@gmod/bam 1.1.17 → 2.0.0

package/dist/bamFile.d.ts

@@ -1,28 +1,27 @@
 /// <reference types="node" />
+import { Buffer } from 'buffer';
 import { GenericFilehandle } from 'generic-filehandle';
+import BAI from './bai';
+import CSI from './csi';
 import Chunk from './chunk';
 import BAMFeature from './record';
 import { BamOpts, BaseOpts } from './util';
 export declare const BAM_MAGIC = 21840194;
 export default class BamFile {
-    private renameRefSeq;
-    private bam;
-    private index;
-    private chunkSizeLimit;
-    private fetchSizeLimit;
-    private header;
-    protected chrToIndex: any;
-    protected indexToChr: any;
-    private yieldThreadTime;
+    renameRefSeq: (a: string) => string;
+    bam: GenericFilehandle;
+    header?: string;
+    chrToIndex?: Record<string, number>;
+    indexToChr?: {
+        refName: string;
+        length: number;
+    }[];
+    yieldThreadTime: number;
+    index?: BAI | CSI;
+    htsget: boolean;
+    headerP?: ReturnType<BamFile['getHeaderPre']>;
     private featureCache;
-    /**
-     * @param {object} args
-     * @param {string} [args.bamPath]
-     * @param {FileHandle} [args.bamFilehandle]
-     * @param {string} [args.baiPath]
-     * @param {FileHandle} [args.baiFilehandle]
-     */
-    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, fetchSizeLimit, chunkSizeLimit, yieldThreadTime, renameRefSeqs, }: {
+    constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime, renameRefSeqs, }: {
         bamFilehandle?: GenericFilehandle;
         bamPath?: string;
         bamUrl?: string;
@@ -32,19 +31,25 @@ export default class BamFile {
         csiPath?: string;
         csiFilehandle?: GenericFilehandle;
         csiUrl?: string;
-        fetchSizeLimit?: number;
-        chunkSizeLimit?: number;
         renameRefSeqs?: (a: string) => string;
         yieldThreadTime?: number;
+        htsget?: boolean;
     });
-    getHeader(origOpts?: AbortSignal | BaseOpts): Promise<{
+    getHeaderPre(origOpts?: BaseOpts): Promise<{
         tag: string;
         data: {
             tag: string;
             value: string;
         }[];
-    }[]>;
-    getHeaderText(opts?: BaseOpts): Promise<any>;
+    }[] | undefined>;
+    getHeader(opts?: BaseOpts): Promise<{
+        tag: string;
+        data: {
+            tag: string;
+            value: string;
+        }[];
+    }[] | undefined>;
+    getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
     _readRefSeqs(start: number, refSeqBytes: number, opts?: BaseOpts): Promise<{
         chrToIndex: {
             [key: string]: number;
@@ -56,19 +61,20 @@ export default class BamFile {
     }>;
     getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
     streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
-    _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
+    _fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
     fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
+    _readRegion(position: number, size: number, opts?: BaseOpts): Promise<Buffer>;
     _readChunk({ chunk, opts }: {
         chunk: Chunk;
         opts: BaseOpts;
     }): Promise<{
-        data: any;
-        cpositions: any;
-        dpositions: any;
+        data: Buffer;
+        cpositions: number[];
+        dpositions: number[];
         chunk: Chunk;
     }>;
     readBamFeatures(ba: Buffer, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
-    hasRefSeq(seqName: string): Promise<boolean>;
+    hasRefSeq(seqName: string): Promise<boolean | undefined>;
     lineCount(seqName: string): Promise<number>;
     indexCov(seqName: string, start?: number, end?: number): Promise<{
         start: number;