@gmod/bam 1.1.8 → 1.1.9

package/dist/bai.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,iDAA2C;AAC3C,kDAA2B;AAE3B,0DAAmC;AACnC,+BAAgF;AAEhF,IAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAED;IAAiC,uBAAS;IAA1C;;IAkNA,CAAC;IA/MC,4BAAc,GAAd,UAAe,KAAa,EAAE,MAAc;QAC1C,IAAM,SAAS,GAAG,IAAA,mBAAY,EAC5B,cAAI,CAAC,WAAW,CACd,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,IAAI,CAAC,KAAK,EAAE,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,CAAC,EAC3D,IAAI,CACL,CACF,CAAA;QACD,OAAO,EAAE,SAAS,WAAA,EAAE,CAAA;IACtB,CAAC;IAEK,uBAAS,GAAf,UAAgB,KAAa,EAAE,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;4BACnC,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAA7B,IAAI,GAAG,SAAsB;wBAC7B,KAAK,GAAG,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACjC,IAAI,CAAC,KAAK,EAAE;4BACV,sBAAO,CAAC,CAAC,EAAA;yBACV;wBACK,GAAG,GAAG,KAAK,CAAC,KAAK,IAAI,EAAE,CAAA;wBAC7B,sBAAO,GAAG,CAAC,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,EAAA;;;;KACxD;IAED,sBAAQ,GAAR,UAAS,IAAmB;QAA5B,iBAQC;QARQ,qBAAA,EAAA,SAAmB;QAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE;YACd,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,UAAA,CAAC;gBAChD,KAAI,CAAC,IAAI,GAAG,SAAS,CAAA;gBACrB,MAAM,CAAC,CAAA;YACT,CAAC,CAAoB,CAAA;SACtB;QACD,OAAO,IAAI,CAAC,IAAI,CAAA;IAClB,CAAC;IAED,4BAA4B;IACtB,oBAAM,GAAZ,UAAa,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;;wBACxB,IAAI,GAA2B,EAAE,GAAG,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,IAAI,EAAE,EAAE,CAAA;wBAC3D,qBAAM,IAAI,CAAC,QAAQ,EAAE;4BAEnC,0BAA0B;0BAFS;;wBAA7B,KAAK,GAAG,SAAqB;wBAEnC,0BAA0B;wBAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;4BACvC,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;yBAClC;wBAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;wBAC9B,KAAK,GAAG,CAAC,CAAA;wBACT,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;wBAEnD,+CAA+C;wBAC/C,IAAI,CAAC,OAAO,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;wBACnC,UAAU,GAAG,CAAC,CAAA;wBACT,CAAC,GAAG,CAAC;;;6BAAE,CAAA,CAAC,GAAG,IAAI,CAAC,QAAQ,CAAA;wBAC/B,qBAAM,IAAA,sBAAe,EAAC,IAAI,CAAC,MAAM,CAAC;4BAElC,oBAAoB;0BAFc;;wBAAlC,SAAkC,CAAA;wBAG5B,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBAC1C,KAAK,SAAA,CAAA;wBAET,UAAU,IAAI,CAAC,CAAA;wBACT,QAAQ,GAA+B,EAAE,CAAA;wBAC/C,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;4BAC9B,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;4BAC1C,UAAU,IAAI,CAAC,CAAA;4BACf,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE;gCACxB,UAAU,IAAI,CAAC,CAAA;gCACf,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gCAC9C,UAAU,IAAI,EAAE,CAAA;6BACjB;iCAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE;gCAC7B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;6BACpE;iCAAM;gCACC,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gCAChD,UAAU,IAAI,CAAC,CAAA;gCACT,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;gCACpC,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;oCAChC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;oCAChC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;oCAC1C,UAAU,IAAI,EAAE,CAAA;oCAChB,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,CAAC,CAAC,CAAA;oCAC5B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,eAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;iCACjC;gCACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;6BACvB;yBACF;wBAEK,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;wBACjD,UAAU,IAAI,CAAC,CAAA;wBAIT,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;wBAC1C,KAAS,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE;4BACvC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,CAAC,CAAA;4BAC7C,UAAU,IAAI,CAAC,CAAA;4BACf,IAAI,CAAC,cAAc,CAAC,IAAI,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;yBAC1C;wBAED,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,QAAQ,UAAA,EAAE,WAAW,aAAA,EAAE,KAAK,OAAA,EAAE,CAAA;;;wBA7CjB,CAAC,IAAI,CAAC,CAAA;;4BAgDzC,sBAAO,IAAI,EAAA;;;;KACZ;IAEK,sBAAQ,GAAd,UACE,KAAa,EACb,KAAc,EACd,GAAY,EACZ,IAAmB;QAAnB,qBAAA,EAAA,SAAmB;;;;;;wBAEb,CAAC,GAAG,KAAK,CAAA;wBACT,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;wBACf,qBAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAAA;;wBAAlC,SAAS,GAAG,SAAsB;wBAClC,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;wBACvC,IAAI,CAAC,MAAM,EAAE;4BACX,sBAAO,EAAE,EAAA;yBACV;wBACO,KAA4B,MAAM,YAAlB,EAAhB,WAAW,mBAAG,EAAE,KAAA,EAAE,KAAK,GAAK,MAAM,MAAX,CAAW;wBAC1C,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE;4BACvB,sBAAO,EAAE,EAAA;yBACV;wBACK,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;wBACtE,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;wBAEvD,IAAI,KAAK,EAAE;4BACT,MAAM,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;yBAChC;6BAAM;4BACL,MAAM,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;yBAC3C;wBACK,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,aAAa,CAAA;wBACnE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE;4BACpC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;yBAC1D;wBAC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package/dist/bamFile.d.ts

@@ -11,7 +11,6 @@ export default class BamFile {
     private chunkSizeLimit;
     private fetchSizeLimit;
     private header;
-    protected featureCache: any;
     protected chrToIndex: any;
     protected indexToChr: any;
     private yieldThreadTime;
@@ -22,7 +21,7 @@ export default class BamFile {
      * @param {string} [args.baiPath]
      * @param {FileHandle} [args.baiFilehandle]
      */
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, cacheSize, fetchSizeLimit, chunkSizeLimit, yieldThreadTime, renameRefSeqs, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, fetchSizeLimit, chunkSizeLimit, yieldThreadTime, renameRefSeqs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -32,7 +31,6 @@ export default class BamFile {
         csiPath?: string;
         csiFilehandle?: GenericFilehandle;
         csiUrl?: string;
-        cacheSize?: number;
         fetchSizeLimit?: number;
         chunkSizeLimit?: number;
         renameRefSeqs?: (a: string) => string;
@@ -60,13 +58,13 @@ export default class BamFile {
     _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     fetchPairs(chrId: number, featPromises: Promise<BAMFeature[]>[], opts: BamOpts): Promise<BAMFeature[]>;
     _readChunk({ chunk, opts }: {
-        chunk: unknown;
+        chunk: Chunk;
         opts: BaseOpts;
-    }, abortSignal?: AbortSignal): Promise<never[] | {
+    }): Promise<{
         data: any;
         cpositions: any;
         dpositions: any;
-        chunk: unknown;
+        chunk: Chunk;
     }>;
     readBamFeatures(ba: Buffer, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
     hasRefSeq(seqName: string): Promise<boolean>;