@gmod/bam 1.1.17 → 2.0.0

package/dist/bamFile.js.map

@@ -1 +1 @@
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package/dist/chunk.d.ts

@@ -1,16 +1,12 @@
+/// <reference types="node" />
 import VirtualOffset from './virtualOffset';
 export default class Chunk {
     minv: VirtualOffset;
     maxv: VirtualOffset;
     bin: number;
-    _fetchedSize?: number;
-    /**
-     * @param {VirtualOffset} minv
-     * @param {VirtualOffset} maxv
-     * @param {number} bin
-     * @param {number} [fetchedSize]
-     */
-    constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, fetchedSize?: undefined);
+    _fetchedSize?: number | undefined;
+    buffer?: Buffer;
+    constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number, _fetchedSize?: number | undefined);
     toUniqueString(): string;
     toString(): string;
     compareTo(b: Chunk): number;

package/dist/chunk.js

@@ -1,38 +1,30 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 // little class representing a chunk in the index
-var Chunk = /** @class */ (function () {
-    /**
-     * @param {VirtualOffset} minv
-     * @param {VirtualOffset} maxv
-     * @param {number} bin
-     * @param {number} [fetchedSize]
-     */
-    function Chunk(minv, maxv, bin, fetchedSize) {
-        if (fetchedSize === void 0) { fetchedSize = undefined; }
+class Chunk {
+    constructor(minv, maxv, bin, _fetchedSize) {
         this.minv = minv;
         this.maxv = maxv;
         this.bin = bin;
-        this._fetchedSize = fetchedSize;
+        this._fetchedSize = _fetchedSize;
     }
-    Chunk.prototype.toUniqueString = function () {
-        return "".concat(this.minv, "..").concat(this.maxv, " (bin ").concat(this.bin, ", fetchedSize ").concat(this.fetchedSize(), ")");
-    };
-    Chunk.prototype.toString = function () {
+    toUniqueString() {
+        return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
+    }
+    toString() {
         return this.toUniqueString();
-    };
-    Chunk.prototype.compareTo = function (b) {
+    }
+    compareTo(b) {
         return (this.minv.compareTo(b.minv) ||
             this.maxv.compareTo(b.maxv) ||
             this.bin - b.bin);
-    };
-    Chunk.prototype.fetchedSize = function () {
+    }
+    fetchedSize() {
         if (this._fetchedSize !== undefined) {
             return this._fetchedSize;
         }
         return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition;
-    };
-    return Chunk;
-}());
+    }
+}
 exports.default = Chunk;
 //# sourceMappingURL=chunk.js.map

package/dist/chunk.js.map

@@ -1 +1 @@
-{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD;IAME;;;;;OAKG;IACH,eACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAuB;QAAvB,4BAAA,EAAA,uBAAuB;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,8BAAc,GAAd;QACE,OAAO,UAAG,IAAI,CAAC,IAAI,eAAK,IAAI,CAAC,IAAI,mBAC/B,IAAI,CAAC,GAAG,2BACO,IAAI,CAAC,WAAW,EAAE,MAAG,CAAA;IACxC,CAAC;IAED,wBAAQ,GAAR;QACE,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,yBAAS,GAAT,UAAU,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,2BAAW,GAAX;QACE,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE;YACnC,OAAO,IAAI,CAAC,YAAY,CAAA;SACzB;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;IACH,YAAC;AAAD,CAAC,AAhDD,IAgDC"}
+{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAGxB,YACS,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAe;QACnB,SAAI,GAAJ,IAAI,CAAe;QACnB,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE;YACnC,OAAO,IAAI,CAAC,YAAY,CAAA;SACzB;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AAlCD,wBAkCC"}

package/dist/csi.d.ts

@@ -1,4 +1,5 @@
 /// <reference types="node" />
+import VirtualOffset from './virtualOffset';
 import Chunk from './chunk';
 import { BaseOpts } from './util';
 import IndexFile from './indexFile';
@@ -6,30 +7,93 @@ export default class CSI extends IndexFile {
     private maxBinNumber;
     private depth;
     private minShift;
-    constructor(args: any);
-    lineCount(refId: number): Promise<number>;
+    setupP?: ReturnType<CSI['_parse']>;
+    lineCount(refId: number, opts?: BaseOpts): Promise<number>;
     indexCov(): Promise<never[]>;
-    parseAuxData(bytes: Buffer, offset: number, auxLength: number): {
-        [key: string]: any;
-    };
-    _parseNameBytes(namesBytes: Buffer): {
+    parseAuxData(bytes: Buffer, offset: number): {
         refNameToId: {
             [key: string]: number;
         };
         refIdToName: string[];
+        columnNumbers: {
+            ref: number;
+            start: number;
+            end: number;
+        };
+        coordinateType: string;
+        metaValue: number;
+        metaChar: string;
+        skipLines: number;
+        format: string;
+        formatFlags: number;
     };
     _parse(opts: {
         signal?: AbortSignal;
     }): Promise<{
-        [key: string]: any;
+        refNameToId?: {
+            [key: string]: number;
+        } | undefined;
+        refIdToName?: string[] | undefined;
+        columnNumbers?: {
+            ref: number;
+            start: number;
+            end: number;
+        } | undefined;
+        coordinateType?: string | undefined;
+        metaValue?: number | undefined;
+        metaChar?: string | undefined;
+        skipLines?: number | undefined;
+        format?: string | undefined;
+        formatFlags?: number | undefined;
+        csiVersion: number;
+        firstDataLine: VirtualOffset | undefined;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            stats?: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        refCount: number;
+        csi: boolean;
+        maxBlockSize: number;
     }>;
-    parsePseudoBin(bytes: Buffer, offset: number): {
-        lineCount: number;
-    };
     blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
     /**
      * calculate the list of bins that may overlap with region [beg,end)
      * (zero-based half-open)
      */
     reg2bins(beg: number, end: number): number[][];
+    parse(opts?: BaseOpts): Promise<{
+        refNameToId?: {
+            [key: string]: number;
+        } | undefined;
+        refIdToName?: string[] | undefined;
+        columnNumbers?: {
+            ref: number;
+            start: number;
+            end: number;
+        } | undefined;
+        coordinateType?: string | undefined;
+        metaValue?: number | undefined;
+        metaChar?: string | undefined;
+        skipLines?: number | undefined;
+        format?: string | undefined;
+        formatFlags?: number | undefined;
+        csiVersion: number;
+        firstDataLine: VirtualOffset | undefined;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            stats?: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        refCount: number;
+        csi: boolean;
+        maxBlockSize: number;
+    }>;
+    hasRefSeq(seqId: number, opts?: BaseOpts): Promise<boolean>;
 }