@gmod/tabix 1.5.0 → 1.5.3
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 +20 -0
- package/README.md +3 -2
- package/dist/chunk.js +34 -62
- package/dist/chunk.js.map +1 -0
- package/dist/csi.d.ts +0 -1
- package/dist/csi.js +329 -533
- package/dist/csi.js.map +1 -0
- package/dist/index.js +12 -36
- package/dist/index.js.map +1 -0
- package/dist/indexFile.d.ts +1 -1
- package/dist/indexFile.js +113 -174
- package/dist/indexFile.js.map +1 -0
- package/dist/tabixIndexedFile.d.ts +8 -4
- package/dist/tabixIndexedFile.js +477 -774
- package/dist/tabixIndexedFile.js.map +1 -0
- package/dist/tbi.js +313 -485
- package/dist/tbi.js.map +1 -0
- package/dist/util.js +133 -148
- package/dist/util.js.map +1 -0
- package/dist/virtualOffset.js +45 -68
- package/dist/virtualOffset.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/csi.d.ts +71 -0
- package/esm/csi.js +230 -0
- package/esm/csi.js.map +1 -0
- package/esm/index.d.ts +4 -0
- package/esm/index.js +5 -0
- package/esm/index.js.map +1 -0
- package/esm/indexFile.d.ts +32 -0
- package/esm/indexFile.js +40 -0
- package/esm/indexFile.js.map +1 -0
- package/esm/tabixIndexedFile.d.ts +118 -0
- package/esm/tabixIndexedFile.js +398 -0
- package/esm/tabixIndexedFile.js.map +1 -0
- package/esm/tbi.d.ts +45 -0
- package/esm/tbi.js +216 -0
- package/esm/tbi.js.map +1 -0
- package/esm/util.d.ts +25 -0
- package/esm/util.js +91 -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 +27 -44
- package/src/chunk.ts +52 -0
- package/src/csi.ts +277 -0
- package/src/declare.d.ts +2 -0
- package/src/index.ts +5 -0
- package/src/indexFile.ts +79 -0
- package/src/tabixIndexedFile.ts +519 -0
- package/src/tbi.ts +250 -0
- package/src/util.ts +103 -0
- package/src/virtualOffset.ts +47 -0
- package/dist/declare.d.js +0 -2
package/dist/tbi.js.map
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var __generator = (this && this.__generator) || function (thisArg, body) {
|
|
27
|
+
var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
|
|
28
|
+
return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
|
|
29
|
+
function verb(n) { return function (v) { return step([n, v]); }; }
|
|
30
|
+
function step(op) {
|
|
31
|
+
if (f) throw new TypeError("Generator is already executing.");
|
|
32
|
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while (_) try {
|
|
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|
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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;
|
|
34
|
+
if (y = 0, t) op = [op[0] & 2, t.value];
|
|
35
|
+
switch (op[0]) {
|
|
36
|
+
case 0: case 1: t = op; break;
|
|
37
|
+
case 4: _.label++; return { value: op[1], done: false };
|
|
38
|
+
case 5: _.label++; y = op[1]; op = [0]; continue;
|
|
39
|
+
case 7: op = _.ops.pop(); _.trys.pop(); continue;
|
|
40
|
+
default:
|
|
41
|
+
if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
|
|
42
|
+
if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
|
|
43
|
+
if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
|
|
44
|
+
if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
|
|
45
|
+
if (t[2]) _.ops.pop();
|
|
46
|
+
_.trys.pop(); continue;
|
|
47
|
+
}
|
|
48
|
+
op = body.call(thisArg, _);
|
|
49
|
+
} catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
|
|
50
|
+
if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
|
|
51
|
+
}
|
|
52
|
+
};
|
|
53
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
54
|
+
exports.optimizeChunks = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = void 0;
|
|
47
55
|
function longToNumber(long) {
|
|
48
|
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|
|
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|
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|
|
50
|
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|
|
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|
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|
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|
|
56
|
+
if (long.greaterThan(Number.MAX_SAFE_INTEGER) ||
|
|
57
|
+
long.lessThan(Number.MIN_SAFE_INTEGER)) {
|
|
58
|
+
throw new Error('integer overflow');
|
|
59
|
+
}
|
|
60
|
+
return long.toNumber();
|
|
53
61
|
}
|
|
54
|
-
|
|
55
|
-
var AbortError =
|
|
56
|
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|
|
57
|
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|
|
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|
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|
|
59
|
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|
|
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|
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function AbortError() {
|
|
61
|
-
var _this;
|
|
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|
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|
|
63
|
-
(0, _classCallCheck2.default)(this, AbortError);
|
|
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|
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|
|
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|
-
for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
|
|
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|
-
args[_key] = arguments[_key];
|
|
62
|
+
exports.longToNumber = longToNumber;
|
|
63
|
+
var AbortError = /** @class */ (function (_super) {
|
|
64
|
+
__extends(AbortError, _super);
|
|
65
|
+
function AbortError() {
|
|
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|
+
return _super !== null && _super.apply(this, arguments) || this;
|
|
67
67
|
}
|
|
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|
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|
|
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|
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|
|
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|
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(0, _defineProperty2.default)((0, _assertThisInitialized2.default)(_this), "code", void 0);
|
|
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|
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return _this;
|
|
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|
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|
|
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|
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|
|
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|
-
return AbortError;
|
|
75
|
-
}( /*#__PURE__*/(0, _wrapNativeSuper2.default)(Error));
|
|
68
|
+
return AbortError;
|
|
69
|
+
}(Error));
|
|
76
70
|
/**
|
|
77
71
|
* Properly check if the given AbortSignal is aborted.
|
|
78
72
|
* Per the standard, if the signal reads as aborted,
|
|
@@ -84,96 +78,87 @@ var AbortError = /*#__PURE__*/function (_Error) {
|
|
|
84
78
|
* @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted` attribute
|
|
85
79
|
* @returns nothing
|
|
86
80
|
*/
|
|
87
|
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|
|
88
|
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|
|
89
81
|
function checkAbortSignal(signal) {
|
|
90
|
-
|
|
91
|
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|
|
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|
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|
|
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|
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|
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|
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97
|
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|
|
98
|
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|
|
82
|
+
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|
|
83
|
+
return;
|
|
84
|
+
}
|
|
85
|
+
if (signal.aborted) {
|
|
86
|
+
// console.log('bam aborted!')
|
|
87
|
+
if (typeof DOMException !== 'undefined') {
|
|
88
|
+
// eslint-disable-next-line no-undef
|
|
89
|
+
throw new DOMException('aborted', 'AbortError');
|
|
90
|
+
}
|
|
91
|
+
else {
|
|
92
|
+
var e = new AbortError('aborted');
|
|
93
|
+
e.code = 'ERR_ABORTED';
|
|
94
|
+
throw e;
|
|
95
|
+
}
|
|
99
96
|
}
|
|
100
|
-
}
|
|
101
97
|
}
|
|
98
|
+
exports.checkAbortSignal = checkAbortSignal;
|
|
102
99
|
/**
|
|
103
100
|
* Skips to the next tick, then runs `checkAbortSignal`.
|
|
104
101
|
* Await this to inside an otherwise synchronous loop to
|
|
105
102
|
* provide a place to break when an abort signal is received.
|
|
106
103
|
* @param {AbortSignal} signal
|
|
107
104
|
*/
|
|
108
|
-
|
|
109
|
-
|
|
110
|
-
function
|
|
111
|
-
|
|
105
|
+
function abortBreakPoint(signal) {
|
|
106
|
+
return __awaiter(this, void 0, void 0, function () {
|
|
107
|
+
return __generator(this, function (_a) {
|
|
108
|
+
switch (_a.label) {
|
|
109
|
+
case 0: return [4 /*yield*/, Promise.resolve()];
|
|
110
|
+
case 1:
|
|
111
|
+
_a.sent();
|
|
112
|
+
checkAbortSignal(signal);
|
|
113
|
+
return [2 /*return*/];
|
|
114
|
+
}
|
|
115
|
+
});
|
|
116
|
+
});
|
|
112
117
|
}
|
|
113
|
-
|
|
114
|
-
function _abortBreakPoint() {
|
|
115
|
-
_abortBreakPoint = (0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee(signal) {
|
|
116
|
-
return _regenerator.default.wrap(function _callee$(_context) {
|
|
117
|
-
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|
|
118
|
-
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|
|
119
|
-
case 0:
|
|
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|
-
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|
|
121
|
-
return _promise.default.resolve();
|
|
122
|
-
|
|
123
|
-
case 2:
|
|
124
|
-
checkAbortSignal(signal);
|
|
125
|
-
|
|
126
|
-
case 3:
|
|
127
|
-
case "end":
|
|
128
|
-
return _context.stop();
|
|
129
|
-
}
|
|
130
|
-
}
|
|
131
|
-
}, _callee);
|
|
132
|
-
}));
|
|
133
|
-
return _abortBreakPoint.apply(this, arguments);
|
|
134
|
-
}
|
|
135
|
-
|
|
118
|
+
exports.abortBreakPoint = abortBreakPoint;
|
|
136
119
|
function canMergeBlocks(chunk1, chunk2) {
|
|
137
|
-
|
|
120
|
+
return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
|
|
121
|
+
chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);
|
|
138
122
|
}
|
|
139
|
-
|
|
123
|
+
exports.canMergeBlocks = canMergeBlocks;
|
|
140
124
|
function optimizeChunks(chunks, lowest) {
|
|
141
|
-
|
|
142
|
-
|
|
143
|
-
|
|
144
|
-
|
|
145
|
-
return chunks;
|
|
146
|
-
}
|
|
147
|
-
|
|
148
|
-
chunks.sort(function (c0, c1) {
|
|
149
|
-
var dif = c0.minv.blockPosition - c1.minv.blockPosition;
|
|
150
|
-
|
|
151
|
-
if (dif !== 0) {
|
|
152
|
-
return dif;
|
|
153
|
-
} else {
|
|
154
|
-
return c0.minv.dataPosition - c1.minv.dataPosition;
|
|
125
|
+
var mergedChunks = [];
|
|
126
|
+
var lastChunk = null;
|
|
127
|
+
if (chunks.length === 0) {
|
|
128
|
+
return chunks;
|
|
155
129
|
}
|
|
156
|
-
|
|
157
|
-
|
|
158
|
-
|
|
159
|
-
|
|
160
|
-
|
|
161
|
-
|
|
162
|
-
|
|
163
|
-
if (canMergeBlocks(lastChunk, chunk)) {
|
|
164
|
-
if (chunk.maxv.compareTo(lastChunk.maxv) > 0) {
|
|
165
|
-
lastChunk.maxv = chunk.maxv;
|
|
166
|
-
}
|
|
167
|
-
} else {
|
|
168
|
-
mergedChunks.push(chunk);
|
|
169
|
-
lastChunk = chunk;
|
|
130
|
+
chunks.sort(function (c0, c1) {
|
|
131
|
+
var dif = c0.minv.blockPosition - c1.minv.blockPosition;
|
|
132
|
+
if (dif !== 0) {
|
|
133
|
+
return dif;
|
|
134
|
+
}
|
|
135
|
+
else {
|
|
136
|
+
return c0.minv.dataPosition - c1.minv.dataPosition;
|
|
170
137
|
}
|
|
171
|
-
|
|
172
|
-
|
|
173
|
-
|
|
174
|
-
|
|
175
|
-
|
|
176
|
-
|
|
177
|
-
|
|
138
|
+
});
|
|
139
|
+
chunks.forEach(function (chunk) {
|
|
140
|
+
if (!lowest || chunk.maxv.compareTo(lowest) > 0) {
|
|
141
|
+
if (lastChunk === null) {
|
|
142
|
+
mergedChunks.push(chunk);
|
|
143
|
+
lastChunk = chunk;
|
|
144
|
+
}
|
|
145
|
+
else {
|
|
146
|
+
if (canMergeBlocks(lastChunk, chunk)) {
|
|
147
|
+
if (chunk.maxv.compareTo(lastChunk.maxv) > 0) {
|
|
148
|
+
lastChunk.maxv = chunk.maxv;
|
|
149
|
+
}
|
|
150
|
+
}
|
|
151
|
+
else {
|
|
152
|
+
mergedChunks.push(chunk);
|
|
153
|
+
lastChunk = chunk;
|
|
154
|
+
}
|
|
155
|
+
}
|
|
156
|
+
}
|
|
157
|
+
// else {
|
|
158
|
+
// console.log(`skipping chunk ${chunk}`)
|
|
159
|
+
// }
|
|
160
|
+
});
|
|
161
|
+
return mergedChunks;
|
|
178
162
|
}
|
|
179
|
-
|
|
163
|
+
exports.optimizeChunks = optimizeChunks;
|
|
164
|
+
//# sourceMappingURL=util.js.map
|
package/dist/util.js.map
ADDED
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAGA,SAAgB,YAAY,CAAC,IAAU;IACrC,IACE,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,gBAAgB,CAAC;QACzC,IAAI,CAAC,QAAQ,CAAC,MAAM,CAAC,gBAAgB,CAAC,EACtC;QACA,MAAM,IAAI,KAAK,CAAC,kBAAkB,CAAC,CAAA;KACpC;IACD,OAAO,IAAI,CAAC,QAAQ,EAAE,CAAA;AACxB,CAAC;AARD,oCAQC;AAED;IAAyB,8BAAK;IAA9B;;IAEA,CAAC;IAAD,iBAAC;AAAD,CAAC,AAFD,CAAyB,KAAK,GAE7B;AACD;;;;;;;;;;GAUG;AACH,SAAgB,gBAAgB,CAAC,MAAoB;IACnD,IAAI,CAAC,MAAM,EAAE;QACX,OAAM;KACP;IAED,IAAI,MAAM,CAAC,OAAO,EAAE;QAClB,8BAA8B;QAC9B,IAAI,OAAO,YAAY,KAAK,WAAW,EAAE;YACvC,qCAAqC;YACrC,MAAM,IAAI,YAAY,CAAC,SAAS,EAAE,YAAY,CAAC,CAAA;SAChD;aAAM;YACL,IAAM,CAAC,GAAG,IAAI,UAAU,CAAC,SAAS,CAAC,CAAA;YACnC,CAAC,CAAC,IAAI,GAAG,aAAa,CAAA;YACtB,MAAM,CAAC,CAAA;SACR;KACF;AACH,CAAC;AAhBD,4CAgBC;AAED;;;;;GAKG;AACH,SAAsB,eAAe,CAAC,MAAoB;;;;wBACxD,qBAAM,OAAO,CAAC,OAAO,EAAE,EAAA;;oBAAvB,SAAuB,CAAA;oBACvB,gBAAgB,CAAC,MAAM,CAAC,CAAA;;;;;CACzB;AAHD,0CAGC;AAED,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AALD,wCAKC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAqB;IACnE,IAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAAS,GAAiB,IAAI,CAAA;IAElC,IAAI,MAAM,CAAC,MAAM,KAAK,CAAC,EAAE;QACvB,OAAO,MAAM,CAAA;KACd;IAED,MAAM,CAAC,IAAI,CAAC,UAAU,EAAE,EAAE,EAAE;QAC1B,IAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,IAAI,GAAG,KAAK,CAAC,EAAE;YACb,OAAO,GAAG,CAAA;SACX;aAAM;YACL,OAAO,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;SACnD;IACH,CAAC,CAAC,CAAA;IAEF,MAAM,CAAC,OAAO,CAAC,UAAA,KAAK;QAClB,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE;YAC/C,IAAI,SAAS,KAAK,IAAI,EAAE;gBACtB,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;gBACxB,SAAS,GAAG,KAAK,CAAA;aAClB;iBAAM;gBACL,IAAI,cAAc,CAAC,SAAS,EAAE,KAAK,CAAC,EAAE;oBACpC,IAAI,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE;wBAC5C,SAAS,CAAC,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;qBAC5B;iBACF;qBAAM;oBACL,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;oBACxB,SAAS,GAAG,KAAK,CAAA;iBAClB;aACF;SACF;QACD,SAAS;QACT,2CAA2C;QAC3C,IAAI;IACN,CAAC,CAAC,CAAA;IAEF,OAAO,YAAY,CAAA;AACrB,CAAC;AAvCD,wCAuCC"}
|
package/dist/virtualOffset.js
CHANGED
|
@@ -1,72 +1,49 @@
|
|
|
1
1
|
"use strict";
|
|
2
|
-
|
|
3
|
-
|
|
4
|
-
|
|
5
|
-
|
|
6
|
-
|
|
7
|
-
|
|
8
|
-
value: true
|
|
9
|
-
});
|
|
10
|
-
|
|
11
|
-
exports.fromBytes = fromBytes;
|
|
12
|
-
exports.default = void 0;
|
|
13
|
-
|
|
14
|
-
var _classCallCheck2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/classCallCheck"));
|
|
15
|
-
|
|
16
|
-
var _createClass2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/createClass"));
|
|
17
|
-
|
|
18
|
-
var _defineProperty2 = _interopRequireDefault(require("@babel/runtime-corejs2/helpers/defineProperty"));
|
|
19
|
-
|
|
20
|
-
var VirtualOffset = /*#__PURE__*/function () {
|
|
21
|
-
function VirtualOffset(blockPosition, dataPosition) {
|
|
22
|
-
(0, _classCallCheck2.default)(this, VirtualOffset);
|
|
23
|
-
(0, _defineProperty2.default)(this, "blockPosition", void 0);
|
|
24
|
-
(0, _defineProperty2.default)(this, "dataPosition", void 0);
|
|
25
|
-
this.blockPosition = blockPosition; // < offset of the compressed data block
|
|
26
|
-
|
|
27
|
-
this.dataPosition = dataPosition; // < offset into the uncompressed data
|
|
28
|
-
}
|
|
29
|
-
|
|
30
|
-
(0, _createClass2.default)(VirtualOffset, [{
|
|
31
|
-
key: "toString",
|
|
32
|
-
value: function toString() {
|
|
33
|
-
return "".concat(this.blockPosition, ":").concat(this.dataPosition);
|
|
34
|
-
}
|
|
35
|
-
}, {
|
|
36
|
-
key: "compareTo",
|
|
37
|
-
value: function compareTo(b) {
|
|
38
|
-
return this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition;
|
|
39
|
-
}
|
|
40
|
-
}], [{
|
|
41
|
-
key: "min",
|
|
42
|
-
value: function min() {
|
|
43
|
-
var min;
|
|
44
|
-
var i = 0;
|
|
45
|
-
|
|
46
|
-
for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {
|
|
47
|
-
args[_key] = arguments[_key];
|
|
48
|
-
}
|
|
49
|
-
|
|
50
|
-
for (; !min; i += 1) {
|
|
51
|
-
min = args[i];
|
|
52
|
-
}
|
|
53
|
-
|
|
54
|
-
for (; i < args.length; i += 1) {
|
|
55
|
-
if (min.compareTo(args[i]) > 0) min = args[i];
|
|
56
|
-
}
|
|
57
|
-
|
|
58
|
-
return min;
|
|
2
|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
exports.fromBytes = void 0;
|
|
4
|
+
var VirtualOffset = /** @class */ (function () {
|
|
5
|
+
function VirtualOffset(blockPosition, dataPosition) {
|
|
6
|
+
this.blockPosition = blockPosition; // < offset of the compressed data block
|
|
7
|
+
this.dataPosition = dataPosition; // < offset into the uncompressed data
|
|
59
8
|
}
|
|
60
|
-
|
|
61
|
-
|
|
62
|
-
}
|
|
63
|
-
|
|
9
|
+
VirtualOffset.prototype.toString = function () {
|
|
10
|
+
return "".concat(this.blockPosition, ":").concat(this.dataPosition);
|
|
11
|
+
};
|
|
12
|
+
VirtualOffset.prototype.compareTo = function (b) {
|
|
13
|
+
return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
|
|
14
|
+
};
|
|
15
|
+
VirtualOffset.min = function () {
|
|
16
|
+
var args = [];
|
|
17
|
+
for (var _i = 0; _i < arguments.length; _i++) {
|
|
18
|
+
args[_i] = arguments[_i];
|
|
19
|
+
}
|
|
20
|
+
var min;
|
|
21
|
+
var i = 0;
|
|
22
|
+
for (; !min; i += 1) {
|
|
23
|
+
min = args[i];
|
|
24
|
+
}
|
|
25
|
+
for (; i < args.length; i += 1) {
|
|
26
|
+
if (min.compareTo(args[i]) > 0) {
|
|
27
|
+
min = args[i];
|
|
28
|
+
}
|
|
29
|
+
}
|
|
30
|
+
return min;
|
|
31
|
+
};
|
|
32
|
+
return VirtualOffset;
|
|
33
|
+
}());
|
|
64
34
|
exports.default = VirtualOffset;
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
35
|
+
function fromBytes(bytes, offset, bigendian) {
|
|
36
|
+
if (offset === void 0) { offset = 0; }
|
|
37
|
+
if (bigendian === void 0) { bigendian = false; }
|
|
38
|
+
if (bigendian) {
|
|
39
|
+
throw new Error('big-endian virtual file offsets not implemented');
|
|
40
|
+
}
|
|
41
|
+
return new VirtualOffset(bytes[offset + 7] * 0x10000000000 +
|
|
42
|
+
bytes[offset + 6] * 0x100000000 +
|
|
43
|
+
bytes[offset + 5] * 0x1000000 +
|
|
44
|
+
bytes[offset + 4] * 0x10000 +
|
|
45
|
+
bytes[offset + 3] * 0x100 +
|
|
46
|
+
bytes[offset + 2], (bytes[offset + 1] << 8) | bytes[offset]);
|
|
71
47
|
}
|
|
72
|
-
|
|
48
|
+
exports.fromBytes = fromBytes;
|
|
49
|
+
//# sourceMappingURL=virtualOffset.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AAAA;IAGE,uBAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,gCAAQ,GAAR;QACE,OAAO,UAAG,IAAI,CAAC,aAAa,cAAI,IAAI,CAAC,YAAY,CAAE,CAAA;IACrD,CAAC;IAED,iCAAS,GAAT,UAAU,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAEM,iBAAG,GAAV;QAAW,cAAwB;aAAxB,UAAwB,EAAxB,qBAAwB,EAAxB,IAAwB;YAAxB,yBAAwB;;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE;YACnB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;SACd;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC9B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE;gBAC9B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;aACd;SACF;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IACH,oBAAC;AAAD,CAAC,AA/BD,IA+BC;;AACD,SAAgB,SAAS,CAAC,KAAa,EAAE,MAAU,EAAE,SAAiB;IAA7B,uBAAA,EAAA,UAAU;IAAE,0BAAA,EAAA,iBAAiB;IACpE,IAAI,SAAS,EAAE;QACb,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;KACnE;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC;AAdD,8BAcC"}
|
package/esm/chunk.d.ts
ADDED
|
@@ -0,0 +1,18 @@
|
|
|
1
|
+
import VirtualOffset from './virtualOffset';
|
|
2
|
+
export default class Chunk {
|
|
3
|
+
minv: VirtualOffset;
|
|
4
|
+
maxv: VirtualOffset;
|
|
5
|
+
bin: number;
|
|
6
|
+
_fetchedSize?: number;
|
|
7
|
+
/**
|
|
8
|
+
* @param {VirtualOffset} minv
|
|
9
|
+
* @param {VirtualOffset} maxv
|
|
10
|
+
* @param {number} bin
|
|
11
|
+
* @param {number} [fetchedSize]
|
|
12
|
+
*/
|
|
13
|
+
constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: undefined);
|
|
14
|
+
toUniqueString(): string;
|
|
15
|
+
toString(): string;
|
|
16
|
+
compareTo(b: Chunk): number;
|
|
17
|
+
fetchedSize(): number;
|
|
18
|
+
}
|
package/esm/chunk.js
ADDED
|
@@ -0,0 +1,33 @@
|
|
|
1
|
+
// little class representing a chunk in the index
|
|
2
|
+
export default class Chunk {
|
|
3
|
+
/**
|
|
4
|
+
* @param {VirtualOffset} minv
|
|
5
|
+
* @param {VirtualOffset} maxv
|
|
6
|
+
* @param {number} bin
|
|
7
|
+
* @param {number} [fetchedSize]
|
|
8
|
+
*/
|
|
9
|
+
constructor(minv, maxv, bin, fetchedSize = undefined) {
|
|
10
|
+
this.minv = minv;
|
|
11
|
+
this.maxv = maxv;
|
|
12
|
+
this.bin = bin;
|
|
13
|
+
this._fetchedSize = fetchedSize;
|
|
14
|
+
}
|
|
15
|
+
toUniqueString() {
|
|
16
|
+
return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
|
|
17
|
+
}
|
|
18
|
+
toString() {
|
|
19
|
+
return this.toUniqueString();
|
|
20
|
+
}
|
|
21
|
+
compareTo(b) {
|
|
22
|
+
return (this.minv.compareTo(b.minv) ||
|
|
23
|
+
this.maxv.compareTo(b.maxv) ||
|
|
24
|
+
this.bin - b.bin);
|
|
25
|
+
}
|
|
26
|
+
fetchedSize() {
|
|
27
|
+
if (this._fetchedSize !== undefined) {
|
|
28
|
+
return this._fetchedSize;
|
|
29
|
+
}
|
|
30
|
+
return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition;
|
|
31
|
+
}
|
|
32
|
+
}
|
|
33
|
+
//# sourceMappingURL=chunk.js.map
|
package/esm/chunk.js.map
ADDED
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IAMxB;;;;;OAKG;IACH,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE;YACnC,OAAO,IAAI,CAAC,YAAY,CAAA;SACzB;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF"}
|
package/esm/csi.d.ts
ADDED
|
@@ -0,0 +1,71 @@
|
|
|
1
|
+
/// <reference types="node" />
|
|
2
|
+
import VirtualOffset from './virtualOffset';
|
|
3
|
+
import Chunk from './chunk';
|
|
4
|
+
import IndexFile, { Options } from './indexFile';
|
|
5
|
+
export default class CSI extends IndexFile {
|
|
6
|
+
private maxBinNumber;
|
|
7
|
+
private depth;
|
|
8
|
+
private minShift;
|
|
9
|
+
constructor(args: any);
|
|
10
|
+
lineCount(refName: string, opts?: Options): Promise<number>;
|
|
11
|
+
indexCov(): Promise<never[]>;
|
|
12
|
+
parseAuxData(bytes: Buffer, offset: number, auxLength: number): {
|
|
13
|
+
refIdToName: never[];
|
|
14
|
+
refNameToId: {};
|
|
15
|
+
skipLines?: undefined;
|
|
16
|
+
metaChar?: undefined;
|
|
17
|
+
columnNumbers?: undefined;
|
|
18
|
+
format?: undefined;
|
|
19
|
+
coordinateType?: undefined;
|
|
20
|
+
} | {
|
|
21
|
+
refIdToName: string[];
|
|
22
|
+
refNameToId: {
|
|
23
|
+
[key: string]: number;
|
|
24
|
+
};
|
|
25
|
+
skipLines: number;
|
|
26
|
+
metaChar: string;
|
|
27
|
+
columnNumbers: {
|
|
28
|
+
ref: number;
|
|
29
|
+
start: number;
|
|
30
|
+
end: number;
|
|
31
|
+
};
|
|
32
|
+
format: string;
|
|
33
|
+
coordinateType: string;
|
|
34
|
+
};
|
|
35
|
+
_parseNameBytes(namesBytes: Buffer): {
|
|
36
|
+
refNameToId: {
|
|
37
|
+
[key: string]: number;
|
|
38
|
+
};
|
|
39
|
+
refIdToName: string[];
|
|
40
|
+
};
|
|
41
|
+
_parse(opts?: Options): Promise<{
|
|
42
|
+
csi: boolean;
|
|
43
|
+
refCount: any;
|
|
44
|
+
maxBlockSize: number;
|
|
45
|
+
firstDataLine: VirtualOffset | undefined;
|
|
46
|
+
csiVersion: number;
|
|
47
|
+
indices: {
|
|
48
|
+
binIndex: {
|
|
49
|
+
[key: string]: Chunk[];
|
|
50
|
+
};
|
|
51
|
+
stats: {
|
|
52
|
+
lineCount: number;
|
|
53
|
+
} | undefined;
|
|
54
|
+
}[];
|
|
55
|
+
depth: number;
|
|
56
|
+
maxBinNumber: number;
|
|
57
|
+
maxRefLength: number;
|
|
58
|
+
refIdToName: string[];
|
|
59
|
+
refNameToId: {
|
|
60
|
+
[key: string]: number;
|
|
61
|
+
};
|
|
62
|
+
}>;
|
|
63
|
+
parsePseudoBin(bytes: Buffer, offset: number): {
|
|
64
|
+
lineCount: number;
|
|
65
|
+
};
|
|
66
|
+
blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
|
|
67
|
+
/**
|
|
68
|
+
* calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
|
|
69
|
+
*/
|
|
70
|
+
reg2bins(beg: number, end: number): number[][];
|
|
71
|
+
}
|