@jbrowse/plugin-gtf 2.2.0 → 2.2.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (4) hide show
  1. package/dist/util.d.ts +1 -1
  2. package/esm/util.d.ts +1 -1
  3. package/package.json +3 -3
  4. package/src/GtfAdapter/__snapshots__/GtfAdapter.test.ts.snap +62 -62
package/dist/util.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export declare type Strand = '+' | '-' | '.' | '?';
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+ export type Strand = '+' | '-' | '.' | '?';
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  export interface FeatureLoc {
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  [key: string]: unknown;
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  start: number;
package/esm/util.d.ts CHANGED
@@ -1,4 +1,4 @@
1
- export declare type Strand = '+' | '-' | '.' | '?';
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+ export type Strand = '+' | '-' | '.' | '?';
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  export interface FeatureLoc {
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  [key: string]: unknown;
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  start: number;
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-gtf",
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- "version": "2.2.0",
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+ "version": "2.2.2",
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  "description": "JBrowse 2 gtf feature adapter",
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  "keywords": [
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  "jbrowse",
@@ -27,7 +27,7 @@
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  "build": "npm-run-all build:*",
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  "test": "cd ../..; jest plugins/gtf --passWithNoTests",
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  "prepublishOnly": "yarn test",
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- "prepack": "yarn build; yarn useDist",
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+ "prepack": "yarn build && yarn useDist",
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  "postpack": "yarn useSrc",
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  "useDist": "node ../../scripts/useDist.js",
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  "useSrc": "node ../../scripts/useSrc.js",
@@ -58,5 +58,5 @@
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  "distModule": "esm/index.js",
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  "srcModule": "src/index.ts",
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  "module": "esm/index.js",
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- "gitHead": "cf31db8d833117f8822510340664fb3f045975cb"
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+ "gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
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  }
package/src/GtfAdapter/__snapshots__/GtfAdapter.test.ts.snap CHANGED
@@ -1,8 +1,8 @@
1
1
  // Jest Snapshot v1, https://goo.gl/fbAQLP
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  exports[`adapter can fetch features from volvox.sorted.gtf test getfeatures on gtf plain text adapter 1`] = `
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- Array [
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- Object {
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+ [
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+ {
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  "end": 9000,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -12,8 +12,8 @@ Array [
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  "source": "example",
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  "start": 1049,
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  "strand": 1,
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- "subfeatures": Array [
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- Object {
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+ "subfeatures": [
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+ {
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  "end": 1500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -28,7 +28,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-0-0",
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  },
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- Object {
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+ {
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  "end": 1200,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -43,7 +43,7 @@ Array [
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  "type": "five_prime_UTR",
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  "uniqueId": "test-ctgA-0-1",
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  },
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- Object {
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+ {
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  "end": 1500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -58,7 +58,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-0-2",
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  },
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- Object {
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+ {
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  "end": 3902,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -73,7 +73,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-0-3",
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  },
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- Object {
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+ {
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  "end": 3902,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -88,7 +88,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-0-4",
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  },
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- Object {
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+ {
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  "end": 5500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -103,7 +103,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-0-5",
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  },
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- Object {
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+ {
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  "end": 5500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -118,7 +118,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-0-6",
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  },
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- Object {
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+ {
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  "end": 7608,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -133,7 +133,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-0-7",
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  },
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- Object {
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+ {
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  "end": 9000,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -148,7 +148,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-0-8",
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  },
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- Object {
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+ {
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  "end": 9000,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -168,7 +168,7 @@ Array [
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  "type": "transcript",
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  "uniqueId": "test-ctgA-0",
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  },
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- Object {
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+ {
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  "end": 9000,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -178,8 +178,8 @@ Array [
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  "source": "example",
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  "start": 1049,
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  "strand": 1,
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- "subfeatures": Array [
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- Object {
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+ "subfeatures": [
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+ {
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  "end": 1500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -194,7 +194,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-1-0",
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  },
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- Object {
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+ {
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  "end": 1200,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -209,7 +209,7 @@ Array [
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  "type": "five_prime_UTR",
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  "uniqueId": "test-ctgA-1-1",
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  },
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- Object {
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+ {
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  "end": 1500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -224,7 +224,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-1-2",
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  },
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- Object {
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+ {
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  "end": 5500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -239,7 +239,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-1-3",
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  },
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- Object {
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+ {
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  "end": 5500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -254,7 +254,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-1-4",
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  },
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- Object {
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+ {
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  "end": 7608,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -269,7 +269,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-1-5",
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  },
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- Object {
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+ {
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  "end": 9000,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -284,7 +284,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-1-6",
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  },
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- Object {
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+ {
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  "end": 9000,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -304,7 +304,7 @@ Array [
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  "type": "transcript",
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  "uniqueId": "test-ctgA-1",
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  },
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- Object {
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+ {
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  "end": 9000,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -314,8 +314,8 @@ Array [
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  "source": "example",
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  "start": 1299,
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  "strand": 1,
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- "subfeatures": Array [
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- Object {
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+ "subfeatures": [
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+ {
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  "end": 1500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -330,7 +330,7 @@ Array [
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  "type": "exon",
331
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  "uniqueId": "test-ctgA-2-0",
332
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  },
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- Object {
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+ {
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  "end": 1500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -345,7 +345,7 @@ Array [
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  "type": "five_prime_UTR",
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  "uniqueId": "test-ctgA-2-1",
347
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  },
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- Object {
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+ {
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  "end": 3902,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -360,7 +360,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-2-2",
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  },
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- Object {
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+ {
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  "end": 3300,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -375,7 +375,7 @@ Array [
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  "type": "five_prime_UTR",
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  "uniqueId": "test-ctgA-2-3",
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  },
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- Object {
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+ {
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  "end": 3902,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -390,7 +390,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-2-4",
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  },
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- Object {
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+ {
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  "end": 5500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -405,7 +405,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-2-5",
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  },
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- Object {
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+ {
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  "end": 5500,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -420,7 +420,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-2-6",
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  },
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- Object {
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+ {
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  "end": 7600,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -435,7 +435,7 @@ Array [
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  "type": "CDS",
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  "uniqueId": "test-ctgA-2-7",
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  },
438
- Object {
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+ {
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  "end": 9000,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -450,7 +450,7 @@ Array [
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  "type": "exon",
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  "uniqueId": "test-ctgA-2-8",
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  },
453
- Object {
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+ {
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  "end": 9000,
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  "gene_id": "EDEN",
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  "gene_name": "EDEN",
@@ -470,7 +470,7 @@ Array [
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  "type": "transcript",
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  "uniqueId": "test-ctgA-2",
472
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  },
473
- Object {
473
+ {
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  "end": 11500,
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  "name": "Apple1",
476
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  "phase": 0,
@@ -478,8 +478,8 @@ Array [
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  "source": "bare_predicted",
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  "start": 9999,
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  "strand": 1,
481
- "subfeatures": Array [
482
- Object {
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+ "subfeatures": [
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+ {
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  "end": 11500,
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  "name": "Apple1",
485
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  "parentId": "test-ctgA-3",
@@ -497,7 +497,7 @@ Array [
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  "type": "transcript",
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  "uniqueId": "test-ctgA-3",
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  },
500
- Object {
500
+ {
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  "end": 17000,
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  "name": "cds-Apple2",
503
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  "phase": 0,
@@ -505,8 +505,8 @@ Array [
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  "source": "predicted",
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  "start": 13499,
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  "strand": 1,
508
- "subfeatures": Array [
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- Object {
508
+ "subfeatures": [
509
+ {
510
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  "end": 13800,
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  "name": "cds-Apple2",
512
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  "parentId": "test-ctgA-4",
@@ -519,7 +519,7 @@ Array [
519
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  "type": "CDS",
520
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  "uniqueId": "test-ctgA-4-0",
521
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  },
522
- Object {
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+ {
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  "end": 15500,
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  "name": "cds-Apple2",
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  "parentId": "test-ctgA-4",
@@ -532,7 +532,7 @@ Array [
532
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  "type": "CDS",
533
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  "uniqueId": "test-ctgA-4-1",
534
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  },
535
- Object {
535
+ {
536
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  "end": 17000,
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  "name": "cds-Apple2",
538
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  "parentId": "test-ctgA-4",
@@ -550,7 +550,7 @@ Array [
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  "type": "transcript",
551
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  "uniqueId": "test-ctgA-4",
552
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  },
553
- Object {
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+ {
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  "end": 23000,
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  "name": "rna-Apple3",
556
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  "phase": 0,
@@ -558,8 +558,8 @@ Array [
558
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  "source": "exonerate",
559
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  "start": 17399,
560
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  "strand": 1,
561
- "subfeatures": Array [
562
- Object {
561
+ "subfeatures": [
562
+ {
563
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  "end": 17999,
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  "name": "rna-Apple3",
565
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  "parentId": "test-ctgA-5",
@@ -572,7 +572,7 @@ Array [
572
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  "type": "UTR",
573
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  "uniqueId": "test-ctgA-5-0",
574
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  },
575
- Object {
575
+ {
576
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  "end": 18800,
577
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  "name": "rna-Apple3",
578
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  "parentId": "test-ctgA-5",
@@ -585,7 +585,7 @@ Array [
585
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  "type": "exon",
586
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  "uniqueId": "test-ctgA-5-1",
587
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  },
588
- Object {
588
+ {
589
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  "end": 18800,
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  "name": "rna-Apple3",
591
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  "parentId": "test-ctgA-5",
@@ -598,7 +598,7 @@ Array [
598
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  "type": "CDS",
599
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  "uniqueId": "test-ctgA-5-2",
600
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  },
601
- Object {
601
+ {
602
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  "end": 19500,
603
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  "name": "rna-Apple3",
604
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  "parentId": "test-ctgA-5",
@@ -611,7 +611,7 @@ Array [
611
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  "type": "CDS",
612
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  "uniqueId": "test-ctgA-5-3",
613
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  },
614
- Object {
614
+ {
615
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  "end": 19500,
616
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  "name": "rna-Apple3",
617
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  "parentId": "test-ctgA-5",
@@ -624,7 +624,7 @@ Array [
624
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  "type": "exon",
625
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  "uniqueId": "test-ctgA-5-4",
626
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  },
627
- Object {
627
+ {
628
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  "end": 21200,
629
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  "name": "rna-Apple3",
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  "parentId": "test-ctgA-5",
@@ -637,7 +637,7 @@ Array [
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  "type": "CDS",
638
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  "uniqueId": "test-ctgA-5-5",
639
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  },
640
- Object {
640
+ {
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  "end": 23000,
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  "name": "rna-Apple3",
643
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  "parentId": "test-ctgA-5",
@@ -650,7 +650,7 @@ Array [
650
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  "type": "exon",
651
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  "uniqueId": "test-ctgA-5-6",
652
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  },
653
- Object {
653
+ {
654
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  "end": 23000,
655
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  "name": "rna-Apple3",
656
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  "parentId": "test-ctgA-5",
@@ -672,8 +672,8 @@ Array [
672
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  `;
673
673
 
674
674
  exports[`can instantiate new GtfAdapter and check for demo data 1`] = `
675
- Array [
676
- Object {
675
+ [
676
+ {
677
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  "end": 107987,
678
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  "gene_biotype": "pseudogene",
679
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  "gene_id": "ENSVPAG00000000407",
@@ -685,8 +685,8 @@ Array [
685
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  "source": "ensembl",
686
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  "start": 107688,
687
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  "strand": 1,
688
- "subfeatures": Array [
689
- Object {
688
+ "subfeatures": [
689
+ {
690
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  "end": 107715,
691
691
  "exon_id": "ENSVPAE00000004844",
692
692
  "exon_number": "1",
@@ -709,7 +709,7 @@ Array [
709
709
  "type": "exon",
710
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  "uniqueId": "test-GeneScaffold_1-0-0",
711
711
  },
712
- Object {
712
+ {
713
713
  "end": 107812,
714
714
  "exon_id": "ENSVPAE00000004847",
715
715
  "exon_number": "2",
@@ -732,7 +732,7 @@ Array [
732
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  "type": "exon",
733
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  "uniqueId": "test-GeneScaffold_1-0-1",
734
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  },
735
- Object {
735
+ {
736
736
  "end": 107877,
737
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  "exon_id": "ENSVPAE00000004849",
738
738
  "exon_number": "3",
@@ -755,7 +755,7 @@ Array [
755
755
  "type": "exon",
756
756
  "uniqueId": "test-GeneScaffold_1-0-2",
757
757
  },
758
- Object {
758
+ {
759
759
  "end": 107895,
760
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  "exon_id": "ENSVPAE00000156282",
761
761
  "exon_number": "4",
@@ -778,7 +778,7 @@ Array [
778
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  "type": "exon",
779
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  "uniqueId": "test-GeneScaffold_1-0-3",
780
780
  },
781
- Object {
781
+ {
782
782
  "end": 107917,
783
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  "exon_id": "ENSVPAE00000188321",
784
784
  "exon_number": "5",
@@ -801,7 +801,7 @@ Array [
801
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  "type": "exon",
802
802
  "uniqueId": "test-GeneScaffold_1-0-4",
803
803
  },
804
- Object {
804
+ {
805
805
  "end": 107987,
806
806
  "exon_id": "ENSVPAE00000004854",
807
807
  "exon_number": "6",