@gmod/bam 5.0.4 → 5.0.6

package/esm/htsget.d.ts

@@ -1,6 +1,6 @@
-import { BaseOpts, BamOpts } from './util';
 import BamFile from './bamFile';
 import Chunk from './chunk';
+import { BamOpts, BaseOpts } from './util';
 export default class HtsgetFile extends BamFile {
     private baseUrl;
     private trackId;

package/esm/htsget.js

@@ -1,7 +1,7 @@
 import { unzip } from '@gmod/bgzf-filehandle';
-import { concatUint8Array } from './util';
 import BamFile, { BAM_MAGIC } from './bamFile';
 import { parseHeaderText } from './sam';
+import { concatUint8Array } from './util';
 async function concat(arr, opts) {
     const res = await Promise.all(arr.map(async (chunk) => {
         const { url, headers } = chunk;
@@ -16,7 +16,7 @@ async function concat(arr, opts) {
             return new Uint8Array(ret);
         }
         else {
-            //remove referer header, it is not even allowed to be specified
+            // remove referer header, it is not even allowed to be specified
             // @ts-expect-error
             const { referer, ...rest } = headers;
             const res = await fetch(url, {

package/esm/htsget.js.map

@@ -1 +1 @@
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+{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,eAAe,EAAE,MAAM,OAAO,CAAA;AACvC,OAAO,EAAqB,gBAAgB,EAAE,MAAM,QAAQ,CAAA;AAM5D,KAAK,UAAU,MAAM,CAAC,GAAkB,EAAE,IAA0B;IAClE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,CAC3B,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,KAAK,EAAC,EAAE;QACpB,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,GAAG,KAAK,CAAA;QAC9B,IAAI,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC;YAC5B,oDAAoD;YACpD,+CAA+C;YAC/C,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;YAC5C,CAAC;YACD,MAAM,GAAG,GAAG,MAAM,GAAG,CAAC,WAAW,EAAE,CAAA;YACnC,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;QAC5B,CAAC;aAAM,CAAC;YACN,gEAAgE;YAChE,mBAAmB;YAEnB,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,CAAA;YACpC,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE;gBAC3B,GAAG,IAAI;gBACP,OAAO,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,GAAG,IAAI,EAAE;aACvC,CAAC,CAAA;YACF,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;gBACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAC1D,CAAA;YACH,CAAC;YACD,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;QAChD,CAAC;IACH,CAAC,CAAC,CACH,CAAA;IAED,OAAO,gBAAgB,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;AACxE,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,OAAO;IACrC,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEvB,YAAY,IAA0C;QACpD,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QACvB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,CAAC,qBAAqB,CAC1B,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,MAAM,EAAE,CAAA;QACV,CAAC;aAAM,CAAC;YACN,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,CAAC,CAAA;YAC5C,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;YACH,CAAC;YACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;YAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;YAE3D,KAAK,CAAC,CAAC,IAAI,CAAC,mBAAmB,CAC7B;gBACE,sCAAsC;gBACtC;oBACE,MAAM,EAAE,KAAK;oBACb,YAAY,EAAE,SAAS;oBACvB,GAAG,EAAE,CAAC;oBACN,SAAS;wBACP,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,cAAc;wBACZ,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;oBACD,WAAW;wBACT,OAAO,CAAC,CAAA;oBACV,CAAC;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,CAAC;wBACf,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,IAAI,EAAE;wBACJ,YAAY,EAAE,MAAM,CAAC,gBAAgB;wBACrC,aAAa,EAAE,CAAC;wBAChB,SAAS,EAAE,GAAG,EAAE,CAAC,CAAC;qBACnB;oBACD,QAAQ;wBACN,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAA;oBAC/B,CAAC;iBACF;aACF,EACD,KAAK,EACL,GAAG,EACH,GAAG,EACH,IAAI,CACL,CAAA;QACH,CAAC;IACH,CAAC;IAED,mBAAmB;IACnB,KAAK,CAAC,UAAU,CAAC,EAAE,KAAK,EAAoC;QAC1D,IAAI,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;YAClB,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;QACpD,CAAC;QACD,OAAO;YACL,IAAI,EAAE,KAAK,CAAC,MAAM;YAClB,UAAU,EAAE,EAAE;YACd,UAAU,EAAE,EAAE;YACd,KAAK;SACN,CAAA;IACH,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAiB,EAAE;QACjC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACrC,IAAI,CAAC,MAAM,CAAC,EAAE,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CACb,QAAQ,MAAM,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,MAAM,CAAC,IAAI,EAAE,EAAE,CAChE,CAAA;QACH,CAAC;QACD,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC7C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAE1C,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;QACvC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAC,CAAA;QACjE,MAAM,SAAS,GAAG,eAAe,CAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC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package/esm/indexFile.d.ts

@@ -1,12 +1,12 @@
-import { GenericFilehandle } from 'generic-filehandle2';
 import Chunk from './chunk';
 import { BaseOpts } from './util';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (s: string) => string;
     /**
      * @param {filehandle} filehandle
-     * @param {function} [renameRefSeqs]
+     * @param {function} renameRefSeqs
      */
     constructor({ filehandle, renameRefSeq, }: {
         filehandle: GenericFilehandle;

package/esm/indexFile.js

@@ -3,7 +3,7 @@ export default class IndexFile {
     renameRefSeq;
     /**
      * @param {filehandle} filehandle
-     * @param {function} [renameRefSeqs]
+     * @param {function} renameRefSeqs
      */
     constructor({ filehandle, renameRefSeq = (n) => n, }) {
         this.filehandle = filehandle;

package/esm/indexFile.js.map

@@ -1 +1 @@
-{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAIA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAC9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAE1C;;;OAGG;IACH,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;CAcF"}
+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAKA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAC9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAE1C;;;OAGG;IACH,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;CAcF"}

package/esm/long.d.ts

@@ -0,0 +1,3 @@
+export declare const TWO_PWR_16_DBL: number;
+export declare const TWO_PWR_32_DBL: number;
+export declare function longFromBytesToUnsigned(source: Uint8Array, i?: number): number;

package/esm/long.js

@@ -0,0 +1,14 @@
+export const TWO_PWR_16_DBL = 1 << 16;
+export const TWO_PWR_32_DBL = TWO_PWR_16_DBL * TWO_PWR_16_DBL;
+export function longFromBytesToUnsigned(source, i = 0) {
+    const low = source[i] |
+        (source[i + 1] << 8) |
+        (source[i + 2] << 16) |
+        (source[i + 3] << 24);
+    const high = source[i + 4] |
+        (source[i + 5] << 8) |
+        (source[i + 6] << 16) |
+        (source[i + 7] << 24);
+    return (high >>> 0) * TWO_PWR_32_DBL + (low >>> 0);
+}
+//# sourceMappingURL=long.js.map

package/esm/long.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,MAAM,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AACrC,MAAM,CAAC,MAAM,cAAc,GAAG,cAAc,GAAG,cAAc,CAAA;AAE7D,MAAM,UAAU,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}

package/esm/nullFilehandle.d.ts

@@ -0,0 +1,6 @@
+export default class NullFilehandle {
+    read(): Promise<any>;
+    stat(): Promise<any>;
+    readFile(): Promise<any>;
+    close(): Promise<any>;
+}

package/esm/nullFilehandle.js

@@ -0,0 +1,15 @@
+export default class NullFilehandle {
+    read() {
+        throw new Error('never called');
+    }
+    stat() {
+        throw new Error('never called');
+    }
+    readFile() {
+        throw new Error('never called');
+    }
+    close() {
+        throw new Error('never called');
+    }
+}
+//# sourceMappingURL=nullFilehandle.js.map

package/esm/nullFilehandle.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"nullFilehandle.js","sourceRoot":"","sources":["../src/nullFilehandle.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,OAAO,cAAc;IAC1B,IAAI;QACT,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IACM,IAAI;QACT,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,QAAQ;QACb,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,KAAK;QACV,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;CACF"}

package/esm/record.js

@@ -327,14 +327,13 @@ export default class BamRecord {
         return (this.seq_length + 1) >> 1;
     }
     get seq() {
-        const { byteArray } = this.bytes;
         const p = this.b0 + this.read_name_length + this.num_cigar_ops * 4;
         const seqBytes = this.num_seq_bytes;
         const len = this.seq_length;
         const buf = [];
         let i = 0;
         for (let j = 0; j < seqBytes; ++j) {
-            const sb = byteArray[p + j];
+            const sb = this.byteArray[p + j];
             buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
             i++;
             if (i < len) {
@@ -403,7 +402,7 @@ export default class BamRecord {
             if (k.startsWith('_') || k === 'bytes') {
                 continue;
             }
-            //@ts-ignore
+            // @ts-ignore
             data[k] = this[k];
         }
         return data;

package/esm/record.js.map

@@ -1 +1 @@
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package/esm/util.d.ts

@@ -1,5 +1,5 @@
 import Chunk from './chunk';
-import VirtualOffset from './virtualOffset';
+import { Offset, VirtualOffset } from './virtualOffset';
 export declare function timeout(ms: number): Promise<unknown>;
 /**
  * Properly check if the given AbortSignal is aborted.
@@ -32,7 +32,7 @@ export interface BaseOpts {
     signal?: AbortSignal;
 }
 export declare function makeOpts(obj?: AbortSignal | BaseOpts): BaseOpts;
-export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
+export declare function optimizeChunks(chunks: Chunk[], lowest?: Offset): Chunk[];
 export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;
 };
@@ -43,3 +43,4 @@ export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (a
 };
 export declare function sum(array: Uint8Array[]): number;
 export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;
+export declare function gen2array<T>(gen: AsyncIterable<T[]>): Promise<T[]>;

package/esm/util.js

@@ -1,4 +1,4 @@
-import { fromBytesLE, toNumber } from 'longfn';
+import { longFromBytesToUnsigned } from './long';
 export function timeout(ms) {
     return new Promise(resolve => setTimeout(resolve, ms));
 }
@@ -22,7 +22,7 @@ export function checkAbortSignal(signal) {
         // console.log('bam aborted!')
         if (typeof DOMException === 'undefined') {
             const e = new Error('aborted');
-            //@ts-ignore
+            // @ts-ignore
             e.code = 'ERR_ABORTED';
             throw e;
         }
@@ -81,7 +81,7 @@ export function optimizeChunks(chunks, lowest) {
 }
 export function parsePseudoBin(bytes, offset) {
     return {
-        lineCount: toNumber(fromBytesLE(bytes.subarray(offset, offset + 8), true)),
+        lineCount: longFromBytesToUnsigned(bytes, offset),
     };
 }
 export function findFirstData(firstDataLine, virtualOffset) {
@@ -129,4 +129,11 @@ export function concatUint8Array(args) {
     }
     return mergedArray;
 }
+export async function gen2array(gen) {
+    let out = [];
+    for await (const x of gen) {
+        out = out.concat(x);
+    }
+    return out;
+}
 //# sourceMappingURL=util.js.map

package/esm/util.js.map

@@ -1 +1 @@
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package/esm/virtualOffset.d.ts

@@ -1,9 +1,14 @@
-export default class VirtualOffset {
+export interface Offset {
+    blockPosition: number;
+    dataPosition: number;
+    toString(): string;
+    compareTo(arg: Offset): number;
+}
+export declare class VirtualOffset {
     blockPosition: number;
     dataPosition: number;
     constructor(blockPosition: number, dataPosition: number);
     toString(): string;
     compareTo(b: VirtualOffset): number;
-    static min(...args: VirtualOffset[]): VirtualOffset;
 }
 export declare function fromBytes(bytes: Uint8Array, offset?: number, bigendian?: boolean): VirtualOffset;

package/esm/virtualOffset.js

@@ -1,4 +1,4 @@
-export default class VirtualOffset {
+export class VirtualOffset {
     blockPosition;
     dataPosition;
     constructor(blockPosition, dataPosition) {
@@ -11,19 +11,6 @@ export default class VirtualOffset {
     compareTo(b) {
         return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
     }
-    static min(...args) {
-        let min;
-        let i = 0;
-        for (; !min; i += 1) {
-            min = args[i];
-        }
-        for (; i < args.length; i += 1) {
-            if (min.compareTo(args[i]) > 0) {
-                min = args[i];
-            }
-        }
-        return min;
-    }
 }
 export function fromBytes(bytes, offset = 0, bigendian = false) {
     if (bigendian) {

package/esm/virtualOffset.js.map

@@ -1 +1 @@
-{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAAA,MAAM,CAAC,OAAO,OAAO,aAAa;IACzB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;IAED,MAAM,CAAC,GAAG,CAAC,GAAG,IAAqB;QACjC,IAAI,GAAG,CAAA;QACP,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,OAAO,CAAC,GAAG,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpB,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACf,CAAC;QACD,OAAO,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC/B,IAAI,GAAG,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC/B,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;YACf,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACxE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,aAAa;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,WAAW;QAC/B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,SAAS;QAC7B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,OAAO;QAC3B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,KAAK;QACzB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,EACnB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAC,CACzC,CAAA;AACH,CAAC"}
+{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":"AAOA,MAAM,OAAO,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;IAED,SAAS,CAAC,CAAgB;QACxB,OAAO,CACL,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAC3E,CAAA;IACH,CAAC;CACF;AACD,MAAM,UAAU,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC,EAAE,SAAS,GAAG,KAAK;IACxE,IAAI,SAAS,EAAE,CAAC;QACd,MAAM,IAAI,KAAK,CAAC,iDAAiD,CAAC,CAAA;IACpE,CAAC;IAED,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "5.0.4",
+  "version": "5.0.6",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -42,22 +42,22 @@
     "@gmod/bgzf-filehandle": "^2.0.1",
     "crc": "^4.3.2",
     "generic-filehandle2": "^1.0.0",
-    "longfn": "^1.3.1",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
     "@types/node": "^20.11.19",
     "@typescript-eslint/eslint-plugin": "^8.1.0",
     "@typescript-eslint/parser": "^8.1.0",
-    "@vitest/coverage-v8": "^2.0.5",
+    "@vitest/coverage-v8": "^3.0.1",
     "eslint": "^9.9.0",
+    "eslint-plugin-import": "^2.31.0",
     "eslint-plugin-unicorn": "^56.0.0",
     "prettier": "^3.3.3",
     "rimraf": "^6.0.1",
     "standard-changelog": "^6.0.0",
     "typescript": "^5.0.4",
     "typescript-eslint": "^8.1.0",
-    "vitest": "^2.0.5"
+    "vitest": "^3.0.1"
   },
   "publishConfig": {
     "access": "public"

package/src/bai.ts

@@ -1,8 +1,9 @@
-import VirtualOffset, { fromBytes } from './virtualOffset'
-import Chunk from './chunk'
+import QuickLRU from 'quick-lru'
 
-import { optimizeChunks, parsePseudoBin, findFirstData, BaseOpts } from './util'
+import Chunk from './chunk'
 import IndexFile from './indexFile'
+import { BaseOpts, findFirstData, optimizeChunks, parsePseudoBin } from './util'
+import { VirtualOffset, fromBytes } from './virtualOffset'
 
 const BAI_MAGIC = 21578050 // BAI\1
 
@@ -13,6 +14,12 @@ function roundUp(n: number, multiple: number) {
   return n - (n % multiple) + multiple
 }
 
+export interface IndexCovEntry {
+  start: number
+  end: number
+  score: number
+}
+
 function reg2bins(beg: number, end: number) {
   end -= 1
   return [
@@ -30,10 +37,9 @@ export default class BAI extends IndexFile {
 
   async lineCount(refId: number, opts?: BaseOpts) {
     const indexData = await this.parse(opts)
-    return indexData.indices[refId]?.stats?.lineCount || 0
+    return indexData.indices(refId)?.stats?.lineCount || 0
   }
 
-  // fetch and parse the index
   async _parse(_opts?: BaseOpts) {
     const bytes = await this.filehandle.readFile()
     const dataView = new DataView(bytes.buffer)
@@ -51,17 +57,53 @@ export default class BAI extends IndexFile {
     let curr = 8
     let firstDataLine: VirtualOffset | undefined
 
-    type BinIndex = Record<string, Chunk[]>
-    type LinearIndex = VirtualOffset[]
-    const indices = new Array<{
-      binIndex: BinIndex
-      linearIndex: LinearIndex
-      stats?: { lineCount: number }
-    }>(refCount)
-
+    const offsets = [] as number[]
     for (let i = 0; i < refCount; i++) {
-      // the binning index
+      offsets.push(curr)
+      const binCount = dataView.getInt32(curr, true)
 
+      curr += 4
+
+      for (let j = 0; j < binCount; j += 1) {
+        const bin = dataView.getUint32(curr, true)
+        curr += 4
+        if (bin === binLimit + 1) {
+          curr += 4
+          curr += 32
+        } else if (bin > binLimit + 1) {
+          throw new Error('bai index contains too many bins, please use CSI')
+        } else {
+          const chunkCount = dataView.getInt32(curr, true)
+          curr += 4
+          for (let k = 0; k < chunkCount; k++) {
+            curr += 8
+            curr += 8
+          }
+        }
+      }
+
+      const linearCount = dataView.getInt32(curr, true)
+      curr += 4
+      // as we're going through the linear index, figure out the smallest
+      // virtual offset in the indexes, which tells us where the BAM header
+      // ends
+      const linearIndex = new Array<VirtualOffset>(linearCount)
+      for (let j = 0; j < linearCount; j++) {
+        const offset = fromBytes(bytes, curr)
+        curr += 8
+        firstDataLine = findFirstData(firstDataLine, offset)
+        linearIndex[j] = offset
+      }
+    }
+    const indicesCache = new QuickLRU<number, ReturnType<typeof getIndices>>({
+      maxSize: 5,
+    })
+
+    function getIndices(refId: number) {
+      let curr = offsets[refId]
+      if (curr === undefined) {
+        return undefined
+      }
       const binCount = dataView.getInt32(curr, true)
       let stats
 
@@ -106,14 +148,27 @@ export default class BAI extends IndexFile {
         linearIndex[j] = offset
       }
 
-      indices[i] = { binIndex, linearIndex, stats }
+      return {
+        binIndex,
+        linearIndex,
+        stats,
+      }
     }
 
     return {
       bai: true,
       firstDataLine,
       maxBlockSize: 1 << 16,
-      indices,
+      indices: (refId: number) => {
+        if (!indicesCache.has(refId)) {
+          const result = getIndices(refId)
+          if (result) {
+            indicesCache.set(refId, result)
+          }
+          return result
+        }
+        return indicesCache.get(refId)
+      },
       refCount,
     }
   }
@@ -122,13 +177,13 @@ export default class BAI extends IndexFile {
     seqId: number,
     start?: number,
     end?: number,
-    opts: BaseOpts = {},
-  ): Promise<{ start: number; end: number; score: number }[]> {
+    opts?: BaseOpts,
+  ): Promise<IndexCovEntry[]> {
     const v = 16384
     const range = start !== undefined
     const indexData = await this.parse(opts)
-    const seqIdx = indexData.indices[seqId]
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    const seqIdx = indexData.indices(seqId)
+
     if (!seqIdx) {
       return []
     }
@@ -141,18 +196,18 @@ export default class BAI extends IndexFile {
     const depths = range
       ? new Array((e - s) / v)
       : new Array(linearIndex.length - 1)
-    const totalSize = linearIndex[linearIndex.length - 1].blockPosition
+    const totalSize = linearIndex[linearIndex.length - 1]!.blockPosition
     if (e > (linearIndex.length - 1) * v) {
       throw new Error('query outside of range of linear index')
     }
-    let currentPos = linearIndex[s / v].blockPosition
+    let currentPos = linearIndex[s / v]!.blockPosition
     for (let i = s / v, j = 0; i < e / v; i++, j++) {
       depths[j] = {
-        score: linearIndex[i + 1].blockPosition - currentPos,
+        score: linearIndex[i + 1]!.blockPosition - currentPos,
         start: i * v,
         end: i * v + v,
       }
-      currentPos = linearIndex[i + 1].blockPosition
+      currentPos = linearIndex[i + 1]!.blockPosition
     }
     return depths.map(d => ({
       ...d,
@@ -175,8 +230,8 @@ export default class BAI extends IndexFile {
     if (!indexData) {
       return []
     }
-    const ba = indexData.indices[refId]
-    // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+    const ba = indexData.indices(refId)
+
     if (!ba) {
       return []
     }
@@ -188,9 +243,8 @@ export default class BAI extends IndexFile {
     // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
     for (const [start, end] of overlappingBins) {
       for (let bin = start; bin <= end; bin++) {
-        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
         if (ba.binIndex[bin]) {
-          const binChunks = ba.binIndex[bin]
+          const binChunks = ba.binIndex[bin]!
           for (const binChunk of binChunks) {
             chunks.push(new Chunk(binChunk.minv, binChunk.maxv, bin))
           }
@@ -207,7 +261,6 @@ export default class BAI extends IndexFile {
     for (let i = minLin; i <= maxLin; ++i) {
       const vp = ba.linearIndex[i]
 
-      // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
       if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
         lowest = vp
       }
@@ -228,6 +281,6 @@ export default class BAI extends IndexFile {
 
   async hasRefSeq(seqId: number, opts: BaseOpts = {}) {
     const header = await this.parse(opts)
-    return !!header.indices[seqId]?.binIndex
+    return !!header.indices(seqId)?.binIndex
   }
 }