@gmod/bam 1.1.8 → 1.1.9
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/CHANGELOG.md +8 -0
- package/README.md +2 -3
- package/dist/bai.d.ts +2 -0
- package/dist/bai.js +300 -548
- package/dist/bai.js.map +1 -0
- package/dist/bamFile.d.ts +4 -6
- package/dist/bamFile.js +675 -1203
- package/dist/bamFile.js.map +1 -0
- package/dist/chunk.js +34 -69
- package/dist/chunk.js.map +1 -0
- package/dist/constants.js +27 -35
- package/dist/constants.js.map +1 -0
- package/dist/csi.js +317 -515
- package/dist/csi.js.map +1 -0
- package/dist/errors.js +64 -120
- package/dist/errors.js.map +1 -0
- package/dist/htsget.js +275 -396
- package/dist/htsget.js.map +1 -0
- package/dist/index.js +16 -54
- package/dist/index.js.map +1 -0
- package/dist/indexFile.d.ts +1 -2
- package/dist/indexFile.js +77 -163
- package/dist/indexFile.js.map +1 -0
- package/dist/record.js +496 -707
- package/dist/record.js.map +1 -0
- package/dist/sam.js +16 -49
- package/dist/sam.js.map +1 -0
- package/dist/util.d.ts +0 -1
- package/dist/util.js +115 -126
- package/dist/util.js.map +1 -0
- package/dist/virtualOffset.js +44 -77
- package/dist/virtualOffset.js.map +1 -0
- package/esm/bai.d.ts +26 -0
- package/esm/bai.js +191 -0
- package/esm/bai.js.map +1 -0
- package/esm/bamFile.d.ts +77 -0
- package/esm/bamFile.js +388 -0
- package/esm/bamFile.js.map +1 -0
- package/esm/chunk.d.ts +18 -0
- package/esm/chunk.js +33 -0
- package/esm/chunk.js.map +1 -0
- package/esm/constants.d.ts +15 -0
- package/esm/constants.js +27 -0
- package/esm/constants.js.map +1 -0
- package/esm/csi.d.ts +35 -0
- package/esm/csi.js +209 -0
- package/esm/csi.js.map +1 -0
- package/esm/errors.d.ts +23 -0
- package/esm/errors.js +24 -0
- package/esm/errors.js.map +1 -0
- package/esm/htsget.d.ts +33 -0
- package/esm/htsget.js +100 -0
- package/esm/htsget.js.map +1 -0
- package/esm/index.d.ts +6 -0
- package/esm/index.js +7 -0
- package/esm/index.js.map +1 -0
- package/esm/indexFile.d.ts +27 -0
- package/esm/indexFile.js +27 -0
- package/esm/indexFile.js.map +1 -0
- package/esm/record.d.ts +88 -0
- package/esm/record.js +534 -0
- package/esm/record.js.map +1 -0
- package/esm/sam.d.ts +7 -0
- package/esm/sam.js +16 -0
- package/esm/sam.js.map +1 -0
- package/esm/util.d.ts +35 -0
- package/esm/util.js +92 -0
- package/esm/util.js.map +1 -0
- package/esm/virtualOffset.d.ts +10 -0
- package/esm/virtualOffset.js +37 -0
- package/esm/virtualOffset.js.map +1 -0
- package/package.json +21 -29
- package/dist/declare.d.js +0 -2
package/dist/htsget.js
CHANGED
|
@@ -1,406 +1,285 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
|
|
3
|
-
var
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
|
|
9
|
-
|
|
10
|
-
|
|
2
|
+
var __extends = (this && this.__extends) || (function () {
|
|
3
|
+
var extendStatics = function (d, b) {
|
|
4
|
+
extendStatics = Object.setPrototypeOf ||
|
|
5
|
+
({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
|
|
6
|
+
function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
|
|
7
|
+
return extendStatics(d, b);
|
|
8
|
+
};
|
|
9
|
+
return function (d, b) {
|
|
10
|
+
if (typeof b !== "function" && b !== null)
|
|
11
|
+
throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
|
|
12
|
+
extendStatics(d, b);
|
|
13
|
+
function __() { this.constructor = d; }
|
|
14
|
+
d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
|
|
15
|
+
};
|
|
16
|
+
})();
|
|
17
|
+
var __assign = (this && this.__assign) || function () {
|
|
18
|
+
__assign = Object.assign || function(t) {
|
|
19
|
+
for (var s, i = 1, n = arguments.length; i < n; i++) {
|
|
20
|
+
s = arguments[i];
|
|
21
|
+
for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p))
|
|
22
|
+
t[p] = s[p];
|
|
23
|
+
}
|
|
24
|
+
return t;
|
|
25
|
+
};
|
|
26
|
+
return __assign.apply(this, arguments);
|
|
27
|
+
};
|
|
28
|
+
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
|
|
29
|
+
if (k2 === undefined) k2 = k;
|
|
30
|
+
Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
|
|
31
|
+
}) : (function(o, m, k, k2) {
|
|
32
|
+
if (k2 === undefined) k2 = k;
|
|
33
|
+
o[k2] = m[k];
|
|
34
|
+
}));
|
|
35
|
+
var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
|
|
36
|
+
Object.defineProperty(o, "default", { enumerable: true, value: v });
|
|
37
|
+
}) : function(o, v) {
|
|
38
|
+
o["default"] = v;
|
|
11
39
|
});
|
|
12
|
-
|
|
13
|
-
|
|
14
|
-
|
|
15
|
-
var
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
var
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
var
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
35
|
-
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
50
|
-
|
|
51
|
-
|
|
52
|
-
|
|
53
|
-
|
|
54
|
-
|
|
55
|
-
var
|
|
56
|
-
|
|
57
|
-
var
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
|
|
61
|
-
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
var
|
|
68
|
-
|
|
69
|
-
var
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
40
|
+
var __importStar = (this && this.__importStar) || function (mod) {
|
|
41
|
+
if (mod && mod.__esModule) return mod;
|
|
42
|
+
var result = {};
|
|
43
|
+
if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
|
|
44
|
+
__setModuleDefault(result, mod);
|
|
45
|
+
return result;
|
|
46
|
+
};
|
|
47
|
+
var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
|
|
48
|
+
function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
|
|
49
|
+
return new (P || (P = Promise))(function (resolve, reject) {
|
|
50
|
+
function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
|
|
51
|
+
function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
|
|
52
|
+
function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
|
|
53
|
+
step((generator = generator.apply(thisArg, _arguments || [])).next());
|
|
54
|
+
});
|
|
55
|
+
};
|
|
56
|
+
var __generator = (this && this.__generator) || function (thisArg, body) {
|
|
57
|
+
var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
|
|
58
|
+
return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
|
|
59
|
+
function verb(n) { return function (v) { return step([n, v]); }; }
|
|
60
|
+
function step(op) {
|
|
61
|
+
if (f) throw new TypeError("Generator is already executing.");
|
|
62
|
+
while (_) try {
|
|
63
|
+
if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
|
|
64
|
+
if (y = 0, t) op = [op[0] & 2, t.value];
|
|
65
|
+
switch (op[0]) {
|
|
66
|
+
case 0: case 1: t = op; break;
|
|
67
|
+
case 4: _.label++; return { value: op[1], done: false };
|
|
68
|
+
case 5: _.label++; y = op[1]; op = [0]; continue;
|
|
69
|
+
case 7: op = _.ops.pop(); _.trys.pop(); continue;
|
|
70
|
+
default:
|
|
71
|
+
if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
|
|
72
|
+
if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
|
|
73
|
+
if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
|
|
74
|
+
if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
|
|
75
|
+
if (t[2]) _.ops.pop();
|
|
76
|
+
_.trys.pop(); continue;
|
|
77
|
+
}
|
|
78
|
+
op = body.call(thisArg, _);
|
|
79
|
+
} catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
|
|
80
|
+
if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
|
|
81
|
+
}
|
|
82
|
+
};
|
|
83
|
+
var __rest = (this && this.__rest) || function (s, e) {
|
|
84
|
+
var t = {};
|
|
85
|
+
for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
|
|
86
|
+
t[p] = s[p];
|
|
87
|
+
if (s != null && typeof Object.getOwnPropertySymbols === "function")
|
|
88
|
+
for (var i = 0, p = Object.getOwnPropertySymbols(s); i < p.length; i++) {
|
|
89
|
+
if (e.indexOf(p[i]) < 0 && Object.prototype.propertyIsEnumerable.call(s, p[i]))
|
|
90
|
+
t[p[i]] = s[p[i]];
|
|
91
|
+
}
|
|
92
|
+
return t;
|
|
93
|
+
};
|
|
94
|
+
var __await = (this && this.__await) || function (v) { return this instanceof __await ? (this.v = v, this) : new __await(v); }
|
|
95
|
+
var __asyncValues = (this && this.__asyncValues) || function (o) {
|
|
96
|
+
if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
|
|
97
|
+
var m = o[Symbol.asyncIterator], i;
|
|
98
|
+
return m ? m.call(o) : (o = typeof __values === "function" ? __values(o) : o[Symbol.iterator](), i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i);
|
|
99
|
+
function verb(n) { i[n] = o[n] && function (v) { return new Promise(function (resolve, reject) { v = o[n](v), settle(resolve, reject, v.done, v.value); }); }; }
|
|
100
|
+
function settle(resolve, reject, d, v) { Promise.resolve(v).then(function(v) { resolve({ value: v, done: d }); }, reject); }
|
|
101
|
+
};
|
|
102
|
+
var __asyncDelegator = (this && this.__asyncDelegator) || function (o) {
|
|
103
|
+
var i, p;
|
|
104
|
+
return i = {}, verb("next"), verb("throw", function (e) { throw e; }), verb("return"), i[Symbol.iterator] = function () { return this; }, i;
|
|
105
|
+
function verb(n, f) { i[n] = o[n] ? function (v) { return (p = !p) ? { value: __await(o[n](v)), done: n === "return" } : f ? f(v) : v; } : f; }
|
|
106
|
+
};
|
|
107
|
+
var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _arguments, generator) {
|
|
108
|
+
if (!Symbol.asyncIterator) throw new TypeError("Symbol.asyncIterator is not defined.");
|
|
109
|
+
var g = generator.apply(thisArg, _arguments || []), i, q = [];
|
|
110
|
+
return i = {}, verb("next"), verb("throw"), verb("return"), i[Symbol.asyncIterator] = function () { return this; }, i;
|
|
111
|
+
function verb(n) { if (g[n]) i[n] = function (v) { return new Promise(function (a, b) { q.push([n, v, a, b]) > 1 || resume(n, v); }); }; }
|
|
112
|
+
function resume(n, v) { try { step(g[n](v)); } catch (e) { settle(q[0][3], e); } }
|
|
113
|
+
function step(r) { r.value instanceof __await ? Promise.resolve(r.value.v).then(fulfill, reject) : settle(q[0][2], r); }
|
|
114
|
+
function fulfill(value) { resume("next", value); }
|
|
115
|
+
function reject(value) { resume("throw", value); }
|
|
116
|
+
function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }
|
|
117
|
+
};
|
|
118
|
+
var __values = (this && this.__values) || function(o) {
|
|
119
|
+
var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
|
|
120
|
+
if (m) return m.call(o);
|
|
121
|
+
if (o && typeof o.length === "number") return {
|
|
122
|
+
next: function () {
|
|
123
|
+
if (o && i >= o.length) o = void 0;
|
|
124
|
+
return { value: o && o[i++], done: !o };
|
|
125
|
+
}
|
|
126
|
+
};
|
|
127
|
+
throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
|
|
128
|
+
};
|
|
129
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
130
|
+
var bamFile_1 = __importStar(require("./bamFile"));
|
|
73
131
|
require("cross-fetch/polyfill");
|
|
74
|
-
|
|
75
|
-
var
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
|
|
80
|
-
|
|
81
|
-
|
|
82
|
-
|
|
83
|
-
|
|
84
|
-
|
|
85
|
-
|
|
86
|
-
|
|
87
|
-
|
|
88
|
-
|
|
132
|
+
var bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
133
|
+
var sam_1 = require("./sam");
|
|
134
|
+
function concat(arr, opts) {
|
|
135
|
+
return __awaiter(this, void 0, void 0, function () {
|
|
136
|
+
var res, _a, _b;
|
|
137
|
+
var _this = this;
|
|
138
|
+
return __generator(this, function (_c) {
|
|
139
|
+
switch (_c.label) {
|
|
140
|
+
case 0: return [4 /*yield*/, Promise.all(arr.map(function (chunk) { return __awaiter(_this, void 0, void 0, function () {
|
|
141
|
+
var url, headers, referer, rest, res_1, _a, _b;
|
|
142
|
+
return __generator(this, function (_c) {
|
|
143
|
+
switch (_c.label) {
|
|
144
|
+
case 0:
|
|
145
|
+
url = chunk.url, headers = chunk.headers;
|
|
146
|
+
if (!url.startsWith('data:')) return [3 /*break*/, 1];
|
|
147
|
+
return [2 /*return*/, Buffer.from(url.split(',')[1], 'base64')];
|
|
148
|
+
case 1:
|
|
149
|
+
referer = headers.referer, rest = __rest(headers, ["referer"]);
|
|
150
|
+
return [4 /*yield*/, fetch(url, __assign(__assign({}, opts), { headers: __assign(__assign({}, opts.headers), rest) }))];
|
|
151
|
+
case 2:
|
|
152
|
+
res_1 = _c.sent();
|
|
153
|
+
if (!res_1.ok) {
|
|
154
|
+
throw new Error("Failed to fetch ".concat(res_1.statusText));
|
|
155
|
+
}
|
|
156
|
+
_b = (_a = Buffer).from;
|
|
157
|
+
return [4 /*yield*/, res_1.arrayBuffer()];
|
|
158
|
+
case 3: return [2 /*return*/, _b.apply(_a, [_c.sent()])];
|
|
159
|
+
}
|
|
160
|
+
});
|
|
161
|
+
}); }))];
|
|
162
|
+
case 1:
|
|
163
|
+
res = _c.sent();
|
|
164
|
+
_b = (_a = Buffer).concat;
|
|
165
|
+
return [4 /*yield*/, Promise.all(res.map(function (elt) { return (0, bgzf_filehandle_1.unzip)(elt); }))];
|
|
166
|
+
case 2: return [2 /*return*/, _b.apply(_a, [_c.sent()])];
|
|
167
|
+
}
|
|
168
|
+
});
|
|
169
|
+
});
|
|
89
170
|
}
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
|
|
93
|
-
|
|
94
|
-
|
|
95
|
-
|
|
96
|
-
|
|
97
|
-
|
|
98
|
-
|
|
99
|
-
|
|
100
|
-
|
|
101
|
-
|
|
102
|
-
|
|
103
|
-
|
|
104
|
-
|
|
105
|
-
|
|
106
|
-
|
|
107
|
-
|
|
108
|
-
|
|
109
|
-
|
|
110
|
-
|
|
111
|
-
|
|
171
|
+
var HtsgetFile = /** @class */ (function (_super) {
|
|
172
|
+
__extends(HtsgetFile, _super);
|
|
173
|
+
function HtsgetFile(args) {
|
|
174
|
+
var _this =
|
|
175
|
+
// @ts-ignore override bam defaults
|
|
176
|
+
_super.call(this, { bamFilehandle: '?', baiFilehandle: '?' }) || this;
|
|
177
|
+
_this.baseUrl = args.baseUrl;
|
|
178
|
+
_this.trackId = args.trackId;
|
|
179
|
+
return _this;
|
|
180
|
+
}
|
|
181
|
+
HtsgetFile.prototype.streamRecordsForRange = function (chr, min, max, opts) {
|
|
182
|
+
if (opts === void 0) { opts = {
|
|
183
|
+
viewAsPairs: false,
|
|
184
|
+
pairAcrossChr: false,
|
|
185
|
+
maxInsertSize: 200000,
|
|
186
|
+
}; }
|
|
187
|
+
return __asyncGenerator(this, arguments, function streamRecordsForRange_1() {
|
|
188
|
+
var base, url, chrId, result, data, uncba, chunk;
|
|
189
|
+
return __generator(this, function (_a) {
|
|
190
|
+
switch (_a.label) {
|
|
191
|
+
case 0:
|
|
192
|
+
base = "".concat(this.baseUrl, "/").concat(this.trackId);
|
|
193
|
+
url = "".concat(base, "?referenceName=").concat(chr, "&start=").concat(min, "&end=").concat(max, "&format=BAM");
|
|
194
|
+
chrId = this.chrToIndex && this.chrToIndex[chr];
|
|
195
|
+
return [4 /*yield*/, __await(fetch(url, __assign({}, opts)))];
|
|
196
|
+
case 1:
|
|
197
|
+
result = _a.sent();
|
|
198
|
+
if (!result.ok) {
|
|
199
|
+
throw new Error(result.statusText);
|
|
112
200
|
}
|
|
113
|
-
|
|
114
|
-
|
|
115
|
-
|
|
116
|
-
|
|
117
|
-
|
|
118
|
-
|
|
119
|
-
|
|
120
|
-
|
|
121
|
-
|
|
122
|
-
|
|
123
|
-
|
|
124
|
-
|
|
125
|
-
|
|
126
|
-
|
|
127
|
-
|
|
128
|
-
|
|
129
|
-
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
throw new Error("Failed to fetch ".concat(_res.statusText));
|
|
135
|
-
|
|
136
|
-
case 11:
|
|
137
|
-
_context15.t0 = Buffer;
|
|
138
|
-
_context15.next = 14;
|
|
139
|
-
return _res.arrayBuffer();
|
|
140
|
-
|
|
141
|
-
case 14:
|
|
142
|
-
_context15.t1 = _context15.sent;
|
|
143
|
-
return _context15.abrupt("return", _context15.t0.from.call(_context15.t0, _context15.t1));
|
|
144
|
-
|
|
145
|
-
case 16:
|
|
146
|
-
case "end":
|
|
147
|
-
return _context15.stop();
|
|
148
|
-
}
|
|
149
|
-
}
|
|
150
|
-
}, _callee4);
|
|
151
|
-
}));
|
|
152
|
-
|
|
153
|
-
return function (_x4) {
|
|
154
|
-
return _ref.apply(this, arguments);
|
|
155
|
-
};
|
|
156
|
-
}()));
|
|
157
|
-
|
|
158
|
-
case 2:
|
|
159
|
-
res = _context16.sent;
|
|
160
|
-
_context16.t0 = (0, _concat2.default)(Buffer);
|
|
161
|
-
_context16.t1 = Buffer;
|
|
162
|
-
_context16.next = 7;
|
|
163
|
-
return _promise.default.all((0, _map.default)(res).call(res, function (elt) {
|
|
164
|
-
return (0, _bgzfFilehandle.unzip)(elt);
|
|
165
|
-
}));
|
|
166
|
-
|
|
167
|
-
case 7:
|
|
168
|
-
_context16.t2 = _context16.sent;
|
|
169
|
-
return _context16.abrupt("return", _context16.t0.call.call(_context16.t0, _context16.t1, _context16.t2));
|
|
170
|
-
|
|
171
|
-
case 9:
|
|
172
|
-
case "end":
|
|
173
|
-
return _context16.stop();
|
|
174
|
-
}
|
|
175
|
-
}
|
|
176
|
-
}, _callee5);
|
|
177
|
-
}));
|
|
178
|
-
return _concat.apply(this, arguments);
|
|
179
|
-
}
|
|
180
|
-
|
|
181
|
-
var HtsgetFile = /*#__PURE__*/function (_BamFile) {
|
|
182
|
-
(0, _inherits2.default)(HtsgetFile, _BamFile);
|
|
183
|
-
|
|
184
|
-
var _super = _createSuper(HtsgetFile);
|
|
185
|
-
|
|
186
|
-
function HtsgetFile(args) {
|
|
187
|
-
var _this2;
|
|
188
|
-
|
|
189
|
-
(0, _classCallCheck2.default)(this, HtsgetFile);
|
|
190
|
-
// @ts-ignore override bam defaults
|
|
191
|
-
_this2 = _super.call(this, {
|
|
192
|
-
bamFilehandle: '?',
|
|
193
|
-
baiFilehandle: '?'
|
|
194
|
-
});
|
|
195
|
-
(0, _defineProperty3.default)((0, _assertThisInitialized2.default)(_this2), "baseUrl", void 0);
|
|
196
|
-
(0, _defineProperty3.default)((0, _assertThisInitialized2.default)(_this2), "trackId", void 0);
|
|
197
|
-
_this2.baseUrl = args.baseUrl;
|
|
198
|
-
_this2.trackId = args.trackId;
|
|
199
|
-
return _this2;
|
|
200
|
-
}
|
|
201
|
-
|
|
202
|
-
(0, _createClass2.default)(HtsgetFile, [{
|
|
203
|
-
key: "streamRecordsForRange",
|
|
204
|
-
value: function streamRecordsForRange(chr, min, max) {
|
|
205
|
-
var _this = this;
|
|
206
|
-
|
|
207
|
-
var opts = arguments.length > 3 && arguments[3] !== undefined ? arguments[3] : {
|
|
208
|
-
viewAsPairs: false,
|
|
209
|
-
pairAcrossChr: false,
|
|
210
|
-
maxInsertSize: 200000
|
|
211
|
-
};
|
|
212
|
-
return (0, _wrapAsyncGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
|
|
213
|
-
var _context, _context2, _context3, _context4, _context5;
|
|
214
|
-
|
|
215
|
-
var base, url, chrId, result, data, uncba, chunk;
|
|
216
|
-
return _regenerator.default.wrap(function _callee$(_context8) {
|
|
217
|
-
while (1) {
|
|
218
|
-
switch (_context8.prev = _context8.next) {
|
|
219
|
-
case 0:
|
|
220
|
-
base = (0, _concat2.default)(_context = "".concat(_this.baseUrl, "/")).call(_context, _this.trackId);
|
|
221
|
-
url = (0, _concat2.default)(_context2 = (0, _concat2.default)(_context3 = (0, _concat2.default)(_context4 = "".concat(base, "?referenceName=")).call(_context4, chr, "&start=")).call(_context3, min, "&end=")).call(_context2, max, "&format=BAM");
|
|
222
|
-
chrId = _this.chrToIndex && _this.chrToIndex[chr];
|
|
223
|
-
_context8.next = 5;
|
|
224
|
-
return (0, _awaitAsyncGenerator2.default)(fetch(url, _objectSpread({}, opts)));
|
|
225
|
-
|
|
226
|
-
case 5:
|
|
227
|
-
result = _context8.sent;
|
|
228
|
-
|
|
229
|
-
if (result.ok) {
|
|
230
|
-
_context8.next = 8;
|
|
231
|
-
break;
|
|
201
|
+
return [4 /*yield*/, __await(result.json())];
|
|
202
|
+
case 2:
|
|
203
|
+
data = _a.sent();
|
|
204
|
+
return [4 /*yield*/, __await(concat(data.htsget.urls.slice(1), opts))];
|
|
205
|
+
case 3:
|
|
206
|
+
uncba = _a.sent();
|
|
207
|
+
chunk = {
|
|
208
|
+
buffer: uncba,
|
|
209
|
+
chunk: { minv: { dataPosition: 0 } },
|
|
210
|
+
toString: function () {
|
|
211
|
+
return "".concat(chr, "_").concat(min, "_").concat(max);
|
|
212
|
+
},
|
|
213
|
+
};
|
|
214
|
+
return [5 /*yield**/, __values(__asyncDelegator(__asyncValues(this._fetchChunkFeatures(
|
|
215
|
+
// @ts-ignore
|
|
216
|
+
[chunk], chrId, min, max, opts))))];
|
|
217
|
+
case 4: return [4 /*yield*/, __await.apply(void 0, [_a.sent()])];
|
|
218
|
+
case 5:
|
|
219
|
+
_a.sent();
|
|
220
|
+
return [2 /*return*/];
|
|
232
221
|
}
|
|
233
|
-
|
|
234
|
-
|
|
235
|
-
|
|
236
|
-
|
|
237
|
-
|
|
238
|
-
|
|
239
|
-
|
|
240
|
-
|
|
241
|
-
data = _context8.sent;
|
|
242
|
-
_context8.next = 13;
|
|
243
|
-
return (0, _awaitAsyncGenerator2.default)(concat((0, _slice.default)(_context5 = data.htsget.urls).call(_context5, 1), opts));
|
|
244
|
-
|
|
245
|
-
case 13:
|
|
246
|
-
uncba = _context8.sent;
|
|
247
|
-
chunk = {
|
|
248
|
-
buffer: uncba,
|
|
249
|
-
chunk: {
|
|
250
|
-
minv: {
|
|
251
|
-
dataPosition: 0
|
|
252
|
-
}
|
|
253
|
-
},
|
|
254
|
-
toString: function toString() {
|
|
255
|
-
var _context6, _context7;
|
|
256
|
-
|
|
257
|
-
return (0, _concat2.default)(_context6 = (0, _concat2.default)(_context7 = "".concat(chr, "_")).call(_context7, min, "_")).call(_context6, max);
|
|
258
|
-
}
|
|
259
|
-
};
|
|
260
|
-
return _context8.delegateYield((0, _asyncGeneratorDelegate2.default)((0, _asyncIterator2.default)(_this._fetchChunkFeatures( // @ts-ignore
|
|
261
|
-
[chunk], chrId, min, max, opts)), _awaitAsyncGenerator2.default), "t0", 16);
|
|
262
|
-
|
|
263
|
-
case 16:
|
|
264
|
-
case "end":
|
|
265
|
-
return _context8.stop();
|
|
266
|
-
}
|
|
267
|
-
}
|
|
268
|
-
}, _callee);
|
|
269
|
-
}))();
|
|
270
|
-
} //@ts-ignore
|
|
271
|
-
|
|
272
|
-
}, {
|
|
273
|
-
key: "_readChunk",
|
|
274
|
-
value: function () {
|
|
275
|
-
var _readChunk2 = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee2(params) {
|
|
276
|
-
var chunk, buffer, c2;
|
|
277
|
-
return _regenerator.default.wrap(function _callee2$(_context9) {
|
|
278
|
-
while (1) {
|
|
279
|
-
switch (_context9.prev = _context9.next) {
|
|
280
|
-
case 0:
|
|
222
|
+
});
|
|
223
|
+
});
|
|
224
|
+
};
|
|
225
|
+
//@ts-ignore
|
|
226
|
+
HtsgetFile.prototype._readChunk = function (params) {
|
|
227
|
+
return __awaiter(this, void 0, void 0, function () {
|
|
228
|
+
var chunk, buffer, c2;
|
|
229
|
+
return __generator(this, function (_a) {
|
|
281
230
|
chunk = params.chunk;
|
|
282
231
|
buffer = chunk.buffer, c2 = chunk.chunk;
|
|
283
|
-
return
|
|
284
|
-
|
|
285
|
-
|
|
286
|
-
|
|
287
|
-
|
|
288
|
-
|
|
289
|
-
|
|
290
|
-
|
|
291
|
-
|
|
292
|
-
|
|
293
|
-
|
|
294
|
-
|
|
295
|
-
|
|
296
|
-
|
|
297
|
-
|
|
298
|
-
|
|
299
|
-
|
|
300
|
-
|
|
301
|
-
|
|
302
|
-
|
|
303
|
-
|
|
304
|
-
|
|
305
|
-
|
|
306
|
-
|
|
307
|
-
|
|
308
|
-
|
|
309
|
-
|
|
310
|
-
|
|
311
|
-
|
|
312
|
-
|
|
313
|
-
|
|
314
|
-
|
|
315
|
-
|
|
316
|
-
|
|
317
|
-
|
|
318
|
-
|
|
319
|
-
|
|
320
|
-
|
|
321
|
-
|
|
322
|
-
|
|
323
|
-
|
|
324
|
-
|
|
325
|
-
|
|
326
|
-
|
|
327
|
-
|
|
328
|
-
|
|
329
|
-
return fetch(url, opts);
|
|
330
|
-
|
|
331
|
-
case 4:
|
|
332
|
-
result = _context12.sent;
|
|
333
|
-
|
|
334
|
-
if (result.ok) {
|
|
335
|
-
_context12.next = 7;
|
|
336
|
-
break;
|
|
337
|
-
}
|
|
338
|
-
|
|
339
|
-
throw new Error("Failed to fetch ".concat(result.statusText));
|
|
340
|
-
|
|
341
|
-
case 7:
|
|
342
|
-
_context12.next = 9;
|
|
343
|
-
return result.json();
|
|
344
|
-
|
|
345
|
-
case 9:
|
|
346
|
-
data = _context12.sent;
|
|
347
|
-
_context12.next = 12;
|
|
348
|
-
return concat(data.htsget.urls, opts);
|
|
349
|
-
|
|
350
|
-
case 12:
|
|
351
|
-
uncba = _context12.sent;
|
|
352
|
-
|
|
353
|
-
if (!(uncba.readInt32LE(0) !== _bamFile.BAM_MAGIC)) {
|
|
354
|
-
_context12.next = 15;
|
|
355
|
-
break;
|
|
232
|
+
return [2 /*return*/, { data: buffer, cpositions: null, dpositions: null, chunk: c2 }];
|
|
233
|
+
});
|
|
234
|
+
});
|
|
235
|
+
};
|
|
236
|
+
HtsgetFile.prototype.getHeader = function (opts) {
|
|
237
|
+
if (opts === void 0) { opts = {}; }
|
|
238
|
+
return __awaiter(this, void 0, void 0, function () {
|
|
239
|
+
var url, result, data, uncba, headLen, headerText, samHeader, idToName, nameToId, sqLines;
|
|
240
|
+
return __generator(this, function (_a) {
|
|
241
|
+
switch (_a.label) {
|
|
242
|
+
case 0:
|
|
243
|
+
url = "".concat(this.baseUrl, "/").concat(this.trackId, "?referenceName=na&class=header");
|
|
244
|
+
return [4 /*yield*/, fetch(url, opts)];
|
|
245
|
+
case 1:
|
|
246
|
+
result = _a.sent();
|
|
247
|
+
if (!result.ok) {
|
|
248
|
+
throw new Error("Failed to fetch ".concat(result.statusText));
|
|
249
|
+
}
|
|
250
|
+
return [4 /*yield*/, result.json()];
|
|
251
|
+
case 2:
|
|
252
|
+
data = _a.sent();
|
|
253
|
+
return [4 /*yield*/, concat(data.htsget.urls, opts)];
|
|
254
|
+
case 3:
|
|
255
|
+
uncba = _a.sent();
|
|
256
|
+
if (uncba.readInt32LE(0) !== bamFile_1.BAM_MAGIC) {
|
|
257
|
+
throw new Error('Not a BAM file');
|
|
258
|
+
}
|
|
259
|
+
headLen = uncba.readInt32LE(4);
|
|
260
|
+
headerText = uncba.toString('utf8', 8, 8 + headLen);
|
|
261
|
+
samHeader = (0, sam_1.parseHeaderText)(headerText);
|
|
262
|
+
idToName = [];
|
|
263
|
+
nameToId = {};
|
|
264
|
+
sqLines = samHeader.filter(function (l) { return l.tag === 'SQ'; });
|
|
265
|
+
sqLines.forEach(function (sqLine, refId) {
|
|
266
|
+
sqLine.data.forEach(function (item) {
|
|
267
|
+
if (item.tag === 'SN') {
|
|
268
|
+
// this is the ref name
|
|
269
|
+
var refName = item.value;
|
|
270
|
+
nameToId[refName] = refId;
|
|
271
|
+
idToName[refId] = refName;
|
|
272
|
+
}
|
|
273
|
+
});
|
|
274
|
+
});
|
|
275
|
+
this.chrToIndex = nameToId;
|
|
276
|
+
this.indexToChr = idToName;
|
|
277
|
+
return [2 /*return*/, samHeader];
|
|
356
278
|
}
|
|
357
|
-
|
|
358
|
-
|
|
359
|
-
|
|
360
|
-
|
|
361
|
-
|
|
362
|
-
headerText = uncba.toString('utf8', 8, 8 + headLen);
|
|
363
|
-
samHeader = (0, _sam.parseHeaderText)(headerText); // use the @SQ lines in the header to figure out the
|
|
364
|
-
// mapping between ref ref ID numbers and names
|
|
365
|
-
|
|
366
|
-
idToName = [];
|
|
367
|
-
nameToId = {};
|
|
368
|
-
sqLines = (0, _filter.default)(samHeader).call(samHeader, function (l) {
|
|
369
|
-
return l.tag === 'SQ';
|
|
370
|
-
});
|
|
371
|
-
(0, _forEach.default)(sqLines).call(sqLines, function (sqLine, refId) {
|
|
372
|
-
var _context11;
|
|
373
|
-
|
|
374
|
-
(0, _forEach.default)(_context11 = sqLine.data).call(_context11, function (item) {
|
|
375
|
-
if (item.tag === 'SN') {
|
|
376
|
-
// this is the ref name
|
|
377
|
-
var refName = item.value;
|
|
378
|
-
nameToId[refName] = refId;
|
|
379
|
-
idToName[refId] = refName;
|
|
380
|
-
}
|
|
381
|
-
});
|
|
382
|
-
});
|
|
383
|
-
this.chrToIndex = nameToId;
|
|
384
|
-
this.indexToChr = idToName;
|
|
385
|
-
return _context12.abrupt("return", samHeader);
|
|
386
|
-
|
|
387
|
-
case 25:
|
|
388
|
-
case "end":
|
|
389
|
-
return _context12.stop();
|
|
390
|
-
}
|
|
391
|
-
}
|
|
392
|
-
}, _callee3, this);
|
|
393
|
-
}));
|
|
394
|
-
|
|
395
|
-
function getHeader() {
|
|
396
|
-
return _getHeader.apply(this, arguments);
|
|
397
|
-
}
|
|
398
|
-
|
|
399
|
-
return getHeader;
|
|
400
|
-
}()
|
|
401
|
-
}]);
|
|
402
|
-
return HtsgetFile;
|
|
403
|
-
}(_bamFile.default);
|
|
404
|
-
|
|
279
|
+
});
|
|
280
|
+
});
|
|
281
|
+
};
|
|
282
|
+
return HtsgetFile;
|
|
283
|
+
}(bamFile_1.default));
|
|
405
284
|
exports.default = HtsgetFile;
|
|
406
|
-
//# sourceMappingURL=data:application/json;charset=utf-8;base64,{"version":3,"sources":["../src/htsget.ts"],"names":["concat","arr","opts","all","chunk","url","headers","Buffer","from","split","referer","rest","fetch","res","ok","Error","statusText","arrayBuffer","elt","HtsgetFile","args","bamFilehandle","baiFilehandle","baseUrl","trackId","chr","min","max","viewAsPairs","pairAcrossChr","maxInsertSize","base","chrId","chrToIndex","result","json","data","htsget","urls","uncba","buffer","minv","dataPosition","toString","_fetchChunkFeatures","params","c2","cpositions","dpositions","readInt32LE","BAM_MAGIC","headLen","headerText","samHeader","idToName","nameToId","sqLines","l","tag","sqLine","refId","item","refName","value","indexToChr","BamFile"],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA;;AACA;;AAEA;;AACA;;;;;;;;;;SAWeA,M;;;;;oFAAf,kBAAsBC,GAAtB,EAA8CC,IAA9C;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,mBACoB,iBAAQC,GAAR,CAChB,kBAAAF,GAAG,MAAH,CAAAA,GAAG;AAAA,iGAAK,kBAAOG,KAAP;AAAA;;AAAA;AAAA;AAAA;AAAA;AACEC,wBAAAA,GADF,GACmBD,KADnB,CACEC,GADF,EACOC,OADP,GACmBF,KADnB,CACOE,OADP;;AAAA,6BAEF,yBAAAD,GAAG,MAAH,CAAAA,GAAG,EAAY,OAAZ,CAFD;AAAA;AAAA;AAAA;;AAAA,2DAGGE,MAAM,CAACC,IAAP,CAAYH,GAAG,CAACI,KAAJ,CAAU,GAAV,EAAe,CAAf,CAAZ,EAA+B,QAA/B,CAHH;;AAAA;AAKJ;AACA;AACA;AACQC,wBAAAA,OARJ,GAQyBJ,OARzB,CAQII,OARJ,EAQgBC,IARhB,0CAQyBL,OARzB;AAAA;AAAA,+BAScM,KAAK,CAACP,GAAD,kCAAWH,IAAX;AAAiBI,0BAAAA,OAAO,kCAAOJ,IAAI,CAACI,OAAZ,GAAwBK,IAAxB;AAAxB,2BATnB;;AAAA;AASEE,wBAAAA,IATF;;AAAA,4BAUCA,IAAG,CAACC,EAVL;AAAA;AAAA;AAAA;;AAAA,8BAWI,IAAIC,KAAJ,2BAA6BF,IAAG,CAACG,UAAjC,EAXJ;;AAAA;AAAA,wCAaGT,MAbH;AAAA;AAAA,+BAaqBM,IAAG,CAACI,WAAJ,EAbrB;;AAAA;AAAA;AAAA,yEAaUT,IAbV;;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,eAAL;;AAAA;AAAA;AAAA;AAAA,gBADa,CADpB;;AAAA;AACQK,YAAAA,GADR;AAAA,kDAoBSN,MApBT;AAAA,4BAoBSA,MApBT;AAAA;AAAA,mBAoB6B,iBAAQJ,GAAR,CAAY,kBAAAU,GAAG,MAAH,CAAAA,GAAG,EAAK,UAAAK,GAAG;AAAA,qBAAI,2BAAMA,GAAN,CAAJ;AAAA,aAAR,CAAf,CApB7B;;AAAA;AAAA;AAAA;;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA,G;;;;IAuBqBC,U;;;;;AAKnB,sBAAYC,IAAZ,EAAwD;AAAA;;AAAA;AACtD;AACA,+BAAM;AAAEC,MAAAA,aAAa,EAAE,GAAjB;AAAsBC,MAAAA,aAAa,EAAE;AAArC,KAAN;AAFsD;AAAA;AAGtD,WAAKC,OAAL,GAAeH,IAAI,CAACG,OAApB;AACA,WAAKC,OAAL,GAAeJ,IAAI,CAACI,OAApB;AAJsD;AAKvD;;;;0CAGCC,G,EACAC,G,EACAC,G,EAEA;AAAA;;AAAA,UADAzB,IACA,uEADgB;AAAE0B,QAAAA,WAAW,EAAE,KAAf;AAAsBC,QAAAA,aAAa,EAAE,KAArC;AAA4CC,QAAAA,aAAa,EAAE;AAA3D,OAChB;AAAA;AAAA;;AAAA;AAAA;AAAA;AAAA;AAAA;AACMC,gBAAAA,IADN,8CACgB,KAAI,CAACR,OADrB,uBACgC,KAAI,CAACC,OADrC;AAEMnB,gBAAAA,GAFN,mHAEe0B,IAFf,sCAEqCN,GAFrC,8BAEkDC,GAFlD,4BAE6DC,GAF7D;AAGMK,gBAAAA,KAHN,GAGc,KAAI,CAACC,UAAL,IAAmB,KAAI,CAACA,UAAL,CAAgBR,GAAhB,CAHjC;AAAA;AAAA,0DAIqBb,KAAK,CAACP,GAAD,oBAAWH,IAAX,EAJ1B;;AAAA;AAIMgC,gBAAAA,MAJN;;AAAA,oBAKKA,MAAM,CAACpB,EALZ;AAAA;AAAA;AAAA;;AAAA,sBAMQ,IAAIC,KAAJ,CAAUmB,MAAM,CAAClB,UAAjB,CANR;;AAAA;AAAA;AAAA,0DAQmBkB,MAAM,CAACC,IAAP,EARnB;;AAAA;AAQMC,gBAAAA,IARN;AAAA;AAAA,0DASoBpC,MAAM,CAAC,gCAAAoC,IAAI,CAACC,MAAL,CAAYC,IAAZ,kBAAuB,CAAvB,CAAD,EAA4BpC,IAA5B,CAT1B;;AAAA;AASMqC,gBAAAA,KATN;AAUMnC,gBAAAA,KAVN,GAUc;AACZoC,kBAAAA,MAAM,EAAED,KADI;AAEZnC,kBAAAA,KAAK,EAAE;AAAEqC,oBAAAA,IAAI,EAAE;AAAEC,sBAAAA,YAAY,EAAE;AAAhB;AAAR,mBAFK;AAGZC,kBAAAA,QAHY,sBAGD;AAAA;;AACT,yGAAUlB,GAAV,wBAAiBC,GAAjB,wBAAwBC,GAAxB;AACD;AALW,iBAVd;AAkBA,kHAAO,KAAI,CAACiB,mBAAL,EACL;AACA,iBAACxC,KAAD,CAFK,EAGL4B,KAHK,EAILN,GAJK,EAKLC,GALK,EAMLzB,IANK,CAAP;;AAlBA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AA0BD,K,CAED;;;;;kHACiB2C,M;;;;;;AACPzC,gBAAAA,K,GAAUyC,M,CAAVzC,K;AACAoC,gBAAAA,M,GAAsBpC,K,CAAtBoC,M,EAAeM,E,GAAO1C,K,CAAdA,K;kDACT;AAAEgC,kBAAAA,IAAI,EAAEI,MAAR;AAAgBO,kBAAAA,UAAU,EAAE,IAA5B;AAAkCC,kBAAAA,UAAU,EAAE,IAA9C;AAAoD5C,kBAAAA,KAAK,EAAE0C;AAA3D,iB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAGO5C,gBAAAA,I,8DAAiB,E;AACzBG,gBAAAA,G,gDAAS,KAAKkB,O,yBAAW,KAAKC,O;;uBACfZ,KAAK,CAACP,GAAD,EAAMH,IAAN,C;;;AAApBgC,gBAAAA,M;;oBACDA,MAAM,CAACpB,E;;;;;sBACJ,IAAIC,KAAJ,2BAA6BmB,MAAM,CAAClB,UAApC,E;;;;uBAEWkB,MAAM,CAACC,IAAP,E;;;AAAbC,gBAAAA,I;;uBACcpC,MAAM,CAACoC,IAAI,CAACC,MAAL,CAAYC,IAAb,EAAmBpC,IAAnB,C;;;AAApBqC,gBAAAA,K;;sBAEFA,KAAK,CAACU,WAAN,CAAkB,CAAlB,MAAyBC,kB;;;;;sBACrB,IAAInC,KAAJ,CAAU,gBAAV,C;;;AAEFoC,gBAAAA,O,GAAUZ,KAAK,CAACU,WAAN,CAAkB,CAAlB,C;AAEVG,gBAAAA,U,GAAab,KAAK,CAACI,QAAN,CAAe,MAAf,EAAuB,CAAvB,EAA0B,IAAIQ,OAA9B,C;AACbE,gBAAAA,S,GAAY,0BAAgBD,UAAhB,C,EAElB;AACA;;AACME,gBAAAA,Q,GAAqB,E;AACrBC,gBAAAA,Q,GAAmC,E;AACnCC,gBAAAA,O,GAAU,qBAAAH,SAAS,MAAT,CAAAA,SAAS,EAAQ,UAACI,CAAD;AAAA,yBAAwBA,CAAC,CAACC,GAAF,KAAU,IAAlC;AAAA,iBAAR,C;AACzB,sCAAAF,OAAO,MAAP,CAAAA,OAAO,EAAS,UAACG,MAAD,EAAiCC,KAAjC,EAAmD;AAAA;;AACjE,qDAAAD,MAAM,CAACvB,IAAP,mBAAoB,UAACyB,IAAD,EAAsB;AACxC,wBAAIA,IAAI,CAACH,GAAL,KAAa,IAAjB,EAAuB;AACrB;AACA,0BAAMI,OAAO,GAAGD,IAAI,CAACE,KAArB;AACAR,sBAAAA,QAAQ,CAACO,OAAD,CAAR,GAAoBF,KAApB;AACAN,sBAAAA,QAAQ,CAACM,KAAD,CAAR,GAAkBE,OAAlB;AACD;AACF,mBAPD;AAQD,iBATM,CAAP;AAUA,qBAAK7B,UAAL,GAAkBsB,QAAlB;AACA,qBAAKS,UAAL,GAAkBV,QAAlB;mDACOD,S;;;;;;;;;;;;;;;;;;EAtF6BY,gB","sourcesContent":["import { BaseOpts, BamOpts } from './util'\nimport BamFile, { BAM_MAGIC } from './bamFile'\nimport 'cross-fetch/polyfill'\nimport Chunk from './chunk'\nimport { unzip } from '@gmod/bgzf-filehandle'\nimport { parseHeaderText } from './sam'\n\ninterface HeaderLine {\n  tag: string\n  value: string\n}\n\ninterface HtsgetChunk {\n  url: string\n  headers?: Record<string, string>\n}\nasync function concat(arr: { url: string }[], opts: Record<string, any>) {\n  const res = await Promise.all(\n    arr.map(async (chunk: HtsgetChunk) => {\n      const { url, headers } = chunk\n      if (url.startsWith('data:')) {\n        return Buffer.from(url.split(',')[1], 'base64')\n      } else {\n        //remove referer header, it is not even allowed to be specified\n        //@ts-ignore\n        //eslint-disable-next-line @typescript-eslint/no-unused-vars\n        const { referer, ...rest } = headers\n        const res = await fetch(url, { ...opts, headers: { ...opts.headers, ...rest } })\n        if (!res.ok) {\n          throw new Error(`Failed to fetch ${res.statusText}`)\n        }\n        return Buffer.from(await res.arrayBuffer())\n      }\n    }),\n  )\n\n  return Buffer.concat(await Promise.all(res.map(elt => unzip(elt))))\n}\n\nexport default class HtsgetFile extends BamFile {\n  private baseUrl: string\n\n  private trackId: string\n\n  constructor(args: { trackId: string; baseUrl: string }) {\n    // @ts-ignore override bam defaults\n    super({ bamFilehandle: '?', baiFilehandle: '?' })\n    this.baseUrl = args.baseUrl\n    this.trackId = args.trackId\n  }\n\n  async *streamRecordsForRange(\n    chr: string,\n    min: number,\n    max: number,\n    opts: BamOpts = { viewAsPairs: false, pairAcrossChr: false, maxInsertSize: 200000 },\n  ) {\n    const base = `${this.baseUrl}/${this.trackId}`\n    const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`\n    const chrId = this.chrToIndex && this.chrToIndex[chr]\n    const result = await fetch(url, { ...opts })\n    if (!result.ok) {\n      throw new Error(result.statusText)\n    }\n    const data = await result.json()\n    const uncba = await concat(data.htsget.urls.slice(1), opts)\n    const chunk = {\n      buffer: uncba,\n      chunk: { minv: { dataPosition: 0 } },\n      toString() {\n        return `${chr}_${min}_${max}`\n      },\n    }\n\n    yield* this._fetchChunkFeatures(\n      // @ts-ignore\n      [chunk],\n      chrId,\n      min,\n      max,\n      opts,\n    )\n  }\n\n  //@ts-ignore\n  async _readChunk(params: { chunk: { buffer: Buffer; chunk: Chunk }; opts: BaseOpts }) {\n    const { chunk } = params\n    const { buffer, chunk: c2 } = chunk\n    return { data: buffer, cpositions: null, dpositions: null, chunk: c2 }\n  }\n\n  async getHeader(opts: BaseOpts = {}) {\n    const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`\n    const result = await fetch(url, opts)\n    if (!result.ok) {\n      throw new Error(`Failed to fetch ${result.statusText}`)\n    }\n    const data = await result.json()\n    const uncba = await concat(data.htsget.urls, opts)\n\n    if (uncba.readInt32LE(0) !== BAM_MAGIC) {\n      throw new Error('Not a BAM file')\n    }\n    const headLen = uncba.readInt32LE(4)\n\n    const headerText = uncba.toString('utf8', 8, 8 + headLen)\n    const samHeader = parseHeaderText(headerText)\n\n    // use the @SQ lines in the header to figure out the\n    // mapping between ref ref ID numbers and names\n    const idToName: string[] = []\n    const nameToId: Record<string, number> = {}\n    const sqLines = samHeader.filter((l: { tag: string }) => l.tag === 'SQ')\n    sqLines.forEach((sqLine: { data: HeaderLine[] }, refId: number) => {\n      sqLine.data.forEach((item: HeaderLine) => {\n        if (item.tag === 'SN') {\n          // this is the ref name\n          const refName = item.value\n          nameToId[refName] = refId\n          idToName[refId] = refName\n        }\n      })\n    })\n    this.chrToIndex = nameToId\n    this.indexToChr = idToName\n    return samHeader\n  }\n}\n"]}
|
|
285
|
+
//# sourceMappingURL=htsget.js.map
|