push({ type: 'fillStyle', style })
+    if (style !== this.currentFillStyle) {
+      this.commands.push({ type: 'fillStyle', style })
+      this.currentFillStyle = style
+    }
   }
 
   set font(style) {

plugins/alignments/src/LinearPileupDisplay/model.ts

@@ -452,6 +452,12 @@ const stateModelFactory = (
                     self.setColorScheme({ type: 'pairOrientation' })
                   },
                 },
+                {
+                  label: 'Per-base quality',
+                  onClick: () => {
+                    self.setColorScheme({ type: 'perBaseQuality' })
+                  },
+                },
                 {
                   label: 'Insert size',
                   onClick: () => {

plugins/alignments/src/PileupRenderer/PileupLayoutSession.ts

@@ -0,0 +1,59 @@
+import deepEqual from 'deep-equal'
+import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType'
+import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
+import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
+import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout'
+import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout'
+import { readConfObject } from '@jbrowse/core/configuration'
+
+export interface PileupLayoutSessionProps {
+  config: AnyConfigurationModel
+  bpPerPx: number
+  filters: SerializableFilterChain
+  sortedBy: unknown
+  showSoftClip: unknown
+}
+
+type MyMultiLayout = MultiLayout<GranularRectLayout<unknown>, unknown>
+interface CachedPileupLayout {
+  layout: MyMultiLayout
+  config: AnyConfigurationModel
+  filters: SerializableFilterChain
+  sortedBy: unknown
+  showSoftClip: boolean
+}
+// Sorting and revealing soft clip changes the layout of Pileup renderer
+// Adds extra conditions to see if cached layout is valid
+export class PileupLayoutSession extends LayoutSession {
+  sortedBy: unknown
+
+  showSoftClip = false
+
+  constructor(args: PileupLayoutSessionProps) {
+    super(args)
+    this.config = args.config
+  }
+
+  cachedLayoutIsValid(cachedLayout: CachedPileupLayout) {
+    return (
+      super.cachedLayoutIsValid(cachedLayout) &&
+      this.showSoftClip === cachedLayout.showSoftClip &&
+      deepEqual(this.sortedBy, cachedLayout.sortedBy)
+    )
+  }
+
+  cachedLayout: CachedPileupLayout | undefined
+
+  get layout(): MyMultiLayout {
+    if (!this.cachedLayout || !this.cachedLayoutIsValid(this.cachedLayout)) {
+      this.cachedLayout = {
+        layout: this.makeLayout(),
+        config: readConfObject(this.config),
+        filters: this.filters,
+        sortedBy: this.sortedBy,
+        showSoftClip: this.showSoftClip,
+      }
+    }
+    return this.cachedLayout.layout
+  }
+}