@gmod/tabix 3.4.1 → 3.4.3
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/dist/chunk.d.ts +2 -1
- package/dist/chunk.js +8 -2
- package/dist/chunk.js.map +1 -1
- package/dist/csi.d.ts +0 -6
- package/dist/csi.js +5 -14
- package/dist/csi.js.map +1 -1
- package/dist/long.d.ts +0 -2
- package/dist/long.js +2 -4
- package/dist/long.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tabixIndexedFile.js +49 -35
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.js +22 -23
- package/dist/tbi.js.map +1 -1
- package/dist/util.d.ts +1 -0
- package/dist/util.js +38 -2
- package/dist/util.js.map +1 -1
- package/esm/chunk.d.ts +2 -1
- package/esm/chunk.js +8 -2
- package/esm/chunk.js.map +1 -1
- package/esm/csi.d.ts +0 -6
- package/esm/csi.js +6 -15
- package/esm/csi.js.map +1 -1
- package/esm/long.d.ts +0 -2
- package/esm/long.js +1 -2
- package/esm/long.js.map +1 -1
- package/esm/tabixIndexedFile.js +49 -35
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/tbi.js +23 -24
- package/esm/tbi.js.map +1 -1
- package/esm/util.d.ts +1 -0
- package/esm/util.js +37 -2
- package/esm/util.js.map +1 -1
- package/package.json +2 -1
- package/src/chunk.ts +13 -2
- package/src/csi.ts +10 -15
- package/src/long.ts +1 -2
- package/src/tabixIndexedFile.ts +70 -30
- package/src/tbi.ts +38 -25
- package/src/util.ts +45 -1
package/dist/tabixIndexedFile.js
CHANGED
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@@ -12,6 +12,7 @@ const tbi_ts_1 = __importDefault(require("./tbi.js"));
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12
12
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const util_ts_1 = require("./util.js");
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13
13
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const TAB = 9;
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14
14
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const NEWLINE = 10;
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15
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+
const CARRIAGE_RETURN = 13;
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15
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const SEMICOLON = 59;
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16
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function resolveFilehandle(filehandle, path, url) {
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if (filehandle) {
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@@ -25,6 +26,35 @@ function resolveFilehandle(filehandle, path, url) {
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}
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throw new TypeError('must provide either filehandle, path, or url');
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}
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+
// An explicitly supplied index always wins over the `<path>.tbi` /
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// `<url>.tbi` names derived from the data file, whichever kind it is.
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31
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function resolveIndex({ tbiFilehandle, csiFilehandle, tbiPath, csiPath, tbiUrl, csiUrl, path, url, }) {
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if (tbiFilehandle) {
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return new tbi_ts_1.default({ filehandle: tbiFilehandle });
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}
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35
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if (csiFilehandle) {
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return new csi_ts_1.default({ filehandle: csiFilehandle });
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}
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38
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if (tbiPath) {
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return new tbi_ts_1.default({ filehandle: new generic_filehandle2_1.LocalFile(tbiPath) });
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}
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if (csiPath) {
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return new csi_ts_1.default({ filehandle: new generic_filehandle2_1.LocalFile(csiPath) });
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}
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if (csiUrl) {
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return new csi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(csiUrl) });
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}
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if (tbiUrl) {
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return new tbi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(tbiUrl) });
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49
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}
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if (path) {
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return new tbi_ts_1.default({ filehandle: new generic_filehandle2_1.LocalFile(`${path}.tbi`) });
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}
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if (url) {
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return new tbi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(`${url}.tbi`) });
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}
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throw new TypeError('must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl');
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}
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function calculateFileOffset(cpositions, dpositions, pos, blockStart, minvDataPosition) {
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return (cpositions[pos] * (1 << 8) +
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60
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(blockStart - dpositions[pos]) +
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@@ -94,33 +124,16 @@ class TabixIndexedFile {
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chunkCache;
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constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = 5 * 2 ** 20, }) {
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this.filehandle = resolveFilehandle(filehandle, path, url);
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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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-
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-
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105
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-
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106
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-
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this.index = new csi_ts_1.default({ filehandle: new generic_filehandle2_1.LocalFile(csiPath) });
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108
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-
}
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109
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-
else if (path) {
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110
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-
this.index = new tbi_ts_1.default({ filehandle: new generic_filehandle2_1.LocalFile(`${path}.tbi`) });
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111
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-
}
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112
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-
else if (csiUrl) {
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113
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this.index = new csi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(csiUrl) });
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114
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-
}
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115
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-
else if (tbiUrl) {
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116
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-
this.index = new tbi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(tbiUrl) });
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-
}
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118
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-
else if (url) {
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119
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-
this.index = new tbi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(`${url}.tbi`) });
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120
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-
}
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121
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-
else {
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122
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throw new TypeError('must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl');
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123
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-
}
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127
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+
this.index = resolveIndex({
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128
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tbiFilehandle,
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+
csiFilehandle,
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130
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+
tbiPath,
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131
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csiPath,
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132
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+
tbiUrl,
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133
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+
csiUrl,
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path,
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135
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url,
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136
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});
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124
137
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this.chunkCache = new abortable_promise_cache_1.default({
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125
138
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cache: new quick_lru_1.default({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
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126
139
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fill: (args, signal) => this.readChunk(args, { signal }),
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@@ -215,15 +228,14 @@ class TabixIndexedFile {
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228
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blockStart = n + 1;
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229
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continue;
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}
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218
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-
// find tab positions
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231
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+
// find tab positions. Columns past the end of the line all get `n`
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232
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// rather than breaking out, which would leave stale offsets from the
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233
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// previous line in the tail of the array.
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tabs[0] = blockStart - 1;
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for (let i = 0; i < maxColumn; i++) {
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-
const
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-
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-
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break;
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-
}
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-
tabs[i + 1] = tabPos;
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const prev = tabs[i];
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const tabPos = prev < n ? buffer.indexOf(TAB, prev + 1) : -1;
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tabs[i + 1] = tabPos === -1 || tabPos >= n ? n : tabPos;
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}
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// compare ref name bytes directly
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const refStart = tabs[refCol - 1] + 1;
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@@ -262,7 +274,9 @@ class TabixIndexedFile {
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endCoordinate = parseIntFromBytes(buffer, tabs[endCol - 1] + 1, tabs[endCol]);
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}
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if (endCoordinate > start) {
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-
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277
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// trim a CRLF terminator, matching htslib's line reader
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const lineEnd = buffer[n - 1] === CARRIAGE_RETURN ? n - 1 : n;
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const line = decoder.decode(buffer.subarray(blockStart, lineEnd));
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callback(line, calculateFileOffset(cpositions, dpositions, pos, blockStart, minvDataPosition), startCoordinate, endCoordinate);
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}
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blockStart = n + 1;
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@@ -1 +1 @@
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1
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-
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AAU,EACV,gBAAgB,CACjB,EACD,eAAe,EACf,aAAa,CACd,CAAA;gBACH,CAAC;gBACD,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;YACpB,CAAC;QACH,CAAC;IACH,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QAClC,OAAO,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,OAAgB,EAAE;QACtC,MAAM,EAAE,aAAa,EAAE,QAAQ,EAAE,YAAY,EAAE,GAC7C,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAE9B,MAAM,QAAQ,GAAG,CAAC,aAAa,EAAE,aAAa,IAAI,CAAC,CAAC,GAAG,YAAY,CAAA;QACnE,uEAAuE;QACvE,8DAA8D;QAE9D,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,QAAQ,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;QACzD,MAAM,KAAK,GAAG,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAe,CAAA;QAE9C,0CAA0C;QAC1C,IAAI,QAAQ,EAAE,CAAC;YACb,IAAI,WAAW,GAAG,CAAC,CAAC,CAAA;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YAEvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC7C,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBACrB,IAAI,CAAC,KAAK,WAAW,GAAG,CAAC,IAAI,IAAI,KAAK,QAAQ,EAAE,CAAC;oBAC/C,MAAK;gBACP,CAAC;gBACD,IAAI,IAAI,KAAK,OAAO,EAAE,CAAC;oBACrB,WAAW,GAAG,CAAC,CAAA;gBACjB,CAAC;YACH,CAAC;YACD,OAAO,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;QAC3C,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAgB,EAAE;QAChC,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9C,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;IACxC,CAAC;IAED,KAAK,CAAC,yBAAyB,CAAC,OAAgB,EAAE;QAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAC7C,OAAO,QAAQ,CAAC,WAAW,CAAA;IAC7B,CAAC;IAED,6CAA6C;IAC7C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,OAAO,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,SAAS,CAAC,CAAQ,EAAE,OAAgB,EAAE;QAC1C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,IAAI,CACpC,CAAC,CAAC,WAAW,EAAE,EACf,CAAC,CAAC,IAAI,CAAC,aAAa,EACpB,IAAI,CACL,CAAA;QACD,OAAO,IAAA,iCAAe,EAAC,GAAG,EAAE,CAAC,CAAC,CAAA;IAChC,CAAC;CACF;AAhTD,mCAgTC"}
|
package/dist/tbi.js
CHANGED
|
@@ -9,21 +9,23 @@ const indexFile_ts_1 = __importDefault(require("./indexFile.js"));
|
|
|
9
9
|
const util_ts_1 = require("./util.js");
|
|
10
10
|
const virtualOffset_ts_1 = require("./virtualOffset.js");
|
|
11
11
|
const TBI_MAGIC = 21_578_324; // TBI\1
|
|
12
|
+
// TBI is always the fixed depth-5, 14-bit-leaf binning scheme
|
|
13
|
+
const TBI_DEPTH = 5;
|
|
14
|
+
const TBI_MAX_REF_LENGTH = 2 ** (14 + TBI_DEPTH * 3);
|
|
12
15
|
/**
|
|
13
16
|
* calculate the list of bins that may overlap with region [beg,end)
|
|
14
17
|
* (zero-based half-open)
|
|
15
18
|
*/
|
|
16
19
|
function reg2bins(beg, end) {
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
[73 + (
|
|
24
|
-
|
|
25
|
-
|
|
26
|
-
];
|
|
20
|
+
// Clamp into the binning scheme's range. Past 2**31 the shifts below
|
|
21
|
+
// truncate to int32 and go negative, which would silently yield no bins.
|
|
22
|
+
const b = Math.min(Math.max(beg, 0), TBI_MAX_REF_LENGTH);
|
|
23
|
+
const e = Math.min(end, TBI_MAX_REF_LENGTH) - 1;
|
|
24
|
+
const bins = [];
|
|
25
|
+
if (b <= e) {
|
|
26
|
+
bins.push([0, 0], [1 + (b >> 26), 1 + (e >> 26)], [9 + (b >> 23), 9 + (e >> 23)], [73 + (b >> 20), 73 + (e >> 20)], [585 + (b >> 17), 585 + (e >> 17)], [4681 + (b >> 14), 4681 + (e >> 14)]);
|
|
27
|
+
}
|
|
28
|
+
return bins;
|
|
27
29
|
}
|
|
28
30
|
class TabixIndex extends indexFile_ts_1.default {
|
|
29
31
|
/** @internal */
|
|
@@ -33,14 +35,12 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
33
35
|
onProgress: opts.onProgress,
|
|
34
36
|
});
|
|
35
37
|
const bytes = (await (0, bgzf_filehandle_1.unzip)(buf));
|
|
36
|
-
const dataView = new DataView(bytes.buffer);
|
|
38
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
37
39
|
if (dataView.getUint32(0, true) !== TBI_MAGIC) {
|
|
38
40
|
throw new Error('Not a TBI file');
|
|
39
41
|
}
|
|
40
42
|
const refCount = dataView.getUint32(4, true);
|
|
41
|
-
const
|
|
42
|
-
const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
|
|
43
|
-
const maxRefLength = 2 ** (14 + depth * 3);
|
|
43
|
+
const maxBinNumber = ((1 << ((TBI_DEPTH + 1) * 3)) - 1) / 7;
|
|
44
44
|
// TBI header layout matches CSI aux data; parseAuxData handles both
|
|
45
45
|
const { refNameToId, refIdToName, coordinateType, format, columnNumbers, metaChar, skipLines, } = (0, util_ts_1.parseAuxData)(bytes, 8);
|
|
46
46
|
// nameSectionLength is at TBI offset 32; re-read to find where bin data starts
|
|
@@ -121,13 +121,14 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
121
121
|
linearIndex[k] = (0, virtualOffset_ts_1.fromBytes)(bytes, pos);
|
|
122
122
|
pos += 8;
|
|
123
123
|
}
|
|
124
|
+
(0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat(), linearIndex.map(v => v.blockPosition));
|
|
124
125
|
return { binIndex, linearIndex, stats };
|
|
125
126
|
}
|
|
126
127
|
return {
|
|
127
128
|
indices: (0, util_ts_1.memoizeByRefId)(getIndices),
|
|
128
129
|
metaChar,
|
|
129
130
|
maxBinNumber,
|
|
130
|
-
maxRefLength,
|
|
131
|
+
maxRefLength: TBI_MAX_REF_LENGTH,
|
|
131
132
|
skipLines,
|
|
132
133
|
firstDataLine,
|
|
133
134
|
columnNumbers,
|
|
@@ -139,9 +140,6 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
139
140
|
};
|
|
140
141
|
}
|
|
141
142
|
async blocksForRange(refName, min, max, opts = {}) {
|
|
142
|
-
if (min < 0) {
|
|
143
|
-
min = 0;
|
|
144
|
-
}
|
|
145
143
|
const indexData = await this.parse(opts);
|
|
146
144
|
const refId = indexData.refNameToId[refName];
|
|
147
145
|
if (refId === undefined) {
|
|
@@ -151,12 +149,12 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
151
149
|
if (!ba) {
|
|
152
150
|
return [];
|
|
153
151
|
}
|
|
154
|
-
|
|
155
|
-
// min >= 2**31 overflows int32 and produces a negative >> 14 result —
|
|
156
|
-
// query is well beyond the indexed range
|
|
157
|
-
if (linearIndex.length > 0 && min >= 2 ** 31) {
|
|
152
|
+
if (min > TBI_MAX_REF_LENGTH) {
|
|
158
153
|
console.warn('querying outside of possible tabix range');
|
|
159
154
|
}
|
|
155
|
+
// clamp before the >> 14 below, which would truncate to int32 and go
|
|
156
|
+
// negative past 2**31
|
|
157
|
+
const beg = Math.min(Math.max(min, 0), TBI_MAX_REF_LENGTH);
|
|
160
158
|
const overlappingBins = reg2bins(min, max); // List of bin #s that overlap min, max
|
|
161
159
|
const chunks = [];
|
|
162
160
|
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
|
|
@@ -173,7 +171,8 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
173
171
|
// The linear index is monotonically non-decreasing, so the minimum virtual
|
|
174
172
|
// offset for chunks that could overlap [min, ...) is at index minLin.
|
|
175
173
|
// SYNC: ~/src/gmod/bam-js/src/bai.ts getLowestChunk
|
|
176
|
-
const
|
|
174
|
+
const linearIndex = ba.linearIndex;
|
|
175
|
+
const lowest = linearIndex?.[Math.min(beg >> 14, linearIndex.length - 1)];
|
|
177
176
|
return (0, util_ts_1.optimizeChunks)(chunks, lowest);
|
|
178
177
|
}
|
|
179
178
|
}
|
package/dist/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAsC;AACtC,
|
|
1
|
+
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAsC;AACtC,uCAOkB;AAClB,yDAA8C;AAK9C,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAErC,8DAA8D;AAC9D,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,MAAM,kBAAkB,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,SAAS,GAAG,CAAC,CAAC,CAAA;AAEpD;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,qEAAqE;IACrE,yEAAyE;IACzE,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,EAAE,kBAAkB,CAAC,CAAA;IACxD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAC/C,MAAM,IAAI,GAAkC,EAAE,CAAA;IAC9C,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QACX,IAAI,CAAC,IAAI,CACP,CAAC,CAAC,EAAE,CAAC,CAAC,EACN,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAC9B,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAC9B,CAAC,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAChC,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAClC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CACrC,CAAA;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAS;IAC/C,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,UAAU,EAAE,IAAI,CAAC,UAAU;SAC5B,CAAC,CAAA;QACF,MAAM,KAAK,GAAG,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAe,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC5C,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAE3D,oEAAoE;QACpE,MAAM,EACJ,WAAW,EACX,WAAW,EACX,cAAc,EACd,MAAM,EACN,aAAa,EACb,QAAQ,EACR,SAAS,GACV,GAAG,IAAA,sBAAY,EAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QAC1B,+EAA+E;QAC/E,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAErD,iEAAiE;QACjE,mEAAmE;QACnE,IAAI,IAAI,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACjC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAa,EAAE,CAAA;QAE5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAChD,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,IAAI,IAAI,EAAE,GAAG,UAAU,CAAA;gBACzB,CAAC;qBAAM,CAAC;oBACN,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;wBACpE,IAAI,IAAI,EAAE,CAAA;oBACZ,CAAC;gBACH,CAAC;YACH,CAAC;YACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;gBACpE,IAAI,IAAI,CAAC,CAAA;YACX,CAAC;QACH,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YAC5B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,GAAG,GAAG,KAAK,CAAA;YACf,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAC7C,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;gBACzC,GAAG,IAAI,CAAC,CAAA;gBACR,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;wBACrB,KAAK,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,GAAG,GAAG,EAAE,CAAC,CAAA;oBACzC,CAAC;oBACD,GAAG,IAAI,EAAE,GAAG,UAAU,CAAA;gBACxB,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC,CAAA;oBACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CACnB,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,CAAC,EACrB,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,GAAG,CAAC,CAAC,EACzB,GAAG,CACJ,CAAA;wBACD,GAAG,IAAI,EAAE,CAAA;oBACX,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAChD,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAgB,EAAE,MAAM,EAAE,WAAW,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|
package/dist/util.d.ts
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
2
|
import type VirtualOffset from './virtualOffset.ts';
|
|
3
3
|
export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
|
|
4
|
+
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
|
|
4
5
|
export declare function findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
|
|
5
6
|
export declare function parseNameBytes(namesBytes: Uint8Array): {
|
|
6
7
|
refNameToId: Record<string, number>;
|
package/dist/util.js
CHANGED
|
@@ -4,6 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
exports.optimizeChunks = optimizeChunks;
|
|
7
|
+
exports.clampChunkEnds = clampChunkEnds;
|
|
7
8
|
exports.findFirstData = findFirstData;
|
|
8
9
|
exports.parseNameBytes = parseNameBytes;
|
|
9
10
|
exports.parseAuxData = parseAuxData;
|
|
@@ -61,7 +62,7 @@ function optimizeChunks(chunks, lowest) {
|
|
|
61
62
|
const cmp = chunkMaxBlock - lastMaxBlock ||
|
|
62
63
|
chunk.maxv.dataPosition - lastChunk.maxv.dataPosition;
|
|
63
64
|
if (cmp > 0) {
|
|
64
|
-
mergedChunks[mergedChunks.length - 1] = new chunk_ts_1.default(lastChunk.minv, chunk.maxv, lastChunk.bin);
|
|
65
|
+
mergedChunks[mergedChunks.length - 1] = new chunk_ts_1.default(lastChunk.minv, chunk.maxv, lastChunk.bin, chunk.endPosition);
|
|
65
66
|
lastMaxBlock = chunkMaxBlock;
|
|
66
67
|
}
|
|
67
68
|
}
|
|
@@ -73,6 +74,41 @@ function optimizeChunks(chunks, lowest) {
|
|
|
73
74
|
}
|
|
74
75
|
return mergedChunks;
|
|
75
76
|
}
|
|
77
|
+
// Tighten each chunk's endPosition (default: a full max-size BGZF block past
|
|
78
|
+
// maxv) down to the next known block boundary. Every chunk min/maxv blockPosition
|
|
79
|
+
// and every extraBoundary (e.g. linear-index entries) is a real BGZF block start;
|
|
80
|
+
// since blocks don't overlap, the first boundary strictly greater than a chunk's
|
|
81
|
+
// maxv.blockPosition is an upper bound on where that final block ends — always at
|
|
82
|
+
// least the true block end, so the clamped fetch still contains the whole block.
|
|
83
|
+
// Shrinks both the byte estimate and the actual fetch with no extra I/O.
|
|
84
|
+
function clampChunkEnds(chunks, extraBoundaries = []) {
|
|
85
|
+
// Array#sort with a comparator beats a Float64Array numeric sort here:
|
|
86
|
+
// extraBoundaries (the linear index) arrives already sorted and TimSort
|
|
87
|
+
// exploits the existing run, which introsort cannot.
|
|
88
|
+
const boundaries = [...extraBoundaries];
|
|
89
|
+
for (const c of chunks) {
|
|
90
|
+
boundaries.push(c.minv.blockPosition, c.maxv.blockPosition);
|
|
91
|
+
}
|
|
92
|
+
boundaries.sort((a, b) => a - b);
|
|
93
|
+
for (const c of chunks) {
|
|
94
|
+
const max = c.maxv.blockPosition;
|
|
95
|
+
// first boundary strictly greater than max
|
|
96
|
+
let lo = 0;
|
|
97
|
+
let hi = boundaries.length;
|
|
98
|
+
while (lo < hi) {
|
|
99
|
+
const mid = (lo + hi) >>> 1;
|
|
100
|
+
if (boundaries[mid] > max) {
|
|
101
|
+
hi = mid;
|
|
102
|
+
}
|
|
103
|
+
else {
|
|
104
|
+
lo = mid + 1;
|
|
105
|
+
}
|
|
106
|
+
}
|
|
107
|
+
if (lo < boundaries.length) {
|
|
108
|
+
c.endPosition = Math.min(c.endPosition, boundaries[lo]);
|
|
109
|
+
}
|
|
110
|
+
}
|
|
111
|
+
}
|
|
76
112
|
function findFirstData(currentFdl, virtualOffset) {
|
|
77
113
|
return !currentFdl || currentFdl.compareTo(virtualOffset) > 0
|
|
78
114
|
? virtualOffset
|
|
@@ -105,7 +141,7 @@ const tabixFormats = {
|
|
|
105
141
|
2: 'VCF',
|
|
106
142
|
};
|
|
107
143
|
function parseAuxData(bytes, offset) {
|
|
108
|
-
const dataView = new DataView(bytes.buffer);
|
|
144
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
109
145
|
const formatFlags = dataView.getInt32(offset, true);
|
|
110
146
|
const coordinateType = formatFlags & 0x1_00_00 ? 'zero-based-half-open' : '1-based-closed';
|
|
111
147
|
const format = tabixFormats[formatFlags & 0xf];
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;AAQA,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;AAQA,wCAuEC;AASD,wCA8BC;AAED,sCAOC;AAED,wCAoBC;AAQD,oCAkCC;AAED,wCAEC;AAGD,wCAgBC;AAtND,mEAAoC;AAEpC,0DAA8B;AAC9B,uCAAmD;AAInD,qDAAqD;AACrD,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;IACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,MAAM,CAAA;IACf,CAAC;IAED,uEAAuE;IACvE,wEAAwE;IACxE,2EAA2E;IAC3E,IAAI,QAAiB,CAAA;IACrB,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,WAAW,GAAG,MAAM,CAAC,aAAa,CAAA;QACxC,MAAM,UAAU,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,QAAQ,GAAG,EAAE,CAAA;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;YACxB,MAAM,GAAG,GACP,KAAK,CAAC,IAAI,CAAC,aAAa,GAAG,WAAW;gBACtC,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,UAAU,CAAA;YACtC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACtB,CAAC;QACH,CAAC;QACD,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,QAAQ,CAAA;QACjB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,QAAQ,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,4EAA4E;IAC5E,0DAA0D;IAC1D,oEAAoE;IACpE,MAAM,YAAY,GAAY,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;IAC5C,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAClD,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAElD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,IACE,aAAa,GAAG,YAAY,GAAG,MAAM;YACrC,aAAa,GAAG,YAAY,GAAG,SAAS,EACxC,CAAC;YACD,MAAM,SAAS,GAAG,YAAY,CAAC,EAAE,CAAC,CAAC,CAAC,CAAE,CAAA;YACtC,MAAM,GAAG,GACP,aAAa,GAAG,YAAY;gBAC5B,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,YAAY,CAAA;YACvD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,YAAY,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,kBAAK,CAC/C,SAAS,CAAC,IAAI,EACd,KAAK,CAAC,IAAI,EACV,SAAS,CAAC,GAAG,EACb,KAAK,CAAC,WAAW,CAClB,CAAA;gBACD,YAAY,GAAG,aAAa,CAAA;YAC9B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACxB,YAAY,GAAG,aAAa,CAAA;YAC5B,YAAY,GAAG,aAAa,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,6EAA6E;AAC7E,kFAAkF;AAClF,kFAAkF;AAClF,iFAAiF;AACjF,kFAAkF;AAClF,iFAAiF;AACjF,yEAAyE;AACzE,SAAgB,cAAc,CAC5B,MAAe,EACf,kBAA4B,EAAE;IAE9B,uEAAuE;IACvE,wEAAwE;IACxE,qDAAqD;IACrD,MAAM,UAAU,GAAG,CAAC,GAAG,eAAe,CAAC,CAAA;IACvC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;IAC7D,CAAC;IACD,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IAEhC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,aAAa,CAAA;QAChC,2CAA2C;QAC3C,IAAI,EAAE,GAAG,CAAC,CAAA;QACV,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;QAC1B,OAAO,EAAE,GAAG,EAAE,EAAE,CAAC;YACf,MAAM,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,CAAA;YAC3B,IAAI,UAAU,CAAC,GAAG,CAAE,GAAG,GAAG,EAAE,CAAC;gBAC3B,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,EAAE,GAAG,GAAG,GAAG,CAAC,CAAA;YACd,CAAC;QACH,CAAC;QACD,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;YAC3B,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,UAAU,CAAC,EAAE,CAAE,CAAC,CAAA;QAC1D,CAAC;IACH,CAAC;AACH,CAAC;AAED,SAAgB,aAAa,CAC3B,UAAqC,EACrC,aAA4B;IAE5B,OAAO,CAAC,UAAU,IAAI,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;QAC3D,CAAC,CAAC,aAAa;QACf,CAAC,CAAC,UAAU,CAAA;AAChB,CAAC;AAED,SAAgB,cAAc,CAAC,UAAsB;IACnD,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,OAAO,CAAC,CAAA;IACxC,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,OAAO,GAAG,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;QAC/B,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;QACtC,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE,CAAC;YACf,MAAK;QACP,CAAC;QACD,IAAI,GAAG,GAAG,GAAG,EAAE,CAAC;YACd,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;YAC7D,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;YAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;QAClC,CAAC;QACD,GAAG,GAAG,GAAG,GAAG,CAAC,CAAA;QACb,SAAS,EAAE,CAAA;IACb,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,MAAM,YAAY,GAA2B;IAC3C,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,KAAK;IACR,CAAC,EAAE,KAAK;CACT,CAAA;AAED,SAAgB,YAAY,CAAC,KAAiB,EAAE,MAAc;IAC5D,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;IACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IACnD,MAAM,cAAc,GAClB,WAAW,GAAG,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;IACrE,MAAM,MAAM,GAAG,YAAY,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;IAC9C,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;IACrE,CAAC;IACD,MAAM,aAAa,GAAG;QACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;QACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;QAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;KAC1C,CAAA;IACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC9D,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,cAAc,CACjD,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CAAA;IACD,OAAO;QACL,WAAW;QACX,WAAW;QACX,SAAS;QACT,QAAQ;QACR,aAAa;QACb,MAAM;QACN,cAAc;KACf,CAAA;AACH,CAAC;AAED,SAAgB,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO,EAAE,SAAS,EAAE,IAAA,iCAAuB,EAAC,KAAK,EAAE,MAAM,CAAC,EAAE,CAAA;AAC9D,CAAC;AAED,0DAA0D;AAC1D,SAAgB,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,GAAG,GAAG,IAAI,mBAAG,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAC3C,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,MAAM,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC7B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,GAAG,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QACxB,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC"}
|
package/esm/chunk.d.ts
CHANGED
|
@@ -3,7 +3,8 @@ export default class Chunk {
|
|
|
3
3
|
minv: VirtualOffset;
|
|
4
4
|
maxv: VirtualOffset;
|
|
5
5
|
bin: number;
|
|
6
|
-
|
|
6
|
+
endPosition: number;
|
|
7
|
+
constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, endPosition?: number);
|
|
7
8
|
toString(): string;
|
|
8
9
|
fetchedSize(): number;
|
|
9
10
|
}
|
package/esm/chunk.js
CHANGED
|
@@ -3,16 +3,22 @@ export default class Chunk {
|
|
|
3
3
|
minv;
|
|
4
4
|
maxv;
|
|
5
5
|
bin;
|
|
6
|
-
|
|
6
|
+
// Absolute byte offset where the fetch for this chunk ends. The compressed
|
|
7
|
+
// size of the final BGZF block (the one at maxv.blockPosition) is unknown
|
|
8
|
+
// from the index, so this defaults to a full max-size block past maxv. It can
|
|
9
|
+
// be tightened to the next known block boundary via clampChunkEnds.
|
|
10
|
+
endPosition;
|
|
11
|
+
constructor(minv, maxv, bin, endPosition = maxv.blockPosition + (1 << 16)) {
|
|
7
12
|
this.minv = minv;
|
|
8
13
|
this.maxv = maxv;
|
|
9
14
|
this.bin = bin;
|
|
15
|
+
this.endPosition = endPosition;
|
|
10
16
|
}
|
|
11
17
|
toString() {
|
|
12
18
|
return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
|
|
13
19
|
}
|
|
14
20
|
fetchedSize() {
|
|
15
|
-
return this.
|
|
21
|
+
return this.endPosition - this.minv.blockPosition;
|
|
16
22
|
}
|
|
17
23
|
}
|
|
18
24
|
//# sourceMappingURL=chunk.js.map
|
package/esm/chunk.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IACjB,IAAI,CAAe;IACnB,IAAI,CAAe;IACnB,GAAG,CAAQ;
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IACjB,IAAI,CAAe;IACnB,IAAI,CAAe;IACnB,GAAG,CAAQ;IAClB,2EAA2E;IAC3E,0EAA0E;IAC1E,8EAA8E;IAC9E,oEAAoE;IAC7D,WAAW,CAAQ;IAE1B,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;QAE5C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACnD,CAAC;CACF"}
|
package/esm/csi.d.ts
CHANGED
|
@@ -2,16 +2,10 @@ import Chunk from './chunk.ts';
|
|
|
2
2
|
import IndexFile from './indexFile.ts';
|
|
3
3
|
import type { Options, RefIndex } from './indexFile.ts';
|
|
4
4
|
import type VirtualOffset from './virtualOffset.ts';
|
|
5
|
-
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
6
5
|
export default class CSI extends IndexFile {
|
|
7
6
|
private maxBinNumber;
|
|
8
7
|
private depth;
|
|
9
8
|
private minShift;
|
|
10
|
-
constructor(args: {
|
|
11
|
-
filehandle: GenericFilehandle;
|
|
12
|
-
});
|
|
13
|
-
/** @internal */
|
|
14
|
-
indexCov(): void;
|
|
15
9
|
/** @internal */
|
|
16
10
|
_parse(opts?: Options): Promise<{
|
|
17
11
|
csi: boolean;
|
package/esm/csi.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
2
|
import Chunk from "./chunk.js";
|
|
3
3
|
import IndexFile from "./indexFile.js";
|
|
4
|
-
import { findFirstData, memoizeByRefId, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
|
|
4
|
+
import { clampChunkEnds, findFirstData, memoizeByRefId, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
|
|
5
5
|
import { fromBytes } from "./virtualOffset.js";
|
|
6
6
|
const CSI1_MAGIC = 21_582_659; // CSI\1
|
|
7
7
|
const CSI2_MAGIC = 38_359_875; // CSI\2
|
|
@@ -14,19 +14,9 @@ function rshift(num, bits) {
|
|
|
14
14
|
return Math.floor(num / 2 ** bits);
|
|
15
15
|
}
|
|
16
16
|
export default class CSI extends IndexFile {
|
|
17
|
-
maxBinNumber;
|
|
18
|
-
depth;
|
|
19
|
-
minShift;
|
|
20
|
-
constructor(args) {
|
|
21
|
-
super(args);
|
|
22
|
-
this.maxBinNumber = 0;
|
|
23
|
-
this.depth = 0;
|
|
24
|
-
this.minShift = 0;
|
|
25
|
-
}
|
|
26
|
-
/** @internal */
|
|
27
|
-
indexCov() {
|
|
28
|
-
throw new Error('CSI indexes do not support indexcov');
|
|
29
|
-
}
|
|
17
|
+
maxBinNumber = 0;
|
|
18
|
+
depth = 0;
|
|
19
|
+
minShift = 0;
|
|
30
20
|
/** @internal */
|
|
31
21
|
async _parse(opts = {}) {
|
|
32
22
|
const buf = await this.filehandle.readFile({
|
|
@@ -34,7 +24,7 @@ export default class CSI extends IndexFile {
|
|
|
34
24
|
onProgress: opts.onProgress,
|
|
35
25
|
});
|
|
36
26
|
const bytes = (await unzip(buf));
|
|
37
|
-
const dataView = new DataView(bytes.buffer);
|
|
27
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
38
28
|
const magic = dataView.getUint32(0, true);
|
|
39
29
|
let csiVersion;
|
|
40
30
|
if (magic === CSI1_MAGIC) {
|
|
@@ -115,6 +105,7 @@ export default class CSI extends IndexFile {
|
|
|
115
105
|
binIndex[bin] = chunks;
|
|
116
106
|
}
|
|
117
107
|
}
|
|
108
|
+
clampChunkEnds(Object.values(binIndex).flat());
|
|
118
109
|
return { binIndex, stats };
|
|
119
110
|
}
|
|
120
111
|
return {
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,aAAa,EACb,cAAc,EACd,cAAc,EACd,YAAY,EACZ,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
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package/esm/long.d.ts
CHANGED
package/esm/long.js
CHANGED
package/esm/long.js.map
CHANGED
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@@ -1 +1 @@
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|
|
1
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-
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|
1
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+
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