@jbrowse/plugin-gff3 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.
- package/dist/Gff3Adapter/index.d.ts +3 -1
- package/dist/Gff3Adapter/index.js +32 -3
- package/dist/Gff3Adapter/index.js.map +1 -1
- package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js +2 -2
- package/dist/Gff3TabixAdapter/Gff3TabixAdapter.js.map +1 -1
- package/dist/Gff3TabixAdapter/index.d.ts +3 -1
- package/dist/Gff3TabixAdapter/index.js +32 -3
- package/dist/Gff3TabixAdapter/index.js.map +1 -1
- package/dist/GuessGff3/index.d.ts +3 -0
- package/dist/GuessGff3/index.js +44 -0
- package/dist/GuessGff3/index.js.map +1 -0
- package/dist/index.js +6 -75
- package/dist/index.js.map +1 -1
- package/esm/Gff3Adapter/index.d.ts +3 -1
- package/esm/Gff3Adapter/index.js +9 -1
- package/esm/Gff3Adapter/index.js.map +1 -1
- package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js +2 -2
- package/esm/Gff3TabixAdapter/Gff3TabixAdapter.js.map +1 -1
- package/esm/Gff3TabixAdapter/index.d.ts +3 -1
- package/esm/Gff3TabixAdapter/index.js +9 -1
- package/esm/Gff3TabixAdapter/index.js.map +1 -1
- package/esm/GuessGff3/index.d.ts +3 -0
- package/esm/GuessGff3/index.js +42 -0
- package/esm/GuessGff3/index.js.map +1 -0
- package/esm/index.js +6 -52
- package/esm/index.js.map +1 -1
- package/package.json +3 -3
- package/src/Gff3Adapter/__snapshots__/Gff3Adapter.test.ts.snap +9 -9
- package/src/Gff3Adapter/index.ts +14 -1
- package/src/Gff3TabixAdapter/Gff3TabixAdapter.ts +2 -2
- package/src/Gff3TabixAdapter/__snapshots__/Gff3TabixAdapter.test.ts.snap +9 -9
- package/src/Gff3TabixAdapter/index.ts +15 -1
- package/src/GuessGff3/index.ts +63 -0
- package/src/index.ts +7 -79
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@@ -1,9 +1,38 @@
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"use strict";
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var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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var desc = Object.getOwnPropertyDescriptor(m, k);
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if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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desc = { enumerable: true, get: function() { return m[k]; } };
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}
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Object.defineProperty(o, k2, desc);
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}) : (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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o[k2] = m[k];
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}));
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var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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Object.defineProperty(o, "default", { enumerable: true, value: v });
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}) : function(o, v) {
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o["default"] = v;
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});
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var __importStar = (this && this.__importStar) || function (mod) {
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if (mod && mod.__esModule) return mod;
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var result = {};
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if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
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__setModuleDefault(result, mod);
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return result;
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};
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var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
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const configSchema_1 = __importDefault(require("./configSchema"));
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exports.default = (pluginManager) => {
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pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
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name: 'Gff3Adapter',
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configSchema: configSchema_1.default,
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getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3Adapter'))).then(r => r.default),
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}));
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};
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//# sourceMappingURL=index.js.map
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3Adapter/index.ts"],"names":[],"mappings":"
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3Adapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+EAAiE;AAEjE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,mCAAW,CAAC;QACd,IAAI,EAAE,aAAa;QACnB,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,kDAAO,eAAe,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
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@@ -41,7 +41,7 @@ class default_1 extends BaseAdapter_1.BaseFeatureDataAdapter {
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getFeatures(query, opts = {}) {
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return (0, rxjs_1.ObservableCreate)(async (observer) => {
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const metadata = await this.gff.getMetadata();
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this.getFeaturesHelper(query, opts, metadata, observer, true);
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await this.getFeaturesHelper(query, opts, metadata, observer, true);
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}, opts.signal);
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}
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async getFeaturesHelper(query, opts = {}, metadata, observer, allowRedispatch, originalQuery = query) {
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if (maxEnd > query.end || minStart < query.start) {
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// make a new feature callback to only return top-level features
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// in the original query range
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this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, metadata, observer, false, query);
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await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, metadata, observer, false, query);
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return;
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}
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}
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@@ -1 +1 @@
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pluginManager.addAdapterType(() => new pluggableElementTypes_1.AdapterType({
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name: 'Gff3TabixAdapter',
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configSchema: configSchema_1.default,
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getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3TabixAdapter'))).then(r => r.default),
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/index.ts"],"names":[],"mappings":"
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+EAAiE;AAEjE,kEAAyC;AAEzC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,mCAAW,CAAC;QACd,IAAI,EAAE,kBAAkB;QACxB,YAAY,EAAZ,sBAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,kDAAO,oBAAoB,IAAE,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
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type: adapterName,
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bamLocation: file,
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gffGzLocation: file,
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index: {
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indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
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const regexGuess = /\.gff3?$/i;
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type: adapterName,
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else if (adapterHint === adapterName) {
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}
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};
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});
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};
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//# sourceMappingURL=index.js.map
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|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GuessGff3/index.ts"],"names":[],"mappings":";;AAEA,sDAKkC;AAElC,kBAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,iBAAiB,CAAA;YACpC,MAAM,WAAW,GAAG,kBAAkB,CAAA;YACtC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;YAClC,MAAM,SAAS,GAAG,KAAK,IAAI,IAAA,oBAAW,EAAC,KAAK,CAAC,CAAA;YAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;gBAC5D,OAAO;oBACL,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,IAAI;oBACjB,aAAa,EAAE,IAAI;oBACnB,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK,IAAI,IAAA,kBAAS,EAAC,IAAI,EAAE,MAAM,CAAC;wBAC1C,SAAS,EAAE,IAAA,sBAAa,EAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;qBAClD;iBACF,CAAA;aACF;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,WAAW,CAAA;YAC9B,MAAM,WAAW,GAAG,aAAa,CAAA;YACjC,MAAM,QAAQ,GAAG,IAAA,oBAAW,EAAC,IAAI,CAAC,CAAA;YAClC,MAAM,GAAG,GAAG;gBACV,IAAI,EAAE,WAAW;gBACjB,WAAW,EAAE,IAAI;aAClB,CAAA;YACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;gBAC7C,OAAO,GAAG,CAAA;aACX;iBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;gBACtC,OAAO,GAAG,CAAA;aACX;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC,CAAA"}
|
package/dist/index.js
CHANGED
|
@@ -1,90 +1,21 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
|
|
3
|
-
if (k2 === undefined) k2 = k;
|
|
4
|
-
var desc = Object.getOwnPropertyDescriptor(m, k);
|
|
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|
-
if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
|
|
6
|
-
desc = { enumerable: true, get: function() { return m[k]; } };
|
|
7
|
-
}
|
|
8
|
-
Object.defineProperty(o, k2, desc);
|
|
9
|
-
}) : (function(o, m, k, k2) {
|
|
10
|
-
if (k2 === undefined) k2 = k;
|
|
11
|
-
o[k2] = m[k];
|
|
12
|
-
}));
|
|
13
|
-
var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
|
|
14
|
-
Object.defineProperty(o, "default", { enumerable: true, value: v });
|
|
15
|
-
}) : function(o, v) {
|
|
16
|
-
o["default"] = v;
|
|
17
|
-
});
|
|
18
|
-
var __importStar = (this && this.__importStar) || function (mod) {
|
|
19
|
-
if (mod && mod.__esModule) return mod;
|
|
20
|
-
var result = {};
|
|
21
|
-
if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
|
|
22
|
-
__setModuleDefault(result, mod);
|
|
23
|
-
return result;
|
|
24
|
-
};
|
|
25
2
|
var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
26
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
27
4
|
};
|
|
28
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
29
|
-
const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
|
|
30
6
|
const Plugin_1 = __importDefault(require("@jbrowse/core/Plugin"));
|
|
31
|
-
const Gff3TabixAdapter_1 = require("./Gff3TabixAdapter");
|
|
32
|
-
const
|
|
33
|
-
const
|
|
7
|
+
const Gff3TabixAdapter_1 = __importDefault(require("./Gff3TabixAdapter"));
|
|
8
|
+
const Gff3Adapter_1 = __importDefault(require("./Gff3Adapter"));
|
|
9
|
+
const GuessGff3_1 = __importDefault(require("./GuessGff3"));
|
|
34
10
|
class default_1 extends Plugin_1.default {
|
|
35
11
|
constructor() {
|
|
36
12
|
super(...arguments);
|
|
37
13
|
this.name = 'GFF3Plugin';
|
|
38
14
|
}
|
|
39
15
|
install(pluginManager) {
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
43
|
-
getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3TabixAdapter/Gff3TabixAdapter'))).then(r => r.default),
|
|
44
|
-
}));
|
|
45
|
-
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
|
|
46
|
-
return (file, index, adapterHint) => {
|
|
47
|
-
const regexGuess = /\.gff3?\.b?gz$/i;
|
|
48
|
-
const adapterName = 'Gff3TabixAdapter';
|
|
49
|
-
const fileName = (0, tracks_1.getFileName)(file);
|
|
50
|
-
const indexName = index && (0, tracks_1.getFileName)(index);
|
|
51
|
-
if (regexGuess.test(fileName) || adapterHint === adapterName) {
|
|
52
|
-
return {
|
|
53
|
-
type: adapterName,
|
|
54
|
-
bamLocation: file,
|
|
55
|
-
gffGzLocation: file,
|
|
56
|
-
index: {
|
|
57
|
-
location: index || (0, tracks_1.makeIndex)(file, '.tbi'),
|
|
58
|
-
indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'TBI'),
|
|
59
|
-
},
|
|
60
|
-
};
|
|
61
|
-
}
|
|
62
|
-
return adapterGuesser(file, index, adapterHint);
|
|
63
|
-
};
|
|
64
|
-
});
|
|
65
|
-
pluginManager.addAdapterType(() => new AdapterType_1.default({
|
|
66
|
-
name: 'Gff3Adapter',
|
|
67
|
-
configSchema: Gff3Adapter_1.configSchema,
|
|
68
|
-
getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./Gff3Adapter/Gff3Adapter'))).then(r => r.default),
|
|
69
|
-
}));
|
|
70
|
-
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
|
|
71
|
-
return (file, index, adapterHint) => {
|
|
72
|
-
const regexGuess = /\.gff3?$/i;
|
|
73
|
-
const adapterName = 'Gff3Adapter';
|
|
74
|
-
const fileName = (0, tracks_1.getFileName)(file);
|
|
75
|
-
const obj = {
|
|
76
|
-
type: adapterName,
|
|
77
|
-
gffLocation: file,
|
|
78
|
-
};
|
|
79
|
-
if (regexGuess.test(fileName) && !adapterHint) {
|
|
80
|
-
return obj;
|
|
81
|
-
}
|
|
82
|
-
else if (adapterHint === adapterName) {
|
|
83
|
-
return obj;
|
|
84
|
-
}
|
|
85
|
-
return adapterGuesser(file, index, adapterHint);
|
|
86
|
-
};
|
|
87
|
-
});
|
|
16
|
+
(0, Gff3TabixAdapter_1.default)(pluginManager);
|
|
17
|
+
(0, Gff3Adapter_1.default)(pluginManager);
|
|
18
|
+
(0, GuessGff3_1.default)(pluginManager);
|
|
88
19
|
}
|
|
89
20
|
}
|
|
90
21
|
exports.default = default_1;
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;AACA,kEAAyC;AAEzC,0EAAkD;AAClD,gEAAwC;AACxC,4DAAoC;AAEpC,eAAqB,SAAQ,gBAAM;IAAnC;;QACE,SAAI,GAAG,YAAY,CAAA;IAOrB,CAAC;IALC,OAAO,CAAC,aAA4B;QAClC,IAAA,0BAAiB,EAAC,aAAa,CAAC,CAAA;QAChC,IAAA,qBAAY,EAAC,aAAa,CAAC,CAAA;QAC3B,IAAA,mBAAU,EAAC,aAAa,CAAC,CAAA;IAC3B,CAAC;CACF;AARD,4BAQC"}
|
package/esm/Gff3Adapter/index.js
CHANGED
|
@@ -1,2 +1,10 @@
|
|
|
1
|
-
|
|
1
|
+
import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
|
|
2
|
+
import configSchema from './configSchema';
|
|
3
|
+
export default (pluginManager) => {
|
|
4
|
+
pluginManager.addAdapterType(() => new AdapterType({
|
|
5
|
+
name: 'Gff3Adapter',
|
|
6
|
+
configSchema,
|
|
7
|
+
getAdapterClass: () => import('./Gff3Adapter').then(r => r.default),
|
|
8
|
+
}));
|
|
9
|
+
};
|
|
2
10
|
//# sourceMappingURL=index.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3Adapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3Adapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,aAAa;QACnB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CAAC,MAAM,CAAC,eAAe,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpE,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
|
|
@@ -36,7 +36,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
36
36
|
getFeatures(query, opts = {}) {
|
|
37
37
|
return ObservableCreate(async (observer) => {
|
|
38
38
|
const metadata = await this.gff.getMetadata();
|
|
39
|
-
this.getFeaturesHelper(query, opts, metadata, observer, true);
|
|
39
|
+
await this.getFeaturesHelper(query, opts, metadata, observer, true);
|
|
40
40
|
}, opts.signal);
|
|
41
41
|
}
|
|
42
42
|
async getFeaturesHelper(query, opts = {}, metadata, observer, allowRedispatch, originalQuery = query) {
|
|
@@ -65,7 +65,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
65
65
|
if (maxEnd > query.end || minStart < query.start) {
|
|
66
66
|
// make a new feature callback to only return top-level features
|
|
67
67
|
// in the original query range
|
|
68
|
-
this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, metadata, observer, false, query);
|
|
68
|
+
await this.getFeaturesHelper({ ...query, start: minStart, end: maxEnd }, opts, metadata, observer, false, query);
|
|
69
69
|
return;
|
|
70
70
|
}
|
|
71
71
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"Gff3TabixAdapter.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/Gff3TabixAdapter.ts"],"names":[],"mappings":"AAAA,yCAAyC;AACzC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAA;AAEzD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,GAA6C,MAAM,WAAW,CAAA;AAErE,OAAO,EACL,cAAc,GAEf,MAAM,6BAA6B,CAAA;AAWpC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAKjD,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,cAAc,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC7D,MAAM,SAAS,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAChE,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC9D,MAAM,cAAc,GAAG,cAAc,CAAC,MAAM,EAAE,gBAAgB,CAAC,CAAA;QAE/D,IAAI,CAAC,cAAc,GAAG,cAAc,IAAI,CAAC,YAAY,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAA;QAC1E,IAAI,CAAC,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC9B,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;YAC3D,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,aAAa,EAAE,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC;SAChC,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YAC7C,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;
|
|
1
|
+
{"version":3,"file":"Gff3TabixAdapter.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/Gff3TabixAdapter.ts"],"names":[],"mappings":"AAAA,yCAAyC;AACzC,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAChD,OAAO,EAAE,cAAc,EAAE,MAAM,0BAA0B,CAAA;AAEzD,OAAO,EAAE,YAAY,EAAE,MAAM,uBAAuB,CAAA;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAA;AAC9C,OAAO,GAA6C,MAAM,WAAW,CAAA;AAErE,OAAO,EACL,cAAc,GAEf,MAAM,6BAA6B,CAAA;AAWpC,MAAM,CAAC,OAAO,MAAO,SAAQ,sBAAsB;IAKjD,YACE,MAA6B,EAC7B,aAAiC,EACjC,aAA6B;QAE7B,KAAK,CAAC,MAAM,EAAE,aAAa,EAAE,aAAa,CAAC,CAAA;QAC3C,MAAM,aAAa,GAAG,cAAc,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;QAC7D,MAAM,SAAS,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC,CAAA;QAChE,MAAM,QAAQ,GAAG,cAAc,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,UAAU,CAAC,CAAC,CAAA;QAC9D,MAAM,cAAc,GAAG,cAAc,CAAC,MAAM,EAAE,gBAAgB,CAAC,CAAA;QAE/D,IAAI,CAAC,cAAc,GAAG,cAAc,IAAI,CAAC,YAAY,EAAE,QAAQ,EAAE,QAAQ,CAAC,CAAA;QAC1E,IAAI,CAAC,GAAG,GAAG,IAAI,gBAAgB,CAAC;YAC9B,UAAU,EAAE,YAAY,CAAC,aAAa,EAAE,IAAI,CAAC,aAAa,CAAC;YAC3D,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,aAAa,EACX,SAAS,KAAK,KAAK;gBACjB,CAAC,CAAC,YAAY,CAAC,QAAQ,EAAE,IAAI,CAAC,aAAa,CAAC;gBAC5C,CAAC,CAAC,SAAS;YACf,cAAc,EAAE,EAAE,GAAG,CAAC,IAAI,EAAE;YAC5B,aAAa,EAAE,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC;SAChC,CAAC,CAAA;IACJ,CAAC;IAEM,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QAC7C,OAAO,IAAI,CAAC,GAAG,CAAC,yBAAyB,CAAC,IAAI,CAAC,CAAA;IACjD,CAAC;IAEM,KAAK,CAAC,SAAS;QACpB,OAAO,IAAI,CAAC,GAAG,CAAC,SAAS,EAAE,CAAA;IAC7B,CAAC;IAEM,WAAW,CAAC,KAAa,EAAE,OAAoB,EAAE;QACtD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,CAAA;YAC7C,MAAM,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,EAAE,QAAQ,EAAE,QAAQ,EAAE,IAAI,CAAC,CAAA;QACrE,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAEO,KAAK,CAAC,iBAAiB,CAC7B,KAAa,EACb,OAAoB,EAAE,EACtB,QAA2D,EAC3D,QAA2B,EAC3B,eAAwB,EACxB,aAAa,GAAG,KAAK;QAErB,IAAI;YACF,MAAM,KAAK,GAAkB,EAAE,CAAA;YAE/B,MAAM,IAAI,CAAC,GAAG,CAAC,QAAQ,CACrB,KAAK,CAAC,OAAO,EACb,KAAK,CAAC,KAAK,EACX,KAAK,CAAC,GAAG,EACT,CAAC,IAAY,EAAE,UAAkB,EAAE,EAAE;gBACnC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,aAAa,EAAE,IAAI,EAAE,UAAU,CAAC,CAAC,CAAA;YACtE,CAAC,CACF,CAAA;YACD,IAAI,eAAe,IAAI,KAAK,CAAC,MAAM,EAAE;gBACnC,IAAI,QAAQ,GAAG,QAAQ,CAAA;gBACvB,IAAI,MAAM,GAAG,CAAC,QAAQ,CAAA;gBACtB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;oBACnB,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,CAAA;oBAClC,yEAAyE;oBACzE,6CAA6C;oBAC7C,IAAI,CAAC,IAAI,CAAC,cAAc,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC9C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA,CAAC,iBAAiB;wBAC9C,IAAI,KAAK,GAAG,QAAQ,EAAE;4BACpB,QAAQ,GAAG,KAAK,CAAA;yBACjB;wBACD,IAAI,IAAI,CAAC,GAAG,GAAG,MAAM,EAAE;4BACrB,MAAM,GAAG,IAAI,CAAC,GAAG,CAAA;yBAClB;qBACF;gBACH,CAAC,CAAC,CAAA;gBACF,IAAI,MAAM,GAAG,KAAK,CAAC,GAAG,IAAI,QAAQ,GAAG,KAAK,CAAC,KAAK,EAAE;oBAChD,gEAAgE;oBAChE,8BAA8B;oBAC9B,MAAM,IAAI,CAAC,iBAAiB,CAC1B,EAAE,GAAG,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,GAAG,EAAE,MAAM,EAAE,EAC1C,IAAI,EACJ,QAAQ,EACR,QAAQ,EACR,KAAK,EACL,KAAK,CACN,CAAA;oBACD,OAAM;iBACP;aACF;YAED,MAAM,IAAI,GAAG,KAAK;iBACf,GAAG,CAAC,CAAC,UAAuB,EAAE,EAAE;gBAC/B,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE;oBACxD,IAAI,CAAC,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,WAAW,CAAC,EAAE;wBAC/C,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,cAAc,UAAU,CAAC,QAAQ,EAAE,CAAA;qBAC5D;iBACF;qBAAM;oBACL,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,aAAa,UAAU,CAAC,QAAQ,EAAE,CAAA;iBAC1D;gBACD,OAAO,UAAU,CAAC,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YACrC,CAAC,CAAC;iBACD,IAAI,CAAC,IAAI,CAAC,CAAA;YAEb,MAAM,QAAQ,GAAG,GAAG,CAAC,eAAe,CAAC,IAAI,EAAE;gBACzC,aAAa,EAAE,IAAI;gBACnB,aAAa,EAAE,KAAK;gBACpB,eAAe,EAAE,KAAK;gBACtB,cAAc,EAAE,KAAK;gBACrB,4BAA4B,EAAE,IAAI;aACnC,CAAC,CAAA;YAEF,QAAQ,CAAC,OAAO,CAAC,WAAW,CAAC,EAAE,CAC7B,IAAI,CAAC,cAAc,CAAC,WAAW,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;gBAC3C,IACE,cAAc,CACZ,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,EACd,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,EACZ,aAAa,CAAC,KAAK,EACnB,aAAa,CAAC,GAAG,CAClB,EACD;oBACA,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;iBACjB;YACH,CAAC,CAAC,CACH,CAAA;YACD,QAAQ,CAAC,QAAQ,EAAE,CAAA;SACpB;QAAC,OAAO,CAAC,EAAE;YACV,QAAQ,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;SAClB;IACH,CAAC;IAEO,SAAS,CACf,aAA6C,EAC7C,IAAY,EACZ,UAAkB;QAElB,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAE/B,yCAAyC;QACzC,OAAO;YACL,KAAK,EAAE,CAAC,MAAM,CAAC,aAAa,CAAC,KAAK,GAAG,CAAC,CAAC;YACvC,GAAG,EAAE,CAAC,MAAM,CAAC,aAAa,CAAC,GAAG,GAAG,CAAC,CAAC;YACnC,QAAQ,EAAE,UAAU;YACpB,MAAM;SACP,CAAA;IACH,CAAC;IAEO,cAAc,CAAC,WAAwB;QAC7C,OAAO,WAAW,CAAC,GAAG,CACpB,UAAU,CAAC,EAAE,CACX,IAAI,aAAa,CAAC;YAChB,IAAI,EAAE,IAAI,CAAC,WAAW,CAAC,UAAU,CAAC;YAClC,oEAAoE;YACpE,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,WAAW,UAAU,CAAC,UAAW,CAAC,SAAU,CAAC,CAAC,CAAC,EAAE;SAChE,CAAC,CACL,CAAA;IACH,CAAC;IAEO,WAAW,CAAC,IAA6B;QAC/C,MAAM,CAAC,GAA4B,EAAE,GAAG,IAAI,EAAE,CAC7C;QAAC,CAAC,CAAC,KAAgB,IAAI,CAAC,CAAA,CAAC,uBAAuB;QACjD,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YACvB,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;SACd;aAAM,IAAI,IAAI,CAAC,MAAM,KAAK,GAAG,EAAE;YAC9B,CAAC,CAAC,MAAM,GAAG,CAAC,CAAA;SACb;aAAM;YACL,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;SACrB;QACD,CAAC,CAAC,KAAK,GAAG,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QAC5B,CAAC,CAAC,OAAO,GAAG,IAAI,CAAC,MAAM,CAAA;QACvB,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,OAAO,CAAC,CAAC,KAAK,CAAA;SACf;QACD,MAAM,aAAa,GAAG;YACpB,OAAO;YACP,KAAK;YACL,QAAQ;YACR,OAAO;YACP,MAAM;YACN,QAAQ;YACR,OAAO;YACP,QAAQ;SACT,CAAA;QACD,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,IAAI,EAAE,CAAA;QAC5C,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACtC,IAAI,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,CAAA;YACvB,IAAI,aAAa,CAAC,QAAQ,CAAC,CAAC,CAAC,EAAE;gBAC7B,gDAAgD;gBAChD,gCAAgC;gBAChC,CAAC,IAAI,GAAG,CAAA;aACT;YACD,IAAI,cAAc,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;gBAC9B,IAAI,IAAI,GAAkC,cAAc,CAAC,CAAC,CAAC,CAAA;gBAC3D,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE;oBAC5C,CAAC;oBAAA,CAAC,IAAI,CAAC,GAAG,IAAI,CAAA;iBACf;gBACD,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;aACZ;QACH,CAAC,CAAC,CAAA;QACF,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,MAAM,CAAA;QAEpB,gFAAgF;QAChF,IAAI,IAAI,CAAC,cAAc,IAAI,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE;YACrD,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,cAAc;iBAChC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,CAAC,IAAI,CAAC,WAAW,CAAC,QAAQ,CAAC,CAAC,CAAC;iBACvE,IAAI,EAAE,CAAA;SACV;QAED,OAAO,CAAC,CAAC,cAAc,CAAA;QACvB,OAAO,CAAC,CAAC,IAAI,CAAA;QACb,4BAA4B;QAC5B,OAAO,CAAC,CAAC,SAAS,CAAA;QAClB,OAAO,CAAC,CAAC,UAAU,CAAA;QACnB,OAAO,CAAC,CAAC,MAAM,CAAA;QAEf,OAAO,CAAC,CAAA;IACV,CAAC;IAEM,aAAa,EAAC,gBAAgB,IAAG,CAAC;CAC1C"}
|
|
@@ -1,2 +1,10 @@
|
|
|
1
|
-
|
|
1
|
+
import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
|
|
2
|
+
import configSchema from './configSchema';
|
|
3
|
+
export default (pluginManager) => {
|
|
4
|
+
pluginManager.addAdapterType(() => new AdapterType({
|
|
5
|
+
name: 'Gff3TabixAdapter',
|
|
6
|
+
configSchema,
|
|
7
|
+
getAdapterClass: () => import('./Gff3TabixAdapter').then(r => r.default),
|
|
8
|
+
}));
|
|
9
|
+
};
|
|
2
10
|
//# sourceMappingURL=index.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,YAAY,EAAE,MAAM,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Gff3TabixAdapter/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,cAAc,CAC1B,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,kBAAkB;QACxB,YAAY;QACZ,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,oBAAoB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;KACpD,CAAC,CACL,CAAA;AACH,CAAC,CAAA"}
|
|
@@ -0,0 +1,42 @@
|
|
|
1
|
+
import { makeIndex, makeIndexType, getFileName, } from '@jbrowse/core/util/tracks';
|
|
2
|
+
export default (pluginManager) => {
|
|
3
|
+
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
|
|
4
|
+
return (file, index, adapterHint) => {
|
|
5
|
+
const regexGuess = /\.gff3?\.b?gz$/i;
|
|
6
|
+
const adapterName = 'Gff3TabixAdapter';
|
|
7
|
+
const fileName = getFileName(file);
|
|
8
|
+
const indexName = index && getFileName(index);
|
|
9
|
+
if (regexGuess.test(fileName) || adapterHint === adapterName) {
|
|
10
|
+
return {
|
|
11
|
+
type: adapterName,
|
|
12
|
+
bamLocation: file,
|
|
13
|
+
gffGzLocation: file,
|
|
14
|
+
index: {
|
|
15
|
+
location: index || makeIndex(file, '.tbi'),
|
|
16
|
+
indexType: makeIndexType(indexName, 'CSI', 'TBI'),
|
|
17
|
+
},
|
|
18
|
+
};
|
|
19
|
+
}
|
|
20
|
+
return adapterGuesser(file, index, adapterHint);
|
|
21
|
+
};
|
|
22
|
+
});
|
|
23
|
+
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
|
|
24
|
+
return (file, index, adapterHint) => {
|
|
25
|
+
const regexGuess = /\.gff3?$/i;
|
|
26
|
+
const adapterName = 'Gff3Adapter';
|
|
27
|
+
const fileName = getFileName(file);
|
|
28
|
+
const obj = {
|
|
29
|
+
type: adapterName,
|
|
30
|
+
gffLocation: file,
|
|
31
|
+
};
|
|
32
|
+
if (regexGuess.test(fileName) && !adapterHint) {
|
|
33
|
+
return obj;
|
|
34
|
+
}
|
|
35
|
+
else if (adapterHint === adapterName) {
|
|
36
|
+
return obj;
|
|
37
|
+
}
|
|
38
|
+
return adapterGuesser(file, index, adapterHint);
|
|
39
|
+
};
|
|
40
|
+
});
|
|
41
|
+
};
|
|
42
|
+
//# sourceMappingURL=index.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/GuessGff3/index.ts"],"names":[],"mappings":"AAEA,OAAO,EACL,SAAS,EACT,aAAa,EACb,WAAW,GAEZ,MAAM,2BAA2B,CAAA;AAElC,eAAe,CAAC,aAA4B,EAAE,EAAE;IAC9C,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,iBAAiB,CAAA;YACpC,MAAM,WAAW,GAAG,kBAAkB,CAAA;YACtC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;YAClC,MAAM,SAAS,GAAG,KAAK,IAAI,WAAW,CAAC,KAAK,CAAC,CAAA;YAC7C,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,WAAW,KAAK,WAAW,EAAE;gBAC5D,OAAO;oBACL,IAAI,EAAE,WAAW;oBACjB,WAAW,EAAE,IAAI;oBACjB,aAAa,EAAE,IAAI;oBACnB,KAAK,EAAE;wBACL,QAAQ,EAAE,KAAK,IAAI,SAAS,CAAC,IAAI,EAAE,MAAM,CAAC;wBAC1C,SAAS,EAAE,aAAa,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC;qBAClD;iBACF,CAAA;aACF;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;IAED,aAAa,CAAC,mBAAmB,CAC/B,8BAA8B,EAC9B,CAAC,cAA8B,EAAE,EAAE;QACjC,OAAO,CACL,IAAkB,EAClB,KAAoB,EACpB,WAAoB,EACpB,EAAE;YACF,MAAM,UAAU,GAAG,WAAW,CAAA;YAC9B,MAAM,WAAW,GAAG,aAAa,CAAA;YACjC,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,CAAA;YAClC,MAAM,GAAG,GAAG;gBACV,IAAI,EAAE,WAAW;gBACjB,WAAW,EAAE,IAAI;aAClB,CAAA;YACD,IAAI,UAAU,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,WAAW,EAAE;gBAC7C,OAAO,GAAG,CAAA;aACX;iBAAM,IAAI,WAAW,KAAK,WAAW,EAAE;gBACtC,OAAO,GAAG,CAAA;aACX;YACD,OAAO,cAAc,CAAC,IAAI,EAAE,KAAK,EAAE,WAAW,CAAC,CAAA;QACjD,CAAC,CAAA;IACH,CAAC,CACF,CAAA;AACH,CAAC,CAAA"}
|
package/esm/index.js
CHANGED
|
@@ -1,62 +1,16 @@
|
|
|
1
|
-
import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
|
|
2
1
|
import Plugin from '@jbrowse/core/Plugin';
|
|
3
|
-
import
|
|
4
|
-
import
|
|
5
|
-
import
|
|
2
|
+
import Gff3TabixAdapterF from './Gff3TabixAdapter';
|
|
3
|
+
import Gff3AdapterF from './Gff3Adapter';
|
|
4
|
+
import GuessGff3F from './GuessGff3';
|
|
6
5
|
export default class extends Plugin {
|
|
7
6
|
constructor() {
|
|
8
7
|
super(...arguments);
|
|
9
8
|
this.name = 'GFF3Plugin';
|
|
10
9
|
}
|
|
11
10
|
install(pluginManager) {
|
|
12
|
-
pluginManager
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
getAdapterClass: () => import('./Gff3TabixAdapter/Gff3TabixAdapter').then(r => r.default),
|
|
16
|
-
}));
|
|
17
|
-
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
|
|
18
|
-
return (file, index, adapterHint) => {
|
|
19
|
-
const regexGuess = /\.gff3?\.b?gz$/i;
|
|
20
|
-
const adapterName = 'Gff3TabixAdapter';
|
|
21
|
-
const fileName = getFileName(file);
|
|
22
|
-
const indexName = index && getFileName(index);
|
|
23
|
-
if (regexGuess.test(fileName) || adapterHint === adapterName) {
|
|
24
|
-
return {
|
|
25
|
-
type: adapterName,
|
|
26
|
-
bamLocation: file,
|
|
27
|
-
gffGzLocation: file,
|
|
28
|
-
index: {
|
|
29
|
-
location: index || makeIndex(file, '.tbi'),
|
|
30
|
-
indexType: makeIndexType(indexName, 'CSI', 'TBI'),
|
|
31
|
-
},
|
|
32
|
-
};
|
|
33
|
-
}
|
|
34
|
-
return adapterGuesser(file, index, adapterHint);
|
|
35
|
-
};
|
|
36
|
-
});
|
|
37
|
-
pluginManager.addAdapterType(() => new AdapterType({
|
|
38
|
-
name: 'Gff3Adapter',
|
|
39
|
-
configSchema: gff3AdapterConfigSchema,
|
|
40
|
-
getAdapterClass: () => import('./Gff3Adapter/Gff3Adapter').then(r => r.default),
|
|
41
|
-
}));
|
|
42
|
-
pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
|
|
43
|
-
return (file, index, adapterHint) => {
|
|
44
|
-
const regexGuess = /\.gff3?$/i;
|
|
45
|
-
const adapterName = 'Gff3Adapter';
|
|
46
|
-
const fileName = getFileName(file);
|
|
47
|
-
const obj = {
|
|
48
|
-
type: adapterName,
|
|
49
|
-
gffLocation: file,
|
|
50
|
-
};
|
|
51
|
-
if (regexGuess.test(fileName) && !adapterHint) {
|
|
52
|
-
return obj;
|
|
53
|
-
}
|
|
54
|
-
else if (adapterHint === adapterName) {
|
|
55
|
-
return obj;
|
|
56
|
-
}
|
|
57
|
-
return adapterGuesser(file, index, adapterHint);
|
|
58
|
-
};
|
|
59
|
-
});
|
|
11
|
+
Gff3TabixAdapterF(pluginManager);
|
|
12
|
+
Gff3AdapterF(pluginManager);
|
|
13
|
+
GuessGff3F(pluginManager);
|
|
60
14
|
}
|
|
61
15
|
}
|
|
62
16
|
//# sourceMappingURL=index.js.map
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AACA,OAAO,MAAM,MAAM,sBAAsB,CAAA;AAEzC,OAAO,iBAAiB,MAAM,oBAAoB,CAAA;AAClD,OAAO,YAAY,MAAM,eAAe,CAAA;AACxC,OAAO,UAAU,MAAM,aAAa,CAAA;AAEpC,MAAM,CAAC,OAAO,MAAO,SAAQ,MAAM;IAAnC;;QACE,SAAI,GAAG,YAAY,CAAA;IAOrB,CAAC;IALC,OAAO,CAAC,aAA4B;QAClC,iBAAiB,CAAC,aAAa,CAAC,CAAA;QAChC,YAAY,CAAC,aAAa,CAAC,CAAA;QAC3B,UAAU,CAAC,aAAa,CAAC,CAAA;IAC3B,CAAC;CACF"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/plugin-gff3",
|
|
3
|
-
"version": "2.2.
|
|
3
|
+
"version": "2.2.2",
|
|
4
4
|
"description": "JBrowse 2 gff3.",
|
|
5
5
|
"keywords": [
|
|
6
6
|
"jbrowse",
|
|
@@ -27,7 +27,7 @@
|
|
|
27
27
|
"build": "npm-run-all build:*",
|
|
28
28
|
"test": "cd ../..; jest plugins/gff3 --passWithNoTests",
|
|
29
29
|
"prepublishOnly": "yarn test",
|
|
30
|
-
"prepack": "yarn build
|
|
30
|
+
"prepack": "yarn build && yarn useDist",
|
|
31
31
|
"postpack": "yarn useSrc",
|
|
32
32
|
"useDist": "node ../../scripts/useDist.js",
|
|
33
33
|
"useSrc": "node ../../scripts/useSrc.js",
|
|
@@ -59,5 +59,5 @@
|
|
|
59
59
|
"distModule": "esm/index.js",
|
|
60
60
|
"srcModule": "src/index.ts",
|
|
61
61
|
"module": "esm/index.js",
|
|
62
|
-
"gitHead": "
|
|
62
|
+
"gitHead": "abbc00e8feedbc58de84a7a3e735ec0224909b29"
|
|
63
63
|
}
|
|
@@ -1,9 +1,9 @@
|
|
|
1
1
|
// Jest Snapshot v1, https://goo.gl/fbAQLP
|
|
2
2
|
|
|
3
3
|
exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = `
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
"derived_features":
|
|
4
|
+
[
|
|
5
|
+
{
|
|
6
|
+
"derived_features": [],
|
|
7
7
|
"end": 6079,
|
|
8
8
|
"name": "ctgB",
|
|
9
9
|
"phase": 0,
|
|
@@ -14,8 +14,8 @@ Array [
|
|
|
14
14
|
"type": "contig",
|
|
15
15
|
"uniqueId": "test-offset-187",
|
|
16
16
|
},
|
|
17
|
-
|
|
18
|
-
"derived_features":
|
|
17
|
+
{
|
|
18
|
+
"derived_features": [],
|
|
19
19
|
"end": 1984,
|
|
20
20
|
"name": "f07",
|
|
21
21
|
"note": "This is an example",
|
|
@@ -27,8 +27,8 @@ Array [
|
|
|
27
27
|
"type": "remark",
|
|
28
28
|
"uniqueId": "test-offset-188",
|
|
29
29
|
},
|
|
30
|
-
|
|
31
|
-
"derived_features":
|
|
30
|
+
{
|
|
31
|
+
"derived_features": [],
|
|
32
32
|
"end": 6130,
|
|
33
33
|
"name": "f06",
|
|
34
34
|
"note": "This is another example",
|
|
@@ -40,8 +40,8 @@ Array [
|
|
|
40
40
|
"type": "remark",
|
|
41
41
|
"uniqueId": "test-offset-189",
|
|
42
42
|
},
|
|
43
|
-
|
|
44
|
-
"derived_features":
|
|
43
|
+
{
|
|
44
|
+
"derived_features": [],
|
|
45
45
|
"end": 5968,
|
|
46
46
|
"name": "f05",
|
|
47
47
|
"note": "ああ、この機能は、世界中を旅しています！",
|
package/src/Gff3Adapter/index.ts
CHANGED
|
@@ -1 +1,14 @@
|
|
|
1
|
-
|
|
1
|
+
import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
|
|
2
|
+
import PluginManager from '@jbrowse/core/PluginManager'
|
|
3
|
+
import configSchema from './configSchema'
|
|
4
|
+
|
|
5
|
+
export default (pluginManager: PluginManager) => {
|
|
6
|
+
pluginManager.addAdapterType(
|
|
7
|
+
() =>
|
|
8
|
+
new AdapterType({
|
|
9
|
+
name: 'Gff3Adapter',
|
|
10
|
+
configSchema,
|
|
11
|
+
getAdapterClass: () => import('./Gff3Adapter').then(r => r.default),
|
|
12
|
+
}),
|
|
13
|
+
)
|
|
14
|
+
}
|
|
@@ -68,7 +68,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
68
68
|
public getFeatures(query: Region, opts: BaseOptions = {}) {
|
|
69
69
|
return ObservableCreate<Feature>(async observer => {
|
|
70
70
|
const metadata = await this.gff.getMetadata()
|
|
71
|
-
this.getFeaturesHelper(query, opts, metadata, observer, true)
|
|
71
|
+
await this.getFeaturesHelper(query, opts, metadata, observer, true)
|
|
72
72
|
}, opts.signal)
|
|
73
73
|
}
|
|
74
74
|
|
|
@@ -111,7 +111,7 @@ export default class extends BaseFeatureDataAdapter {
|
|
|
111
111
|
if (maxEnd > query.end || minStart < query.start) {
|
|
112
112
|
// make a new feature callback to only return top-level features
|
|
113
113
|
// in the original query range
|
|
114
|
-
this.getFeaturesHelper(
|
|
114
|
+
await this.getFeaturesHelper(
|
|
115
115
|
{ ...query, start: minStart, end: maxEnd },
|
|
116
116
|
opts,
|
|
117
117
|
metadata,
|
|
@@ -1,9 +1,9 @@
|
|
|
1
1
|
// Jest Snapshot v1, https://goo.gl/fbAQLP
|
|
2
2
|
|
|
3
3
|
exports[`adapter can fetch features from volvox.gff3 test getfeatures on gff plain text adapter 1`] = `
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
"derived_features":
|
|
4
|
+
[
|
|
5
|
+
{
|
|
6
|
+
"derived_features": [],
|
|
7
7
|
"end": 6079,
|
|
8
8
|
"name": "ctgB",
|
|
9
9
|
"phase": 0,
|
|
@@ -14,8 +14,8 @@ Array [
|
|
|
14
14
|
"type": "contig",
|
|
15
15
|
"uniqueId": "test-offset-794327",
|
|
16
16
|
},
|
|
17
|
-
|
|
18
|
-
"derived_features":
|
|
17
|
+
{
|
|
18
|
+
"derived_features": [],
|
|
19
19
|
"end": 1984,
|
|
20
20
|
"name": "f07",
|
|
21
21
|
"note": "This is an example",
|
|
@@ -27,8 +27,8 @@ Array [
|
|
|
27
27
|
"type": "remark",
|
|
28
28
|
"uniqueId": "test-offset-794370",
|
|
29
29
|
},
|
|
30
|
-
|
|
31
|
-
"derived_features":
|
|
30
|
+
{
|
|
31
|
+
"derived_features": [],
|
|
32
32
|
"end": 6130,
|
|
33
33
|
"name": "f06",
|
|
34
34
|
"note": "This is another example",
|
|
@@ -40,8 +40,8 @@ Array [
|
|
|
40
40
|
"type": "remark",
|
|
41
41
|
"uniqueId": "test-offset-794439",
|
|
42
42
|
},
|
|
43
|
-
|
|
44
|
-
"derived_features":
|
|
43
|
+
{
|
|
44
|
+
"derived_features": [],
|
|
45
45
|
"end": 5968,
|
|
46
46
|
"name": "f05",
|
|
47
47
|
"note": "ああ、この機能は、世界中を旅しています！",
|
|
@@ -1 +1,15 @@
|
|
|
1
|
-
|
|
1
|
+
import { AdapterType } from '@jbrowse/core/pluggableElementTypes'
|
|
2
|
+
import PluginManager from '@jbrowse/core/PluginManager'
|
|
3
|
+
import configSchema from './configSchema'
|
|
4
|
+
|
|
5
|
+
export default (pluginManager: PluginManager) => {
|
|
6
|
+
pluginManager.addAdapterType(
|
|
7
|
+
() =>
|
|
8
|
+
new AdapterType({
|
|
9
|
+
name: 'Gff3TabixAdapter',
|
|
10
|
+
configSchema,
|
|
11
|
+
getAdapterClass: () =>
|
|
12
|
+
import('./Gff3TabixAdapter').then(r => r.default),
|
|
13
|
+
}),
|
|
14
|
+
)
|
|
15
|
+
}
|
|
@@ -0,0 +1,63 @@
|
|
|
1
|
+
import PluginManager from '@jbrowse/core/PluginManager'
|
|
2
|
+
import { FileLocation } from '@jbrowse/core/util/types'
|
|
3
|
+
import {
|
|
4
|
+
makeIndex,
|
|
5
|
+
makeIndexType,
|
|
6
|
+
getFileName,
|
|
7
|
+
AdapterGuesser,
|
|
8
|
+
} from '@jbrowse/core/util/tracks'
|
|
9
|
+
|
|
10
|
+
export default (pluginManager: PluginManager) => {
|
|
11
|
+
pluginManager.addToExtensionPoint(
|
|
12
|
+
'Core-guessAdapterForLocation',
|
|
13
|
+
(adapterGuesser: AdapterGuesser) => {
|
|
14
|
+
return (
|
|
15
|
+
file: FileLocation,
|
|
16
|
+
index?: FileLocation,
|
|
17
|
+
adapterHint?: string,
|
|
18
|
+
) => {
|
|
19
|
+
const regexGuess = /\.gff3?\.b?gz$/i
|
|
20
|
+
const adapterName = 'Gff3TabixAdapter'
|
|
21
|
+
const fileName = getFileName(file)
|
|
22
|
+
const indexName = index && getFileName(index)
|
|
23
|
+
if (regexGuess.test(fileName) || adapterHint === adapterName) {
|
|
24
|
+
return {
|
|
25
|
+
type: adapterName,
|
|
26
|
+
bamLocation: file,
|
|
27
|
+
gffGzLocation: file,
|
|
28
|
+
index: {
|
|
29
|
+
location: index || makeIndex(file, '.tbi'),
|
|
30
|
+
indexType: makeIndexType(indexName, 'CSI', 'TBI'),
|
|
31
|
+
},
|
|
32
|
+
}
|
|
33
|
+
}
|
|
34
|
+
return adapterGuesser(file, index, adapterHint)
|
|
35
|
+
}
|
|
36
|
+
},
|
|
37
|
+
)
|
|
38
|
+
|
|
39
|
+
pluginManager.addToExtensionPoint(
|
|
40
|
+
'Core-guessAdapterForLocation',
|
|
41
|
+
(adapterGuesser: AdapterGuesser) => {
|
|
42
|
+
return (
|
|
43
|
+
file: FileLocation,
|
|
44
|
+
index?: FileLocation,
|
|
45
|
+
adapterHint?: string,
|
|
46
|
+
) => {
|
|
47
|
+
const regexGuess = /\.gff3?$/i
|
|
48
|
+
const adapterName = 'Gff3Adapter'
|
|
49
|
+
const fileName = getFileName(file)
|
|
50
|
+
const obj = {
|
|
51
|
+
type: adapterName,
|
|
52
|
+
gffLocation: file,
|
|
53
|
+
}
|
|
54
|
+
if (regexGuess.test(fileName) && !adapterHint) {
|
|
55
|
+
return obj
|
|
56
|
+
} else if (adapterHint === adapterName) {
|
|
57
|
+
return obj
|
|
58
|
+
}
|
|
59
|
+
return adapterGuesser(file, index, adapterHint)
|
|
60
|
+
}
|
|
61
|
+
},
|
|
62
|
+
)
|
|
63
|
+
}
|
package/src/index.ts
CHANGED
|
@@ -1,88 +1,16 @@
|
|
|
1
|
-
import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
|
|
2
1
|
import PluginManager from '@jbrowse/core/PluginManager'
|
|
3
2
|
import Plugin from '@jbrowse/core/Plugin'
|
|
4
|
-
|
|
5
|
-
import
|
|
6
|
-
import
|
|
7
|
-
|
|
8
|
-
makeIndexType,
|
|
9
|
-
AdapterGuesser,
|
|
10
|
-
getFileName,
|
|
11
|
-
} from '@jbrowse/core/util/tracks'
|
|
12
|
-
import { configSchema as gff3AdapterConfigSchema } from './Gff3Adapter'
|
|
3
|
+
|
|
4
|
+
import Gff3TabixAdapterF from './Gff3TabixAdapter'
|
|
5
|
+
import Gff3AdapterF from './Gff3Adapter'
|
|
6
|
+
import GuessGff3F from './GuessGff3'
|
|
13
7
|
|
|
14
8
|
export default class extends Plugin {
|
|
15
9
|
name = 'GFF3Plugin'
|
|
16
10
|
|
|
17
11
|
install(pluginManager: PluginManager) {
|
|
18
|
-
pluginManager
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
name: 'Gff3TabixAdapter',
|
|
22
|
-
configSchema: gff3TabixAdapterConfigSchema,
|
|
23
|
-
getAdapterClass: () =>
|
|
24
|
-
import('./Gff3TabixAdapter/Gff3TabixAdapter').then(r => r.default),
|
|
25
|
-
}),
|
|
26
|
-
)
|
|
27
|
-
pluginManager.addToExtensionPoint(
|
|
28
|
-
'Core-guessAdapterForLocation',
|
|
29
|
-
(adapterGuesser: AdapterGuesser) => {
|
|
30
|
-
return (
|
|
31
|
-
file: FileLocation,
|
|
32
|
-
index?: FileLocation,
|
|
33
|
-
adapterHint?: string,
|
|
34
|
-
) => {
|
|
35
|
-
const regexGuess = /\.gff3?\.b?gz$/i
|
|
36
|
-
const adapterName = 'Gff3TabixAdapter'
|
|
37
|
-
const fileName = getFileName(file)
|
|
38
|
-
const indexName = index && getFileName(index)
|
|
39
|
-
if (regexGuess.test(fileName) || adapterHint === adapterName) {
|
|
40
|
-
return {
|
|
41
|
-
type: adapterName,
|
|
42
|
-
bamLocation: file,
|
|
43
|
-
gffGzLocation: file,
|
|
44
|
-
index: {
|
|
45
|
-
location: index || makeIndex(file, '.tbi'),
|
|
46
|
-
indexType: makeIndexType(indexName, 'CSI', 'TBI'),
|
|
47
|
-
},
|
|
48
|
-
}
|
|
49
|
-
}
|
|
50
|
-
return adapterGuesser(file, index, adapterHint)
|
|
51
|
-
}
|
|
52
|
-
},
|
|
53
|
-
)
|
|
54
|
-
pluginManager.addAdapterType(
|
|
55
|
-
() =>
|
|
56
|
-
new AdapterType({
|
|
57
|
-
name: 'Gff3Adapter',
|
|
58
|
-
configSchema: gff3AdapterConfigSchema,
|
|
59
|
-
getAdapterClass: () =>
|
|
60
|
-
import('./Gff3Adapter/Gff3Adapter').then(r => r.default),
|
|
61
|
-
}),
|
|
62
|
-
)
|
|
63
|
-
pluginManager.addToExtensionPoint(
|
|
64
|
-
'Core-guessAdapterForLocation',
|
|
65
|
-
(adapterGuesser: AdapterGuesser) => {
|
|
66
|
-
return (
|
|
67
|
-
file: FileLocation,
|
|
68
|
-
index?: FileLocation,
|
|
69
|
-
adapterHint?: string,
|
|
70
|
-
) => {
|
|
71
|
-
const regexGuess = /\.gff3?$/i
|
|
72
|
-
const adapterName = 'Gff3Adapter'
|
|
73
|
-
const fileName = getFileName(file)
|
|
74
|
-
const obj = {
|
|
75
|
-
type: adapterName,
|
|
76
|
-
gffLocation: file,
|
|
77
|
-
}
|
|
78
|
-
if (regexGuess.test(fileName) && !adapterHint) {
|
|
79
|
-
return obj
|
|
80
|
-
} else if (adapterHint === adapterName) {
|
|
81
|
-
return obj
|
|
82
|
-
}
|
|
83
|
-
return adapterGuesser(file, index, adapterHint)
|
|
84
|
-
}
|
|
85
|
-
},
|
|
86
|
-
)
|
|
12
|
+
Gff3TabixAdapterF(pluginManager)
|
|
13
|
+
Gff3AdapterF(pluginManager)
|
|
14
|
+
GuessGff3F(pluginManager)
|
|
87
15
|
}
|
|
88
16
|
}
|