@gmod/tabix 3.4.2 → 3.5.0
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/csi.d.ts +8 -6
- package/dist/csi.js +33 -17
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +2 -0
- package/dist/indexFile.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 +21 -23
- package/dist/tbi.js.map +1 -1
- package/dist/util.js +4 -1
- package/dist/util.js.map +1 -1
- package/esm/csi.d.ts +8 -6
- package/esm/csi.js +33 -17
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +2 -0
- package/esm/indexFile.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 +21 -23
- package/esm/tbi.js.map +1 -1
- package/esm/util.js +4 -1
- package/esm/util.js.map +1 -1
- package/package.json +3 -1
- package/src/csi.ts +41 -18
- package/src/indexFile.ts +2 -0
- package/src/long.ts +1 -2
- package/src/tabixIndexedFile.ts +70 -30
- package/src/tbi.ts +33 -25
- package/src/util.ts +12 -2
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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29
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+
// An explicitly supplied index always wins over the `<path>.tbi` /
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30
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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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32
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if (tbiFilehandle) {
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33
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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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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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(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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-
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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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-
}
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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(`${path}.tbi`) });
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111
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-
}
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-
else if (csiUrl) {
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113
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this.index = new csi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(csiUrl) });
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114
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-
}
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115
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-
else if (tbiUrl) {
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116
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-
this.index = new tbi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(tbiUrl) });
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-
}
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-
else if (url) {
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119
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this.index = new tbi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(`${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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csiPath,
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+
tbiUrl,
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133
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csiUrl,
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path,
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url,
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});
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137
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this.chunkCache = new abortable_promise_cache_1.default({
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138
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cache: new quick_lru_1.default({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
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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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continue;
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}
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-
// find tab positions
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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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|
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
|
|
@@ -128,7 +128,7 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
128
128
|
indices: (0, util_ts_1.memoizeByRefId)(getIndices),
|
|
129
129
|
metaChar,
|
|
130
130
|
maxBinNumber,
|
|
131
|
-
maxRefLength,
|
|
131
|
+
maxRefLength: TBI_MAX_REF_LENGTH,
|
|
132
132
|
skipLines,
|
|
133
133
|
firstDataLine,
|
|
134
134
|
columnNumbers,
|
|
@@ -140,9 +140,6 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
140
140
|
};
|
|
141
141
|
}
|
|
142
142
|
async blocksForRange(refName, min, max, opts = {}) {
|
|
143
|
-
if (min < 0) {
|
|
144
|
-
min = 0;
|
|
145
|
-
}
|
|
146
143
|
const indexData = await this.parse(opts);
|
|
147
144
|
const refId = indexData.refNameToId[refName];
|
|
148
145
|
if (refId === undefined) {
|
|
@@ -152,12 +149,12 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
152
149
|
if (!ba) {
|
|
153
150
|
return [];
|
|
154
151
|
}
|
|
155
|
-
|
|
156
|
-
// min >= 2**31 overflows int32 and produces a negative >> 14 result —
|
|
157
|
-
// query is well beyond the indexed range
|
|
158
|
-
if (linearIndex.length > 0 && min >= 2 ** 31) {
|
|
152
|
+
if (min > TBI_MAX_REF_LENGTH) {
|
|
159
153
|
console.warn('querying outside of possible tabix range');
|
|
160
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);
|
|
161
158
|
const overlappingBins = reg2bins(min, max); // List of bin #s that overlap min, max
|
|
162
159
|
const chunks = [];
|
|
163
160
|
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
|
|
@@ -174,7 +171,8 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
174
171
|
// The linear index is monotonically non-decreasing, so the minimum virtual
|
|
175
172
|
// offset for chunks that could overlap [min, ...) is at index minLin.
|
|
176
173
|
// SYNC: ~/src/gmod/bam-js/src/bai.ts getLowestChunk
|
|
177
|
-
const
|
|
174
|
+
const linearIndex = ba.linearIndex;
|
|
175
|
+
const lowest = linearIndex?.[Math.min(beg >> 14, linearIndex.length - 1)];
|
|
178
176
|
return (0, util_ts_1.optimizeChunks)(chunks, lowest);
|
|
179
177
|
}
|
|
180
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,uCAOkB;AAClB,yDAA8C;AAK9C,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAErC;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,
|
|
1
|
+
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|
package/dist/util.js
CHANGED
|
@@ -82,6 +82,9 @@ function optimizeChunks(chunks, lowest) {
|
|
|
82
82
|
// least the true block end, so the clamped fetch still contains the whole block.
|
|
83
83
|
// Shrinks both the byte estimate and the actual fetch with no extra I/O.
|
|
84
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.
|
|
85
88
|
const boundaries = [...extraBoundaries];
|
|
86
89
|
for (const c of chunks) {
|
|
87
90
|
boundaries.push(c.minv.blockPosition, c.maxv.blockPosition);
|
|
@@ -138,7 +141,7 @@ const tabixFormats = {
|
|
|
138
141
|
2: 'VCF',
|
|
139
142
|
};
|
|
140
143
|
function parseAuxData(bytes, offset) {
|
|
141
|
-
const dataView = new DataView(bytes.buffer);
|
|
144
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
142
145
|
const formatFlags = dataView.getInt32(offset, true);
|
|
143
146
|
const coordinateType = formatFlags & 0x1_00_00 ? 'zero-based-half-open' : '1-based-closed';
|
|
144
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,wCAuEC;AASD,
|
|
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,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|
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;
|
|
@@ -56,6 +50,14 @@ export default class CSI extends IndexFile {
|
|
|
56
50
|
format: string;
|
|
57
51
|
}>;
|
|
58
52
|
blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
|
|
53
|
+
/**
|
|
54
|
+
* CSI's equivalent of the BAI/TBI linear index: the loffset of the deepest
|
|
55
|
+
* indexed bin covering `beg` is the earliest virtual offset any record
|
|
56
|
+
* overlapping `beg` can have, so chunks ending at or before it are dead.
|
|
57
|
+
* Walks leaf -> previous sibling -> parent until an indexed bin is found.
|
|
58
|
+
* SYNC: htslib hts_itr_query min_off computation
|
|
59
|
+
*/
|
|
60
|
+
private minOffset;
|
|
59
61
|
/** @internal */
|
|
60
62
|
reg2bins(beg: number, end: number): (readonly [number, number])[];
|
|
61
63
|
}
|
package/esm/csi.js
CHANGED
|
@@ -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) {
|
|
@@ -95,6 +85,7 @@ export default class CSI extends IndexFile {
|
|
|
95
85
|
const binCount = dataView.getInt32(pos, true);
|
|
96
86
|
pos += 4;
|
|
97
87
|
const binIndex = {};
|
|
88
|
+
const loffsets = {};
|
|
98
89
|
let stats;
|
|
99
90
|
for (let j = 0; j < binCount; j++) {
|
|
100
91
|
const bin = dataView.getUint32(pos, true);
|
|
@@ -104,7 +95,8 @@ export default class CSI extends IndexFile {
|
|
|
104
95
|
pos += 28 + 16;
|
|
105
96
|
}
|
|
106
97
|
else {
|
|
107
|
-
|
|
98
|
+
loffsets[bin] = fromBytes(bytes, pos);
|
|
99
|
+
pos += 8;
|
|
108
100
|
const chunkCount = dataView.getInt32(pos, true);
|
|
109
101
|
pos += 4;
|
|
110
102
|
const chunks = Array.from({ length: chunkCount });
|
|
@@ -116,7 +108,7 @@ export default class CSI extends IndexFile {
|
|
|
116
108
|
}
|
|
117
109
|
}
|
|
118
110
|
clampChunkEnds(Object.values(binIndex).flat());
|
|
119
|
-
return { binIndex, stats };
|
|
111
|
+
return { binIndex, loffsets, stats };
|
|
120
112
|
}
|
|
121
113
|
return {
|
|
122
114
|
...aux,
|
|
@@ -158,7 +150,31 @@ export default class CSI extends IndexFile {
|
|
|
158
150
|
}
|
|
159
151
|
}
|
|
160
152
|
}
|
|
161
|
-
return optimizeChunks(chunks);
|
|
153
|
+
return optimizeChunks(chunks, this.minOffset(ba.loffsets, min));
|
|
154
|
+
}
|
|
155
|
+
/**
|
|
156
|
+
* CSI's equivalent of the BAI/TBI linear index: the loffset of the deepest
|
|
157
|
+
* indexed bin covering `beg` is the earliest virtual offset any record
|
|
158
|
+
* overlapping `beg` can have, so chunks ending at or before it are dead.
|
|
159
|
+
* Walks leaf -> previous sibling -> parent until an indexed bin is found.
|
|
160
|
+
* SYNC: htslib hts_itr_query min_off computation
|
|
161
|
+
*/
|
|
162
|
+
minOffset(loffsets, beg) {
|
|
163
|
+
let found;
|
|
164
|
+
if (loffsets) {
|
|
165
|
+
// first bin of the deepest level, i.e. (8**depth - 1) / 7
|
|
166
|
+
let bin = (lshift(1, 3 * this.depth) - 1) / 7 + rshift(beg, this.minShift);
|
|
167
|
+
while (found === undefined && bin > 0) {
|
|
168
|
+
found = loffsets[bin];
|
|
169
|
+
if (found === undefined) {
|
|
170
|
+
const parent = Math.floor((bin - 1) / 8);
|
|
171
|
+
const firstChild = parent * 8 + 1;
|
|
172
|
+
bin = bin > firstChild ? bin - 1 : parent;
|
|
173
|
+
}
|
|
174
|
+
}
|
|
175
|
+
found ??= loffsets[0];
|
|
176
|
+
}
|
|
177
|
+
return found;
|
|
162
178
|
}
|
|
163
179
|
/** @internal */
|
|
164
180
|
reg2bins(beg, end) {
|
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,cAAc,EACd,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/indexFile.d.ts
CHANGED
|
@@ -16,6 +16,8 @@ export interface RefIndex {
|
|
|
16
16
|
lineCount: number;
|
|
17
17
|
};
|
|
18
18
|
linearIndex?: VirtualOffset[];
|
|
19
|
+
/** CSI only: per-bin loffset, the linear index's equivalent for pruning */
|
|
20
|
+
loffsets?: Record<number, VirtualOffset>;
|
|
19
21
|
}
|
|
20
22
|
export interface IndexData {
|
|
21
23
|
refNameToId: Record<string, number>;
|
package/esm/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAyCA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAC9B,UAAU,CAAmB;IAC5B,MAAM,CAAqB;IAEnC,YAAY,EAAE,UAAU,EAAqC;QAC3D,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;IAC9B,CAAC;IAID,gBAAgB;IACT,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACxD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAA;IACzD,CAAC;IAED,gBAAgB;IACT,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IAUD,gBAAgB;IAChB,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;YACzD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,MAAM,KAAK,CAAA;QACb,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IACvC,CAAC;CACF"}
|
package/esm/long.d.ts
CHANGED
package/esm/long.js
CHANGED
package/esm/long.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"AAAA,MAAM,
|
|
1
|
+
{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"AAAA,MAAM,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AAE9B,MAAM,UAAU,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}
|