@jbrowse/plugin-alignments 2.0.0 → 2.1.2

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.0.0",
+  "version": "2.1.2",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -37,19 +37,18 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@babel/runtime": "^7.17.9",
     "@gmod/bam": "^1.1.15",
     "@gmod/cram": "^1.6.4",
     "@mui/icons-material": "^5.0.1",
     "color": "^3.1.2",
     "copy-to-clipboard": "^3.3.1",
     "fast-deep-equal": "^3.1.3",
-    "generic-filehandle": "^2.2.2"
+    "generic-filehandle": "^3.0.0"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^1.0.0",
-    "@jbrowse/plugin-linear-genome-view": "^1.0.0",
-    "@jbrowse/plugin-wiggle": "^1.0.0",
+    "@jbrowse/core": "^2.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^2.0.0",
+    "@jbrowse/plugin-wiggle": "^2.0.0",
     "@mui/material": "^5.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^7.0.0",
@@ -65,5 +64,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "ecc7f5d47351a5ea04bc00f3a6eb6dfb607342e6"
+  "gitHead": "449b17325c9a4a97181f7ddddf48e80219f03b8d"
 }

package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap

@@ -345,7 +345,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -379,7 +379,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -413,7 +413,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -447,7 +447,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -481,7 +481,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -515,7 +515,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -549,7 +549,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -583,7 +583,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -617,7 +617,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -651,7 +651,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -685,7 +685,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -719,7 +719,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiCheckbox-root MuiCheckbox-colorPrimary MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"

package/src/BamAdapter/BamAdapter.ts

@@ -105,7 +105,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     return this.samHeader
   }
 
-  private async setup(opts?: BaseOptions) {
+  async setup(opts?: BaseOptions) {
     if (!this.setupP) {
       this.setupP = this.setupPre(opts).catch(e => {
         this.setupP = undefined

package/src/BamAdapter/MismatchParser.ts

@@ -11,8 +11,8 @@ export interface Mismatch {
 }
 const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi)
 const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/)
-export function parseCigar(cigar: string) {
-  return (cigar || '').split(/([MIDNSHPX=])/)
+export function parseCigar(cigar = '') {
+  return cigar.split(/([MIDNSHPX=])/).slice(0, -1)
 }
 export function cigarToMismatches(
   ops: string[],

package/src/LinearPileupDisplay/model.ts

@@ -34,6 +34,7 @@ import FilterListIcon from '@mui/icons-material/ClearAll'
 import { LinearPileupDisplayConfigModel } from './configSchema'
 import LinearPileupDisplayBlurb from './components/LinearPileupDisplayBlurb'
 import { getUniqueTagValues, getUniqueModificationValues } from '../shared'
+import { SimpleFeatureSerialized } from '@jbrowse/core/util/simpleFeature'
 
 // async
 const ColorByTagDlg = lazy(() => import('./components/ColorByTag'))
@@ -529,10 +530,9 @@ const stateModelFactory = (configSchema: LinearPileupDisplayConfigModel) =>
                       layoutId: getContainingView(self).id,
                       rendererType: 'PileupRenderer',
                     },
-                  )) as { feature: unknown }
+                  )) as { feature: SimpleFeatureSerialized }
 
                   if (feature) {
-                    // @ts-ignore
                     self.setContextMenuFeature(new SimpleFeature(feature))
                   }
                 }

package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
 import React from 'react'
 import { observer } from 'mobx-react'
 import { Feature } from '@jbrowse/core/util/simpleFeature'
@@ -31,8 +30,8 @@ const en = (n: number) => n.toLocaleString('en-US')
 const toP = (s = 0) => +(+s).toFixed(1)
 const pct = (n: number, total: number) => `${toP((n / (total || 1)) * 100)}%`
 
-const TooltipContents = React.forwardRef(
-  ({ feature }: { feature: Feature }, reactRef: any) => {
+const TooltipContents = React.forwardRef<HTMLDivElement, { feature: Feature }>(
+  ({ feature }, reactRef) => {
     const start = feature.get('start')
     const end = feature.get('end')
     const name = feature.get('refName')
@@ -109,7 +108,7 @@ type Coord = [number, number]
 
 const SNPCoverageTooltip = observer(
   (props: {
-    model: any
+    model: { featureUnderMouse: Feature }
     height: number
     offsetMouseCoord: Coord
     clientMouseCoord: Coord

package/src/LinearSNPCoverageDisplay/models/model.ts

@@ -7,12 +7,14 @@ import {
   AnyConfigurationModel,
 } from '@jbrowse/core/configuration'
 import { linearWiggleDisplayModelFactory } from '@jbrowse/plugin-wiggle'
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getContainingView } from '@jbrowse/core/util'
+
+// locals
 import Tooltip from '../components/Tooltip'
 import { getUniqueModificationValues } from '../../shared'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
 
 // using a map because it preserves order
 const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']])

package/src/PileupRenderer/PileupRenderer.tsx

@@ -63,7 +63,6 @@ function fillRect(
 }
 
 function getColorBaseMap(theme: Theme) {
-  // @ts-ignore
   const { bases } = theme.palette
   return {
     A: bases.A.main,
@@ -1060,7 +1059,6 @@ export default class PileupRenderer extends BoxRendererType {
     const mismatches: Mismatch[] = feature.get('mismatches')
     const seq = feature.get('seq')
     const { charWidth, charHeight } = this.getCharWidthHeight(ctx)
-    // @ts-ignore
     const { bases } = theme.palette
     const colorForBase: { [key: string]: string } = {
       A: bases.A.main,
@@ -1292,23 +1290,19 @@ export default class PileupRenderer extends BoxRendererType {
     const width = (end - start) / bpPerPx
     const height = Math.max(layout.getTotalHeight(), 1)
     const Color = await import('color').then(f => f.default)
-    const res = await renderToAbstractCanvas(
-      width,
-      height,
-      renderProps,
-      (ctx: CanvasRenderingContext2D) =>
-        this.makeImageData({
-          ctx,
-          layoutRecords,
-          canvasWidth: width,
-          renderArgs: {
-            ...renderProps,
-            layout,
-            features,
-            regionSequence,
-            Color,
-          },
-        }),
+    const res = await renderToAbstractCanvas(width, height, renderProps, ctx =>
+      this.makeImageData({
+        ctx,
+        layoutRecords,
+        canvasWidth: width,
+        renderArgs: {
+          ...renderProps,
+          layout,
+          features,
+          regionSequence,
+          Color,
+        },
+      }),
     )
 
     const results = await super.render({

package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts

@@ -88,14 +88,15 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
       )
 
       bins.forEach((bin, index) => {
+        const start = region.start + index
         observer.next(
           new SimpleFeature({
-            id: `${this.id}-${region.start + index}`,
+            id: `${this.id}-${start}`,
             data: {
               score: bin.total,
               snpinfo: bin,
-              start: region.start + index,
-              end: region.start + index + 1,
+              start,
+              end: start + 1,
               refName: region.refName,
             },
           }),

package/src/SNPCoverageRenderer/SNPCoverageRenderer.ts

@@ -1,6 +1,5 @@
 import { createJBrowseTheme } from '@jbrowse/core/ui'
-import { featureSpanPx, bpSpanPx } from '@jbrowse/core/util'
-import { Feature } from '@jbrowse/core/util/simpleFeature'
+import { featureSpanPx, bpSpanPx, Feature } from '@jbrowse/core/util'
 import { readConfObject } from '@jbrowse/core/configuration'
 import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType'
 import {
@@ -94,7 +93,6 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     const indicatorToHeight = (n: number) =>
       indicatorToY(getOrigin('linear')) - indicatorToY(n)
 
-    // @ts-ignore
     const { bases } = theme.palette
     const colorForBase: { [key: string]: string } = {
       A: bases.A.main,