Performance optimizations for alignments tracks, particularly those with many short reads

packages/core/pluggableElementTypes/renderers/BoxRendererType.ts

@@ -57,7 +57,7 @@ export class LayoutSession implements LayoutSessionProps {
       maxHeight: readConfObject(this.config, 'maxHeight'),
       displayMode: readConfObject(this.config, 'displayMode'),
       pitchX: this.bpPerPx,
-      spacing: readConfObject(this.config, 'noSpacing') ? 0 : 2,
+      pitchY: readConfObject(this.config, 'noSpacing') ? 1 : 3,
     })
   }
 

packages/core/rpc/WebWorkerRpcDriver.ts

@@ -60,12 +60,14 @@ export default class WebWorkerRpcDriver extends BaseRpcDriver {
   }
 
   makeWorker() {
-    // note that we are making a Rpc.Client connection with a worker pool of one for each worker,
-    // because we want to do our own state-group-aware load balancing rather than using librpc's
-    // builtin round-robin
+    // note that we are making a Rpc.Client connection with a worker pool of
+    // one for each worker, because we want to do our own state-group-aware
+    // load balancing rather than using librpc's builtin round-robin
     const worker = new WebWorkerHandle({ workers: [new this.WorkerClass()] })
+
     // send the worker its boot configuration using info from the pluginManager
     worker.workers[0].postMessage(this.workerBootConfiguration)
+
     return worker
   }
 }

packages/core/util/layouts/BaseLayout.ts

@@ -10,6 +10,7 @@ export interface Rectangle<T> {
   r: number
   top: number | null
   h: number
+  originalHeight: number
   data?: Record<string, T>
 }
 
@@ -22,6 +23,8 @@ export interface BaseLayout<T> {
     data?: Record<string, T>,
   ): number | null
   collides(rect: Rectangle<T>, top: number): boolean
+  addRectToBitmap(rect: Rectangle<T>, data: Record<string, T>): void
+  getRectangles(): Map<string, RectTuple>
   discardRange(left: number, right: number): void
   serializeRegion(region: { start: number; end: number }): SerializedLayout
   getTotalHeight(): number

packages/core/util/layouts/GranularRectLayout.test.js

@@ -2,7 +2,7 @@ import Layout from './GranularRectLayout'
 
 describe('GranularRectLayout', () => {
   it('lays out non-overlapping features end to end', () => {
-    const l = new Layout()
+    const l = new Layout({ pitchX: 10, pitchY: 4 })
     const testRects = [
       ['1,0', 4133, 5923, 16],
       ['1,1', 11299, 12389, 16],
@@ -46,7 +46,7 @@ describe('GranularRectLayout', () => {
   })
 
   it('stacks up overlapping features', () => {
-    const l = new Layout()
+    const l = new Layout({ pitchX: 10, pitchY: 4 })
 
     const testRects = []
     for (let i = 1; i <= 20; i += 1) {
@@ -55,26 +55,37 @@ describe('GranularRectLayout', () => {
 
     for (let i = 0; i < testRects.length; i += 1) {
       const top = l.addRect(...testRects[i])
-      expect(top).toEqual((i % 2) * 3)
+      expect(top).toEqual((i % 2) * 4)
     }
   })
 
   it('discards regions', () => {
-    const l = new Layout()
+    const l = new Layout({ pitchX: 10, pitchY: 4 })
     for (let i = 0; i < 20; i += 1) {
       const top = l.addRect(
         `feature-${i}`,
         10000 * i + 4000,
         10000 * i + 16000,
         1,
       )
-      expect(top).toEqual((i % 2) * 3)
+      expect(top).toEqual((i % 2) * 4)
     }
+
+    expect(l.bitmap[0].rowState.bits.length).toBe(34812)
+    expect(l.bitmap[1].rowState.bits.length).toBe(34812)
+    l.discardRange(190000, 220000)
+    expect(l.bitmap[0].rowState.bits.length).toBe(24802)
+    expect(l.bitmap[1].rowState.bits.length).toBe(23802)
+    l.discardRange(0, 100000)
+    expect(l.bitmap[0].rowState.bits.length).toBe(19001)
+    expect(l.bitmap[1].rowState.bits.length).toBe(23802)
+    l.discardRange(0, 220000)
+    expect(l.bitmap[0].rowState).toBeUndefined()
   })
 
   // see issue #486
   it('tests that adding +/- pitchX fixes resolution causing errors', () => {
-    const l = new Layout()
+    const l = new Layout({ pitchX: 91.21851599727707, pitchY: 3 })
 
     l.addRect('test', 2581541, 2581542, 1)
 
@@ -83,16 +94,34 @@ describe('GranularRectLayout', () => {
     ).toBeTruthy()
   })
 
+  it('tests reinitializing layout due to throwing away old one', () => {
+    const spy = jest.spyOn(console, 'warn').mockImplementation(() => {})
+    const l = new Layout({
+      pitchX: 1,
+      pitchY: 1,
+      maxHeight: 600,
+    })
+
+    l.addRect('test1', 0, 10000, 1)
+    l.addRect('test2', 1000000, 1000100, 1)
+    l.addRect('test3', 0, 10000, 1)
+    expect(l.rectangles.size).toBe(3)
+    expect(spy).toHaveBeenCalled()
+    spy.mockRestore()
+  })
+
   it('tests adding a gigantic feature that fills entire row with another smaller added on top', () => {
     const l = new Layout({
+      pitchX: 100,
+      pitchY: 1,
       maxHeight: 600,
     })
 
     expect(l.getByCoord(50000, 0)).toEqual(undefined)
-    l.addRect('test1', 0, 10000000, 1)
-    expect(l.getByCoord(50000, 0)).toEqual('test1')
-    l.addRect('test2', 0, 1000, 1)
-    expect(l.getByCoord(500, 2)).toEqual('test2')
+    l.addRect('test1', 0, 100000000, 1, { id: 'feat1' })
+    expect(l.getByCoord(50000, 0)).toEqual({ id: 'feat1' })
+    l.addRect('test2', 0, 1000, 1, { id: 'feat2' })
+    expect(l.getByCoord(500, 1)).toEqual({ id: 'feat2' })
     expect(l.rectangles.size).toBe(2)
   })
 })