@gmod/tabix 1.5.7 → 1.5.9
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 +11 -1
- package/README.md +19 -22
- package/dist/csi.js +2 -2
- package/dist/csi.js.map +1 -1
- package/dist/index.js +1 -0
- package/dist/index.js.map +1 -1
- package/dist/tabixIndexedFile.d.ts +1 -1
- package/dist/tabixIndexedFile.js +3 -3
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.js +2 -2
- package/dist/tbi.js.map +1 -1
- package/esm/csi.js +2 -2
- package/esm/csi.js.map +1 -1
- package/esm/index.js +1 -0
- package/esm/index.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +1 -1
- package/esm/tabixIndexedFile.js +3 -3
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/tbi.js +2 -2
- package/esm/tbi.js.map +1 -1
- package/package.json +1 -1
- package/src/csi.ts +2 -2
- package/src/index.ts +1 -0
- package/src/tabixIndexedFile.ts +4 -4
- package/src/tbi.ts +2 -2
package/CHANGELOG.md
CHANGED
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@@ -1,7 +1,17 @@
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## [1.5.
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## [1.5.9](https://github.com/GMOD/tabix-js/compare/v1.5.8...v1.5.9) (2023-03-27)
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- Revert the Buffer::slice -> Buffer::subarray change due to use with polyfills
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## [1.5.8](https://github.com/GMOD/tabix-js/compare/v1.5.7...v1.5.8) (2023-03-24)
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- Make yieldTime optional
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## [1.5.7](https://github.com/GMOD/tabix-js/compare/v1.5.6...v1.5.7) (2023-03-24)
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- Add yieldTime parameter
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- Improve typescripting
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package/README.md
CHANGED
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@@ -14,7 +14,7 @@ Read Tabix-indexed files using either .tbi or .csi indexes.
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### Importing the module
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```
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```typescript
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// import with require in node.js
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const { TabixIndexedFile } = require('@gmod/tabix')
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@@ -28,7 +28,7 @@ Basic usage of TabixIndexedFile under node.js supplies a path and optionally a
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tbiPath to the constructor. If no tbiPath is supplied, it assumes that the
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path+'.tbi' is the location of the tbiPath.
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```
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```typescript
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// basic usage under node.js provides a file path on the filesystem to bgzipped file
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// it assumes the tbi file is path+'.tbi' if no tbiPath is supplied
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const tbiIndexed = new TabixIndexedFile({
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@@ -43,7 +43,7 @@ The renameRefSeqs callback makes it so that you can use
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file.getLines('1',0,100,...) even when the file itself contains names like
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'chr1' (can also do the reverse by customizing the renameRefSeqs callback)
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```
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```typescript
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// can also open tabix files that have a .csi index
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// note also usage of renameRefSeqs callback to trim chr off the chr names
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const csiIndexed = new TabixIndexedFile({
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[generic-filehandle](https://github.com/GMOD/generic-filehandle) module
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RemoteFile filehandle, as seen below
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```
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```typescript
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// use a remote file or other filehandle, note RemoteFile comes from https://github.com/GMOD/generic-filehandle
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const {RemoteFile} = require('generic-filehandle')
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const { RemoteFile } = require('generic-filehandle')
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const remoteTbiIndexed = new TabixIndexedFile({
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filehandle: new RemoteFile('http://yourhost/file.vcf.gz'),
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tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi') // can also be csiFilehandle
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tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi'), // can also be csiFilehandle
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})
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```
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@@ -72,12 +72,12 @@ This works in both the browser and in node.js, but note that in node.js you have
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to also supply a custom fetch function to the RemoteFile constructor e.g. like
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this
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```
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```typescript
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// for node.js you have to manually supply a fetch function e.g. node-fetch to RemoteFile
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const fetch = require('node-fetch')
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const remoteTbiIndexedForNodeJs = new TabixIndexedFile({
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filehandle: new RemoteFile('http://yourhost/file.vcf.gz', {fetch}),
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tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi', {fetch}) // can also be csiFilehandle
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filehandle: new RemoteFile('http://yourhost/file.vcf.gz', { fetch }),
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tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi', { fetch }), // can also be csiFilehandle
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})
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```
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0-based half-open coordinates. This is different from the 1-based values that
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are supplied to the tabix command line tool
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```
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```typescript
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// iterate over lines in the specified region
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const lines = []
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await tbiIndexed.getLines('ctgA',200,300, function(line, fileOffset) {
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await tbiIndexed.getLines('ctgA', 200, 300, function (line, fileOffset) {
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lines.push(line)
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})
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```
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After running this, your `lines` array would contain an array of lines from the
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You can also supply some extra arguments to getLines with this format, but these
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are sort of obscure and only used in some circumstances
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```
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```typescript
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const lines = []
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const aborter = new AbortController()
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await tbiIndexed.getLines('ctgA',200,300, {
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await tbiIndexed.getLines('ctgA', 200, 300, {
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lineCallback: (line, fileOffset) => lines.push(line),
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signal: aborter.signal // an optional AbortSignal from an AbortController
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signal: aborter.signal, // an optional AbortSignal from an AbortController
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})
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```
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After running the above demo, lines is now an array of strings, containing the
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start going to the end of the contig e.g.
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```
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```typescript
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const lines = []
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await tbiIndexed.getLines('ctgA', 0, undefined, line=>lines.push(line))`
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console.log(lines)
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### lineCount
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```
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```typescript
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// get the approximate number of data lines in the
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// file for the given reference sequence, excluding header, comment, and whitespace lines
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// uses the extra bin from tabix
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const numLines = await tbiIndexed.lineCount('ctgA')
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// or const numLines = await tbiIndexed.lineCount('ctgA', { signal: aborter.signal })
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```
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### getHeader
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```
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```typescript
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// get the "header text" string from the file, which is the first contiguous
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// set of lines in the file that all start with a "meta" character (usually #)
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const headerText = await tbiIndexed.getHeader()
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#### getHeaderBuffer
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```
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```typescript
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// or if you want a nodejs Buffer object instead, there is getHeaderBuffer()
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const headerBuffer = await tbiIndexed.getHeaderBuffer()
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// or const headerBuffer = await tbiIndexed.getHeaderBuffer({ signal: aborter.signal })
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package/dist/csi.js
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const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
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const skipLines = bytes.readInt32LE(offset + 20);
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const { refIdToName, refNameToId } = this._parseNameBytes(bytes.
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const { refIdToName, refNameToId } = this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength));
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}
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const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.
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const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
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}
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package/dist/csi.js.map
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+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gDAAuB;AACvB,2DAA6C;AAE7C,iEAA0D;AAC1D,oDAA2B;AAC3B,iCAAqD;AAErD,4DAAgD;AAEhD,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACK,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;;YACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,GAAG,EAAE;gBACR,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,KAAK,EAAE;gBACT,OAAO,KAAK,CAAC,SAAS,CAAA;aACvB;YACD,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;KAAA;IACK,QAAQ;;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;QACxD,CAAC;KAAA;IAED,YAAY,CAAC,KAAa,EAAE,MAAc;QACxC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACtE,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;SACpE;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC1D,CAAA;QAED,OAAO;YACL,WAAW;YACX,WAAW;YACX,SAAS;YACT,QAAQ;YACR,aAAa;YACb,MAAM;YACN,cAAc;SACf,CAAA;IACH,CAAC;IAED,eAAe,CAAC,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,MAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IAEtB,MAAM,CAAC,OAAgB,EAAE;;YAC7B,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAC,CAAA;YAE3E,0BAA0B;YAC1B,IAAI,UAAU,CAAA;YACd,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;gBACxC,UAAU,GAAG,CAAC,CAAA;aACf;iBAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;gBAC/C,UAAU,GAAG,CAAC,CAAA;aACf;iBAAM;gBACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;aACrD;YAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YAC3D,MAAM,YAAY,GAAG,SAAA,CAAC,EAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA,CAAA;YAC1D,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,MAAM,GAAG,GACP,SAAS,IAAI,SAAS,IAAI,EAAE;gBAC1B,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC;gBAC9B,CAAC,CAAC;oBACE,WAAW,EAAE,EAAE;oBACf,WAAW,EAAE,EAAE;oBACf,QAAQ,EAAE,IAAI;oBACd,aAAa,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE;oBAC3C,cAAc,EAAE,sBAAsB;oBACtC,MAAM,EAAE,SAAS;iBAClB,CAAA;YACP,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;YAElD,+CAA+C;YAC/C,IAAI,aAAwC,CAAA;YAC5C,IAAI,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;YACnC,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;gBACnD,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBAC9C,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;gBAC/C,IAAI,KAAK,CAAA,CAAC,iDAAiD;gBAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;oBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;oBAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;wBAC3B,yDAAyD;wBACzD,qCAAqC;wBACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;qBAClC;yBAAM;wBACL,MAAM,OAAO,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GA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|
package/dist/index.js
CHANGED
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,0EAAiD;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,0EAAiD;AAKxC,2BALF,0BAAgB,CAKE;AAJzB,gDAAuB;AAII,cAJpB,aAAG,CAIoB;AAH9B,gDAAuB;AAGS,cAHzB,aAAG,CAGyB;AADnC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA"}
|
|
@@ -35,7 +35,7 @@ export default class TabixIndexedFile {
|
|
|
35
35
|
tbiFilehandle?: GenericFilehandle;
|
|
36
36
|
csiPath?: string;
|
|
37
37
|
csiFilehandle?: GenericFilehandle;
|
|
38
|
-
yieldTime
|
|
38
|
+
yieldTime?: number;
|
|
39
39
|
chunkSizeLimit?: number;
|
|
40
40
|
renameRefSeqs?: (n: string) => string;
|
|
41
41
|
chunkCacheSize?: number;
|
package/dist/tabixIndexedFile.js
CHANGED
|
@@ -154,7 +154,7 @@ class TabixIndexedFile {
|
|
|
154
154
|
if (n === -1) {
|
|
155
155
|
break;
|
|
156
156
|
}
|
|
157
|
-
const b = buffer.
|
|
157
|
+
const b = buffer.slice(blockStart, n);
|
|
158
158
|
const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
|
|
159
159
|
if (dpositions) {
|
|
160
160
|
while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
|
|
@@ -244,7 +244,7 @@ class TabixIndexedFile {
|
|
|
244
244
|
lastNewline = i;
|
|
245
245
|
}
|
|
246
246
|
}
|
|
247
|
-
bytes = bytes.
|
|
247
|
+
bytes = bytes.slice(0, lastNewline + 1);
|
|
248
248
|
}
|
|
249
249
|
return bytes;
|
|
250
250
|
});
|
|
@@ -400,7 +400,7 @@ class TabixIndexedFile {
|
|
|
400
400
|
return __awaiter(this, void 0, void 0, function* () {
|
|
401
401
|
const b = Buffer.alloc(size);
|
|
402
402
|
const { bytesRead, buffer } = yield this.filehandle.read(b, 0, size, pos, opts);
|
|
403
|
-
return buffer.
|
|
403
|
+
return buffer.slice(0, bytesRead);
|
|
404
404
|
});
|
|
405
405
|
}
|
|
406
406
|
/**
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
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package/dist/tbi.js
CHANGED
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@@ -114,7 +114,7 @@ class TabixIndex extends indexFile_1.default {
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|
|
114
114
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const skipLines = bytes.readInt32LE(28);
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|
115
115
|
// read sequence dictionary
|
|
116
116
|
const nameSectionLength = bytes.readInt32LE(32);
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|
117
|
-
const { refNameToId, refIdToName } = this._parseNameBytes(bytes.
|
|
117
|
+
const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
|
|
118
118
|
// read the indexes for each reference sequence
|
|
119
119
|
let currOffset = 36 + nameSectionLength;
|
|
120
120
|
let firstDataLine;
|
|
@@ -180,7 +180,7 @@ class TabixIndex extends indexFile_1.default {
|
|
|
180
180
|
});
|
|
181
181
|
}
|
|
182
182
|
parsePseudoBin(bytes, offset) {
|
|
183
|
-
const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.
|
|
183
|
+
const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
|
|
184
184
|
return { lineCount };
|
|
185
185
|
}
|
|
186
186
|
_parseNameBytes(namesBytes) {
|
package/dist/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gDAAuB;AACvB,iEAA0D;AAC1D,oDAA2B;AAC3B,2DAA6C;AAC7C,iCAAuE;AACvE,4DAAgD;AAEhD,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;GAEG;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;KACzC,CAAA;AACH,CAAC;AAED,MAAqB,UAAW,SAAQ,mBAAS;IACzC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;;YACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,GAAG,EAAE;gBACR,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,KAAK,EAAE;gBACT,OAAO,KAAK,CAAC,SAAS,CAAA;aACvB;YACD,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;KAAA;IAED,4BAA4B;IACtB,MAAM,CAAC,OAAgB,EAAE;;YAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YAChD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAA;YAC9B,IAAA,uBAAgB,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YAE7B,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,aAAa,EAAE;gBACrD,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;aACrD;YAED,6CAA6C;YAC7C,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACrC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACxC,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;YACnE,MAAM,UAAU,GAA8B;gBAC5C,CAAC,EAAE,SAAS;gBACZ,CAAC,EAAE,KAAK;gBACR,CAAC,EAAE,KAAK;aACT,CAAA;YACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,EAAE;gBACX,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;aACpE;YACD,MAAM,aAAa,GAAG;gBACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC1B,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC5B,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;aAC3B,CAAA;YACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,MAAM,KAAK,GAAG,CAAC,CAAA;YACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YACvD,MAAM,YAAY,GAAG,SAAA,CAAC,EAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA,CAAA;YAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;YAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAEvC,2BAA2B;YAC3B,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAC/C,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,
|
|
1
|
+
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gDAAuB;AACvB,iEAA0D;AAC1D,oDAA2B;AAC3B,2DAA6C;AAC7C,iCAAuE;AACvE,4DAAgD;AAEhD,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;GAEG;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;KACzC,CAAA;AACH,CAAC;AAED,MAAqB,UAAW,SAAQ,mBAAS;IACzC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;;YACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,GAAG,EAAE;gBACR,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,KAAK,EAAE;gBACT,OAAO,KAAK,CAAC,SAAS,CAAA;aACvB;YACD,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;KAAA;IAED,4BAA4B;IACtB,MAAM,CAAC,OAAgB,EAAE;;YAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YAChD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAA;YAC9B,IAAA,uBAAgB,EAAC,IAAI,CAAC,MAAM,CAAC,CAAA;YAE7B,0BAA0B;YAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,aAAa,EAAE;gBACrD,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;aACrD;YAED,6CAA6C;YAC7C,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACrC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACxC,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;YACnE,MAAM,UAAU,GAA8B;gBAC5C,CAAC,EAAE,SAAS;gBACZ,CAAC,EAAE,KAAK;gBACR,CAAC,EAAE,KAAK;aACT,CAAA;YACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,EAAE;gBACX,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;aACpE;YACD,MAAM,aAAa,GAAG;gBACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC1B,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;gBAC5B,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;aAC3B,CAAA;YACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,MAAM,KAAK,GAAG,CAAC,CAAA;YACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YACvD,MAAM,YAAY,GAAG,SAAA,CAAC,EAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA,CAAA;YAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;YAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAEvC,2BAA2B;YAC3B,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YAC/C,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CACxC,CAAA;YAED,+CAA+C;YAC/C,IAAI,UAAU,GAAG,EAAE,GAAG,iBAAiB,CAAA;YACvC,IAAI,aAAwC,CAAA;YAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;gBACnD,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBAC9C,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;gBAC/C,IAAI,KAAK,CAAA;gBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;oBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;oBAC1C,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE;wBAC1B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;qBACF;yBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE;wBACnC,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAChD,UAAU,IAAI,CAAC,CAAA;wBACf,IAAI,UAAU,KAAK,CAAC,EAAE;4BACpB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;yBAC/C;wBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;qBAC9B;yBAAM;wBACL,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAChD,UAAU,IAAI,CAAC,CAAA;wBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;wBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;4BACtC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;4BACtC,MAAM,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;4BAC1C,UAAU,IAAI,EAAE,CAAA;4BAChB,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;4BACrD,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;yBACjC;wBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;qBACvB;iBACF;gBAED,mBAAmB;gBACnB,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBACjD,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;gBAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE;oBACvC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oBAC7C,UAAU,IAAI,CAAC,CAAA;oBACf,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;iBACnE;gBACD,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;YACzC,CAAC,CAAC,CAAA;YAEF,OAAO;gBACL,OAAO;gBACP,QAAQ;gBACR,YAAY;gBACZ,YAAY;gB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|
package/esm/csi.js
CHANGED
|
@@ -54,7 +54,7 @@ export default class CSI extends IndexFile {
|
|
|
54
54
|
const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
|
|
55
55
|
const skipLines = bytes.readInt32LE(offset + 20);
|
|
56
56
|
const nameSectionLength = bytes.readInt32LE(offset + 24);
|
|
57
|
-
const { refIdToName, refNameToId } = this._parseNameBytes(bytes.
|
|
57
|
+
const { refIdToName, refNameToId } = this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength));
|
|
58
58
|
return {
|
|
59
59
|
refIdToName,
|
|
60
60
|
refNameToId,
|
|
@@ -164,7 +164,7 @@ export default class CSI extends IndexFile {
|
|
|
164
164
|
};
|
|
165
165
|
}
|
|
166
166
|
parsePseudoBin(bytes, offset) {
|
|
167
|
-
const lineCount = longToNumber(Long.fromBytesLE(bytes.
|
|
167
|
+
const lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
|
|
168
168
|
return { lineCount };
|
|
169
169
|
}
|
|
170
170
|
async blocksForRange(refName, min, max, opts = {}) {
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,QAAQ,CAAA;AAErD,OAAO,SAAsB,MAAM,aAAa,CAAA;AAEhD,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,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,IAAI,CAAC,SAAS,EAAE;YACd,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE;YACR,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE;YACT,OAAO,KAAK,CAAC,SAAS,CAAA;SACvB;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,YAAY,CAAC,KAAa,EAAE,MAAc;QACxC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACtE,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;SACpE;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,MAAM,QAAQ,CAAA;AAErD,OAAO,SAAsB,MAAM,aAAa,CAAA;AAEhD,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,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,IAAI,CAAC,SAAS,EAAE;YACd,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE;YACR,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE;YACT,OAAO,KAAK,CAAC,SAAS,CAAA;SACvB;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;IACxD,CAAC;IAED,YAAY,CAAC,KAAa,EAAE,MAAc;QACxC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACtE,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;SACpE;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC1D,CAAA;QAED,OAAO;YACL,WAAW;YACX,WAAW;YACX,SAAS;YACT,QAAQ;YACR,aAAa;YACb,MAAM;YACN,cAAc;SACf,CAAA;IACH,CAAC;IAED,eAAe,CAAC,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,MAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IAE5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAC,CAAA;QAE3E,0BAA0B;QAC1B,IAAI,UAAU,CAAA;QACd,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;YACxC,UAAU,GAAG,CAAC,CAAA;SACf;aAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;YAC/C,UAAU,GAAG,CAAC,CAAA;SACf;aAAM;YACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACjC,oDAAoD;SACrD;QAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACjC,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,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QACvC,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,IAAI;gBACd,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,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;QAElD,+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,oBAAoB;YACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC9C,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;YAC/C,IAAI,KAAK,CAAA,CAAC,iDAAiD;YAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gBAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;oBAC3B,yDAAyD;oBACzD,qCAAqC;oBACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oBAClD,UAAU,IAAI,CAAC,GAAG,CAAC,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|
package/esm/index.js
CHANGED
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AAEvB,OAAO,EAAE,gBAAgB,EAAE,GAAG,EAAE,GAAG,EAAE,CAAA"}
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,gBAAgB,MAAM,oBAAoB,CAAA;AACjD,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AAEvB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;AAClB,OAAO,EAAE,gBAAgB,EAAE,GAAG,EAAE,GAAG,EAAE,CAAA"}
|
|
@@ -35,7 +35,7 @@ export default class TabixIndexedFile {
|
|
|
35
35
|
tbiFilehandle?: GenericFilehandle;
|
|
36
36
|
csiPath?: string;
|
|
37
37
|
csiFilehandle?: GenericFilehandle;
|
|
38
|
-
yieldTime
|
|
38
|
+
yieldTime?: number;
|
|
39
39
|
chunkSizeLimit?: number;
|
|
40
40
|
renameRefSeqs?: (n: string) => string;
|
|
41
41
|
chunkCacheSize?: number;
|
package/esm/tabixIndexedFile.js
CHANGED
|
@@ -139,7 +139,7 @@ export default class TabixIndexedFile {
|
|
|
139
139
|
if (n === -1) {
|
|
140
140
|
break;
|
|
141
141
|
}
|
|
142
|
-
const b = buffer.
|
|
142
|
+
const b = buffer.slice(blockStart, n);
|
|
143
143
|
const line = (decoder === null || decoder === void 0 ? void 0 : decoder.decode(b)) || b.toString();
|
|
144
144
|
if (dpositions) {
|
|
145
145
|
while (blockStart + c.minv.dataPosition >= dpositions[pos++]) { }
|
|
@@ -225,7 +225,7 @@ export default class TabixIndexedFile {
|
|
|
225
225
|
lastNewline = i;
|
|
226
226
|
}
|
|
227
227
|
}
|
|
228
|
-
bytes = bytes.
|
|
228
|
+
bytes = bytes.slice(0, lastNewline + 1);
|
|
229
229
|
}
|
|
230
230
|
return bytes;
|
|
231
231
|
}
|
|
@@ -373,7 +373,7 @@ export default class TabixIndexedFile {
|
|
|
373
373
|
async _readRegion(pos, size, opts = {}) {
|
|
374
374
|
const b = Buffer.alloc(size);
|
|
375
375
|
const { bytesRead, buffer } = await this.filehandle.read(b, 0, size, pos, opts);
|
|
376
|
-
return buffer.
|
|
376
|
+
return buffer.slice(0, bytesRead);
|
|
377
377
|
}
|
|
378
378
|
/**
|
|
379
379
|
* read and uncompress the data in a chunk (composed of one or more
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
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package/esm/tbi.js
CHANGED
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@@ -74,7 +74,7 @@ export default class TabixIndex extends IndexFile {
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|
|
74
74
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const skipLines = bytes.readInt32LE(28);
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|
75
75
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// read sequence dictionary
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|
76
76
|
const nameSectionLength = bytes.readInt32LE(32);
|
|
77
|
-
const { refNameToId, refIdToName } = this._parseNameBytes(bytes.
|
|
77
|
+
const { refNameToId, refIdToName } = this._parseNameBytes(bytes.slice(36, 36 + nameSectionLength));
|
|
78
78
|
// read the indexes for each reference sequence
|
|
79
79
|
let currOffset = 36 + nameSectionLength;
|
|
80
80
|
let firstDataLine;
|
|
@@ -139,7 +139,7 @@ export default class TabixIndex extends IndexFile {
|
|
|
139
139
|
};
|
|
140
140
|
}
|
|
141
141
|
parsePseudoBin(bytes, offset) {
|
|
142
|
-
const lineCount = longToNumber(Long.fromBytesLE(bytes.
|
|
142
|
+
const lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
|
|
143
143
|
return { lineCount };
|
|
144
144
|
}
|
|
145
145
|
_parseNameBytes(namesBytes) {
|
package/esm/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
package/src/csi.ts
CHANGED
|
@@ -66,7 +66,7 @@ export default class CSI extends IndexFile {
|
|
|
66
66
|
const nameSectionLength = bytes.readInt32LE(offset + 24)
|
|
67
67
|
|
|
68
68
|
const { refIdToName, refNameToId } = this._parseNameBytes(
|
|
69
|
-
bytes.
|
|
69
|
+
bytes.slice(offset + 28, offset + 28 + nameSectionLength),
|
|
70
70
|
)
|
|
71
71
|
|
|
72
72
|
return {
|
|
@@ -187,7 +187,7 @@ export default class CSI extends IndexFile {
|
|
|
187
187
|
parsePseudoBin(bytes: Buffer, offset: number) {
|
|
188
188
|
const lineCount = longToNumber(
|
|
189
189
|
Long.fromBytesLE(
|
|
190
|
-
bytes.
|
|
190
|
+
bytes.slice(offset + 28, offset + 36) as unknown as number[],
|
|
191
191
|
true,
|
|
192
192
|
),
|
|
193
193
|
)
|
package/src/index.ts
CHANGED
package/src/tabixIndexedFile.ts
CHANGED
|
@@ -68,7 +68,7 @@ export default class TabixIndexedFile {
|
|
|
68
68
|
tbiFilehandle?: GenericFilehandle
|
|
69
69
|
csiPath?: string
|
|
70
70
|
csiFilehandle?: GenericFilehandle
|
|
71
|
-
yieldTime
|
|
71
|
+
yieldTime?: number
|
|
72
72
|
chunkSizeLimit?: number
|
|
73
73
|
renameRefSeqs?: (n: string) => string
|
|
74
74
|
chunkCacheSize?: number
|
|
@@ -203,7 +203,7 @@ export default class TabixIndexedFile {
|
|
|
203
203
|
if (n === -1) {
|
|
204
204
|
break
|
|
205
205
|
}
|
|
206
|
-
const b = buffer.
|
|
206
|
+
const b = buffer.slice(blockStart, n)
|
|
207
207
|
const line = decoder?.decode(b) || b.toString()
|
|
208
208
|
|
|
209
209
|
if (dpositions) {
|
|
@@ -311,7 +311,7 @@ export default class TabixIndexedFile {
|
|
|
311
311
|
lastNewline = i
|
|
312
312
|
}
|
|
313
313
|
}
|
|
314
|
-
bytes = bytes.
|
|
314
|
+
bytes = bytes.slice(0, lastNewline + 1)
|
|
315
315
|
}
|
|
316
316
|
return bytes
|
|
317
317
|
}
|
|
@@ -482,7 +482,7 @@ export default class TabixIndexedFile {
|
|
|
482
482
|
opts,
|
|
483
483
|
)
|
|
484
484
|
|
|
485
|
-
return buffer.
|
|
485
|
+
return buffer.slice(0, bytesRead)
|
|
486
486
|
}
|
|
487
487
|
|
|
488
488
|
/**
|
package/src/tbi.ts
CHANGED
|
@@ -83,7 +83,7 @@ export default class TabixIndex extends IndexFile {
|
|
|
83
83
|
// read sequence dictionary
|
|
84
84
|
const nameSectionLength = bytes.readInt32LE(32)
|
|
85
85
|
const { refNameToId, refIdToName } = this._parseNameBytes(
|
|
86
|
-
bytes.
|
|
86
|
+
bytes.slice(36, 36 + nameSectionLength),
|
|
87
87
|
)
|
|
88
88
|
|
|
89
89
|
// read the indexes for each reference sequence
|
|
@@ -155,7 +155,7 @@ export default class TabixIndex extends IndexFile {
|
|
|
155
155
|
parsePseudoBin(bytes: Buffer, offset: number) {
|
|
156
156
|
const lineCount = longToNumber(
|
|
157
157
|
Long.fromBytesLE(
|
|
158
|
-
bytes.
|
|
158
|
+
bytes.slice(offset + 16, offset + 24) as unknown as number[],
|
|
159
159
|
true,
|
|
160
160
|
),
|
|
161
161
|
)
|