@gmod/cram 1.6.3 → 1.7.0

package/dist/cramFile/slice/index.js.map

@@ -1 +1 @@
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package/dist/cramFile/util.d.ts

@@ -1,5 +1,11 @@
-export function itf8Size(v: any): 1 | 2 | 3 | 4 | 5;
-export function parseItf8(buffer: any, initialOffset: any): any[];
-export function parseItem(buffer: any, parser: any, startBufferPosition?: number, startFilePosition?: number): any;
-export function tinyMemoize(_class: any, methodName: any): void;
-export function sequenceMD5(seq: any): any;
+/// <reference types="node" />
+import { Parser } from '@gmod/binary-parser';
+export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
+export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
+export declare type ParsedItem<T> = T & {
+    _endPosition: number;
+    _size: number;
+};
+export declare function parseItem<T>(buffer: Buffer, parser: Parser<T>, startBufferPosition?: number, startFilePosition?: number): ParsedItem<T>;
+export declare function tinyMemoize(_class: any, methodName: any): void;
+export declare function sequenceMD5(seq: string): string;

package/dist/cramFile/util.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.sequenceMD5 = exports.tinyMemoize = exports.parseItem = exports.parseItf8 = exports.itf8Size = void 0;
-var md5_1 = __importDefault(require("md5"));
-var errors_1 = require("../errors");
+const md5_1 = __importDefault(require("md5"));
+const getBits_1 = require("./codecs/getBits");
 function itf8Size(v) {
     if (!(v & ~0x7f)) {
         return 1;
@@ -23,22 +23,22 @@ function itf8Size(v) {
 }
 exports.itf8Size = itf8Size;
 function parseItf8(buffer, initialOffset) {
-    var offset = initialOffset;
-    var countFlags = buffer[offset];
-    var result;
+    let offset = initialOffset;
+    const countFlags = buffer[offset];
+    let result;
     if (countFlags < 0x80) {
         result = countFlags;
-        offset += 1;
+        offset = offset + 1;
     }
     else if (countFlags < 0xc0) {
         result = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff;
-        offset += 2;
+        offset = offset + 2;
     }
     else if (countFlags < 0xe0) {
         result =
             ((countFlags << 16) | (buffer[offset + 1] << 8) | buffer[offset + 2]) &
                 0x1fffff;
-        offset += 3;
+        offset = offset + 3;
     }
     else if (countFlags < 0xf0) {
         result =
@@ -47,7 +47,7 @@ function parseItf8(buffer, initialOffset) {
                 (buffer[offset + 2] << 8) |
                 buffer[offset + 3]) &
                 0x0fffffff;
-        offset += 4;
+        offset = offset + 4;
     }
     else {
         result =
@@ -58,94 +58,17 @@ function parseItf8(buffer, initialOffset) {
                 (buffer[offset + 4] & 0x0f);
         // x=((0xff & 0x0f)<<28) | (0xff<<20) | (0xff<<12) | (0xff<<4) | (0x0f & 0x0f);
         // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
-        offset += 5;
+        offset = offset + 5;
     }
     if (offset > buffer.length) {
-        throw new errors_1.CramBufferOverrunError('Attempted to read beyond end of buffer; this file seems truncated.');
+        throw new getBits_1.CramBufferOverrunError('Attempted to read beyond end of buffer; this file seems truncated.');
     }
     return [result, offset - initialOffset];
 }
 exports.parseItf8 = parseItf8;
-// parseLtf8(buffer, initialOffset) {
-//   let offset = initialOffset
-//   const countFlags = buffer[offset]
-//   let result
-//   if (countFlags < 0x80) {
-//     result = countFlags
-//     offset += 1
-//   } else if (countFlags < 0xc0) {
-//     result = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff
-//     offset += 2
-//   } else if (countFlags < 0xe0) {
-//     result =
-//       ((buffer[offset] << 16) |
-//         (buffer[offset + 1] << 8) |
-//         buffer[offset + 2]) &
-//       0x1fffff
-//     offset += 3
-//   } else if (countFlags < 0xf0) {
-//     result =
-//       ((buffer[offset] << 24) |
-//         (buffer[offset + 1] << 16) |
-//         (buffer[offset + 2] << 8) |
-//         buffer[offset + 3]) &
-//       0x0fffffff
-//     offset += 4
-//   } else if (countFlags < 0xf8) {
-//     result =
-//       ((buffer[offset] & 15) * Math.pow(2,32) + (buffer[offset + 1] << 24)) |
-//       ((buffer[offset + 2] << 16) |
-//         (buffer[offset + 3] << 8) |
-//         buffer[offset + 4])
-//     // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
-//     offset += 5
-//   } else if (countFlags < 0xfc) {
-//     result =
-//       ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2,32) +
-//         (buffer[offset + 2] << 24)) |
-//       ((buffer[offset + 3] << 16) |
-//         (buffer[offset + 4] << 8) |
-//         buffer[offset + 5])
-//     offset += 6
-//   } else if (countFlags < 0xfe) {
-//     result =
-//       ((((buffer[offset] & 3) << 16) |
-//         (buffer[offset + 1] << 8) |
-//         buffer[offset + 2]) *
-//         Math.pow(2,32) +
-//         (buffer[offset + 3] << 24)) |
-//       ((buffer[offset + 4] << 16) |
-//         (buffer[offset + 5] << 8) |
-//         buffer[offset + 6])
-//     offset += 7
-//   } else if (countFlags < 0xff) {
-//     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 8))
-//     if (
-//       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
-//       result.lessThan(Number.MIN_SAFE_INTEGER)
-//     )
-//       throw new CramUnimplementedError('integer overflow')
-//     result = result.toNumber()
-//     offset += 8
-//   } else {
-//     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 9))
-//     if (
-//       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
-//       result.lessThan(Number.MIN_SAFE_INTEGER)
-//     )
-//       throw new CramUnimplementedError('integer overflow')
-//     result = result.toNumber()
-//     offset += 9
-//   }
-//   return [result, offset - initialOffset]
-// },
-function parseItem(buffer, parser, startBufferPosition, startFilePosition) {
-    if (startBufferPosition === void 0) { startBufferPosition = 0; }
-    if (startFilePosition === void 0) { startFilePosition = 0; }
-    var _a = parser.parse(buffer), offset = _a.offset, result = _a.result;
-    result._endPosition = offset + startFilePosition;
-    result._size = offset - startBufferPosition;
-    return result;
+function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition = 0) {
+    const { offset, result } = parser.parse(buffer);
+    return Object.assign(Object.assign({}, result), { _endPosition: offset + startFilePosition, _size: offset - startBufferPosition });
 }
 exports.parseItem = parseItem;
 // this would be nice as a decorator, but i'm a little worried about
@@ -153,15 +76,14 @@ exports.parseItem = parseItem;
 // memoizes a method in the stupidest possible way, with no regard for the
 // arguments.  actually, this only works on methods that take no arguments
 function tinyMemoize(_class, methodName) {
-    var method = _class.prototype[methodName];
-    var memoAttrName = "_memo_".concat(methodName);
+    const method = _class.prototype[methodName];
+    const memoAttrName = `_memo_${methodName}`;
     _class.prototype[methodName] = function _tinyMemoized() {
-        var _this = this;
         if (!(memoAttrName in this)) {
-            var res = method.call(this);
+            const res = method.call(this);
             this[memoAttrName] = res;
-            Promise.resolve(res).catch(function () {
-                delete _this[memoAttrName];
+            Promise.resolve(res).catch(() => {
+                delete this[memoAttrName];
             });
         }
         return this[memoAttrName];

package/dist/cramFile/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/cramFile/util.ts"],"names":[],"mappings":";;;;;;AAAA,8CAAqB;AAErB,8CAAyD;AAEzD,SAAgB,QAAQ,CAAC,CAAS;IAChC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;QAChB,OAAO,CAAC,CAAA;KACT;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;QAClB,OAAO,CAAC,CAAA;KACT;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE;QACpB,OAAO,CAAC,CAAA;KACT;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE;QACrB,OAAO,CAAC,CAAA;KACT;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAdD,4BAcC;AAED,SAAgB,SAAS,CACvB,MAAkB,EAClB,aAAqB;IAErB,IAAI,MAAM,GAAG,aAAa,CAAA;IAC1B,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,CAAC,CAAA;IACjC,IAAI,MAAM,CAAA;IACV,IAAI,UAAU,GAAG,IAAI,EAAE;QACrB,MAAM,GAAG,UAAU,CAAA;QACnB,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE;QAC5B,MAAM,GAAG,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;QAC1D,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE;QAC5B,MAAM;YACJ,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrE,QAAQ,CAAA;QACV,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE;QAC5B,MAAM;YACJ,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC;gBACjB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrB,UAAU,CAAA;QACZ,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;SAAM;QACL,MAAM;YACJ,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;gBAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,CAAA;QAC7B,+EAA+E;QAC/E,+EAA+E;QAC/E,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;IACD,IAAI,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE;QAC1B,MAAM,IAAI,gCAAsB,CAC9B,oEAAoE,CACrE,CAAA;KACF;IACD,OAAO,CAAC,MAAM,EAAE,MAAM,GAAG,aAAa,CAAC,CAAA;AACzC,CAAC;AA3CD,8BA2CC;AAiFD,SAAgB,SAAS,CACvB,MAAc,EACd,MAAiB,EACjB,mBAAmB,GAAG,CAAC,EACvB,iBAAiB,GAAG,CAAC;IAErB,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAC/C,uCACK,MAAM,KACT,YAAY,EAAE,MAAM,GAAG,iBAAiB,EACxC,KAAK,EAAE,MAAM,GAAG,mBAAmB,IACpC;AACH,CAAC;AAZD,8BAYC;AAED,oEAAoE;AACpE,+CAA+C;AAC/C,0EAA0E;AAC1E,0EAA0E;AAC1E,SAAgB,WAAW,CAAC,MAAW,EAAE,UAAe;IACtD,MAAM,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,CAAA;IAC3C,MAAM,YAAY,GAAG,SAAS,UAAU,EAAE,CAAA;IAC1C,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,GAAG,SAAS,aAAa;QACnD,IAAI,CAAC,CAAC,YAAY,IAAI,IAAI,CAAC,EAAE;YAC3B,MAAM,GAAG,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAC7B,IAAI,CAAC,YAAY,CAAC,GAAG,GAAG,CAAA;YACxB,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE;gBAC9B,OAAO,IAAI,CAAC,YAAY,CAAC,CAAA;YAC3B,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,YAAY,CAAC,CAAA;IAC3B,CAAC,CAAA;AACH,CAAC;AAbD,kCAaC;AAED,SAAgB,WAAW,CAAC,GAAW;IACrC,OAAO,IAAA,aAAG,EAAC,GAAG,CAAC,WAAW,EAAE,CAAC,OAAO,CAAC,eAAe,EAAE,EAAE,CAAC,CAAC,CAAA;AAC5D,CAAC;AAFD,kCAEC"}

package/dist/errors.d.ts

@@ -1,23 +1,18 @@
-export class CramError extends Error {
+export declare class CramError extends Error {
 }
 /** Error caused by encountering a part of the CRAM spec that has not yet been implemented */
-export class CramUnimplementedError extends Error {
+export declare class CramUnimplementedError extends Error {
 }
 /** An error caused by malformed data.  */
-export class CramMalformedError extends CramError {
-}
-/**
- * An error caused by attempting to read beyond the end of the defined data.
- */
-export class CramBufferOverrunError extends CramMalformedError {
+export declare class CramMalformedError extends CramError {
 }
 /**
  * An error caused by data being too big, exceeding a size limit.
  */
-export class CramSizeLimitError extends CramError {
+export declare class CramSizeLimitError extends CramError {
 }
 /**
  * An invalid argument was supplied to a cram-js method or object.
  */
-export class CramArgumentError extends CramError {
+export declare class CramArgumentError extends CramError {
 }

package/dist/errors.js

@@ -1,78 +1,27 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CramArgumentError = exports.CramSizeLimitError = exports.CramBufferOverrunError = exports.CramMalformedError = exports.CramUnimplementedError = exports.CramError = void 0;
-var CramError = /** @class */ (function (_super) {
-    __extends(CramError, _super);
-    function CramError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return CramError;
-}(Error));
+exports.CramArgumentError = exports.CramSizeLimitError = exports.CramMalformedError = exports.CramUnimplementedError = exports.CramError = void 0;
+class CramError extends Error {
+}
 exports.CramError = CramError;
 /** Error caused by encountering a part of the CRAM spec that has not yet been implemented */
-var CramUnimplementedError = /** @class */ (function (_super) {
-    __extends(CramUnimplementedError, _super);
-    function CramUnimplementedError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return CramUnimplementedError;
-}(Error));
+class CramUnimplementedError extends Error {
+}
 exports.CramUnimplementedError = CramUnimplementedError;
 /** An error caused by malformed data.  */
-var CramMalformedError = /** @class */ (function (_super) {
-    __extends(CramMalformedError, _super);
-    function CramMalformedError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return CramMalformedError;
-}(CramError));
+class CramMalformedError extends CramError {
+}
 exports.CramMalformedError = CramMalformedError;
-/**
- * An error caused by attempting to read beyond the end of the defined data.
- */
-var CramBufferOverrunError = /** @class */ (function (_super) {
-    __extends(CramBufferOverrunError, _super);
-    function CramBufferOverrunError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return CramBufferOverrunError;
-}(CramMalformedError));
-exports.CramBufferOverrunError = CramBufferOverrunError;
 /**
  * An error caused by data being too big, exceeding a size limit.
  */
-var CramSizeLimitError = /** @class */ (function (_super) {
-    __extends(CramSizeLimitError, _super);
-    function CramSizeLimitError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return CramSizeLimitError;
-}(CramError));
+class CramSizeLimitError extends CramError {
+}
 exports.CramSizeLimitError = CramSizeLimitError;
 /**
  * An invalid argument was supplied to a cram-js method or object.
  */
-var CramArgumentError = /** @class */ (function (_super) {
-    __extends(CramArgumentError, _super);
-    function CramArgumentError() {
-        return _super !== null && _super.apply(this, arguments) || this;
-    }
-    return CramArgumentError;
-}(CramError));
+class CramArgumentError extends CramError {
+}
 exports.CramArgumentError = CramArgumentError;
 //# sourceMappingURL=errors.js.map

package/dist/errors.js.map

@@ -1 +1 @@
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+{"version":3,"file":"errors.js","sourceRoot":"","sources":["../src/errors.ts"],"names":[],"mappings":";;;AAAA,MAAa,SAAU,SAAQ,KAAK;CAAG;AAAvC,8BAAuC;AAEvC,6FAA6F;AAC7F,MAAa,sBAAuB,SAAQ,KAAK;CAAG;AAApD,wDAAoD;AAEpD,0CAA0C;AAC1C,MAAa,kBAAmB,SAAQ,SAAS;CAAG;AAApD,gDAAoD;AAEpD;;GAEG;AACH,MAAa,kBAAmB,SAAQ,SAAS;CAAG;AAApD,gDAAoD;AAEpD;;GAEG;AACH,MAAa,iBAAkB,SAAQ,SAAS;CAAG;AAAnD,8CAAmD"}

package/dist/index.d.ts

@@ -1,4 +1,4 @@
-import CramFile from "./cramFile";
-import IndexedCramFile from "./indexedCramFile";
-import CraiIndex from "./craiIndex";
+import CramFile from './cramFile';
+import IndexedCramFile from './indexedCramFile';
+import CraiIndex from './craiIndex';
 export { CramFile, IndexedCramFile, CraiIndex };

package/dist/index.js

@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.CraiIndex = exports.IndexedCramFile = exports.CramFile = void 0;
-var cramFile_1 = __importDefault(require("./cramFile"));
+const cramFile_1 = __importDefault(require("./cramFile"));
 exports.CramFile = cramFile_1.default;
-var indexedCramFile_1 = __importDefault(require("./indexedCramFile"));
+const indexedCramFile_1 = __importDefault(require("./indexedCramFile"));
 exports.IndexedCramFile = indexedCramFile_1.default;
-var craiIndex_1 = __importDefault(require("./craiIndex"));
+const craiIndex_1 = __importDefault(require("./craiIndex"));
 exports.CraiIndex = craiIndex_1.default;
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":";;;;;;AAAA,wDAAiC;AAIxB,mBAJF,kBAAQ,CAIE;AAHjB,sEAA+C;AAG5B,0BAHZ,yBAAe,CAGY;AAFlC,0DAAmC;AAEC,oBAF7B,mBAAS,CAE6B"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,0DAAiC;AAIxB,mBAJF,kBAAQ,CAIE;AAHjB,wEAA+C;AAG5B,0BAHZ,yBAAe,CAGY;AAFlC,4DAAmC;AAEC,oBAF7B,mBAAS,CAE6B"}

package/dist/indexedCramFile.d.ts

@@ -1,4 +1,21 @@
+import CramFile from './cramFile';
+import CramRecord from './cramFile/record';
+import { SeqFetch } from './cramFile/file';
+import { Filehandle } from './cramFile/filehandle';
+import { Slice } from './craiIndex';
+export declare type CramFileSource = {
+    cramFilehandle?: Filehandle;
+    cramUrl?: string;
+    cramPath?: string;
+};
+export declare type CramIndexLike = {
+    getEntriesForRange: (seqId: number, start: number, end: number) => Promise<Slice[]>;
+    hasDataForReferenceSequence: (seqId: number) => Promise<boolean>;
+};
 export default class IndexedCramFile {
+    cram: CramFile;
+    index: CramIndexLike;
+    private fetchSizeLimit;
     /**
      *
      * @param {object} args
@@ -10,11 +27,16 @@ export default class IndexedCramFile {
      * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
      */
     constructor(args: {
+        index: CramIndexLike;
+        fetchSizeLimit?: number;
+    } & ({
         cram: CramFile;
-    });
-    cram: CramFile;
-    index: any;
-    fetchSizeLimit: any;
+    } | ({
+        cram?: undefined;
+        seqFetch: SeqFetch;
+        checkSequenceMD5: boolean;
+        cacheSize?: number;
+    } & CramFileSource)));
     /**
      *
      * @param {number} seq numeric ID of the reference sequence
@@ -22,18 +44,21 @@ export default class IndexedCramFile {
      * @param {number} end end of the range of interest. 1-based closed coordinates.
      * @returns {Promise[Array[CramRecord]]}
      */
-    getRecordsForRange(seq: number, start: number, end: number, opts?: {}): Promise<any>[any[][CramRecord]];
-    getRecordsInSlice({ containerStart, sliceStart, sliceBytes }: {
-        containerStart: any;
-        sliceStart: any;
-        sliceBytes: any;
-    }, filterFunction: any): Promise<any>;
+    getRecordsForRange(seq: number, start: number, end: number, opts?: {
+        viewAsPairs?: boolean;
+        pairAcrossChr?: boolean;
+        maxInsertSize?: number;
+    }): Promise<CramRecord[]>;
+    getRecordsInSlice({ containerStart, sliceStart, sliceBytes, }: {
+        containerStart: number;
+        sliceStart: number;
+        sliceBytes: number;
+    }, filterFunction: (r: CramRecord) => boolean): Promise<CramRecord[]>;
     /**
      *
      * @param {number} seqId
      * @returns {Promise} true if the CRAM file contains data for the given
      * reference sequence numerical ID
      */
-    hasDataForReferenceSequence(seqId: number): Promise<any>;
+    hasDataForReferenceSequence(seqId: number): Promise<boolean>;
 }
-import CramFile from "./cramFile";