@gmod/bam 1.1.17 → 1.1.18
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 +5 -1
- package/README.md +15 -2
- package/dist/bai.js +164 -253
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.js +331 -556
- package/dist/bamFile.js.map +1 -1
- package/dist/chunk.js +12 -14
- package/dist/chunk.js.map +1 -1
- package/dist/csi.js +145 -232
- package/dist/csi.js.map +1 -1
- package/dist/errors.js +12 -57
- package/dist/errors.js.map +1 -1
- package/dist/htsget.js +92 -206
- package/dist/htsget.js.map +1 -1
- package/dist/index.js +5 -5
- package/dist/index.js.map +1 -1
- package/dist/indexFile.js +20 -59
- package/dist/indexFile.js.map +1 -1
- package/dist/record.js +169 -172
- package/dist/record.js.map +1 -1
- package/dist/sam.js +7 -7
- package/dist/sam.js.map +1 -1
- package/dist/util.js +11 -46
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.js +13 -20
- package/dist/virtualOffset.js.map +1 -1
- package/package.json +13 -13
package/dist/csi.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"
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1
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+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gDAAuB;AACvB,2DAA6C;AAC7C,iEAA0D;AAC1D,oDAA2B;AAC3B,iCAAgF;AAEhF,4DAAmC;AAEnC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACK,SAAS,CAAC,KAAa;;YAC3B,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,EAAE,CAAA;YACpC,IAAI,CAAC,SAAS,EAAE;gBACd,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,GAAG,EAAE;gBACR,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,KAAK,EAAE;gBACT,OAAO,KAAK,CAAC,SAAS,CAAA;aACvB;YACD,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;KAAA;IAEK,QAAQ;;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;KAAA;IAED,YAAY,CAAC,KAAa,EAAE,MAAc,EAAE,SAAiB;QAC3D,IAAI,SAAS,GAAG,EAAE,EAAE;YAClB,OAAO,EAAE,CAAA;SACV;QAED,MAAM,IAAI,GAA2B,EAAE,CAAA;QACvC,IAAI,CAAC,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC5C,IAAI,CAAC,cAAc;YACjB,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACxE,IAAI,CAAC,MAAM,GACT,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAGnC,CAAC,IAAI,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACzB,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,qCAAqC,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;SACzE;QACD,IAAI,CAAC,aAAa,GAAG;YACnB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QACzE,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAC/C,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,CAAC,MAAM,CACX,IAAI,EACJ,IAAI,CAAC,eAAe,CAClB,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CACF,CAAA;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,eAAe,CAAC,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,MAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IACtB,MAAM,CAAC,IAA8B;;YACzC,MAAM,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;YACzE,MAAM,MAAM,GAAG,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAA;YAC/D,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;YAEjC,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;gBACxC,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;aACpB;iBAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;gBAC/C,IAAI,CAAC,UAAU,GAAG,CAAC,CAAA;aACpB;iBAAM;gBACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;aACrD;YAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YAC3D,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,IAAI,SAAS,EAAE;gBACb,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,EAAE,SAAS,CAAC,CAAC,CAAA;aAC7D;YACD,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;YAEjD,+CAA+C;YAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YACvC,IAAI,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;YACnC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gBACzC,MAAM,IAAA,sBAAe,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;gBAClC,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBAC9C,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;gBAC/C,IAAI,KAAK,CAAA,CAAC,iDAAiD;gBAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;oBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;oBAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;wBAC3B,yDAAyD;wBACzD,qCAAqC;wBACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;qBAClC;yBAAM;wBACL,MAAM,OAAO,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAChD,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;wBAClC,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-
return _super !== null && _super.apply(this, arguments) || this;
|
|
74
|
-
}
|
|
75
|
-
return BamArgumentError;
|
|
76
|
-
}(BamError));
|
|
30
|
+
class BamArgumentError extends BamError {
|
|
31
|
+
}
|
|
77
32
|
exports.BamArgumentError = BamArgumentError;
|
|
78
33
|
//# sourceMappingURL=errors.js.map
|
package/dist/errors.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"errors.js","sourceRoot":"","sources":["../src/errors.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"errors.js","sourceRoot":"","sources":["../src/errors.ts"],"names":[],"mappings":";;;AAAA,MAAa,QAAS,SAAQ,KAAK;CAAG;AAAtC,4BAAsC;AAEtC,4FAA4F;AAC5F,MAAa,qBAAsB,SAAQ,KAAK;CAAG;AAAnD,sDAAmD;AAEnD,0CAA0C;AAC1C,MAAa,iBAAkB,SAAQ,QAAQ;CAAG;AAAlD,8CAAkD;AAElD;;GAEG;AACH,MAAa,qBAAsB,SAAQ,iBAAiB;CAAG;AAA/D,sDAA+D;AAE/D;;GAEG;AACH,MAAa,iBAAkB,SAAQ,QAAQ;CAAG;AAAlD,8CAAkD;AAElD;;GAEG;AACH,MAAa,gBAAiB,SAAQ,QAAQ;CAAG;AAAjD,4CAAiD"}
|
package/dist/htsget.js
CHANGED
|
@@ -1,30 +1,4 @@
|
|
|
1
1
|
"use strict";
|
|
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
2
|
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
|
|
29
3
|
if (k2 === undefined) k2 = k;
|
|
30
4
|
var desc = Object.getOwnPropertyDescriptor(m, k);
|
|
@@ -57,33 +31,6 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
|
|
|
57
31
|
step((generator = generator.apply(thisArg, _arguments || [])).next());
|
|
58
32
|
});
|
|
59
33
|
};
|
|
60
|
-
var __generator = (this && this.__generator) || function (thisArg, body) {
|
|
61
|
-
var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
|
|
62
|
-
return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
|
|
63
|
-
function verb(n) { return function (v) { return step([n, v]); }; }
|
|
64
|
-
function step(op) {
|
|
65
|
-
if (f) throw new TypeError("Generator is already executing.");
|
|
66
|
-
while (_) try {
|
|
67
|
-
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;
|
|
68
|
-
if (y = 0, t) op = [op[0] & 2, t.value];
|
|
69
|
-
switch (op[0]) {
|
|
70
|
-
case 0: case 1: t = op; break;
|
|
71
|
-
case 4: _.label++; return { value: op[1], done: false };
|
|
72
|
-
case 5: _.label++; y = op[1]; op = [0]; continue;
|
|
73
|
-
case 7: op = _.ops.pop(); _.trys.pop(); continue;
|
|
74
|
-
default:
|
|
75
|
-
if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
|
|
76
|
-
if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
|
|
77
|
-
if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
|
|
78
|
-
if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
|
|
79
|
-
if (t[2]) _.ops.pop();
|
|
80
|
-
_.trys.pop(); continue;
|
|
81
|
-
}
|
|
82
|
-
op = body.call(thisArg, _);
|
|
83
|
-
} catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
|
|
84
|
-
if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
|
|
85
|
-
}
|
|
86
|
-
};
|
|
87
34
|
var __rest = (this && this.__rest) || function (s, e) {
|
|
88
35
|
var t = {};
|
|
89
36
|
for (var p in s) if (Object.prototype.hasOwnProperty.call(s, p) && e.indexOf(p) < 0)
|
|
@@ -119,171 +66,110 @@ var __asyncGenerator = (this && this.__asyncGenerator) || function (thisArg, _ar
|
|
|
119
66
|
function reject(value) { resume("throw", value); }
|
|
120
67
|
function settle(f, v) { if (f(v), q.shift(), q.length) resume(q[0][0], q[0][1]); }
|
|
121
68
|
};
|
|
122
|
-
var __values = (this && this.__values) || function(o) {
|
|
123
|
-
var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
|
|
124
|
-
if (m) return m.call(o);
|
|
125
|
-
if (o && typeof o.length === "number") return {
|
|
126
|
-
next: function () {
|
|
127
|
-
if (o && i >= o.length) o = void 0;
|
|
128
|
-
return { value: o && o[i++], done: !o };
|
|
129
|
-
}
|
|
130
|
-
};
|
|
131
|
-
throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
|
|
132
|
-
};
|
|
133
69
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
134
|
-
|
|
70
|
+
const bamFile_1 = __importStar(require("./bamFile"));
|
|
135
71
|
require("cross-fetch/polyfill");
|
|
136
|
-
|
|
137
|
-
|
|
72
|
+
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
73
|
+
const sam_1 = require("./sam");
|
|
138
74
|
function concat(arr, opts) {
|
|
139
|
-
return __awaiter(this, void 0, void 0, function () {
|
|
140
|
-
|
|
141
|
-
|
|
142
|
-
|
|
143
|
-
|
|
144
|
-
case 0: return [4 /*yield*/, Promise.all(arr.map(function (chunk) { return __awaiter(_this, void 0, void 0, function () {
|
|
145
|
-
var url, headers, referer, rest, res_1, _a, _b;
|
|
146
|
-
return __generator(this, function (_c) {
|
|
147
|
-
switch (_c.label) {
|
|
148
|
-
case 0:
|
|
149
|
-
url = chunk.url, headers = chunk.headers;
|
|
150
|
-
if (!url.startsWith('data:')) return [3 /*break*/, 1];
|
|
151
|
-
return [2 /*return*/, Buffer.from(url.split(',')[1], 'base64')];
|
|
152
|
-
case 1:
|
|
153
|
-
referer = headers.referer, rest = __rest(headers, ["referer"]);
|
|
154
|
-
return [4 /*yield*/, fetch(url, __assign(__assign({}, opts), { headers: __assign(__assign({}, opts.headers), rest) }))];
|
|
155
|
-
case 2:
|
|
156
|
-
res_1 = _c.sent();
|
|
157
|
-
if (!res_1.ok) {
|
|
158
|
-
throw new Error("Failed to fetch ".concat(res_1.statusText));
|
|
159
|
-
}
|
|
160
|
-
_b = (_a = Buffer).from;
|
|
161
|
-
return [4 /*yield*/, res_1.arrayBuffer()];
|
|
162
|
-
case 3: return [2 /*return*/, _b.apply(_a, [_c.sent()])];
|
|
163
|
-
}
|
|
164
|
-
});
|
|
165
|
-
}); }))];
|
|
166
|
-
case 1:
|
|
167
|
-
res = _c.sent();
|
|
168
|
-
_b = (_a = Buffer).concat;
|
|
169
|
-
return [4 /*yield*/, Promise.all(res.map(function (elt) { return (0, bgzf_filehandle_1.unzip)(elt); }))];
|
|
170
|
-
case 2: return [2 /*return*/, _b.apply(_a, [_c.sent()])];
|
|
75
|
+
return __awaiter(this, void 0, void 0, function* () {
|
|
76
|
+
const res = yield Promise.all(arr.map((chunk) => __awaiter(this, void 0, void 0, function* () {
|
|
77
|
+
const { url, headers } = chunk;
|
|
78
|
+
if (url.startsWith('data:')) {
|
|
79
|
+
return Buffer.from(url.split(',')[1], 'base64');
|
|
171
80
|
}
|
|
172
|
-
|
|
81
|
+
else {
|
|
82
|
+
//remove referer header, it is not even allowed to be specified
|
|
83
|
+
//@ts-ignore
|
|
84
|
+
//eslint-disable-next-line @typescript-eslint/no-unused-vars
|
|
85
|
+
const { referer } = headers, rest = __rest(headers, ["referer"]);
|
|
86
|
+
const res = yield fetch(url, Object.assign(Object.assign({}, opts), { headers: Object.assign(Object.assign({}, opts.headers), rest) }));
|
|
87
|
+
if (!res.ok) {
|
|
88
|
+
throw new Error(`Failed to fetch ${res.statusText}`);
|
|
89
|
+
}
|
|
90
|
+
return Buffer.from(yield res.arrayBuffer());
|
|
91
|
+
}
|
|
92
|
+
})));
|
|
93
|
+
return Buffer.concat(yield Promise.all(res.map(elt => (0, bgzf_filehandle_1.unzip)(elt))));
|
|
173
94
|
});
|
|
174
95
|
}
|
|
175
|
-
|
|
176
|
-
|
|
177
|
-
function HtsgetFile(args) {
|
|
178
|
-
var _this =
|
|
96
|
+
class HtsgetFile extends bamFile_1.default {
|
|
97
|
+
constructor(args) {
|
|
179
98
|
// @ts-ignore override bam defaults
|
|
180
|
-
|
|
181
|
-
|
|
182
|
-
|
|
183
|
-
return _this;
|
|
99
|
+
super({ bamFilehandle: '?', baiFilehandle: '?' });
|
|
100
|
+
this.baseUrl = args.baseUrl;
|
|
101
|
+
this.trackId = args.trackId;
|
|
184
102
|
}
|
|
185
|
-
|
|
186
|
-
|
|
187
|
-
|
|
188
|
-
|
|
189
|
-
|
|
190
|
-
|
|
191
|
-
|
|
192
|
-
|
|
193
|
-
|
|
194
|
-
|
|
195
|
-
|
|
196
|
-
|
|
197
|
-
|
|
198
|
-
|
|
199
|
-
|
|
200
|
-
|
|
201
|
-
|
|
202
|
-
|
|
203
|
-
|
|
204
|
-
|
|
205
|
-
|
|
206
|
-
|
|
207
|
-
|
|
208
|
-
|
|
209
|
-
|
|
210
|
-
uncba = _a.sent();
|
|
211
|
-
chunk = {
|
|
212
|
-
buffer: uncba,
|
|
213
|
-
chunk: { minv: { dataPosition: 0 } },
|
|
214
|
-
toString: function () {
|
|
215
|
-
return "".concat(chr, "_").concat(min, "_").concat(max);
|
|
216
|
-
},
|
|
217
|
-
};
|
|
218
|
-
return [5 /*yield**/, __values(__asyncDelegator(__asyncValues(this._fetchChunkFeatures(
|
|
219
|
-
// @ts-ignore
|
|
220
|
-
[chunk], chrId, min, max, opts))))];
|
|
221
|
-
case 4: return [4 /*yield*/, __await.apply(void 0, [_a.sent()])];
|
|
222
|
-
case 5:
|
|
223
|
-
_a.sent();
|
|
224
|
-
return [2 /*return*/];
|
|
225
|
-
}
|
|
226
|
-
});
|
|
103
|
+
streamRecordsForRange(chr, min, max, opts = {
|
|
104
|
+
viewAsPairs: false,
|
|
105
|
+
pairAcrossChr: false,
|
|
106
|
+
maxInsertSize: 200000,
|
|
107
|
+
}) {
|
|
108
|
+
return __asyncGenerator(this, arguments, function* streamRecordsForRange_1() {
|
|
109
|
+
const base = `${this.baseUrl}/${this.trackId}`;
|
|
110
|
+
const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
|
|
111
|
+
const chrId = this.chrToIndex && this.chrToIndex[chr];
|
|
112
|
+
const result = yield __await(fetch(url, Object.assign({}, opts)));
|
|
113
|
+
if (!result.ok) {
|
|
114
|
+
throw new Error(result.statusText);
|
|
115
|
+
}
|
|
116
|
+
const data = yield __await(result.json());
|
|
117
|
+
const uncba = yield __await(concat(data.htsget.urls.slice(1), opts));
|
|
118
|
+
const chunk = {
|
|
119
|
+
buffer: uncba,
|
|
120
|
+
chunk: { minv: { dataPosition: 0 } },
|
|
121
|
+
toString() {
|
|
122
|
+
return `${chr}_${min}_${max}`;
|
|
123
|
+
},
|
|
124
|
+
};
|
|
125
|
+
yield __await(yield* __asyncDelegator(__asyncValues(this._fetchChunkFeatures(
|
|
126
|
+
// @ts-ignore
|
|
127
|
+
[chunk], chrId, min, max, opts))));
|
|
227
128
|
});
|
|
228
|
-
}
|
|
129
|
+
}
|
|
229
130
|
//@ts-ignore
|
|
230
|
-
|
|
231
|
-
return __awaiter(this, void 0, void 0, function () {
|
|
232
|
-
|
|
233
|
-
|
|
234
|
-
|
|
235
|
-
buffer = chunk.buffer, c2 = chunk.chunk;
|
|
236
|
-
return [2 /*return*/, { data: buffer, cpositions: null, dpositions: null, chunk: c2 }];
|
|
237
|
-
});
|
|
131
|
+
_readChunk(params) {
|
|
132
|
+
return __awaiter(this, void 0, void 0, function* () {
|
|
133
|
+
const { chunk } = params;
|
|
134
|
+
const { buffer, chunk: c2 } = chunk;
|
|
135
|
+
return { data: buffer, cpositions: null, dpositions: null, chunk: c2 };
|
|
238
136
|
});
|
|
239
|
-
}
|
|
240
|
-
|
|
241
|
-
|
|
242
|
-
|
|
243
|
-
|
|
244
|
-
|
|
245
|
-
|
|
246
|
-
|
|
247
|
-
|
|
248
|
-
|
|
249
|
-
|
|
250
|
-
|
|
251
|
-
|
|
252
|
-
|
|
253
|
-
|
|
254
|
-
|
|
255
|
-
|
|
256
|
-
|
|
257
|
-
|
|
258
|
-
|
|
259
|
-
|
|
260
|
-
|
|
261
|
-
|
|
262
|
-
|
|
263
|
-
|
|
264
|
-
|
|
265
|
-
|
|
266
|
-
idToName =
|
|
267
|
-
|
|
268
|
-
|
|
269
|
-
sqLines.forEach(function (sqLine, refId) {
|
|
270
|
-
sqLine.data.forEach(function (item) {
|
|
271
|
-
if (item.tag === 'SN') {
|
|
272
|
-
// this is the ref name
|
|
273
|
-
var refName = item.value;
|
|
274
|
-
nameToId[refName] = refId;
|
|
275
|
-
idToName[refId] = refName;
|
|
276
|
-
}
|
|
277
|
-
});
|
|
278
|
-
});
|
|
279
|
-
this.chrToIndex = nameToId;
|
|
280
|
-
this.indexToChr = idToName;
|
|
281
|
-
return [2 /*return*/, samHeader];
|
|
282
|
-
}
|
|
137
|
+
}
|
|
138
|
+
getHeader(opts = {}) {
|
|
139
|
+
return __awaiter(this, void 0, void 0, function* () {
|
|
140
|
+
const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
|
|
141
|
+
const result = yield fetch(url, opts);
|
|
142
|
+
if (!result.ok) {
|
|
143
|
+
throw new Error(`Failed to fetch ${result.statusText}`);
|
|
144
|
+
}
|
|
145
|
+
const data = yield result.json();
|
|
146
|
+
const uncba = yield concat(data.htsget.urls, opts);
|
|
147
|
+
if (uncba.readInt32LE(0) !== bamFile_1.BAM_MAGIC) {
|
|
148
|
+
throw new Error('Not a BAM file');
|
|
149
|
+
}
|
|
150
|
+
const headLen = uncba.readInt32LE(4);
|
|
151
|
+
const headerText = uncba.toString('utf8', 8, 8 + headLen);
|
|
152
|
+
const samHeader = (0, sam_1.parseHeaderText)(headerText);
|
|
153
|
+
// use the @SQ lines in the header to figure out the
|
|
154
|
+
// mapping between ref ref ID numbers and names
|
|
155
|
+
const idToName = [];
|
|
156
|
+
const nameToId = {};
|
|
157
|
+
const sqLines = samHeader.filter((l) => l.tag === 'SQ');
|
|
158
|
+
sqLines.forEach((sqLine, refId) => {
|
|
159
|
+
sqLine.data.forEach((item) => {
|
|
160
|
+
if (item.tag === 'SN') {
|
|
161
|
+
// this is the ref name
|
|
162
|
+
const refName = item.value;
|
|
163
|
+
nameToId[refName] = refId;
|
|
164
|
+
idToName[refId] = refName;
|
|
165
|
+
}
|
|
166
|
+
});
|
|
283
167
|
});
|
|
168
|
+
this.chrToIndex = nameToId;
|
|
169
|
+
this.indexToChr = idToName;
|
|
170
|
+
return samHeader;
|
|
284
171
|
});
|
|
285
|
-
}
|
|
286
|
-
|
|
287
|
-
}(bamFile_1.default));
|
|
172
|
+
}
|
|
173
|
+
}
|
|
288
174
|
exports.default = HtsgetFile;
|
|
289
175
|
//# sourceMappingURL=htsget.js.map
|
package/dist/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AACA,qDAA8C;AAC9C,gCAA6B;AAE7B,2DAA6C;AAC7C,+BAAuC;AAWvC,SAAe,MAAM,CAAC,GAAsB,EAAE,IAAyB;;QACrE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,CAAO,KAAkB,EAAE,EAAE;YACnC,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;YAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE;gBAC3B,OAAO,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;aAChD;iBAAM;gBACL,+DAA+D;gBAC/D,YAAY;gBACZ,4DAA4D;gBAC5D,MAAM,EAAE,OAAO,KAAc,OAAO,EAAhB,IAAI,UAAK,OAAO,EAA9B,WAAoB,CAAU,CAAA;gBACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,kCACtB,IAAI,KACP,OAAO,kCAAO,IAAI,CAAC,OAAO,GAAK,IAAI,KACnC,CAAA;gBACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE;oBACX,MAAM,IAAI,KAAK,CAAC,mBAAmB,GAAG,CAAC,UAAU,EAAE,CAAC,CAAA;iBACrD;gBACD,OAAO,MAAM,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;aAC5C;QACH,CAAC,CAAA,CAAC,CACH,CAAA;QAED,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;IACrE,CAAC;CAAA;AAED,MAAqB,UAAW,SAAQ,iBAAO;IAK7C,YAAY,IAA0C;QACpD,mCAAmC;QACnC,KAAK,CAAC,EAAE,aAAa,EAAE,GAAG,EAAE,aAAa,EAAE,GAAG,EAAE,CAAC,CAAA;QACjD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAEM,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,OAAgB;QACd,WAAW,EAAE,KAAK;QAClB,aAAa,EAAE,KAAK;QACpB,aAAa,EAAE,MAAM;KACtB;;YAED,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;YAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;YAC7E,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,IAAI,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;YACrD,MAAM,MAAM,GAAG,cAAM,KAAK,CAAC,GAAG,oBAAO,IAAI,EAAG,CAAA,CAAA;YAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;gBACd,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,UAAU,CAAC,CAAA;aACnC;YACD,MAAM,IAAI,GAAG,cAAM,MAAM,CAAC,IAAI,EAAE,CAAA,CAAA;YAChC,MAAM,KAAK,GAAG,cAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA,CAAA;YAC3D,MAAM,KAAK,GAAG;gBACZ,MAAM,EAAE,KAAK;gBACb,KAAK,EAAE,EAAE,IAAI,EAAE,EAAE,YAAY,EAAE,CAAC,EAAE,EAAE;gBACpC,QAAQ;oBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;gBAC/B,CAAC;aACF,CAAA;YAED,cAAA,KAAK,CAAC,CAAC,iBAAA,cAAA,IAAI,CAAC,mBAAmB;YAC7B,aAAa;YACb,CAAC,KAAK,CAAC,EACP,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA,CAAA,CAAA,CAAA;QACH,CAAC;KAAA;IAED,YAAY;IACN,UAAU,CAAC,MAGhB;;YACC,MAAM,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;YACxB,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,EAAE,EAAE,GAAG,KAAK,CAAA;YACnC,OAAO,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,IAAI,EAAE,UAAU,EAAE,IAAI,EAAE,KAAK,EAAE,EAAE,EAAE,CAAA;QACxE,CAAC;KAAA;IAEK,SAAS,CAAC,OAAiB,EAAE;;YACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;YAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE;gBACd,MAAM,IAAI,KAAK,CAAC,mBAAmB,MAAM,CAAC,UAAU,EAAE,CAAC,CAAA;aACxD;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAElD,IAAI,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,KAAK,mBAAS,EAAE;gBACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;aAClC;YACD,MAAM,OAAO,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YAEpC,MAAM,UAAU,GAAG,KAAK,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAA;YACzD,MAAM,SAAS,GAAG,IAAA,qBAAe,EAAC,UAAU,CAAC,CAAA;YAE7C,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,QAAQ,GAAa,EAAE,CAAA;YAC7B,MAAM,QAAQ,GAA2B,EAAE,CAAA;YAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAkB,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;YACxE,OAAO,CAAC,OAAO,CAAC,CAAC,MAA8B,EAAE,KAAa,EAAE,EAAE;gBAChE,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,IAAgB,EAAE,EAAE;oBACvC,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE;wBACrB,uBAAuB;wBACvB,MAAM,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;wBAC1B,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;wBACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;qBAC1B;gBACH,CAAC,CAAC,CAAA;YACJ,CAAC,CAAC,CAAA;YACF,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;YAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;YAC1B,OAAO,SAAS,CAAA;QAClB,CAAC;KAAA;CACF;AA/FD,6BA+FC"}
|
package/dist/index.js
CHANGED
|
@@ -4,14 +4,14 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
exports.HtsgetFile = exports.BamRecord = exports.BamFile = exports.CSI = exports.BAI = void 0;
|
|
7
|
-
|
|
7
|
+
const bai_1 = __importDefault(require("./bai"));
|
|
8
8
|
exports.BAI = bai_1.default;
|
|
9
|
-
|
|
9
|
+
const csi_1 = __importDefault(require("./csi"));
|
|
10
10
|
exports.CSI = csi_1.default;
|
|
11
|
-
|
|
11
|
+
const bamFile_1 = __importDefault(require("./bamFile"));
|
|
12
12
|
exports.BamFile = bamFile_1.default;
|
|
13
|
-
|
|
13
|
+
const htsget_1 = __importDefault(require("./htsget"));
|
|
14
14
|
exports.HtsgetFile = htsget_1.default;
|
|
15
|
-
|
|
15
|
+
const record_1 = __importDefault(require("./record"));
|
|
16
16
|
exports.BamRecord = record_1.default;
|
|
17
17
|
//# sourceMappingURL=index.js.map
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,gDAAuB;AAMd,cANF,aAAG,CAME;AALZ,gDAAuB;AAKT,cALP,aAAG,CAKO;AAJjB,wDAA+B;AAIZ,kBAJZ,iBAAO,CAIY;AAH1B,sDAAiC;AAGM,qBAHhC,gBAAU,CAGgC;AAFjD,sDAAgC;AAEJ,oBAFrB,gBAAS,CAEqB"}
|