@gmod/bbi 2.0.5 → 3.0.0
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/CHANGELOG.md +5 -3
- package/CHANGELOG.md.orig +200 -0
- package/README.md +90 -75
- package/dist/bbi.js +16 -18
- package/dist/bbi.js.map +1 -1
- package/dist/bigbed.js +1 -1
- package/dist/bigbed.js.map +1 -1
- package/esm/bbi.js +18 -20
- package/esm/bbi.js.map +1 -1
- package/esm/bigbed.js +2 -2
- package/esm/bigbed.js.map +1 -1
- package/package.json +11 -11
- package/src/bbi.ts +5 -7
- package/src/bigbed.ts +3 -6
package/CHANGELOG.md
CHANGED
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@@ -1,12 +1,14 @@
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# [3.0.0](https://github.com/GMOD/bbi-js/compare/v2.0.5...v3.0.0) (2023-01-11)
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- Update to rxjs 7
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## [2.0.
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## [2.0.5](https://github.com/GMOD/bbi-js/compare/v2.0.4...v2.0.5) (2022-12-17)
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- Cleanup package.json and README
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## [2.0.4](https://github.com/GMOD/bbi-js/compare/v2.0.3...v2.0.4) (2022-10-15)
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- Use plain TextDecoder for decoding autoSql
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<<<<<<< Updated upstream
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## [2.0.5](https://github.com/GMOD/bbi-js/compare/v2.0.4...v2.0.5) (2022-12-17)
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- Cleanup package.json and README
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=======
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- Update to rxjs 7
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>>>>>>> Stashed changes
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## [2.0.4](https://github.com/GMOD/bbi-js/compare/v2.0.3...v2.0.4) (2022-10-15)
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- Use plain TextDecoder for decoding autoSql
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## [2.0.3](https://github.com/GMOD/bbi-js/compare/v2.0.2...v2.0.3) (2022-10-10)
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- Add BigInt64 polyfill for older safari
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## [2.0.2](https://github.com/GMOD/bbi-js/compare/v2.0.1...v2.0.2) (2022-07-18)
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- Make basesCovered a number instead of BigInt
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## [2.0.1](https://github.com/GMOD/bbi-js/compare/v2.0.0...v2.0.1) (2022-07-18)
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- Bump generic-filehandle 2->3
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# [2.0.0](https://github.com/GMOD/bbi-js/compare/v1.0.35...v2.0.0) (2022-07-18)
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- Use binary-parser instead of @gmod/binary-parser, with some optimizations.
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This uses BigInt and TextDecoder, so requires a major version bump
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## [1.0.35](https://github.com/GMOD/bbi-js/compare/v1.0.34...v1.0.35) (2022-04-22)
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- Produce actual ESM module for the "module" field in package.json, was commonJS
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- Add sourceMap:true to tsconfig
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## [1.0.34](https://github.com/GMOD/bbi-js/compare/v1.0.33...v1.0.34) (2022-03-11)
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### Reverts
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- Revert "Use subarray instead of slice since slice is deprecated under node xref 'https://nodejs.org/api/buffer.html#bufslicestart-end'" ([44116cc](https://github.com/GMOD/bbi-js/commit/44116cce54601727d37f1c449bfcc60c1b4e602d))
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* Back to slice instead of subarray, as subarray returned a UInt8Array instead
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of a true Buffer
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## [1.0.33](https://github.com/GMOD/bbi-js/compare/v1.0.32...v1.0.33) (2022-02-25)
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- Use subarray instead of slice since slice is deprecated under node xref
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'https://nodejs.org/api/buffer.html#bufslicestart-end'"
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## [1.0.32](https://github.com/GMOD/bbi-js/compare/v1.0.31...v1.0.32) (2022-02-16)
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- Use pako to decode on command line instead of using zlib to avoid need to
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manually polyfill zlib
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## [1.0.31](https://github.com/GMOD/bbi-js/compare/v1.0.30...v1.0.31) (2021-12-14)
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- Add esm module builds with less babelification for smaller bundle sizes
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## [1.0.30](https://github.com/GMOD/bbi-js/compare/v1.0.29...v1.0.30) (2020-06-25)
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- Use abortable-promise-cache instead of abortable-memoize
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- Allow opts parameter to getHeader instead of just abortsignal
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## [1.0.29](https://github.com/GMOD/bbi-js/compare/v1.0.28...v1.0.29) (2020-01-28)
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- Accidentally made the package include itself as dependency in 1.0.28, republish
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## [1.0.28](https://github.com/GMOD/bbi-js/compare/v1.0.27...v1.0.28) (2020-01-28)
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- Change typescript interface to use object keys instead of Map type for refsByName, refsById
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- Typescript only release change
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## [1.0.27](https://github.com/GMOD/bbi-js/compare/v1.0.26...v1.0.27) (2020-01-10)
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- Reduce number of requests needed on initial header
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- Add definedFieldCount to the returned Header
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Thanks to @skinner for both of these contributions!
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## [1.0.26](https://github.com/GMOD/bbi-js/compare/v1.0.25...v1.0.26) (2019-11-10)
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- Fix important bug with fixed step bigwig files not using the proper start coordinate
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## [1.0.25](https://github.com/GMOD/bbi-js/compare/v1.0.24...v1.0.25) (2019-11-03)
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- Add fix for files with a large header, if autoSql is large in a bigbed file would be likely scenario
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## [1.0.24](https://github.com/GMOD/bbi-js/compare/v1.0.23...v1.0.24) (2019-10-29)
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- Fix the uniqueIds generated via the bigbed features
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## [1.0.23](https://github.com/GMOD/bbi-js/compare/v1.0.22...v1.0.23) (2019-10-06)
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- Small refactor of `filehandle.read()` to make it more robust
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## [1.0.22](https://github.com/GMOD/bbi-js/compare/v1.0.21...v1.0.22) (2019-06-13)
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- Bump generic-filehandle
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- Add more checks for abort signal to allow early bailing
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## [1.0.21](https://github.com/GMOD/bbi-js/compare/v1.0.20...v1.0.21) (2019-05-09)
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- Add fix for reading files with greater than 256 contigs
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## [1.0.20](https://github.com/GMOD/bbi-js/compare/v1.0.19...v1.0.20) (2019-05-06)
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- Add fix that prevented accessing the lowest zoom/reduction level
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## [1.0.19](https://github.com/GMOD/bbi-js/compare/v1.0.18...v1.0.19) (2019-05-02)
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- Add regression fix since 1.0.16 for uncompressed files. Thanks to @lidaof for reporting!
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## [1.0.18](https://github.com/GMOD/bbi-js/compare/v1.0.17...v1.0.18) (2019-05-02)
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- Improve error handling of the observables (issue #20, pull #21)
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- Bump generic-filehandle to 1.0.9 to fix compatibility with native browser fetch
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## [1.0.17](https://github.com/GMOD/bbi-js/compare/v1.0.16...v1.0.17) (2019-04-30)
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- Use some standard rxjs notions for combining operator results
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- Add parsing of the extraIndex data in BigBed, allowing you to call bigbed.searchExtraIndex(name[,opts])
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## [1.0.16](https://github.com/GMOD/bbi-js/compare/v1.0.15...v1.0.16) (2019-04-23)
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- Pre-compile binary-parser instances for faster
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- Important: fixed bug that caused bigwig summary blocks to not be returned in output
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## [1.0.15](https://github.com/GMOD/bbi-js/compare/v1.0.14...v1.0.15) (2019-04-18)
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- Make important performance improvement for BigWig data
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## [1.0.14](https://github.com/GMOD/bbi-js/compare/v1.0.12...v1.0.14) (2019-04-17)
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- Improve documentation for integration with @gmod/bed@2
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- Fix some cases where abortSignal was passed incorrectly to filehandle
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## [1.0.13](https://github.com/GMOD/bbi-js/compare/v1.0.12...v1.0.13) (2019-04-14)
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- Added uniqueId to objects returned from BigBed to avoid issue with duplicates
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## [1.0.12](https://github.com/GMOD/bbi-js/compare/v1.0.11...v1.0.12) (2019-04-12)
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- Fix returning bigbed objects on empty regions
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## [1.0.11](https://github.com/GMOD/bbi-js/compare/v1.0.10...v1.0.11) (2019-04-10)
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- Removed polyfill of Array.prototype.flat which modifies global scope
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## [1.0.10](https://github.com/GMOD/bbi-js/compare/v1.0.9...v1.0.10) (2019-04-09)
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- Fix misinterpretation of variable step wig files in this module (the span is not variable in variable step files, only the step, use bedGraphToBigWig for variable span)
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- Improved docs
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## [1.0.9](https://github.com/GMOD/bbi-js/compare/v1.0.8...v1.0.9) (2019-04-05)
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- Added caching of networking requests (thanks @rbuels for the abortable-promise-cache module!)
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- Fix some type errors on the range class
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- Correct using span on fixed size wiggle types
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## [1.0.8](https://github.com/GMOD/bbi-js/compare/v1.0.7...v1.0.8) (2019-04-01)
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- Fix @babel/runtime in deployed package
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- Bugfix to the url argument to the BigWig/BigBed
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## [1.0.7](https://github.com/GMOD/bbi-js/compare/v1.0.6...v1.0.7) (2019-04-01)
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- Added getFeatureStream which returns an Observable from rxjs
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- Added url option to BigWig and BigBed constructors to allow usage of RemoteFile filehandle
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- Added typescript backend for better processing
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## [1.0.6](https://github.com/GMOD/bbi-js/compare/v1.0.5...v1.0.6) (2019-03-15)
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- Fix issue with fixed step and variable step bigwig files not working at all
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## [1.0.5](https://github.com/GMOD/bbi-js/compare/v1.0.4...v1.0.5) (2019-03-07)
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- Fix issue with jest being in deps instead of devDeps
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## [1.0.4](https://github.com/GMOD/bbi-js/compare/v1.0.3...v1.0.4) (2019-01-28)
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- Add renameRefSeqs functionality where you can apply a callback to the refseq names
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- Consistently apply start/end coordinate filters at different zoom levels
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## [1.0.3](https://github.com/GMOD/bbi-js/compare/v1.0.2...v1.0.3) (2019-01-27)
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- Fix issue with properly inflating chunks (issue #1)
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## [1.0.2](https://github.com/GMOD/bbi-js/compare/v1.0.1...v1.0.2) (2019-01-24)
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- Added regenerator-runtime to babel dist compilation
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## [1.0.1](https://github.com/GMOD/bbi-js/compare/v1.0.0...v1.0.1) (2019-01-24)
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- Added exports for BigWig and BigBed. const {BigWig, BigBed} = require('@gmod/bbi')
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# 1.0.0 (2019-01-23)
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- Initial version
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- Has support for bigwig and bigbed files
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```ts
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const { BigWig } = require('@gmod/bbi')
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const file = new BigWig({
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path: 'volvox.bw',
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})
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;(async () => {
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await file.getHeader()
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const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 })
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})()
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```
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If using remotely, you can use it in combination with generic-filehandle or your own implementation of something like generic-filehandle
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```ts
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const { BigWig } = require('@gmod/bbi')
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const { RemoteFile } = require('generic-filehandle')
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// if running in the browser, RemoteFile will use the the global fetch
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const file = new BigWig({
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filehandle: new RemoteFile('volvox.bw'),
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// if running under node.js you must supply the fetch function to RemoteFile
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const file = new BigWig({
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filehandle: new RemoteFile('volvox.bw', { fetch }),
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})
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;(async () => {
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const feats = await file.getFeatures('chr1', 0, 100, { scale: 1 })
|
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+
})()
|
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+
```
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## Documentation
|
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49
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Example:
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-
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+
```ts
|
|
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|
+
const feats = await bigwig.getFeatures('chr1', 0, 100)
|
|
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|
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// returns array of features with start, end, score
|
|
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+
// coordinates on returned data are are 0-based half open
|
|
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// no conversion to 1-based as in wig is done)
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|
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// note refseq is not returned on the object, it is clearly chr1 from the query though
|
|
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+
```
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|
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|
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### Understanding scale and reductionLevel
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@@ -89,14 +94,20 @@ Here is what the reductionLevel structure looks like in a file. The zoomLevel th
|
|
|
89
94
|
|
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95
|
Same as getFeatures but returns an RxJS observable stream, useful for very large queries
|
|
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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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|
-
|
|
98
|
-
|
|
99
|
-
|
|
97
|
+
```ts
|
|
98
|
+
const observer = await bigwig.getFeatureStream('chr1', 0, 100)
|
|
99
|
+
observer.subscribe(
|
|
100
|
+
chunk => {
|
|
101
|
+
/* chunk contains array of features with start, end, score */
|
|
102
|
+
},
|
|
103
|
+
error => {
|
|
104
|
+
/* process error */
|
|
105
|
+
},
|
|
106
|
+
() => {
|
|
107
|
+
/* completed */
|
|
108
|
+
},
|
|
109
|
+
)
|
|
110
|
+
```
|
|
100
111
|
|
|
101
112
|
### BigBed
|
|
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113
|
|
|
@@ -128,49 +139,53 @@ Returns a Promise to an array of Features, with an extra field indicating the fi
|
|
|
128
139
|
|
|
129
140
|
The BigBed line contents are returned as a raw text line e.g. {start: 0, end:100, rest: "ENST00000456328.2\t1000\t..."} where "rest" contains tab delimited text for the fields from 4 and on in the BED format. Since BED files from BigBed format often come with autoSql (a description of all the columns) it can be useful to parse it with BED parser that can handle autoSql. The rest line can be parsed by the @gmod/bed module, which is not by default integrated with this module, but can be combined with it as follows
|
|
130
141
|
|
|
131
|
-
```
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
136
|
-
|
|
137
|
-
|
|
138
|
-
|
|
139
|
-
|
|
140
|
-
|
|
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|
-
|
|
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|
-
|
|
143
|
-
|
|
144
|
-
|
|
145
|
-
|
|
146
|
-
|
|
147
|
-
|
|
142
|
+
```ts
|
|
143
|
+
import {BigBed} from '@gmod/bbi'
|
|
144
|
+
import BED from '@gmod/bed'
|
|
145
|
+
|
|
146
|
+
const ti = new BigBed({
|
|
147
|
+
filehandle: new LocalFile(require.resolve('./data/hg18.bb')),
|
|
148
|
+
})
|
|
149
|
+
const {autoSql} = await ti.getHeader()
|
|
150
|
+
const feats = await ti.getFeatures('chr7', 0, 100000)
|
|
151
|
+
const parser = new BED({autoSql})
|
|
152
|
+
const lines = feats.map(f => {
|
|
153
|
+
const { start, end, rest, uniqueId } = f
|
|
154
|
+
return parser.parseLine(`chr7\t${start}\t${end}\t${rest}, { uniqueId })\
|
|
155
|
+
})
|
|
156
|
+
// @gmod/bbi returns features with {uniqueId, start, end, rest}
|
|
157
|
+
// we reconstitute this as a line for @gmod/bed with a template string
|
|
158
|
+
// note: the uniqueId is based on file offsets and helps to deduplicate exact feature copies if they exist
|
|
148
159
|
```
|
|
149
160
|
|
|
150
161
|
Features before parsing with @gmod/bed:
|
|
151
162
|
|
|
152
|
-
```
|
|
153
|
-
|
|
154
|
-
|
|
155
|
-
|
|
156
|
-
|
|
157
|
-
|
|
163
|
+
```json
|
|
164
|
+
{
|
|
165
|
+
"chromId": 0,
|
|
166
|
+
"start": 64068,
|
|
167
|
+
"end": 64107,
|
|
168
|
+
"rest": "uc003sil.1\t0\t-\t64068\t64068\t255,0,0\t.\tDQ584609",
|
|
169
|
+
"uniqueId": "bb-171"
|
|
170
|
+
}
|
|
158
171
|
```
|
|
159
172
|
|
|
160
173
|
Features after parsing with @gmod/bed:
|
|
161
174
|
|
|
162
|
-
```
|
|
163
|
-
|
|
164
|
-
|
|
165
|
-
|
|
166
|
-
|
|
167
|
-
|
|
168
|
-
|
|
169
|
-
|
|
170
|
-
|
|
171
|
-
|
|
172
|
-
|
|
173
|
-
|
|
175
|
+
```json
|
|
176
|
+
{
|
|
177
|
+
"uniqueId": "bb-0",
|
|
178
|
+
"chrom": "chr7",
|
|
179
|
+
"chromStart": 54028,
|
|
180
|
+
"chromEnd": 73584,
|
|
181
|
+
"name": "uc003sii.2",
|
|
182
|
+
"score": 0,
|
|
183
|
+
"strand": -1,
|
|
184
|
+
"thickStart": 54028,
|
|
185
|
+
"thickEnd": 54028,
|
|
186
|
+
"reserved": "255,0,0",
|
|
187
|
+
"spID": "AL137655"
|
|
188
|
+
}
|
|
174
189
|
```
|
|
175
190
|
|
|
176
191
|
## Academic Use
|
package/dist/bbi.js
CHANGED
|
@@ -78,6 +78,20 @@ function getParsers(isBE) {
|
|
|
78
78
|
};
|
|
79
79
|
}
|
|
80
80
|
class BBI {
|
|
81
|
+
/* fetch and parse header information from a bigwig or bigbed file
|
|
82
|
+
* @param abortSignal - abort the operation, can be null
|
|
83
|
+
* @return a Header object
|
|
84
|
+
*/
|
|
85
|
+
getHeader(opts = {}) {
|
|
86
|
+
const options = 'aborted' in opts ? { signal: opts } : opts;
|
|
87
|
+
if (!this.headerP) {
|
|
88
|
+
this.headerP = this._getHeader(options).catch(e => {
|
|
89
|
+
this.headerP = undefined;
|
|
90
|
+
throw e;
|
|
91
|
+
});
|
|
92
|
+
}
|
|
93
|
+
return this.headerP;
|
|
94
|
+
}
|
|
81
95
|
/*
|
|
82
96
|
* @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
|
|
83
97
|
* @param path - a Local file path as a string
|
|
@@ -100,20 +114,6 @@ class BBI {
|
|
|
100
114
|
throw new Error('no file given');
|
|
101
115
|
}
|
|
102
116
|
}
|
|
103
|
-
/* fetch and parse header information from a bigwig or bigbed file
|
|
104
|
-
* @param abortSignal - abort the operation, can be null
|
|
105
|
-
* @return a Header object
|
|
106
|
-
*/
|
|
107
|
-
getHeader(opts = {}) {
|
|
108
|
-
const options = 'aborted' in opts ? { signal: opts } : opts;
|
|
109
|
-
if (!this.headerP) {
|
|
110
|
-
this.headerP = this._getHeader(options).catch(e => {
|
|
111
|
-
this.headerP = undefined;
|
|
112
|
-
throw e;
|
|
113
|
-
});
|
|
114
|
-
}
|
|
115
|
-
return this.headerP;
|
|
116
|
-
}
|
|
117
117
|
_getHeader(opts) {
|
|
118
118
|
return __awaiter(this, void 0, void 0, function* () {
|
|
119
119
|
const header = yield this._getMainHeader(opts);
|
|
@@ -270,10 +270,8 @@ class BBI {
|
|
|
270
270
|
}) {
|
|
271
271
|
return __awaiter(this, void 0, void 0, function* () {
|
|
272
272
|
const ob = yield this.getFeatureStream(refName, start, end, opts);
|
|
273
|
-
const ret = yield ob
|
|
274
|
-
|
|
275
|
-
.toPromise();
|
|
276
|
-
return ret || [];
|
|
273
|
+
const ret = yield (0, rxjs_1.firstValueFrom)(ob.pipe((0, operators_1.toArray)()));
|
|
274
|
+
return ret.flat();
|
|
277
275
|
});
|
|
278
276
|
}
|
|
279
277
|
}
|
package/dist/bbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,iDAAsC;AACtC,2DAA6E;AAC7E,+
|
|
1
|
+
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":";;;;;;;;;;;;AAAA,iDAAsC;AACtC,2DAA6E;AAC7E,+BAA2D;AAC3D,8CAAwC;AACxC,2CAAuC;AAEvC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AACjC,MAAM,aAAa,GAAG,CAAC,UAAU,CAAA;AAEjC,SAAS,QAAQ,CAAC,GAAe;IAC/B,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;AACtC,CAAC;AAyCD;;;;GAIG;AACH,SAAS,UAAU,CAAC,IAAa;IAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;IAClC,MAAM,YAAY,GAAG,IAAI,sBAAM,EAAE;SAC9B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,OAAO,CAAC;SACd,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,eAAe,CAAC;SACvB,MAAM,CAAC,iBAAiB,CAAC;SACzB,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,qBAAqB,CAAC;SAC7B,MAAM,CAAC,YAAY,CAAC;SACpB,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,UAAU,CAAC,CAAC,iCAAiC;SACpD,MAAM,CAAC,oBAAoB,CAAC;SAC5B,MAAM,CAAC,mBAAmB,CAAC;SAC3B,MAAM,CAAC,iBAAiB,CAAC,CAAC,oCAAoC;SAC9D,KAAK,CAAC,YAAY,EAAE;QACnB,MAAM,EAAE,eAAe;QACvB,IAAI,EAAE,IAAI,sBAAM,EAAE;aACf,SAAS,CAAC,EAAE,CAAC;aACb,MAAM,CAAC,gBAAgB,CAAC;aACxB,MAAM,CAAC,UAAU,CAAC;aAClB,MAAM,CAAC,YAAY,CAAC;aACpB,MAAM,CAAC,aAAa,CAAC;KACzB,CAAC,CAAA;IAEJ,MAAM,kBAAkB,GAAG,IAAI,sBAAM,EAAE;SACpC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,cAAc,CAAC;SACtB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,UAAU,CAAC;SACpB,QAAQ,CAAC,iBAAiB,CAAC,CAAA;IAE9B,MAAM,eAAe,GAAG,IAAI,sBAAM,EAAE;SACjC,SAAS,CAAC,EAAE,CAAC;SACb,MAAM,CAAC,OAAO,CAAC;SACf,MAAM,CAAC,WAAW,CAAC;SACnB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,SAAS,CAAC;SACjB,MAAM,CAAC,WAAW,CAAC,CAAA;IAEtB,MAAM,UAAU,GAAG,IAAI,sBAAM,EAAE;SAC5B,SAAS,CAAC,EAAE,CAAC;SACb,KAAK,CAAC,YAAY,CAAC;SACnB,IAAI,CAAC,CAAC,CAAC;SACP,MAAM,CAAC,KAAK,CAAC;SACb,UAAU,CAAC,QAAQ,CAAC,CAAA;IAEvB,OAAO;QACL,eAAe;QACf,kBAAkB;QAClB,YAAY;QACZ,UAAU;KACX,CAAA;AACH,CAAC;AAQD,MAAsB,GAAG;IAOvB;;;OAGG;IACI,SAAS,CAAC,OAAqC,EAAE;QACtD,MAAM,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,IAAmB,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;QAC1E,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE;YACjB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;gBAChD,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA;gBACxB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,OAAO,CAAA;IACrB,CAAC;IAED;;;;;OAKG;IACH,YACE,UAKI,EAAE;QAEN,MAAM,EAAE,UAAU,EAAE,aAAa,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,OAAO,CAAA;QACjE,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA;QAClC,IAAI,UAAU,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,UAAU,CAAA;SACtB;aAAM,IAAI,GAAG,EAAE;YACd,IAAI,CAAC,GAAG,GAAG,IAAI,+BAAU,CAAC,GAAG,CAAC,CAAA;SAC/B;aAAM,IAAI,IAAI,EAAE;YACf,IAAI,CAAC,GAAG,GAAG,IAAI,8BAAS,CAAC,IAAI,CAAC,CAAA;SAC/B;aAAM;YACL,MAAM,IAAI,KAAK,CAAC,eAAe,CAAC,CAAA;SACjC;IACH,CAAC;IAEa,UAAU,CAAC,IAAoB;;YAC3C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;YAC9C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;YACtD,uCAAY,MAAM,GAAK,MAAM,EAAE;QACjC,CAAC;KAAA;IAEa,cAAc,CAC1B,IAAoB,EACpB,WAAW,GAAG,IAAI;;YAElB,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,WAAW,CAAC,EACzB,CAAC,EACD,WAAW,EACX,CAAC,EACD,IAAI,CACL,CAAA;YACD,MAAM,WAAW,GAAG,IAAI,CAAC,YAAY,CAAC,MAAM,CAAC,CAAA;YAC7C,MAAM,GAAG,GAAG,UAAU,CAAC,WAAW,CAAC,CAAA;YACnC,MAAM,MAAM,GAAG,GAAG,CAAC,YAAY,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;YAC7C,MAAM,EAAE,KAAK,EAAE,QAAQ,EAAE,kBAAkB,EAAE,GAAG,MAAM,CAAA;YACtD,MAAM,CAAC,QAAQ,GAAG,KAAK,KAAK,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAA;YAC/D,IAAI,QAAQ,GAAG,WAAW,IAAI,kBAAkB,GAAG,WAAW,EAAE;gBAC9D,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;aAClD;YACD,IAAI,QAAQ,EAAE;gBACZ,MAAM,GAAG,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;gBACnC,MAAM,CAAC,OAAO,GAAG,QAAQ,CAAC,MAAM,CAAC,QAAQ,CAAC,GAAG,EAAE,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAA;aACxE;YACD,IAAI,MAAM,CAAC,kBAAkB,GAAG,WAAW,EAAE;gBAC3C,OAAO,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;aAClD;YACD,IAAI,MAAM,CAAC,kBAAkB,EAAE;gBAC7B,MAAM,IAAI,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAC,CAAA;gBAC/D,MAAM,GAAG,GAAG,GAAG,CAAC,kBAAkB,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBAC9C,MAAM,CAAC,YAAY,mCAAQ,GAAG,KAAE,YAAY,EAAE,MAAM,CAAC,GAAG,CAAC,YAAY,CAAC,GAAE,CAAA;aACzE;YACD,uCAAY,MAAM,KAAE,WAAW,IAAE;QACnC,CAAC;KAAA;IAEO,YAAY,CAAC,MAAc;QACjC,IAAI,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC/B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,KAAK,CAAA;SACb;QACD,GAAG,GAAG,MAAM,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3B,IAAI,GAAG,KAAK,aAAa,IAAI,GAAG,KAAK,aAAa,EAAE;YAClD,OAAO,IAAI,CAAA;SACZ;QACD,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;IAC7C,CAAC;IAED,qCAAqC;IACvB,cAAc,CAAC,MAAc,EAAE,IAA8B;;YACzE,MAAM,IAAI,GAAG,MAAM,CAAC,WAAW,CAAA;YAC/B,MAAM,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;YAClC,MAAM,YAAY,GAEd,EAAE,CAAA;YACN,MAAM,UAAU,GAA8B,EAAE,CAAA;YAEhD,IAAI,kBAAkB,GAAG,MAAM,CAAC,MAAM,CAAC,kBAAkB,CAAC,CAAA;YAC1D,MAAM,eAAe,GAAG,MAAM,CAAC,MAAM,CAAC,eAAe,CAAC,CAAA;YACtD,OAAO,kBAAkB,GAAG,CAAC,KAAK,CAAC,EAAE;gBACnC,kBAAkB,IAAI,CAAC,CAAA;aACxB;YACD,MAAM,GAAG,GAAG,kBAAkB,GAAG,eAAe,CAAA;YAChD,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,MAAM,CAAC,eAAe,CAAC,EACvB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|
package/dist/bigbed.js
CHANGED
|
@@ -194,7 +194,7 @@ class BigBed extends bbi_1.BBI {
|
|
|
194
194
|
return x;
|
|
195
195
|
}));
|
|
196
196
|
});
|
|
197
|
-
const ret = yield (0, rxjs_1.merge)(...res)
|
|
197
|
+
const ret = yield (0, rxjs_1.firstValueFrom)((0, rxjs_1.merge)(...res));
|
|
198
198
|
return ret.filter(f => { var _a; return ((_a = f.rest) === null || _a === void 0 ? void 0 : _a.split('\t')[(f.field || 0) - 3]) === name; });
|
|
199
199
|
});
|
|
200
200
|
}
|
package/dist/bigbed.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;AAAA,iDAAsC;AACtC,+
|
|
1
|
+
{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;AAAA,iDAAsC;AACtC,+BAAwD;AACxD,8CAA4C;AAC5C,sFAA2D;AAC3D,0DAAgC;AAEhC,+BAAoD;AAiBpD,SAAgB,WAAW,CAAI,EAAqB;IAClD,OAAO,EAAE,CAAC,MAAM,CAAC,CAAC,CAAgB,EAAU,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrD,CAAC;AAFD,kCAEC;AAED,MAAa,MAAO,SAAQ,SAAG;IAA/B;;QACS,qBAAgB,GAAG,IAAI,iCAAqB,CAAC;YAClD,KAAK,EAAE,IAAI,mBAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;YACnC,IAAI,EAAE,CAAO,IAAS,EAAE,MAAoB,EAAE,EAAE;gBAC9C,OAAO,IAAI,CAAC,YAAY,iCAAM,IAAI,KAAE,MAAM,IAAG,CAAA;YAC/C,CAAC,CAAA;SACF,CAAC,CAAA;IA+MJ,CAAC;IA7MQ,WAAW,CAAC,OAAqC,EAAE;QACxD,MAAM,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;QAC3D,OAAO,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAC9B,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,EACvB,OAAO,EACP,OAAO,CAAC,MAAM,CACf,CAAA;IACH,CAAC;IAED;;;;;OAKG;IACa,OAAO,CACrB,MAAc,EACd,IAAoB;;YAEpB,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QACnC,CAAC;KAAA;IAED;;;;OAIG;IACW,YAAY,CAAC,IAAoB;;YAC7C,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YACnE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,eAAe,CAAC,CACxB,CAAA;YACD,MAAM,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;YACzC,MAAM,GAAG,GAAG,IAAI,sBAAM,EAAE;iBACrB,SAAS,CAAC,EAAE,CAAC;iBACb,MAAM,CAAC,MAAM,CAAC;iBACd,MAAM,CAAC,OAAO,CAAC;iBACf,MAAM,CAAC,QAAQ,CAAC;iBAChB,KAAK,CAAC,IAAI,CAAC,CAAA;YAEd,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,GAAG,CAAA;YAE7B,wCAAwC;YACxC,IAAI,KAAK,KAAK,CAAC,EAAE;gBACf,OAAO,EAAE,CAAA;aACV;YAED,MAAM,QAAQ,GAAG,EAAE,CAAA;YACnB,MAAM,GAAG,GAAG,QAAQ,GAAG,KAAK,CAAA;YAC5B,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,MAAM,CAAC,MAAM,CAAC,CACf,CAAA;YACD,MAAM,SAAS,GAAG,IAAI,sBAAM,EAAE;iBAC3B,SAAS,CAAC,EAAE,CAAC;iBACb,KAAK,CAAC,MAAM,CAAC;iBACb,KAAK,CAAC,YAAY,CAAC;iBACnB,MAAM,CAAC,QAAQ,CAAC;iBAChB,IAAI,CAAC,CAAC,CAAC;iBACP,KAAK,CAAC,OAAO,CAAC,CAAA;YACjB,MAAM,OAAO,GAAG,EAAa,CAAA;YAE7B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE;gBACjC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;aAC7D;YACD,OAAO,OAAO,CAAA;QAChB,CAAC;KAAA;IAED;;;;;;;OAOG;IACW,sBAAsB,CAClC,IAAY,EACZ,OAAuB,EAAE;;YAEzB,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;YAClD,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;YAC5C,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE;gBACnB,OAAO,EAAE,CAAA;aACV;YACD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,CAAO,KAAU,EAA4B,EAAE;gBACtE,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;gBAC/B,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,MAAM,CAAC,EACd,IAAI,CACL,CAAA;gBACD,MAAM,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;gBACzC,MAAM,CAAC,GAAG,IAAI,sBAAM,EAAE;qBACnB,SAAS,CAAC,EAAE,CAAC;qBACb,KAAK,CAAC,OAAO,CAAC;qBACd,KAAK,CAAC,WAAW,CAAC;qBAClB,KAAK,CAAC,SAAS,CAAC;qBAChB,KAAK,CAAC,SAAS,CAAC;qBAChB,MAAM,CAAC,WAAW,CAAC,CAAA;gBAEtB,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;gBACrD,2CAA2C;gBAC3C,MAAM,GAAG,GAAG,IAAI,sBAAM,EAAE;qBACrB,SAAS,CAAC,EAAE,CAAC;qBACb,IAAI,CAAC,UAAU,CAAC;qBAChB,IAAI,CAAC,CAAC,CAAC;qBACP,KAAK,CAAC,KAAK,CAAC;qBACZ,MAAM,CAAC;oBACN,GAAG,EAAE,UAAU;oBACf,OAAO,EAAE;wBACP,CAAC,EAAE,IAAI,sBAAM,EAAE,CAAC,KAAK,CAAC,UAAU,EAAE;4BAChC,MAAM,EAAE,KAAK;4BACb,IAAI,EAAE,IAAI,sBAAM,EAAE;iCACf,SAAS,CAAC,EAAE,CAAC;iCACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;iCACnD,MAAM,CAAC,QAAQ,CAAC;yBACpB,CAAC;wBACF,CAAC,EAAE,IAAI,sBAAM,EAAE,CAAC,KAAK,CAAC,MAAM,EAAE;4BAC5B,MAAM,EAAE,KAAK;4BACb,IAAI,EAAE,IAAI,sBAAM,EAAE;iCACf,SAAS,CAAC,EAAE,CAAC;iCACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;iCACnD,MAAM,CAAC,QAAQ,CAAC;iCAChB,MAAM,CAAC,QAAQ,CAAC;iCAChB,MAAM,CAAC,UAAU,CAAC;yBACtB,CAAC;qBACH;iBACF,CAAC,CAAA;gBAEJ,MAAM,WAAW,GAAG,CAClB,UAAkB,EACQ,EAAE;oBAC5B,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,CAAA;oBAC9B,MAAM,GAAG,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,OAAO,GAAG,OAAO,CAAC,CAAA;oBAC/C,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;oBACD,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;oBAC9B,IAAI,IAAI,CAAC,QAAQ,EAAE;wBACjB,IAAI,UAAU,CAAA;wBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;4BAChD,MAAM,EAAE,GAAG,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;4BAChC,IAAI,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,EAAE;gCAC7C,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;6BAC/B;4BACD,UAAU,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;yBACrC;wBACD,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;qBAC/B;oBACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;wBAC5C,IAAI,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,EAAE;4BAC7B,uCAAY,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,KAAE,KAAK,IAAE;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|
package/esm/bbi.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { Parser } from 'binary-parser';
|
|
2
2
|
import { LocalFile, RemoteFile } from 'generic-filehandle';
|
|
3
|
-
import { Observable } from 'rxjs';
|
|
4
|
-
import {
|
|
3
|
+
import { firstValueFrom, Observable } from 'rxjs';
|
|
4
|
+
import { toArray } from 'rxjs/operators';
|
|
5
5
|
import { BlockView } from './blockView';
|
|
6
6
|
const BIG_WIG_MAGIC = -2003829722;
|
|
7
7
|
const BIG_BED_MAGIC = -2021002517;
|
|
@@ -66,6 +66,20 @@ function getParsers(isBE) {
|
|
|
66
66
|
};
|
|
67
67
|
}
|
|
68
68
|
export class BBI {
|
|
69
|
+
/* fetch and parse header information from a bigwig or bigbed file
|
|
70
|
+
* @param abortSignal - abort the operation, can be null
|
|
71
|
+
* @return a Header object
|
|
72
|
+
*/
|
|
73
|
+
getHeader(opts = {}) {
|
|
74
|
+
const options = 'aborted' in opts ? { signal: opts } : opts;
|
|
75
|
+
if (!this.headerP) {
|
|
76
|
+
this.headerP = this._getHeader(options).catch(e => {
|
|
77
|
+
this.headerP = undefined;
|
|
78
|
+
throw e;
|
|
79
|
+
});
|
|
80
|
+
}
|
|
81
|
+
return this.headerP;
|
|
82
|
+
}
|
|
69
83
|
/*
|
|
70
84
|
* @param filehandle - a filehandle from generic-filehandle or implementing something similar to the node10 fs.promises API
|
|
71
85
|
* @param path - a Local file path as a string
|
|
@@ -88,20 +102,6 @@ export class BBI {
|
|
|
88
102
|
throw new Error('no file given');
|
|
89
103
|
}
|
|
90
104
|
}
|
|
91
|
-
/* fetch and parse header information from a bigwig or bigbed file
|
|
92
|
-
* @param abortSignal - abort the operation, can be null
|
|
93
|
-
* @return a Header object
|
|
94
|
-
*/
|
|
95
|
-
getHeader(opts = {}) {
|
|
96
|
-
const options = 'aborted' in opts ? { signal: opts } : opts;
|
|
97
|
-
if (!this.headerP) {
|
|
98
|
-
this.headerP = this._getHeader(options).catch(e => {
|
|
99
|
-
this.headerP = undefined;
|
|
100
|
-
throw e;
|
|
101
|
-
});
|
|
102
|
-
}
|
|
103
|
-
return this.headerP;
|
|
104
|
-
}
|
|
105
105
|
async _getHeader(opts) {
|
|
106
106
|
const header = await this._getMainHeader(opts);
|
|
107
107
|
const chroms = await this._readChromTree(header, opts);
|
|
@@ -247,10 +247,8 @@ export class BBI {
|
|
|
247
247
|
scale: 1,
|
|
248
248
|
}) {
|
|
249
249
|
const ob = await this.getFeatureStream(refName, start, end, opts);
|
|
250
|
-
const ret = await ob
|
|
251
|
-
|
|
252
|
-
.toPromise();
|
|
253
|
-
return ret || [];
|
|
250
|
+
const ret = await firstValueFrom(ob.pipe(toArray()));
|
|
251
|
+
return ret.flat();
|
|
254
252
|
}
|
|
255
253
|
}
|
|
256
254
|
//# sourceMappingURL=bbi.js.map
|
package/esm/bbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bbi.js","sourceRoot":"","sources":["../src/bbi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAqB,MAAM,oBAAoB,CAAA;AAC7E,OAAO,EAAE,UAAU,EAAY,MAAM,MAAM,CAAA;
|
|
1
|
+
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|
package/esm/bigbed.js
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { Parser } from 'binary-parser';
|
|
2
|
-
import { Observable, merge } from 'rxjs';
|
|
2
|
+
import { Observable, merge, firstValueFrom } from 'rxjs';
|
|
3
3
|
import { map, reduce } from 'rxjs/operators';
|
|
4
4
|
import AbortablePromiseCache from 'abortable-promise-cache';
|
|
5
5
|
import QuickLRU from 'quick-lru';
|
|
@@ -171,7 +171,7 @@ export class BigBed extends BBI {
|
|
|
171
171
|
return x;
|
|
172
172
|
}));
|
|
173
173
|
});
|
|
174
|
-
const ret = await merge(...res)
|
|
174
|
+
const ret = await firstValueFrom(merge(...res));
|
|
175
175
|
return ret.filter(f => { var _a; return ((_a = f.rest) === null || _a === void 0 ? void 0 : _a.split('\t')[(f.field || 0) - 3]) === name; });
|
|
176
176
|
}
|
|
177
177
|
}
|
package/esm/bigbed.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,MAAM,MAAM,CAAA;
|
|
1
|
+
{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,MAAM,EAAE,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,UAAU,EAAE,KAAK,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AACxD,OAAO,EAAE,GAAG,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAA;AAC5C,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,OAAO,QAAQ,MAAM,WAAW,CAAA;AAEhC,OAAO,EAAE,GAAG,EAA2B,MAAM,OAAO,CAAA;AAiBpD,MAAM,UAAU,WAAW,CAAI,EAAqB;IAClD,OAAO,EAAE,CAAC,MAAM,CAAC,CAAC,CAAgB,EAAU,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,MAAM,OAAO,MAAO,SAAQ,GAAG;IAA/B;;QACS,qBAAgB,GAAG,IAAI,qBAAqB,CAAC;YAClD,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;YACnC,IAAI,EAAE,KAAK,EAAE,IAAS,EAAE,MAAoB,EAAE,EAAE;gBAC9C,OAAO,IAAI,CAAC,YAAY,CAAC,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;YAC/C,CAAC;SACF,CAAC,CAAA;IA+MJ,CAAC;IA7MQ,WAAW,CAAC,OAAqC,EAAE;QACxD,MAAM,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAA;QAC3D,OAAO,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAC9B,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,EACvB,OAAO,EACP,OAAO,CAAC,MAAM,CACf,CAAA;IACH,CAAC;IAED;;;;;OAKG;IACO,KAAK,CAAC,OAAO,CACrB,MAAc,EACd,IAAoB;QAEpB,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;IAED;;;;OAIG;IACK,KAAK,CAAC,YAAY,CAAC,IAAoB;QAC7C,MAAM,EAAE,eAAe,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QACnE,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,eAAe,CAAC,CACxB,CAAA;QACD,MAAM,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;QACzC,MAAM,GAAG,GAAG,IAAI,MAAM,EAAE;aACrB,SAAS,CAAC,EAAE,CAAC;aACb,MAAM,CAAC,MAAM,CAAC;aACd,MAAM,CAAC,OAAO,CAAC;aACf,MAAM,CAAC,QAAQ,CAAC;aAChB,KAAK,CAAC,IAAI,CAAC,CAAA;QAEd,MAAM,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,GAAG,CAAA;QAE7B,wCAAwC;QACxC,IAAI,KAAK,KAAK,CAAC,EAAE;YACf,OAAO,EAAE,CAAA;SACV;QAED,MAAM,QAAQ,GAAG,EAAE,CAAA;QACnB,MAAM,GAAG,GAAG,QAAQ,GAAG,KAAK,CAAA;QAC5B,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,MAAM,CAAC,MAAM,CAAC,CACf,CAAA;QACD,MAAM,SAAS,GAAG,IAAI,MAAM,EAAE;aAC3B,SAAS,CAAC,EAAE,CAAC;aACb,KAAK,CAAC,MAAM,CAAC;aACb,KAAK,CAAC,YAAY,CAAC;aACnB,MAAM,CAAC,QAAQ,CAAC;aAChB,IAAI,CAAC,CAAC,CAAC;aACP,KAAK,CAAC,OAAO,CAAC,CAAA;QACjB,MAAM,OAAO,GAAG,EAAa,CAAA;QAE7B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE;YACjC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;SAC7D;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;IAED;;;;;;;OAOG;IACK,KAAK,CAAC,sBAAsB,CAClC,IAAY,EACZ,OAAuB,EAAE;QAEzB,MAAM,EAAE,WAAW,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAClD,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAC5C,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE;YACnB,OAAO,EAAE,CAAA;SACV;QACD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,EAAE,KAAU,EAA4B,EAAE;YACtE,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;YAC/B,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CAC1C,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC,EAChB,CAAC,EACD,EAAE,EACF,MAAM,CAAC,MAAM,CAAC,EACd,IAAI,CACL,CAAA;YACD,MAAM,EAAE,GAAG,WAAW,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAA;YACzC,MAAM,CAAC,GAAG,IAAI,MAAM,EAAE;iBACnB,SAAS,CAAC,EAAE,CAAC;iBACb,KAAK,CAAC,OAAO,CAAC;iBACd,KAAK,CAAC,WAAW,CAAC;iBAClB,KAAK,CAAC,SAAS,CAAC;iBAChB,KAAK,CAAC,SAAS,CAAC;iBAChB,MAAM,CAAC,WAAW,CAAC,CAAA;YAEtB,MAAM,EAAE,SAAS,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACrD,2CAA2C;YAC3C,MAAM,GAAG,GAAG,IAAI,MAAM,EAAE;iBACrB,SAAS,CAAC,EAAE,CAAC;iBACb,IAAI,CAAC,UAAU,CAAC;iBAChB,IAAI,CAAC,CAAC,CAAC;iBACP,KAAK,CAAC,KAAK,CAAC;iBACZ,MAAM,CAAC;gBACN,GAAG,EAAE,UAAU;gBACf,OAAO,EAAE;oBACP,CAAC,EAAE,IAAI,MAAM,EAAE,CAAC,KAAK,CAAC,UAAU,EAAE;wBAChC,MAAM,EAAE,KAAK;wBACb,IAAI,EAAE,IAAI,MAAM,EAAE;6BACf,SAAS,CAAC,EAAE,CAAC;6BACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;6BACnD,MAAM,CAAC,QAAQ,CAAC;qBACpB,CAAC;oBACF,CAAC,EAAE,IAAI,MAAM,EAAE,CAAC,KAAK,CAAC,MAAM,EAAE;wBAC5B,MAAM,EAAE,KAAK;wBACb,IAAI,EAAE,IAAI,MAAM,EAAE;6BACf,SAAS,CAAC,EAAE,CAAC;6BACb,MAAM,CAAC,KAAK,EAAE,EAAE,MAAM,EAAE,OAAO,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC;6BACnD,MAAM,CAAC,QAAQ,CAAC;6BAChB,MAAM,CAAC,QAAQ,CAAC;6BAChB,MAAM,CAAC,UAAU,CAAC;qBACtB,CAAC;iBACH;aACF,CAAC,CAAA;YAEJ,MAAM,WAAW,GAAG,KAAK,EACvB,UAAkB,EACQ,EAAE;gBAC5B,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,CAAA;gBAC9B,MAAM,GAAG,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,OAAO,GAAG,OAAO,CAAC,CAAA;gBAC/C,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,IAAI,CAAC,GAAG,CAAC,IAAI,CACpC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,EACjB,CAAC,EACD,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;gBACD,MAAM,IAAI,GAAG,GAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;gBAC9B,IAAI,IAAI,CAAC,QAAQ,EAAE;oBACjB,IAAI,UAAU,CAAA;oBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;wBAChD,MAAM,EAAE,GAAG,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,EAAE;4BAC7C,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;yBAC/B;wBACD,UAAU,GAAG,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;qBACrC;oBACD,OAAO,WAAW,CAAC,UAAU,CAAC,CAAA;iBAC/B;gBACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAA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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/bbi",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "3.0.0",
|
|
4
4
|
"description": "Parser for BigWig/BigBed files",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/bbi-js",
|
|
@@ -46,28 +46,28 @@
|
|
|
46
46
|
"generic-filehandle": "^3.0.0",
|
|
47
47
|
"pako": "^2.0.0",
|
|
48
48
|
"quick-lru": "^4.0.0",
|
|
49
|
-
"rxjs": "^
|
|
49
|
+
"rxjs": "^7.8.0"
|
|
50
50
|
},
|
|
51
51
|
"devDependencies": {
|
|
52
52
|
"@gmod/bed": "^2.1.2",
|
|
53
|
-
"@types/jest": "^29.
|
|
53
|
+
"@types/jest": "^29.2.4",
|
|
54
54
|
"@types/long": "^5.0.0",
|
|
55
|
-
"@types/node": "^18.11.
|
|
55
|
+
"@types/node": "^18.11.15",
|
|
56
56
|
"@types/pako": "^2.0.0",
|
|
57
|
-
"@typescript-eslint/eslint-plugin": "^5.
|
|
58
|
-
"@typescript-eslint/parser": "^5.
|
|
57
|
+
"@typescript-eslint/eslint-plugin": "^5.46.1",
|
|
58
|
+
"@typescript-eslint/parser": "^5.46.1",
|
|
59
59
|
"cross-fetch": "^3.0.2",
|
|
60
|
-
"eslint": "^8.
|
|
60
|
+
"eslint": "^8.29.0",
|
|
61
61
|
"eslint-config-prettier": "^8.3.0",
|
|
62
62
|
"eslint-plugin-import": "^2.25.3",
|
|
63
63
|
"eslint-plugin-prettier": "^4.0.0",
|
|
64
|
-
"jest": "^29.
|
|
65
|
-
"jest-environment-jsdom": "^29.
|
|
66
|
-
"prettier": "^2.
|
|
64
|
+
"jest": "^29.3.1",
|
|
65
|
+
"jest-environment-jsdom": "^29.3.1",
|
|
66
|
+
"prettier": "^2.8.1",
|
|
67
67
|
"rimraf": "^3.0.2",
|
|
68
68
|
"standard-changelog": "^2.0.11",
|
|
69
69
|
"ts-jest": "^29.0.3",
|
|
70
|
-
"typescript": "^4.
|
|
70
|
+
"typescript": "^4.9.4"
|
|
71
71
|
},
|
|
72
72
|
"publishConfig": {
|
|
73
73
|
"access": "public"
|
package/src/bbi.ts
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { Parser } from 'binary-parser'
|
|
2
2
|
import { LocalFile, RemoteFile, GenericFilehandle } from 'generic-filehandle'
|
|
3
|
-
import { Observable, Observer } from 'rxjs'
|
|
4
|
-
import {
|
|
3
|
+
import { firstValueFrom, Observable, Observer } from 'rxjs'
|
|
4
|
+
import { toArray } from 'rxjs/operators'
|
|
5
5
|
import { BlockView } from './blockView'
|
|
6
6
|
|
|
7
7
|
const BIG_WIG_MAGIC = -2003829722
|
|
@@ -367,12 +367,10 @@ export abstract class BBI {
|
|
|
367
367
|
opts: RequestOptions & { scale?: number; basesPerSpan?: number } = {
|
|
368
368
|
scale: 1,
|
|
369
369
|
},
|
|
370
|
-
)
|
|
370
|
+
) {
|
|
371
371
|
const ob = await this.getFeatureStream(refName, start, end, opts)
|
|
372
372
|
|
|
373
|
-
const ret = await ob
|
|
374
|
-
|
|
375
|
-
.toPromise()
|
|
376
|
-
return ret || []
|
|
373
|
+
const ret = await firstValueFrom(ob.pipe(toArray()))
|
|
374
|
+
return ret.flat()
|
|
377
375
|
}
|
|
378
376
|
}
|
package/src/bigbed.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
import { Parser } from 'binary-parser'
|
|
2
|
-
import { Observable, merge } from 'rxjs'
|
|
2
|
+
import { Observable, merge, firstValueFrom } from 'rxjs'
|
|
3
3
|
import { map, reduce } from 'rxjs/operators'
|
|
4
4
|
import AbortablePromiseCache from 'abortable-promise-cache'
|
|
5
5
|
import QuickLRU from 'quick-lru'
|
|
@@ -216,10 +216,7 @@ export class BigBed extends BBI {
|
|
|
216
216
|
* @param opts - a SearchOptions argument with optional signal
|
|
217
217
|
* @return a Promise for an array of Feature
|
|
218
218
|
*/
|
|
219
|
-
public async searchExtraIndex(
|
|
220
|
-
name: string,
|
|
221
|
-
opts: RequestOptions = {},
|
|
222
|
-
): Promise<Feature[]> {
|
|
219
|
+
public async searchExtraIndex(name: string, opts: RequestOptions = {}) {
|
|
223
220
|
const blocks = await this.searchExtraIndexBlocks(name, opts)
|
|
224
221
|
if (!blocks.length) {
|
|
225
222
|
return []
|
|
@@ -238,7 +235,7 @@ export class BigBed extends BBI {
|
|
|
238
235
|
}),
|
|
239
236
|
)
|
|
240
237
|
})
|
|
241
|
-
const ret = await merge(...res)
|
|
238
|
+
const ret = await firstValueFrom(merge(...res))
|
|
242
239
|
return ret.filter(f => f.rest?.split('\t')[(f.field || 0) - 3] === name)
|
|
243
240
|
}
|
|
244
241
|
}
|