@jbrowse/plugin-gtf 2.15.0 → 2.15.1
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.
|
@@ -9,7 +9,7 @@ const rxjs_1 = require("@jbrowse/core/util/rxjs");
|
|
|
9
9
|
const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
|
|
10
10
|
const util_1 = require("@jbrowse/core/util");
|
|
11
11
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
12
|
-
const
|
|
12
|
+
const gtf_nostream_1 = require("gtf-nostream");
|
|
13
13
|
// locals
|
|
14
14
|
const util_2 = require("../util");
|
|
15
15
|
const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
|
|
@@ -60,12 +60,7 @@ class GtfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
|
|
|
60
60
|
if (!this.calculatedIntervalTreeMap[refName]) {
|
|
61
61
|
sc === null || sc === void 0 ? void 0 : sc('Parsing GTF data');
|
|
62
62
|
const intervalTree = new interval_tree_1.default();
|
|
63
|
-
|
|
64
|
-
parseFeatures: true,
|
|
65
|
-
parseComments: false,
|
|
66
|
-
parseDirectives: false,
|
|
67
|
-
parseSequences: false,
|
|
68
|
-
})
|
|
63
|
+
(0, gtf_nostream_1.parseStringSync)(lines)
|
|
69
64
|
.flat()
|
|
70
65
|
.map((f, i) => new util_1.SimpleFeature({
|
|
71
66
|
data: (0, util_2.featureData)(f),
|
|
@@ -4,7 +4,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
|
|
|
4
4
|
import IntervalTree from '@flatten-js/interval-tree';
|
|
5
5
|
import { SimpleFeature, updateStatus, isGzip, } from '@jbrowse/core/util';
|
|
6
6
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
7
|
-
import
|
|
7
|
+
import { parseStringSync } from 'gtf-nostream';
|
|
8
8
|
// locals
|
|
9
9
|
import { featureData } from '../util';
|
|
10
10
|
const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
|
|
@@ -55,12 +55,7 @@ export default class GtfAdapter extends BaseFeatureDataAdapter {
|
|
|
55
55
|
if (!this.calculatedIntervalTreeMap[refName]) {
|
|
56
56
|
sc === null || sc === void 0 ? void 0 : sc('Parsing GTF data');
|
|
57
57
|
const intervalTree = new IntervalTree();
|
|
58
|
-
|
|
59
|
-
parseFeatures: true,
|
|
60
|
-
parseComments: false,
|
|
61
|
-
parseDirectives: false,
|
|
62
|
-
parseSequences: false,
|
|
63
|
-
})
|
|
58
|
+
parseStringSync(lines)
|
|
64
59
|
.flat()
|
|
65
60
|
.map((f, i) => new SimpleFeature({
|
|
66
61
|
data: featureData(f),
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-gtf",
|
|
3
|
-
"version": "2.15.
|
|
3
|
+
"version": "2.15.1",
|
|
4
4
|
"description": "JBrowse 2 gtf feature adapter",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -38,7 +38,7 @@
|
|
|
38
38
|
"dependencies": {
|
|
39
39
|
"@flatten-js/interval-tree": "^1.0.15",
|
|
40
40
|
"@gmod/bgzf-filehandle": "^1.4.3",
|
|
41
|
-
"
|
|
41
|
+
"gtf-nostream": "^1.0.0"
|
|
42
42
|
},
|
|
43
43
|
"peerDependencies": {
|
|
44
44
|
"@jbrowse/core": "^2.0.0",
|
|
@@ -56,5 +56,5 @@
|
|
|
56
56
|
"distModule": "esm/index.js",
|
|
57
57
|
"srcModule": "src/index.ts",
|
|
58
58
|
"module": "esm/index.js",
|
|
59
|
-
"gitHead": "
|
|
59
|
+
"gitHead": "86ed70124fc5a0b1161266659d1ca9f8796bf3fe"
|
|
60
60
|
}
|