@gmod/tabix 3.1.0 → 3.1.1
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 +3 -1
- package/dist/csi.d.ts +0 -4
- package/dist/csi.js +1 -23
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +4 -0
- package/dist/indexFile.js +22 -0
- package/dist/indexFile.js.map +1 -1
- package/dist/package.json +1 -0
- package/dist/tabix-bundle.js +1 -0
- package/dist/tabixIndexedFile.d.ts +1 -0
- package/dist/tabixIndexedFile.js +68 -62
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.d.ts +0 -4
- package/dist/tbi.js +1 -23
- package/dist/tbi.js.map +1 -1
- package/esm/csi.d.ts +0 -4
- package/esm/csi.js +1 -23
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +4 -0
- package/esm/indexFile.js +22 -0
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +1 -0
- package/esm/tabixIndexedFile.js +68 -62
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/tbi.d.ts +0 -4
- package/esm/tbi.js +1 -23
- package/esm/tbi.js.map +1 -1
- package/package.json +8 -8
- package/src/csi.ts +1 -26
- package/src/indexFile.ts +25 -0
- package/src/tabixIndexedFile.ts +107 -69
- package/src/tbi.ts +1 -26
package/dist/tbi.js
CHANGED
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@@ -92,7 +92,7 @@ class TabixIndex extends indexFile_ts_1.default {
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92
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1: 'SAM',
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2: 'VCF',
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};
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-
const format = formatOpts[formatFlags &
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+
const format = formatOpts[formatFlags & 0xf];
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if (!format) {
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throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
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}
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@@ -182,28 +182,6 @@ class TabixIndex extends indexFile_ts_1.default {
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lineCount: (0, long_ts_1.longFromBytesToUnsigned)(bytes, offset + 16),
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183
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};
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}
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185
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-
_parseNameBytes(namesBytes) {
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186
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-
let currRefId = 0;
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187
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-
let currNameStart = 0;
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188
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-
const refIdToName = [];
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-
const refNameToId = {};
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-
const decoder = new TextDecoder('utf8');
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-
for (let i = 0; i < namesBytes.length; i += 1) {
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-
if (!namesBytes[i]) {
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193
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-
if (currNameStart < i) {
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-
const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
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-
refIdToName[currRefId] = refName;
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196
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-
refNameToId[refName] = currRefId;
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-
}
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-
currNameStart = i + 1;
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-
currRefId += 1;
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-
}
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-
}
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-
return {
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-
refNameToId,
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-
refIdToName,
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-
};
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-
}
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async blocksForRange(refName, min, max, opts = {}) {
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if (min < 0) {
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min = 0;
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package/dist/tbi.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
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+
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAmD;AACnD,uCAAmD;AACnD,uCAA4D;AAC5D,uEAA6D;AAE7D,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAS;IAC/C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,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,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAA;IACxD,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAChD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAA;QAC9B,IAAA,0BAAgB,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAC7B,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,KAAK,KAAK,SAAS,CAAC,aAAa,EAAE,CAAC;YACtC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,6CAA6C;QAC7C,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC/C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,UAAU,GAA2B;YACzC,CAAC,EAAE,SAAS;YACZ,CAAC,EAAE,KAAK;YACR,CAAC,EAAE,KAAK;SACT,CAAA;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC5C,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;YAChC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;YAClC,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC;SACjC,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAE7C,2BAA2B;QAC3B,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QACrD,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CACxC,CAAA;QAED,+CAA+C;QAC/C,IAAI,UAAU,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACvC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;YACnD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACpD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;gBAChD,UAAU,IAAI,CAAC,CAAA;gBACf,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,UAAU,EAAE,IAAI,CAAC,CAAA;oBACtD,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;wBACrB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAChD,CAAC;oBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;gBAC/B,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;oBACtD,UAAU,IAAI,CAAC,CAAA;oBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBACrD,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,mBAAmB;YACnB,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACvD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;YAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACxC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gBAC7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|
package/esm/csi.d.ts
CHANGED
|
@@ -21,10 +21,6 @@ export default class CSI extends IndexFile {
|
|
|
21
21
|
format: string;
|
|
22
22
|
coordinateType: string;
|
|
23
23
|
};
|
|
24
|
-
_parseNameBytes(namesBytes: Uint8Array): {
|
|
25
|
-
refNameToId: Record<string, number>;
|
|
26
|
-
refIdToName: string[];
|
|
27
|
-
};
|
|
28
24
|
_parse(opts?: Options): Promise<{
|
|
29
25
|
csi: boolean;
|
|
30
26
|
refCount: number;
|
package/esm/csi.js
CHANGED
|
@@ -47,7 +47,7 @@ export default class CSI extends IndexFile {
|
|
|
47
47
|
const dataView = new DataView(bytes.buffer);
|
|
48
48
|
const formatFlags = dataView.getInt32(offset, true);
|
|
49
49
|
const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
|
|
50
|
-
const format = formats[(formatFlags &
|
|
50
|
+
const format = formats[(formatFlags & 0xf)];
|
|
51
51
|
if (!format) {
|
|
52
52
|
throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
|
|
53
53
|
}
|
|
@@ -71,28 +71,6 @@ export default class CSI extends IndexFile {
|
|
|
71
71
|
coordinateType,
|
|
72
72
|
};
|
|
73
73
|
}
|
|
74
|
-
_parseNameBytes(namesBytes) {
|
|
75
|
-
let currRefId = 0;
|
|
76
|
-
let currNameStart = 0;
|
|
77
|
-
const refIdToName = [];
|
|
78
|
-
const refNameToId = {};
|
|
79
|
-
const decoder = new TextDecoder('utf8');
|
|
80
|
-
for (let i = 0; i < namesBytes.length; i += 1) {
|
|
81
|
-
if (!namesBytes[i]) {
|
|
82
|
-
if (currNameStart < i) {
|
|
83
|
-
const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
|
|
84
|
-
refIdToName[currRefId] = refName;
|
|
85
|
-
refNameToId[refName] = currRefId;
|
|
86
|
-
}
|
|
87
|
-
currNameStart = i + 1;
|
|
88
|
-
currRefId += 1;
|
|
89
|
-
}
|
|
90
|
-
}
|
|
91
|
-
return {
|
|
92
|
-
refNameToId,
|
|
93
|
-
refIdToName,
|
|
94
|
-
};
|
|
95
|
-
}
|
|
96
74
|
async _parse(opts = {}) {
|
|
97
75
|
const bytes = await unzip(await this.filehandle.readFile(opts));
|
|
98
76
|
const dataView = new DataView(bytes.buffer);
|
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,SAAsB,MAAM,gBAAgB,CAAA;AACnD,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AACnD,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC1C,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAE7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,OAAO,GAAG;IACd,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,KAAK;IACR,CAAC,EAAE,KAAK;CACT,CAAA;AAED,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,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,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE,CAAC;YACV,OAAO,KAAK,CAAC,SAAS,CAAA;QACxB,CAAC;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACnD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,WAAW,GAAG,GAAG,CAAc,CAAC,CAAA;QACxD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CAAA;QAED,OAAO;YACL,WAAW;YACX,WAAW;YACX,SAAS;YACT,QAAQ;YACR,aAAa;YACb,MAAM;YACN,cAAc;SACf,CAAA;IACH,CAAC;IAED,
|
|
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,SAAsB,MAAM,gBAAgB,CAAA;AACnD,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AACnD,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC1C,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAE7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,OAAO,GAAG;IACd,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,KAAK;IACR,CAAC,EAAE,KAAK;CACT,CAAA;AAED,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACD,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,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,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE,CAAC;YACT,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE,CAAC;YACV,OAAO,KAAK,CAAC,SAAS,CAAA;QACxB,CAAC;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,QAAQ;QACN,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACnD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,OAAO,CAAC,CAAC,WAAW,GAAG,GAAG,CAAc,CAAC,CAAA;QACxD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CAAA;QAED,OAAO;YACL,WAAW;YACX,WAAW;YACX,SAAS;YACT,QAAQ;YACR,aAAa;YACb,MAAM;YACN,cAAc;SACf,CAAA;IACH,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAA;QAC/D,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,0BAA0B;QAC1B,IAAI,UAAU,CAAA;QACd,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,UAAU,EAAE,CAAC;YAC/C,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,UAAU,EAAE,CAAC;YACtD,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1D,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GACP,SAAS,IAAI,SAAS,IAAI,EAAE;YAC1B,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC;YAC9B,CAAC,CAAC;gBACE,WAAW,EAAE,EAAE;gBACf,WAAW,EAAE,EAAE;gBACf,QAAQ,EAAE,SAAS;gBACnB,aAAa,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE;gBAC3C,cAAc,EAAE,sBAAsB;gBACtC,MAAM,EAAE,SAAS;aAClB,CAAA;QACP,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,aAAwC,CAAA;QAC5C,IAAI,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QACnC,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;YACnD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACpD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;gBAChD,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,mEAAmE;oBACnE,2BAA2B;oBAC3B,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oBAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;gBACnC,CAAC;qBAAM,CAAC;oBACN,MAAM,OAAO,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oBAChD,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,OAAO,CAAC,CAAA;oBAC3D,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;oBAC3D,UAAU,IAAI,EAAE,CAAA;oBAChB,MAAM,MAAM,GAAG,IAA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|
package/esm/indexFile.d.ts
CHANGED
|
@@ -44,4 +44,8 @@ export default abstract class IndexFile {
|
|
|
44
44
|
_findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
|
|
45
45
|
parse(opts?: Options): Promise<IndexData>;
|
|
46
46
|
hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
|
|
47
|
+
_parseNameBytes(namesBytes: Uint8Array): {
|
|
48
|
+
refNameToId: Record<string, number>;
|
|
49
|
+
refIdToName: string[];
|
|
50
|
+
};
|
|
47
51
|
}
|
package/esm/indexFile.js
CHANGED
|
@@ -30,5 +30,27 @@ export default class IndexFile {
|
|
|
30
30
|
const idx = await this.parse(opts);
|
|
31
31
|
return !!idx.indices[seqId]?.binIndex;
|
|
32
32
|
}
|
|
33
|
+
_parseNameBytes(namesBytes) {
|
|
34
|
+
let currRefId = 0;
|
|
35
|
+
let currNameStart = 0;
|
|
36
|
+
const refIdToName = [];
|
|
37
|
+
const refNameToId = {};
|
|
38
|
+
const decoder = new TextDecoder('utf8');
|
|
39
|
+
for (let i = 0; i < namesBytes.length; i += 1) {
|
|
40
|
+
if (!namesBytes[i]) {
|
|
41
|
+
if (currNameStart < i) {
|
|
42
|
+
const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
|
|
43
|
+
refIdToName[currRefId] = refName;
|
|
44
|
+
refNameToId[refName] = currRefId;
|
|
45
|
+
}
|
|
46
|
+
currNameStart = i + 1;
|
|
47
|
+
currRefId += 1;
|
|
48
|
+
}
|
|
49
|
+
}
|
|
50
|
+
return {
|
|
51
|
+
refNameToId,
|
|
52
|
+
refIdToName,
|
|
53
|
+
};
|
|
54
|
+
}
|
|
33
55
|
}
|
|
34
56
|
//# sourceMappingURL=indexFile.js.map
|
package/esm/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAmBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,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;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;gBACvD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,KAAK,CAAA;YACb,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,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"}
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAmBA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMM,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;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE,CAAC;YACf,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,OAAO,aAAa,CAAA;QACtB,CAAC;IACH,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;gBACvD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,KAAK,CAAA;YACb,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,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;IAED,eAAe,CAAC,UAAsB;QACpC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAa,EAAE,CAAA;QAChC,MAAM,WAAW,GAA2B,EAAE,CAAA;QAC9C,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;QACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;gBACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;oBACtB,MAAM,OAAO,GAAG,IAAI,CAAC,YAAY,CAC/B,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,CAAC,CAAC,CAAC,CACtD,CAAA;oBACD,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;gBAClC,CAAC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QACD,OAAO;YACL,WAAW;YACX,WAAW;SACZ,CAAA;IACH,CAAC;CACF"}
|
|
@@ -69,6 +69,7 @@ export default class TabixIndexedFile {
|
|
|
69
69
|
* @returns promise that is resolved when the whole read is finished,
|
|
70
70
|
* rejected on error
|
|
71
71
|
*/
|
|
72
|
+
private calculateFileOffset;
|
|
72
73
|
getLines(refName: string, s: number | undefined, e: number | undefined, opts: GetLinesOpts | GetLinesCallback): Promise<void>;
|
|
73
74
|
getMetadata(opts?: Options): Promise<{
|
|
74
75
|
[key: string]: any;
|
package/esm/tabixIndexedFile.js
CHANGED
|
@@ -5,10 +5,6 @@ import LRU from 'quick-lru';
|
|
|
5
5
|
import CSI from "./csi.js";
|
|
6
6
|
import TBI from "./tbi.js";
|
|
7
7
|
import { checkAbortSignal } from "./util.js";
|
|
8
|
-
function isASCII(str) {
|
|
9
|
-
// eslint-disable-next-line no-control-regex
|
|
10
|
-
return /^[\u0000-\u007F]*$/.test(str);
|
|
11
|
-
}
|
|
12
8
|
export default class TabixIndexedFile {
|
|
13
9
|
/**
|
|
14
10
|
* @param {object} args
|
|
@@ -119,6 +115,12 @@ export default class TabixIndexedFile {
|
|
|
119
115
|
* @returns promise that is resolved when the whole read is finished,
|
|
120
116
|
* rejected on error
|
|
121
117
|
*/
|
|
118
|
+
calculateFileOffset(cpositions, dpositions, pos, blockStart, minvDataPosition) {
|
|
119
|
+
return (cpositions[pos] * (1 << 8) +
|
|
120
|
+
(blockStart - dpositions[pos]) +
|
|
121
|
+
minvDataPosition +
|
|
122
|
+
1);
|
|
123
|
+
}
|
|
122
124
|
async getLines(refName, s, e, opts) {
|
|
123
125
|
let signal;
|
|
124
126
|
let options = {};
|
|
@@ -151,60 +153,71 @@ export default class TabixIndexedFile {
|
|
|
151
153
|
let blockStart = 0;
|
|
152
154
|
let pos = 0;
|
|
153
155
|
// fast path, Buffer is just ASCII chars and not gigantor, can be
|
|
154
|
-
// converted to string and processed directly.
|
|
155
|
-
//
|
|
156
|
+
// converted to string and processed directly.
|
|
157
|
+
//
|
|
158
|
+
// if it is not ASCII or, we have to decode line by line, as it is
|
|
159
|
+
// otherwise hard to get the right 'fileOffset' based feature IDs
|
|
160
|
+
//
|
|
161
|
+
// we use a basic check for isASCII: string length equals buffer length
|
|
162
|
+
// if it is ASCII...no multi-byte decodings
|
|
156
163
|
const str = decoder.decode(buffer);
|
|
157
|
-
const strIsASCII =
|
|
158
|
-
|
|
159
|
-
|
|
160
|
-
|
|
161
|
-
if (strIsASCII) {
|
|
162
|
-
n = str.indexOf('\n', blockStart);
|
|
164
|
+
const strIsASCII = buffer.length == str.length;
|
|
165
|
+
if (strIsASCII) {
|
|
166
|
+
while (blockStart < str.length) {
|
|
167
|
+
const n = str.indexOf('\n', blockStart);
|
|
163
168
|
if (n === -1) {
|
|
164
169
|
break;
|
|
165
170
|
}
|
|
166
|
-
line = str.slice(blockStart, n);
|
|
171
|
+
const line = str.slice(blockStart, n);
|
|
172
|
+
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
|
|
173
|
+
if (dpositions) {
|
|
174
|
+
const target = blockStart + c.minv.dataPosition;
|
|
175
|
+
while (pos < dpositions.length && target >= dpositions[pos]) {
|
|
176
|
+
pos++;
|
|
177
|
+
}
|
|
178
|
+
}
|
|
179
|
+
// filter the line for whether it is within the requested range
|
|
180
|
+
const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
|
|
181
|
+
if (overlaps) {
|
|
182
|
+
callback(line, this.calculateFileOffset(cpositions, dpositions, pos, blockStart, c.minv.dataPosition));
|
|
183
|
+
}
|
|
184
|
+
else if (startCoordinate !== undefined && startCoordinate >= end) {
|
|
185
|
+
// the lines were overlapping the region, but now have stopped, so we
|
|
186
|
+
// must be at the end of the relevant data and we can stop processing
|
|
187
|
+
// data now
|
|
188
|
+
return;
|
|
189
|
+
}
|
|
190
|
+
blockStart = n + 1;
|
|
167
191
|
}
|
|
168
|
-
|
|
169
|
-
|
|
192
|
+
}
|
|
193
|
+
else {
|
|
194
|
+
while (blockStart < buffer.length) {
|
|
195
|
+
const n = buffer.indexOf('\n'.charCodeAt(0), blockStart);
|
|
170
196
|
if (n === -1) {
|
|
171
197
|
break;
|
|
172
198
|
}
|
|
173
199
|
const b = buffer.slice(blockStart, n);
|
|
174
|
-
line = decoder.decode(b);
|
|
175
|
-
|
|
176
|
-
|
|
177
|
-
|
|
178
|
-
|
|
179
|
-
|
|
180
|
-
|
|
181
|
-
|
|
182
|
-
|
|
183
|
-
|
|
184
|
-
|
|
185
|
-
|
|
186
|
-
|
|
187
|
-
|
|
188
|
-
|
|
189
|
-
|
|
190
|
-
|
|
191
|
-
|
|
192
|
-
|
|
193
|
-
|
|
194
|
-
// multiplied by (1 << 8) these uncompressed offsets get a unique
|
|
195
|
-
// space
|
|
196
|
-
cpositions[pos] * (1 << 8) +
|
|
197
|
-
(blockStart - dpositions[pos]) +
|
|
198
|
-
c.minv.dataPosition +
|
|
199
|
-
1);
|
|
200
|
-
}
|
|
201
|
-
else if (startCoordinate !== undefined && startCoordinate >= end) {
|
|
202
|
-
// the lines were overlapping the region, but now have stopped, so we
|
|
203
|
-
// must be at the end of the relevant data and we can stop processing
|
|
204
|
-
// data now
|
|
205
|
-
return;
|
|
200
|
+
const line = decoder.decode(b);
|
|
201
|
+
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
|
|
202
|
+
if (dpositions) {
|
|
203
|
+
const target = blockStart + c.minv.dataPosition;
|
|
204
|
+
while (pos < dpositions.length && target >= dpositions[pos]) {
|
|
205
|
+
pos++;
|
|
206
|
+
}
|
|
207
|
+
}
|
|
208
|
+
// filter the line for whether it is within the requested range
|
|
209
|
+
const { startCoordinate, overlaps } = this.checkLine(metadata, refName, start, end, line);
|
|
210
|
+
if (overlaps) {
|
|
211
|
+
callback(line, this.calculateFileOffset(cpositions, dpositions, pos, blockStart, c.minv.dataPosition));
|
|
212
|
+
}
|
|
213
|
+
else if (startCoordinate !== undefined && startCoordinate >= end) {
|
|
214
|
+
// the lines were overlapping the region, but now have stopped, so we
|
|
215
|
+
// must be at the end of the relevant data and we can stop processing
|
|
216
|
+
// data now
|
|
217
|
+
return;
|
|
218
|
+
}
|
|
219
|
+
blockStart = n + 1;
|
|
206
220
|
}
|
|
207
|
-
blockStart = n + 1;
|
|
208
221
|
}
|
|
209
222
|
}
|
|
210
223
|
}
|
|
@@ -349,11 +362,11 @@ export default class TabixIndexedFile {
|
|
|
349
362
|
};
|
|
350
363
|
}
|
|
351
364
|
}
|
|
352
|
-
|
|
353
|
-
currentColumnNumber += 1;
|
|
354
|
-
if (currentColumnNumber > maxColumn) {
|
|
365
|
+
if (currentColumnNumber === maxColumn) {
|
|
355
366
|
break;
|
|
356
367
|
}
|
|
368
|
+
currentColumnStart = i + 1;
|
|
369
|
+
currentColumnNumber += 1;
|
|
357
370
|
}
|
|
358
371
|
}
|
|
359
372
|
return {
|
|
@@ -370,17 +383,10 @@ export default class TabixIndexedFile {
|
|
|
370
383
|
// be another pairwise feature at the end of this one
|
|
371
384
|
const isTRA = info.includes('SVTYPE=TRA');
|
|
372
385
|
if (info[0] !== '.' && !isTRA) {
|
|
373
|
-
|
|
374
|
-
|
|
375
|
-
|
|
376
|
-
|
|
377
|
-
if (valueEnd === -1) {
|
|
378
|
-
valueEnd = info.length;
|
|
379
|
-
}
|
|
380
|
-
endCoordinate = Number.parseInt(info.slice(j + 4, valueEnd), 10);
|
|
381
|
-
break;
|
|
382
|
-
}
|
|
383
|
-
prevChar = info[j];
|
|
386
|
+
const endRegex = /(?:^|;)END=([^;]+)/;
|
|
387
|
+
const match = endRegex.exec(info);
|
|
388
|
+
if (match) {
|
|
389
|
+
endCoordinate = Number.parseInt(match[1], 10);
|
|
384
390
|
}
|
|
385
391
|
}
|
|
386
392
|
else if (isTRA) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
{"version":3,"file":"tabixIndexedFile.js","sourceRoot":"","sources":["../src/tabixIndexedFile.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,+BAA+B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAA;AAC9D,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AAC3D,OAAO,GAAG,MAAM,WAAW,CAAA;AAG3B,OAAO,GAAG,MAAM,UAAU,CAAA;AAE1B,OAAO,GAAG,MAAM,UAAU,CAAA;AAC1B,OAAO,EAAE,gBAAgB,EAAE,MAAM,WAAW,CAAA;AAkB5C,MAAM,CAAC,OAAO,OAAO,gBAAgB;IASnC;;;;;;;;;;;;;;;;;;;;;;;;;OAyBG;IACH,YAAY,EACV,IAAI,EACJ,UAAU,EACV,GAAG,EACH,OAAO,EACP,MAAM,EACN,aAAa,EACb,OAAO,EACP,MAAM,EACN,aAAa,EACb,aAAa,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EACtB,cAAc,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,GAa7B;QAtDM,UAAK,GAAG,IAAI,GAAG,CAAiD;YACrE,OAAO,EAAE,IAAI;SACd,CAAC,CAAA;QAqDA,IAAI,UAAU,EAAE,CAAC;YACf,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC9B,CAAC;aAAM,IAAI,IAAI,EAAE,CAAC;YAChB,IAAI,CAAC,UAAU,GAAG,IAAI,SAAS,CAAC,IAAI,CAAC,CAAA;QACvC,CAAC;aAAM,IAAI,GAAG,EAAE,CAAC;YACf,IAAI,CAAC,UAAU,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;QACvC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,SAAS,CAAC,wCAAwC,CAAC,CAAA;QAC/D,CAAC;QAED,IAAI,aAAa,EAAE,CAAC;YAClB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,aAAa;gBACzB,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,aAAa,EAAE,CAAC;YACzB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,aAAa;gBACzB,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,SAAS,CAAC,OAAO,CAAC;gBAClC,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,OAAO,EAAE,CAAC;YACnB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,SAAS,CAAC,OAAO,CAAC;gBAClC,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,IAAI,EAAE,CAAC;YAChB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,SAAS,CAAC,GAAG,IAAI,MAAM,CAAC;gBACxC,aAAa;aACd,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,MAAM,EAAE,CAAC;YAClB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,UAAU,CAAC,MAAM,CAAC;aACnC,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,MAAM,EAAE,CAAC;YAClB,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,UAAU,CAAC,MAAM,CAAC;aACnC,CAAC,CAAA;QACJ,CAAC;aAAM,IAAI,GAAG,EAAE,CAAC;YACf,IAAI,CAAC,KAAK,GAAG,IAAI,GAAG,CAAC;gBACnB,UAAU,EAAE,IAAI,UAAU,CAAC,GAAG,GAAG,MAAM,CAAC;aACzC,CAAC,CAAA;QACJ,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,SAAS,CACjB,oFAAoF,CACrF,CAAA;QACH,CAAC;QAED,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;QACjC,IAAI,CAAC,UAAU,GAAG,IAAI,qBAAqB,CAAmB;YAC5D,KAAK,EAAE,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC;YACnE,IAAI,EAAE,CAAC,IAAW,EAAE,MAAoB,EAAE,EAAE,CAC1C,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,MAAM,EAAE,CAAC;SACnC,CAAC,CAAA;IACJ,CAAC;IAED;;;;;;;;;;;;OAYG;IACK,mBAAmB,CACzB,UAAoB,EACpB,UAAoB,EACpB,GAAW,EACX,UAAkB,EAClB,gBAAwB;QAExB,OAAO,CACL,UAAU,CAAC,GAAG,CAAE,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;YAC3B,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAE,CAAC;YAC/B,gBAAgB;YAChB,CAAC,CACF,CAAA;IACH,CAAC;IAED,KAAK,CAAC,QAAQ,CACZ,OAAe,EACf,CAAqB,EACrB,CAAqB,EACrB,IAAqC;QAErC,IAAI,MAA+B,CAAA;QACnC,IAAI,OAAO,GAAY,EAAE,CAAA;QACzB,IAAI,QAAoD,CAAA;QAExD,IAAI,OAAO,IAAI,KAAK,UAAU,EAAE,CAAC;YAC/B,QAAQ,GAAG,IAAI,CAAA;QACjB,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,IAAI,CAAA;YACd,QAAQ,GAAG,IAAI,CAAC,YAAY,CAAA;YAC5B,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;QACtB,CAAC;QAED,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACtD,gBAAgB,CAAC,MAAM,CAAC,CAAA;QACxB,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;QACpB,MAAM,GAAG,GAAG,CAAC,IAAI,QAAQ,CAAC,YAAY,CAAA;QACtC,IAAI,CAAC,CAAC,KAAK,IAAI,GAAG,CAAC,EAAE,CAAC;YACpB,MAAM,IAAI,SAAS,CACjB,4EAA4E,CAC7E,CAAA;QACH,CAAC;QACD,IAAI,KAAK,KAAK,GAAG,EAAE,CAAC;YAClB,OAAM;QACR,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,CAAC,CAAA;QAC5E,gBAAgB,CAAC,MAAM,CAAC,CAAA;QACxB,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;QAEvC,qEAAqE;QACrE,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;YACvB,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,GAAG,CAClE,CAAC,CAAC,QAAQ,EAAE,EACZ,CAAC,EACD,MAAM,CACP,CAAA;YAED,gBAAgB,CAAC,MAAM,CAAC,CAAA;YACxB,IAAI,UAAU,GAAG,CAAC,CAAA;YAClB,IAAI,GAAG,GAAG,CAAC,CAAA;YAEX,iEAAiE;YACjE,8CAA8C;YAC9C,EAAE;YACF,kEAAkE;YAClE,iEAAiE;YACjE,EAAE;YACF,uEAAuE;YACvE,2CAA2C;YAC3C,MAAM,GAAG,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;YAClC,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,IAAI,GAAG,CAAC,MAAM,CAAA;YAC9C,IAAI,UAAU,EAAE,CAAC;gBACf,OAAO,UAAU,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC;oBAC/B,MAAM,CAAC,GAAG,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,UAAU,CAAC,CAAA;oBACvC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;wBACb,MAAK;oBACP,CAAC;oBACD,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,UAAU,EAAE,CAAC,CAAC,CAAA;oBAErC,uEAAuE;oBACvE,IAAI,UAAU,EAAE,CAAC;wBACf,MAAM,MAAM,GAAG,UAAU,GAAG,CAAC,CAAC,IAAI,CAAC,YAAY,CAAA;wBAC/C,OAAO,GAAG,GAAG,UAAU,CAAC,MAAM,IAAI,MAAM,IAAI,UAAU,CAAC,GAAG,CAAE,EAAE,CAAC;4BAC7D,GAAG,EAAE,CAAA;wBACP,CAAC;oBACH,CAAC;oBAED,+DAA+D;oBAC/D,MAAM,EAAE,eAAe,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,SAAS,CAClD,QAAQ,EACR,OAAO,EACP,KAAK,EACL,GAAG,EACH,IAAI,CACL,CAAA;oBAED,IAAI,QAAQ,EAAE,CAAC;wBACb,QAAQ,CACN,IAAI,EACJ,IAAI,CAAC,mBAAmB,CACtB,UAAU,EACV,UAAU,EACV,GAAG,EACH,UAAU,EACV,CAAC,CAAC,IAAI,CAAC,YAAY,CACpB,CACF,CAAA;oBACH,CAAC;yBAAM,IAAI,eAAe,KAAK,SAAS,IAAI,eAAe,IAAI,GAAG,E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|
package/esm/tbi.d.ts
CHANGED
|
@@ -30,9 +30,5 @@ export default class TabixIndex extends IndexFile {
|
|
|
30
30
|
parsePseudoBin(bytes: Uint8Array, offset: number): {
|
|
31
31
|
lineCount: number;
|
|
32
32
|
};
|
|
33
|
-
_parseNameBytes(namesBytes: Uint8Array): {
|
|
34
|
-
refNameToId: Record<string, number>;
|
|
35
|
-
refIdToName: string[];
|
|
36
|
-
};
|
|
37
33
|
blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
|
|
38
34
|
}
|
package/esm/tbi.js
CHANGED
|
@@ -54,7 +54,7 @@ export default class TabixIndex extends IndexFile {
|
|
|
54
54
|
1: 'SAM',
|
|
55
55
|
2: 'VCF',
|
|
56
56
|
};
|
|
57
|
-
const format = formatOpts[formatFlags &
|
|
57
|
+
const format = formatOpts[formatFlags & 0xf];
|
|
58
58
|
if (!format) {
|
|
59
59
|
throw new Error(`invalid Tabix preset format flags ${formatFlags}`);
|
|
60
60
|
}
|
|
@@ -144,28 +144,6 @@ export default class TabixIndex extends IndexFile {
|
|
|
144
144
|
lineCount: longFromBytesToUnsigned(bytes, offset + 16),
|
|
145
145
|
};
|
|
146
146
|
}
|
|
147
|
-
_parseNameBytes(namesBytes) {
|
|
148
|
-
let currRefId = 0;
|
|
149
|
-
let currNameStart = 0;
|
|
150
|
-
const refIdToName = [];
|
|
151
|
-
const refNameToId = {};
|
|
152
|
-
const decoder = new TextDecoder('utf8');
|
|
153
|
-
for (let i = 0; i < namesBytes.length; i += 1) {
|
|
154
|
-
if (!namesBytes[i]) {
|
|
155
|
-
if (currNameStart < i) {
|
|
156
|
-
const refName = this.renameRefSeq(decoder.decode(namesBytes.subarray(currNameStart, i)));
|
|
157
|
-
refIdToName[currRefId] = refName;
|
|
158
|
-
refNameToId[refName] = currRefId;
|
|
159
|
-
}
|
|
160
|
-
currNameStart = i + 1;
|
|
161
|
-
currRefId += 1;
|
|
162
|
-
}
|
|
163
|
-
}
|
|
164
|
-
return {
|
|
165
|
-
refNameToId,
|
|
166
|
-
refIdToName,
|
|
167
|
-
};
|
|
168
|
-
}
|
|
169
147
|
async blocksForRange(refName, min, max, opts = {}) {
|
|
170
148
|
if (min < 0) {
|
|
171
149
|
min = 0;
|
package/esm/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/tabix",
|
|
3
|
-
"version": "3.1.
|
|
3
|
+
"version": "3.1.1",
|
|
4
4
|
"description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
|
|
5
5
|
"type": "module",
|
|
6
6
|
"types": "./dist/index.d.ts",
|
|
@@ -35,14 +35,14 @@
|
|
|
35
35
|
"format": "prettier --write .",
|
|
36
36
|
"docs": "documentation readme --shallow src/tabixIndexedFile.ts --section TabixIndexedFile",
|
|
37
37
|
"clean": "rimraf dist esm",
|
|
38
|
-
"prebuild": "
|
|
38
|
+
"prebuild": "yarn clean",
|
|
39
39
|
"build:esm": "tsc --target es2020 --outDir esm",
|
|
40
40
|
"build:es5": "tsc --target es2020 --module commonjs --outDir dist",
|
|
41
41
|
"postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
|
|
42
|
-
"build": "
|
|
42
|
+
"build": "yarn build:esm && yarn build:es5",
|
|
43
43
|
"postbuild": "webpack",
|
|
44
|
-
"preversion": "
|
|
45
|
-
"prepublishOnly": "
|
|
44
|
+
"preversion": "yarn lint && npm test run && yarn build",
|
|
45
|
+
"prepublishOnly": "yarn lint && npm test run && yarn build",
|
|
46
46
|
"version": "standard-changelog && git add CHANGELOG.md",
|
|
47
47
|
"postversion": "git push --follow-tags"
|
|
48
48
|
},
|
|
@@ -59,17 +59,17 @@
|
|
|
59
59
|
},
|
|
60
60
|
"devDependencies": {
|
|
61
61
|
"@types/node": "^22.15.3",
|
|
62
|
-
"@vitest/coverage-v8": "^
|
|
62
|
+
"@vitest/coverage-v8": "^4.0.6",
|
|
63
63
|
"documentation": "^14.0.3",
|
|
64
64
|
"eslint": "^9.9.0",
|
|
65
65
|
"eslint-plugin-import": "^2.31.0",
|
|
66
|
-
"eslint-plugin-unicorn": "^
|
|
66
|
+
"eslint-plugin-unicorn": "^62.0.0",
|
|
67
67
|
"prettier": "^3.3.3",
|
|
68
68
|
"rimraf": "^6.0.1",
|
|
69
69
|
"standard-changelog": "^7.0.1",
|
|
70
70
|
"typescript": "^5.7.0",
|
|
71
71
|
"typescript-eslint": "^8.0.1",
|
|
72
|
-
"vitest": "^
|
|
72
|
+
"vitest": "^4.0.6",
|
|
73
73
|
"webpack": "^5.93.0",
|
|
74
74
|
"webpack-cli": "^6.0.1"
|
|
75
75
|
},
|