jbrowse-plugin-mafviewer 1.2.0 → 1.2.1

package/package.json

@@ -1,5 +1,5 @@
 {
-  "version": "1.2.0",
+  "version": "1.2.1",
   "license": "MIT",
   "name": "jbrowse-plugin-mafviewer",
   "keywords": [
@@ -66,6 +66,7 @@
     "buffer": "^6.0.3",
     "d3-array": "^3.2.4",
     "d3-hierarchy": "^3.1.2",
+    "fast-deep-equal": "^3.1.3",
     "generic-filehandle2": "^1.0.0",
     "long": "^5.2.3"
   }

package/src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts

@@ -17,9 +17,9 @@ import VirtualOffset from './virtualOffset'
 import parseNewick from '../parseNewick'
 import { normalize } from '../util'
 import { parseRowInstructions } from './rowInstructions'
+import { parseLineByLine } from './util'
 
 import type { IndexData, OrganismRecord } from './types'
-import { parseLineByLine } from './util'
 interface Entry {
   type: string
   row: number
@@ -101,7 +101,6 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
 
   getFeatures(query: Region, opts?: BaseOptions) {
     const { statusCallback = () => {} } = opts || {}
-    console.log(query.start, query.end, 'wtf')
     return ObservableCreate<Feature>(async observer => {
       try {
         const byteRanges = await this.setup()

package/src/LinearMafDisplay/stateModel.ts

@@ -3,9 +3,9 @@ import { getEnv, getSession } from '@jbrowse/core/util'
 import { getRpcSessionId } from '@jbrowse/core/util/tracks'
 import { ascending } from 'd3-array'
 import { cluster, hierarchy } from 'd3-hierarchy'
+import deepEqual from 'fast-deep-equal'
 import { autorun } from 'mobx'
 import { addDisposer, isAlive, types } from 'mobx-state-tree'
-import deepEqual from 'fast-deep-equal'
 
 import SetRowHeightDialog from './components/SetRowHeight'
 import { maxLength, setBrLength } from './types'

package/src/LinearMafRenderer/makeImageData.ts

@@ -40,7 +40,6 @@ export function makeImageData({
     samples,
     rowProportion,
     features,
-    statusCallback,
   } = renderArgs
   const region = regions[0]!
   const canvasWidth = (region.end - region.start) / bpPerPx

package/src/LinearMafRenderer/util.ts

@@ -1,4 +1,5 @@
 import { measureText } from '@jbrowse/core/util'
+
 import type { Theme } from '@mui/material'
 
 export function getContrastBaseMap(theme: Theme) {

package/src/MafTabixAdapter/MafTabixAdapter.ts

@@ -85,6 +85,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
           const data = (feature.get('field5') as string).split(',')
           const alignments = {} as Record<string, OrganismRecord>
 
+          // eslint-disable-next-line @typescript-eslint/prefer-for-of
           for (let j = 0; j < data.length; j++) {
             const elt = data[j]!
             const seq = elt.split(':')[5]!
@@ -116,17 +117,6 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
             }
           }
 
-          console.log(
-            {
-              alignments,
-              firstAssemblyNameFound,
-              refAssemblyName,
-              q: query.assemblyName,
-            },
-            alignments[refAssemblyName],
-            alignments[query.assemblyName],
-            alignments[firstAssemblyNameFound],
-          )
           observer.next(
             new SimpleFeature({
               id: feature.id(),