@jbrowse/plugin-alignments 1.6.9 → 1.7.3

package/src/PileupRenderer/PileupRenderer.tsx

@@ -670,8 +670,7 @@ export default class PileupRenderer extends BoxRendererType {
         // this coloring is similar to igv.js, and is helpful to color negative
         // strand reads differently because their c-g will be flipped (e.g. g-c
         // read right to left)
-        const flags = feature.get('flags')
-        if (flags & 16) {
+        if (feature.get('flags') & 16) {
           ctx.fillStyle = '#c8dcc8'
         } else {
           ctx.fillStyle = '#c8c8c8'
@@ -789,10 +788,8 @@ export default class PileupRenderer extends BoxRendererType {
 
         if (widthPx >= charWidth && heightPx >= heightLim) {
           // normal SNP coloring
-          ctx.fillStyle = getAlphaColor(
-            contrastForBase[mismatch.base],
-            mismatch,
-          )
+          const contrast = contrastForBase[mismatch.base] || 'black'
+          ctx.fillStyle = getAlphaColor(contrast, mismatch)
           ctx.fillText(
             mbase,
             leftPx + (widthPx - charWidth) / 2 + 1,

package/src/SNPCoverageAdapter/SNPCoverageAdapter.ts

@@ -4,7 +4,6 @@ import {
 } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { AugmentedRegion as Region } from '@jbrowse/core/util/types'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { toArray } from 'rxjs/operators'
 import {
@@ -20,10 +19,6 @@ import {
   Mismatch,
 } from '../BamAdapter/MismatchParser'
 
-interface SNPCoverageOptions extends BaseOptions {
-  filters?: SerializableFilterChain
-}
-
 function mismatchLen(mismatch: Mismatch) {
   return !isInterbase(mismatch.type) ? mismatch.length : 1
 }
@@ -34,11 +29,15 @@ function isInterbase(type: string) {
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function inc(bin: any, strand: number, type: string, field: string) {
-  if (!bin[type][field]) {
-    bin[type][field] = { total: 0, strands: { '-1': 0, '0': 0, '1': 0 } }
+  let thisBin = bin[type][field]
+  if (!thisBin) {
+    thisBin = bin[type][field] = {
+      total: 0,
+      strands: { '-1': 0, '0': 0, '1': 0 },
+    }
   }
-  bin[type][field].total++
-  bin[type][field].strands[strand]++
+  thisBin.total++
+  thisBin.strands[strand]++
 }
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function dec(bin: any, strand: number, type: string, field: string) {
@@ -80,19 +79,14 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     return fetchSequence(region, sequenceAdapter)
   }
 
-  getFeatures(region: Region, opts: SNPCoverageOptions = {}) {
+  getFeatures(region: Region, opts: BaseOptions = {}) {
     return ObservableCreate<Feature>(async observer => {
       const { subadapter } = await this.configure()
-      let feats = await subadapter
+      const feats = await subadapter
         .getFeatures(region, opts)
         .pipe(toArray())
         .toPromise()
 
-      if (opts.filters) {
-        const { filters } = opts
-        feats = feats.filter(f => filters.passes(f, opts))
-      }
-
       const { bins, skipmap } = await this.generateCoverageBins(
         feats,
         region,
@@ -102,7 +96,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
       bins.forEach((bin, index) => {
         observer.next(
           new SimpleFeature({
-            id: `${this.id}-${region.start}-${index}`,
+            id: `${this.id}-${region.start + index}`,
             data: {
               score: bin.total,
               snpinfo: bin,

package/dist/AlignmentsFeatureDetail/index.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/LinearAlignmentsDisplay/models/configSchema.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/LinearPileupDisplay/configSchema.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/LinearSNPCoverageDisplay/models/configSchema.test.d.ts

@@ -1 +0,0 @@
-export {};

package/dist/PileupRenderer/components/PileupRendering.test.d.ts

@@ -1 +0,0 @@
-export {};