@jbrowse/plugin-gff3 1.5.1 → 1.5.5

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-gff3",
-  "version": "1.5.1",
+  "version": "1.5.5",
   "description": "JBrowse 2 gff3.",
   "keywords": [
     "jbrowse",
@@ -35,11 +35,11 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@flatten-js/interval-tree": "^1.0.14",
-    "@gmod/bgzf-filehandle": "^1.3.4",
-    "@gmod/gff": "^1.1.2",
-    "@gmod/tabix": "^1.5.0",
-    "generic-filehandle": "^2.2.0"
+    "@flatten-js/interval-tree": "^1.0.15",
+    "@gmod/bgzf-filehandle": "^1.4.2",
+    "@gmod/gff": "^1.2.0",
+    "@gmod/tabix": "^1.5.2",
+    "generic-filehandle": "^2.2.2"
   },
   "peerDependencies": {
     "@jbrowse/core": "^1.0.0",
@@ -54,5 +54,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "284e408c72a3d4d7a0d603197501a8fc8f68c4bc"
+  "gitHead": "214a3bed2d2722f0971c0d0eed37c8d801f086d7"
 }

package/src/Gff3Adapter/Gff3Adapter.ts

@@ -10,9 +10,7 @@ import IntervalTree from '@flatten-js/interval-tree'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
 import { unzip } from '@gmod/bgzf-filehandle'
 
-import gff from '@gmod/gff'
-
-import { FeatureLoc } from '../util'
+import gff, { GFF3FeatureLineWithRefs } from '@gmod/gff'
 
 function isGzip(buf: Buffer) {
   return buf[0] === 31 && buf[1] === 139 && buf[2] === 8
@@ -29,7 +27,7 @@ export default class extends BaseFeatureDataAdapter {
       readConfObject(this.config, 'gffLocation'),
       this.pluginManager,
     ).readFile()
-    const buf = isGzip(buffer as Buffer) ? await unzip(buffer) : buffer
+    const buf = isGzip(buffer) ? await unzip(buffer) : buffer
     // 512MB  max chrome string length is 512MB
     if (buf.length > 536_870_888) {
       throw new Error('Data exceeds maximum string length (512MB)')
@@ -47,7 +45,7 @@ export default class extends BaseFeatureDataAdapter {
       parseComments: false,
       parseDirectives: false,
       parseSequences: false,
-    }) as FeatureLoc[][]
+    })
 
     const intervalTree = feats
       .flat()
@@ -106,10 +104,18 @@ export default class extends BaseFeatureDataAdapter {
     }, opts.signal)
   }
 
-  private featureData(data: FeatureLoc) {
+  private featureData(data: GFF3FeatureLineWithRefs) {
     const f: Record<string, unknown> = { ...data }
     ;(f.start as number) -= 1 // convert to interbase
-    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand] // convert strand
+    if (data.strand === '+') {
+      f.strand = 1
+    } else if (data.strand === '-') {
+      f.strand = -1
+    } else if (data.strand === '.') {
+      f.strand = 0
+    } else {
+      f.strand = undefined
+    }
     f.phase = Number(data.phase)
     f.refName = data.seq_id
     if (data.score === null) {
@@ -128,15 +134,16 @@ export default class extends BaseFeatureDataAdapter {
       'phase',
       'strand',
     ]
-    Object.keys(data.attributes).forEach(a => {
+    const dataAttributes = data.attributes || {}
+    Object.keys(dataAttributes).forEach(a => {
       let b = a.toLowerCase()
       if (defaultFields.includes(b)) {
         // add "suffix" to tag name if it already exists
         // reproduces behavior of NCList
         b += '2'
       }
-      if (data.attributes[a] !== null) {
-        let attr = data.attributes[a]
+      if (dataAttributes[a] !== null) {
+        let attr: string | string[] | undefined = dataAttributes[a]
         if (Array.isArray(attr) && attr.length === 1) {
           ;[attr] = attr
         }

package/src/Gff3TabixAdapter/Gff3TabixAdapter.ts

@@ -9,7 +9,7 @@ import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
 import { TabixIndexedFile } from '@gmod/tabix'
-import gff from '@gmod/gff'
+import gff, { GFF3Feature, GFF3FeatureLineWithRefs } from '@gmod/gff'
 import { Observer } from 'rxjs'
 
 import { Instance } from 'mobx-state-tree'
@@ -17,7 +17,6 @@ import { readConfObject } from '@jbrowse/core/configuration'
 import MyConfigSchema from './configSchema'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
-import { FeatureLoc } from '../util'
 
 interface LineFeature {
   start: number
@@ -110,12 +109,8 @@ export default class extends BaseFeatureDataAdapter {
           }
         })
         if (maxEnd > query.end || minStart < query.start) {
-          // console.log(
-          //   `redispatching ${query.start}-${query.end} => ${minStart}-${maxEnd}`,
-          // )
           // make a new feature callback to only return top-level features
           // in the original query range
-
           this.getFeaturesHelper(
             { ...query, start: minStart, end: maxEnd },
             opts,
@@ -146,7 +141,7 @@ export default class extends BaseFeatureDataAdapter {
         parseComments: false,
         parseDirectives: false,
         parseSequences: false,
-      }) as FeatureLoc[][]
+      })
 
       features.forEach(featureLocs =>
         this.formatFeatures(featureLocs).forEach(f => {
@@ -184,20 +179,29 @@ export default class extends BaseFeatureDataAdapter {
     }
   }
 
-  private formatFeatures(featureLocs: FeatureLoc[]) {
+  private formatFeatures(featureLocs: GFF3Feature) {
     return featureLocs.map(
       featureLoc =>
         new SimpleFeature({
           data: this.featureData(featureLoc),
-          id: `${this.id}-offset-${featureLoc.attributes._lineHash[0]}`,
+          // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
+          id: `${this.id}-offset-${featureLoc.attributes!._lineHash![0]}`,
         }),
     )
   }
 
-  private featureData(data: FeatureLoc) {
+  private featureData(data: GFF3FeatureLineWithRefs) {
     const f: Record<string, unknown> = { ...data }
     ;(f.start as number) -= 1 // convert to interbase
-    f.strand = { '+': 1, '-': -1, '.': 0, '?': undefined }[data.strand] // convert strand
+    if (data.strand === '+') {
+      f.strand = 1
+    } else if (data.strand === '-') {
+      f.strand = -1
+    } else if (data.strand === '.') {
+      f.strand = 0
+    } else {
+      f.strand = undefined
+    }
     f.phase = Number(data.phase)
     f.refName = data.seq_id
     if (data.score === null) {
@@ -216,15 +220,16 @@ export default class extends BaseFeatureDataAdapter {
       'phase',
       'strand',
     ]
-    Object.keys(data.attributes).forEach(a => {
+    const dataAttributes = data.attributes || {}
+    Object.keys(dataAttributes).forEach(a => {
       let b = a.toLowerCase()
       if (defaultFields.includes(b)) {
         // add "suffix" to tag name if it already exists
         // reproduces behavior of NCList
         b += '2'
       }
-      if (data.attributes[a] !== null) {
-        let attr = data.attributes[a]
+      if (dataAttributes[a] !== null) {
+        let attr: string | string[] | undefined = dataAttributes[a]
         if (Array.isArray(attr) && attr.length === 1) {
           ;[attr] = attr
         }

package/dist/util.d.ts

@@ -1,14 +0,0 @@
-export declare type Strand = '+' | '-' | '.' | '?';
-export interface FeatureLoc {
-    [key: string]: unknown;
-    start: number;
-    end: number;
-    strand: Strand;
-    seq_id: string;
-    child_features: FeatureLoc[][];
-    data: unknown;
-    derived_features: unknown;
-    attributes: {
-        [key: string]: unknown[];
-    };
-}

package/src/declare.d.ts

@@ -1,2 +0,0 @@
-declare module '@gmod/gff'
-declare module '@gmod/bgzf-filehandle'

package/src/util.ts

@@ -1,12 +0,0 @@
-export type Strand = '+' | '-' | '.' | '?'
-export interface FeatureLoc {
-  [key: string]: unknown
-  start: number
-  end: number
-  strand: Strand
-  seq_id: string
-  child_features: FeatureLoc[][]
-  data: unknown
-  derived_features: unknown
-  attributes: { [key: string]: unknown[] }
-}