@gmod/cram 4.0.4 → 4.0.5
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- package/README.md +53 -51
- package/dist/cram-bundle.js +1 -1
- package/dist/cramFile/codecs/_base.d.ts +1 -1
- package/dist/cramFile/codecs/byteArrayLength.js +3 -2
- package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/dist/cramFile/codecs/external.d.ts +1 -1
- package/dist/cramFile/codecs/external.js +1 -4
- package/dist/cramFile/codecs/external.js.map +1 -1
- package/dist/cramFile/container/index.d.ts +16 -34
- package/dist/cramFile/container/index.js +5 -20
- package/dist/cramFile/container/index.js.map +1 -1
- package/dist/cramFile/file.d.ts +8 -6
- package/dist/cramFile/file.js +37 -73
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/record.js.map +1 -1
- package/dist/cramFile/sectionParsers.js +3 -2
- package/dist/cramFile/sectionParsers.js.map +1 -1
- package/dist/cramFile/slice/decodeRecord.d.ts +2 -2
- package/dist/cramFile/slice/decodeRecord.js +7 -4
- package/dist/cramFile/slice/decodeRecord.js.map +1 -1
- package/dist/cramFile/slice/index.js +14 -16
- package/dist/cramFile/slice/index.js.map +1 -1
- package/dist/cramFile/util.d.ts +5 -0
- package/dist/cramFile/util.js +75 -51
- package/dist/cramFile/util.js.map +1 -1
- package/esm/cramFile/codecs/_base.d.ts +1 -1
- package/esm/cramFile/codecs/byteArrayLength.js +3 -2
- package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/esm/cramFile/codecs/external.d.ts +1 -1
- package/esm/cramFile/codecs/external.js +2 -5
- package/esm/cramFile/codecs/external.js.map +1 -1
- package/esm/cramFile/container/index.d.ts +16 -34
- package/esm/cramFile/container/index.js +5 -20
- package/esm/cramFile/container/index.js.map +1 -1
- package/esm/cramFile/file.d.ts +8 -6
- package/esm/cramFile/file.js +37 -73
- package/esm/cramFile/file.js.map +1 -1
- package/esm/cramFile/record.js.map +1 -1
- package/esm/cramFile/sectionParsers.js +3 -2
- package/esm/cramFile/sectionParsers.js.map +1 -1
- package/esm/cramFile/slice/decodeRecord.d.ts +2 -2
- package/esm/cramFile/slice/decodeRecord.js +7 -4
- package/esm/cramFile/slice/decodeRecord.js.map +1 -1
- package/esm/cramFile/slice/index.js +14 -16
- package/esm/cramFile/slice/index.js.map +1 -1
- package/esm/cramFile/util.d.ts +5 -0
- package/esm/cramFile/util.js +74 -51
- package/esm/cramFile/util.js.map +1 -1
- package/package.json +3 -5
- package/src/cramFile/codecs/_base.ts +1 -1
- package/src/cramFile/codecs/byteArrayLength.ts +4 -12
- package/src/cramFile/codecs/external.ts +3 -7
- package/src/cramFile/container/index.ts +5 -24
- package/src/cramFile/file.ts +41 -77
- package/src/cramFile/record.ts +1 -1
- package/src/cramFile/sectionParsers.ts +5 -2
- package/src/cramFile/slice/decodeRecord.ts +26 -23
- package/src/cramFile/slice/index.ts +25 -31
- package/src/cramFile/util.ts +107 -73
- package/errors.js +0 -27
package/README.md
CHANGED
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@@ -142,6 +142,7 @@ directory for usage with script tag
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##### Table of Contents
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- [CramRecord](#cramrecord)
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+
- [Parameters](#parameters)
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- [isPaired](#ispaired)
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- [isProperlyPaired](#isproperlypaired)
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- [isSegmentUnmapped](#issegmentunmapped)
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@@ -161,12 +162,34 @@ directory for usage with script tag
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- [getReadBases](#getreadbases)
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- [getPairOrientation](#getpairorientation)
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- [addReferenceSequence](#addreferencesequence)
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- [Parameters](#parameters)
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- [Parameters](#parameters-1)
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#### CramRecord
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Class of each CRAM record returned by this API.
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##### Parameters
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- `$0` **any** 
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- `$0.flags`  
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- `$0.cramFlags`  
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- `$0.readLength`  
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- `$0.mappingQuality`  
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- `$0.lengthOnRef`  
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- `$0.qualityScores`  
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- `$0.mateRecordNumber`  
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- `$0.readBases`  
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- `$0.readFeatures`  
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- `$0.mateToUse`  
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- `$0.readGroupId`  
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- `$0.readName`  
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- `$0.sequenceId`  
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- `$0.uniqueId`  
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- `$0.templateSize`  
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- `$0.alignmentStart`  
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- `$0.tags`  
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##### isPaired
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Returns
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@@ -282,23 +305,23 @@ of paired orientatin
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##### addReferenceSequence
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Annotates this feature with the given reference sequence basepair information.
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This will add a `sub` and a `ref` item to base
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This will add a `sub` and a `ref` item to base substitution read features given
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the actual substituted and reference base pairs, and will make the
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`getReadSequence()` method work.
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###### Parameters
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- `refRegion`
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
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- `refRegion.start`
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
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- `refRegion.end`
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
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- `refRegion.seq`
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**[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)
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**[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)** 
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- `compressionScheme` **CramContainerCompressionScheme
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- `compressionScheme` **CramContainerCompressionScheme** 
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Returns
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**[undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined)**
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@@ -336,9 +359,9 @@ that show insertions, deletions, substitutions, etc.
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##### Parameters
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- `args`
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
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- `args.cram` **CramFile
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- `args.cram` **CramFile** 
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- `args.index` **Index-like** object that supports
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getEntriesForRange(seqId,start,end) -> Promise\[Array\[index entries]]
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- `args.cacheSize`
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@@ -363,14 +386,20 @@ that show insertions, deletions, substitutions, etc.
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- `end`
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
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end of the range of interest. 1-based closed coordinates.
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- `opts`
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- `opts` **{viewAsPairs:
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[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?,
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pairAcrossChr:
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[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?,
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maxInsertSize:
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[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?}**
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(optional, default `{}`)
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#### hasDataForReferenceSequence
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##### Parameters
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- `seqId`
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
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Returns
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**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)**
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##### Table of Contents
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- [constructor](#constructor)
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- [Parameters](#parameters)
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- [containerCount](#containercount)
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#### constructor
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##### Parameters
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- `args`
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
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-
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- `args.filehandle`
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?**
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a filehandle that implements the stat() and read() methods of the Node
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filehandle API <https://nodejs.org/api/fs.html#fs_class_filehandle>
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- `args.path`
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?**
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path to the cram file
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)?**
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url for the cram file. also supports file:// urls for local files
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- `args.seqFetch`
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**[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)?**
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a function with signature `(seqId, startCoordinate, endCoordinate)` that
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returns a promise for a string of sequence bases
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?**
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optional maximum number of CRAM records to cache. default 20,000
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**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?**
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default true. if false, disables verifying the MD5 checksum of the reference
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sequence underlying a slice. In some applications, this check can cause an
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inconvenient amount (many megabases) of sequences to be fetched.
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-
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#### containerCount
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Returns
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**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)<([number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
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[undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined))>** 
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### CraiIndex
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<!-- Generated by documentation.js. Update this documentation by updating the source code. -->
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##### Parameters
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- `args`
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)
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**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)** 
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- `args.path`
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**[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)
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**[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** 
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**[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)
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- `args.filehandle` **FileHandle
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**[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?** 
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- `args.filehandle` **FileHandle?** 
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#### hasDataForReferenceSequence
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##### Parameters
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- `seqId`
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
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**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)**
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##### Parameters
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
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- `queryStart`
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
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- `queryEnd`
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)** 
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Returns
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**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)**
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