@gmod/cram 4.0.9 → 5.0.0

package/esm/cramFile/container/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AACjD,SAAS;AACT,OAAO,SAAS,MAAM,UAAU,CAAA;AAChC,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAC1D,OAAO,8BAA8B,MAAM,qBAAqB,CAAA;AAEhE,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAA;AAErD,MAAM,CAAC,OAAO,OAAO,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAED,KAAK,CAAC,yBAAyB;QAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAE9C,yEAAyE;QACzE,SAAS;QACT,IAAI,CAAC,eAAe,CAAC,UAAU,EAAE,CAAC;YAChC,OAAO,IAAI,CAAA;QACb,CAAC;QACD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QAEtD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACxC,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;YAC/C,MAAM,IAAI,kBAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,8BAA8B,CACxE,CAAA;QACH,CAAC;QAED,MAAM,OAAO,GAAG,SAAS,CACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;QACD,OAAO;YACL,GAAG,KAAK;YACR,aAAa,EAAE,OAAO;SACvB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED,2EAA2E;IAC3E,SAAS;IACT,KAAK,CAAC,oBAAoB;QACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;QACrD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,OAAO,IAAI,8BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IACjE,CAAC;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,SAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,QAAgB;QACzC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QACtD,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAErE,wEAAwE;QACxE,iDAAiD;QACjD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CACjC,oBAAoB,CAAC,SAAS,EAC9B,QAAQ,CACT,CAAA;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAC9D,MAAM,gBAAgB,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QAEvD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CACjC,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,EACpD,QAAQ,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,CAC5C,CAAA;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/D,MAAM,IAAI,CAAC,IAAI,CAAC,UAAU,CACxB,QAAQ,EACR,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,CAAC,EACpD,OAAO,CAAC,KAAK,EACb,0CAA0C,QAAQ,EAAE,CACrD,CAAA;QACH,CAAC;QAED,OAAO;YACL,GAAG,OAAO;YACV,GAAG,OAAO;YACV,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;YACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;SAC1E,CAAA;IACH,CAAC;CACF;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE;IAChB,WAAW,CAAC,aAAa,EAAE,MAAM,CAAC,CAAA;AACpC,CAAC,CAAC,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAA;AACpD,OAAO,SAAS,MAAM,mBAAmB,CAAA;AACzC,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,YAAY,CAAA;AAC7D,OAAO,8BAA8B,MAAM,wBAAwB,CAAA;AAEnE,OAAO,EAAE,iBAAiB,EAAE,MAAM,sBAAsB,CAAA;AAExD,MAAM,CAAC,OAAO,OAAO,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAED,KAAK,CAAC,yBAAyB;QAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAE9C,yEAAyE;QACzE,SAAS;QACT,IAAI,CAAC,eAAe,CAAC,UAAU,EAAE,CAAC;YAChC,OAAO,IAAI,CAAA;QACb,CAAC;QACD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QAEtD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACxC,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;YAC/C,MAAM,IAAI,kBAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,8BAA8B,CACxE,CAAA;QACH,CAAC;QAED,MAAM,OAAO,GAAG,SAAS,CACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;QACD,OAAO;YACL,GAAG,KAAK;YACR,aAAa,EAAE,OAAO;SACvB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC9C,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED,2EAA2E;IAC3E,SAAS;IACT,KAAK,CAAC,oBAAoB;QACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;QACrD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,OAAO,IAAI,8BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IACjE,CAAC;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,SAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,QAAgB;QACzC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QACtD,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAErE,wEAAwE;QACxE,iDAAiD;QACjD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CACjC,oBAAoB,CAAC,SAAS,EAC9B,QAAQ,CACT,CAAA;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAC9D,MAAM,gBAAgB,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QAEvD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CACjC,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,EACpD,QAAQ,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,CAC5C,CAAA;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/D,MAAM,IAAI,CAAC,IAAI,CAAC,UAAU,CACxB,QAAQ,EACR,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,CAAC,EACpD,OAAO,CAAC,KAAK,EACb,0CAA0C,QAAQ,EAAE,CACrD,CAAA;QACH,CAAC;QAED,OAAO;YACL,GAAG,OAAO;YACV,GAAG,OAAO;YACV,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;YACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;SAC1E,CAAA;IACH,CAAC;CACF;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE;IAChB,WAAW,CAAC,aAAa,EAAE,MAAM,CAAC,CAAA;AACpC,CAAC,CAAC,CAAA"}

package/esm/cramFile/file.d.ts

@@ -1,7 +1,7 @@
 import QuickLRU from 'quick-lru';
-import CramContainer from './container';
-import CramRecord from './record';
-import { BlockHeader, CompressionMethod } from './sectionParsers';
+import CramContainer from './container/index.ts';
+import CramRecord from './record.ts';
+import { BlockHeader, CompressionMethod } from './sectionParsers.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 export interface CramFileSource {
     filehandle?: GenericFilehandle;

package/esm/cramFile/file.js

@@ -1,19 +1,16 @@
-// import bzip2 from 'bzip2'
-// import BZip2 from 'bzip2-wasm'
-// import { decompress } from 'bz2'
 import crc32 from 'crc/calculators/crc32';
 import QuickLRU from 'quick-lru';
-import Bunzip from 'seek-bzip';
 import { XzReadableStream } from 'xz-decompress';
-import { CramMalformedError, CramUnimplementedError } from '../errors';
-import * as htscodecs from '../htscodecs';
-import { open } from '../io';
-import ransuncompress from '../rans';
-import { parseHeaderText } from '../sam';
-import { unzip } from '../unzip';
-import CramContainer from './container';
-import { cramFileDefinition, getSectionParsers, } from './sectionParsers';
-import { parseItem, tinyMemoize } from './util';
+import { CramMalformedError, CramUnimplementedError } from "../errors.js";
+import * as htscodecs from "../htscodecs/index.js";
+import { open } from "../io.js";
+import ransuncompress from "../rans/index.js";
+import { parseHeaderText } from "../sam.js";
+import { decode } from "../seek-bzip/index.js";
+import { unzip } from "../unzip.js";
+import CramContainer from "./container/index.js";
+import { cramFileDefinition, getSectionParsers, } from "./sectionParsers.js";
+import { parseItem, tinyMemoize } from "./util.js";
 function bufferToStream(buf) {
     return new ReadableStream({
         start(controller) {
@@ -190,14 +187,10 @@ export default class CramFile {
     async _uncompressPre(compressionMethod, inputBuffer, uncompressedSize) {
         // console.log({ compressionMethod })
         if (compressionMethod === 'gzip') {
-            const ret = unzip(inputBuffer);
-            if (ret[0] === 24) {
-                // console.log(ret.slice(0, 500).join(','))
-            }
-            return ret;
+            return unzip(inputBuffer);
         }
         else if (compressionMethod === 'bzip2') {
-            return Bunzip.decode(inputBuffer);
+            return decode(inputBuffer);
         }
         else if (compressionMethod === 'lzma') {
             const decompressedResponse = new Response(new XzReadableStream(bufferToStream(inputBuffer)));
@@ -207,8 +200,6 @@ export default class CramFile {
             const outputBuffer = new Uint8Array(uncompressedSize);
             ransuncompress(inputBuffer, outputBuffer);
             return outputBuffer;
-            // htscodecs r4x8 is slower, but compatible.
-            // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
         }
         else if (compressionMethod === 'rans4x16') {
             return htscodecs.r4x16_uncompress(inputBuffer);

package/esm/cramFile/file.js.map

@@ -1 +1 @@
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package/esm/cramFile/index.d.ts

@@ -1,2 +1,2 @@
-export { default as CramRecord } from './record';
-export { default } from './file';
+export { default as CramRecord } from './record.ts';
+export { default } from './file.ts';

package/esm/cramFile/index.js

@@ -1,3 +1,3 @@
-export { default as CramRecord } from './record';
-export { default } from './file';
+export { default as CramRecord } from "./record.js";
+export { default } from "./file.js";
 //# sourceMappingURL=index.js.map

package/esm/cramFile/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,UAAU,CAAA;AAEhD,OAAO,EAAE,OAAO,EAAE,MAAM,QAAQ,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA;AAEnD,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA"}

package/esm/cramFile/record.d.ts

@@ -1,5 +1,5 @@
-import CramContainerCompressionScheme from './container/compressionScheme';
-import type decodeRecord from './slice/decodeRecord';
+import CramContainerCompressionScheme from './container/compressionScheme.ts';
+import type decodeRecord from './slice/decodeRecord.ts';
 export interface RefRegion {
     start: number;
     end: number;

package/esm/cramFile/record.js

@@ -1,4 +1,4 @@
-import Constants from './constants';
+import Constants from "./constants.js";
 function decodeReadSequence(cramRecord, refRegion) {
     // if it has no length, it has no sequence
     if (!cramRecord.lengthOnRef && !cramRecord.readLength) {

package/esm/cramFile/record.js.map

@@ -1 +1 @@
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package/esm/cramFile/sectionParsers.d.ts

@@ -1,6 +1,6 @@
-import { TupleOf } from '../typescript';
-import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes';
-import { CramEncoding } from './encoding';
+import { TupleOf } from '../typescript.ts';
+import { DataSeriesEncodingMap } from './codecs/dataSeriesTypes.ts';
+import { CramEncoding } from './encoding.ts';
 export declare function cramFileDefinition(): {
     parser: (b: Uint8Array, _startOffset?: number) => {
         value: {

package/esm/cramFile/sectionParsers.js

@@ -1,4 +1,4 @@
-import { parseItf8, parseLtf8 } from './util';
+import { parseItf8, parseLtf8 } from "./util.js";
 export function cramFileDefinition() {
     return {
         parser: (b, _startOffset = 0) => {

package/esm/cramFile/sectionParsers.js.map

@@ -1 +1 @@
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package/esm/cramFile/slice/decodeRecord.d.ts

@@ -1,9 +1,9 @@
-import { Cursors, DataTypeMapping } from '../codecs/_base';
-import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes';
-import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/compressionScheme';
-import { ReadFeature } from '../record';
-import CramSlice, { SliceHeader } from './index';
-import { CramFileBlock } from '../file';
+import { Cursors, DataTypeMapping } from '../codecs/_base.ts';
+import { DataSeriesEncodingKey } from '../codecs/dataSeriesTypes.ts';
+import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/compressionScheme.ts';
+import { ReadFeature } from '../record.ts';
+import CramSlice, { SliceHeader } from './index.ts';
+import { CramFileBlock } from '../file.ts';
 export type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]] | undefined;
 export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSeriesDecoder, compressionScheme: CramContainerCompressionScheme, sliceHeader: SliceHeader, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, majorVersion: number, recordNumber: number): {
     readLength: number;

package/esm/cramFile/slice/decodeRecord.js

@@ -1,6 +1,6 @@
-import { CramMalformedError } from '../../errors';
-import { BamFlagsDecoder, CramFlagsDecoder, MateFlagsDecoder, } from '../record';
-import { isMappedSliceHeader } from '../sectionParsers';
+import { CramMalformedError } from "../../errors.js";
+import { BamFlagsDecoder, CramFlagsDecoder, MateFlagsDecoder, } from "../record.js";
+import { isMappedSliceHeader } from "../sectionParsers.js";
 /**
  * given a Buffer, read a string up to the first null character
  * @private

package/esm/cramFile/slice/decodeRecord.js.map

@@ -1 +1 @@
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package/esm/cramFile/slice/index.d.ts

@@ -1,7 +1,7 @@
-import CramContainer from '../container';
-import { CramFileBlock } from '../file';
-import CramRecord from '../record';
-import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers';
+import CramContainer from '../container/index.ts';
+import { CramFileBlock } from '../file.ts';
+import CramRecord from '../record.ts';
+import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers.ts';
 export type SliceHeader = CramFileBlock & {
     parsedContent: MappedSliceHeader | UnmappedSliceHeader;
 };
@@ -23,7 +23,7 @@ export default class CramSlice {
             _endPosition: number;
             _size: number;
         };
-        compressionMethod: import("../sectionParsers").CompressionMethod;
+        compressionMethod: import("../sectionParsers.ts").CompressionMethod;
         contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
         contentId: number;
         compressedSize: number;

package/esm/cramFile/slice/index.js

@@ -1,18 +1,15 @@
-import { CramArgumentError, CramMalformedError } from '../../errors';
-import { CramBufferOverrunError } from '../codecs/getBits';
-import Constants from '../constants';
-import decodeRecord from './decodeRecord';
-import CramRecord from '../record';
-import { getSectionParsers, isMappedSliceHeader, } from '../sectionParsers';
-import { parseItem, sequenceMD5, tinyMemoize } from '../util';
+import { CramArgumentError, CramMalformedError } from "../../errors.js";
+import { CramBufferOverrunError } from "../codecs/getBits.js";
+import Constants from "../constants.js";
+import decodeRecord from "./decodeRecord.js";
+import CramRecord from "../record.js";
+import { getSectionParsers, isMappedSliceHeader, } from "../sectionParsers.js";
+import { parseItem, sequenceMD5, tinyMemoize } from "../util.js";
 /**
- * @private
- * Try to estimate the template length from a bunch of interrelated multi-segment reads.
- * @param {Array[CramRecord]} allRecords
- * @param {number} currentRecordNumber
- * @param {CramRecord} thisRecord
+ * Try to estimate the template length from a bunch of interrelated
+ * multi-segment reads.
  */
-function calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumber, thisRecord) {
+function calculateMultiSegmentMatedTemplateLength(allRecords, _currentRecordNumber, thisRecord) {
     function getAllMatedRecords(startRecord) {
         const records = [startRecord];
         if (startRecord.mateRecordNumber !== undefined &&
@@ -39,15 +36,13 @@ function calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumbe
     }
 }
 /**
- * @private
- * Attempt to calculate the `templateLength` for a pair of intra-slice paired reads.
- * Ported from htslib. Algorithm is imperfect.
- * @param {CramRecord} thisRecord
- * @param {CramRecord} mateRecord
+ * Attempt to calculate the `templateLength` for a pair of intra-slice paired
+ * reads. Ported from htslib. Algorithm is imperfect.
  */
 function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
-    // this just estimates the template length by using the simple (non-gapped) end coordinate of each
-    // read, because gapping in the alignment doesn't mean the template is longer or shorter
+    // this just estimates the template length by using the simple (non-gapped)
+    // end coordinate of each read, because gapping in the alignment doesn't mean
+    // the template is longer or shorter
     const start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart);
     const end = Math.max(thisRecord.alignmentStart + thisRecord.readLength - 1, mateRecord.alignmentStart + mateRecord.readLength - 1);
     const lengthEstimate = end - start + 1;
@@ -55,10 +50,9 @@ function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
     mateRecord.templateLength = lengthEstimate;
 }
 /**
- * @private establishes a mate-pair relationship between two records in the
- * same slice. CRAM compresses mate-pair relationships between records in the
- * same slice down into just one record having the index in the slice of its
- * mate
+ * establishes a mate-pair relationship between two records in the same slice.
+ * CRAM compresses mate-pair relationships between records in the same slice
+ * down into just one record having the index in the slice of its mate
  */
 function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, mateRecord) {
     const complicatedMultiSegment = !!(mateRecord.mate ||

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

@@ -1 +1 @@
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package/esm/htscodecs/arith_gen.d.ts

@@ -1,4 +1,4 @@
-import IOStream from './iostream';
+import IOStream from './iostream.ts';
 export default class RangeCoderGen {
     stream: IOStream;
     decode(src: Uint8Array): Uint8Array<any>;