@gmod/cram 4.0.9 → 5.0.0

package/dist/cramFile/sectionParsers.js

@@ -7,7 +7,7 @@ exports.cramTagDictionary = cramTagDictionary;
 exports.cramPreservationMap = cramPreservationMap;
 exports.isMappedSliceHeader = isMappedSliceHeader;
 exports.getSectionParsers = getSectionParsers;
-const util_1 = require("./util");
+const util_ts_1 = require("./util.js");
 function cramFileDefinition() {
     return {
         parser: (b, _startOffset = 0) => {
@@ -71,11 +71,11 @@ function cramBlockHeader() {
             throw new Error(`invalid block content type id ${c}`);
         }
         offset += 1;
-        const [contentId, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+        const [contentId, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
         offset += newOffset1;
-        const [compressedSize, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+        const [compressedSize, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
         offset += newOffset2;
-        const [uncompressedSize, newOffset3] = (0, util_1.parseItf8)(buffer, offset);
+        const [uncompressedSize, newOffset3] = (0, util_ts_1.parseItf8)(buffer, offset);
         offset += newOffset3;
         return {
             offset,
@@ -119,7 +119,7 @@ function makeTagSet(buffer, stringStart, stringEnd) {
 function cramTagDictionary() {
     return {
         parser: (buffer, offset) => {
-            const [size, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+            const [size, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset1;
             const subbuf = buffer.subarray(offset, offset + size);
             offset += size;
@@ -150,9 +150,9 @@ function cramPreservationMap() {
         parser: (buffer, offset) => {
             const b = buffer;
             const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-            const [mapSize, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+            const [mapSize, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset1;
-            const [mapCount, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+            const [mapCount, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset2;
             const ents = [];
             for (let i = 0; i < mapCount; i++) {
@@ -226,30 +226,30 @@ function cramUnmappedSliceHeader(majorVersion) {
     maxLength += 5 * 2;
     maxLength += 16;
     const parser = (buffer, offset) => {
-        const [numRecords, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+        const [numRecords, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
         offset += newOffset1;
         let recordCounter = 0;
         // recordCounter is itf8 in a CRAM v2 file, absent in CRAM v1
         if (majorVersion >= 3) {
-            const [rc, newOffset2] = (0, util_1.parseLtf8)(buffer, offset);
+            const [rc, newOffset2] = (0, util_ts_1.parseLtf8)(buffer, offset);
             offset += newOffset2;
             recordCounter = rc;
         }
         else if (majorVersion === 2) {
-            const [rc, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+            const [rc, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset2;
             recordCounter = rc;
         }
         else {
             console.warn('recordCounter=0');
         }
-        const [numBlocks, newOffset3] = (0, util_1.parseItf8)(buffer, offset);
+        const [numBlocks, newOffset3] = (0, util_ts_1.parseItf8)(buffer, offset);
         offset += newOffset3;
-        const [numContentIds, newOffset4] = (0, util_1.parseItf8)(buffer, offset);
+        const [numContentIds, newOffset4] = (0, util_ts_1.parseItf8)(buffer, offset);
         offset += newOffset4;
         const contentIds = [];
         for (let i = 0; i < numContentIds; i++) {
-            const [id, newOffset5] = (0, util_1.parseItf8)(buffer, offset);
+            const [id, newOffset5] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset5;
             contentIds.push(id);
         }
@@ -287,24 +287,24 @@ function cramMappedSliceHeader(majorVersion) {
     return {
         parser: (buffer, offset) => {
             // L0
-            const [refSeqId, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+            const [refSeqId, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset1;
-            const [refSeqStart, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+            const [refSeqStart, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset2;
-            const [refSeqSpan, newOffset3] = (0, util_1.parseItf8)(buffer, offset);
+            const [refSeqSpan, newOffset3] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset3;
-            const [numRecords, newOffset4] = (0, util_1.parseItf8)(buffer, offset);
+            const [numRecords, newOffset4] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset4;
             // EL0
             // L1
             let recordCounter = 0;
             if (majorVersion >= 3) {
-                const [rc, newOffset5] = (0, util_1.parseLtf8)(buffer, offset);
+                const [rc, newOffset5] = (0, util_ts_1.parseLtf8)(buffer, offset);
                 offset += newOffset5;
                 recordCounter = rc;
             }
             else if (majorVersion === 2) {
-                const [rc, newOffset5] = (0, util_1.parseItf8)(buffer, offset);
+                const [rc, newOffset5] = (0, util_ts_1.parseItf8)(buffer, offset);
                 offset += newOffset5;
                 recordCounter = rc;
             }
@@ -313,17 +313,17 @@ function cramMappedSliceHeader(majorVersion) {
             }
             // EL1
             // L2
-            const [numBlocks, newOffset6] = (0, util_1.parseItf8)(buffer, offset);
+            const [numBlocks, newOffset6] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset6;
-            const [numContentIds, newOffset7] = (0, util_1.parseItf8)(buffer, offset);
+            const [numContentIds, newOffset7] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset7;
             const contentIds = [];
             for (let i = 0; i < numContentIds; i++) {
-                const [id, newOffset5] = (0, util_1.parseItf8)(buffer, offset);
+                const [id, newOffset5] = (0, util_ts_1.parseItf8)(buffer, offset);
                 offset += newOffset5;
                 contentIds.push(id);
             }
-            const [refBaseBlockId, newOffset8] = (0, util_1.parseItf8)(buffer, offset);
+            const [refBaseBlockId, newOffset8] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset8;
             // EL2
             // the md5 sum is missing in cram v1
@@ -359,9 +359,9 @@ function cramEncoding() {
 function cramEncodingSub(buffer, offset) {
     const b = buffer;
     const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-    const [codecId, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+    const [codecId, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
     offset += newOffset1;
-    const [parametersBytes, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+    const [parametersBytes, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
     offset += newOffset2;
     const parameters = {};
     if (codecId === 0) {
@@ -369,32 +369,32 @@ function cramEncodingSub(buffer, offset) {
     }
     else if (codecId === 1) {
         // EXTERNAL
-        const [bc, newOffset3] = (0, util_1.parseItf8)(buffer, offset);
+        const [bc, newOffset3] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.blockContentId = bc;
         offset += newOffset3;
     }
     else if (codecId === 2) {
         // GOLUMB
-        const [off, newOffset3] = (0, util_1.parseItf8)(buffer, offset);
+        const [off, newOffset3] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.offset = off;
         offset += newOffset3;
-        const [M2, newOffset4] = (0, util_1.parseItf8)(buffer, offset);
+        const [M2, newOffset4] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.M = M2;
         offset += newOffset4;
     }
     else if (codecId === 3) {
         // HUFFMAN_INT
-        const val = (0, util_1.parseItf8)(buffer, offset);
+        const val = (0, util_ts_1.parseItf8)(buffer, offset);
         const numCodes = val[0];
         offset += val[1];
         const symbols = [];
         for (let i = 0; i < numCodes; i++) {
-            const code = (0, util_1.parseItf8)(buffer, offset);
+            const code = (0, util_ts_1.parseItf8)(buffer, offset);
             symbols.push(code[0]);
             offset += code[1];
         }
         parameters.symbols = symbols;
-        const val2 = (0, util_1.parseItf8)(buffer, offset);
+        const val2 = (0, util_ts_1.parseItf8)(buffer, offset);
         const numLengths = val[0];
         parameters.numLengths = numLengths;
         parameters.numCodes = numCodes;
@@ -402,7 +402,7 @@ function cramEncodingSub(buffer, offset) {
         offset += val2[1];
         const bitLengths = [];
         for (let i = 0; i < numLengths; i++) {
-            const len = (0, util_1.parseItf8)(buffer, offset);
+            const len = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += len[1];
             bitLengths.push(len[0]);
         }
@@ -421,40 +421,40 @@ function cramEncodingSub(buffer, offset) {
         // BYTE_ARRAY_STOP
         parameters.stopByte = dataView.getUint8(offset);
         offset += 1;
-        const [blockContentId, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+        const [blockContentId, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.blockContentId = blockContentId;
         offset += newOffset1;
     }
     else if (codecId === 6) {
         // BETA
-        const [off, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+        const [off, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.offset = off;
         offset += newOffset1;
-        const [len, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+        const [len, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.length = len;
         offset += newOffset2;
     }
     else if (codecId === 7) {
         // SUBEXP
-        const [off, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+        const [off, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.offset = off;
         offset += newOffset1;
-        const [K, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+        const [K, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.K = K;
         offset += newOffset2;
     }
     else if (codecId === 8) {
         // GOLOMB_RICE
-        const [off, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+        const [off, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.offset = off;
         offset += newOffset1;
-        const [l2m, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+        const [l2m, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.log2m = l2m;
         offset += newOffset2;
     }
     else if (codecId === 9) {
         // GAMMA
-        const [off, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+        const [off, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
         parameters.offset = off;
         offset += newOffset1;
     }
@@ -473,9 +473,9 @@ function cramEncodingSub(buffer, offset) {
 function cramDataSeriesEncodingMap() {
     return {
         parser: (buffer, offset) => {
-            const [mapSize, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+            const [mapSize, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset1;
-            const [mapCount, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+            const [mapCount, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset2;
             const ents = [];
             for (let i = 0; i < mapCount; i++) {
@@ -500,13 +500,13 @@ function cramDataSeriesEncodingMap() {
 function cramTagEncodingMap() {
     return {
         parser: (buffer, offset) => {
-            const [mapSize, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+            const [mapSize, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset1;
-            const [mapCount, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+            const [mapCount, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset2;
             const ents = [];
             for (let i = 0; i < mapCount; i++) {
-                const [k0, newOffset3] = (0, util_1.parseItf8)(buffer, offset);
+                const [k0, newOffset3] = (0, util_ts_1.parseItf8)(buffer, offset);
                 offset += newOffset3;
                 const key = String.fromCharCode((k0 >> 16) & 0xff) +
                     String.fromCharCode((k0 >> 8) & 0xff) +
@@ -566,22 +566,22 @@ function cramContainerHeader1(majorVersion) {
             // reference sequence identifier:
             // -1 for unmapped reads,
             // -2 for multiple reference sequences
-            const [refSeqId, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+            const [refSeqId, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset1;
-            const [refSeqStart, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+            const [refSeqStart, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset2;
-            const [alignmentSpan, newOffset3] = (0, util_1.parseItf8)(buffer, offset);
+            const [alignmentSpan, newOffset3] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset3;
-            const [numRecords, newOffset4] = (0, util_1.parseItf8)(buffer, offset);
+            const [numRecords, newOffset4] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset4;
             let recordCounter = 0;
             if (majorVersion >= 3) {
-                const [rc, newOffset5] = (0, util_1.parseLtf8)(buffer, offset);
+                const [rc, newOffset5] = (0, util_ts_1.parseLtf8)(buffer, offset);
                 recordCounter = rc;
                 offset += newOffset5;
             }
             else if (majorVersion === 2) {
-                const [rc, newOffset5] = (0, util_1.parseItf8)(buffer, offset);
+                const [rc, newOffset5] = (0, util_ts_1.parseItf8)(buffer, offset);
                 recordCounter = rc;
                 offset += newOffset5;
             }
@@ -590,13 +590,13 @@ function cramContainerHeader1(majorVersion) {
             }
             let numBases;
             if (majorVersion > 1) {
-                const [n, newOffset5] = (0, util_1.parseLtf8)(buffer, offset);
+                const [n, newOffset5] = (0, util_ts_1.parseLtf8)(buffer, offset);
                 numBases = n;
                 offset += newOffset5;
             }
-            const [numBlocks, newOffset6] = (0, util_1.parseItf8)(buffer, offset);
+            const [numBlocks, newOffset6] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset6;
-            const [numLandmarks, newOffset7] = (0, util_1.parseItf8)(buffer, offset);
+            const [numLandmarks, newOffset7] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset7;
             return {
                 value: {
@@ -620,11 +620,11 @@ function cramContainerHeader2(majorVersion) {
         parser: (buffer, offset) => {
             const b = buffer;
             const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-            const [numLandmarks, newOffset1] = (0, util_1.parseItf8)(buffer, offset);
+            const [numLandmarks, newOffset1] = (0, util_ts_1.parseItf8)(buffer, offset);
             offset += newOffset1;
             const landmarks = [];
             for (let i = 0; i < numLandmarks; i++) {
-                const [landmark, newOffset2] = (0, util_1.parseItf8)(buffer, offset);
+                const [landmark, newOffset2] = (0, util_ts_1.parseItf8)(buffer, offset);
                 offset += newOffset2;
                 landmarks.push(landmark);
             }

package/dist/cramFile/sectionParsers.js.map

@@ -1 +1 @@
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package/dist/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/dist/cramFile/slice/decodeRecord.js

@@ -1,9 +1,9 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = decodeRecord;
-const errors_1 = require("../../errors");
-const record_1 = require("../record");
-const sectionParsers_1 = require("../sectionParsers");
+const errors_ts_1 = require("../../errors.js");
+const record_ts_1 = require("../record.js");
+const sectionParsers_ts_1 = require("../sectionParsers.js");
 /**
  * given a Buffer, read a string up to the first null character
  * @private
@@ -107,7 +107,7 @@ function parseTagData(tagType, buffer) {
     if (tagType === 'B') {
         return parseTagValueArray(buffer);
     }
-    throw new errors_1.CramMalformedError(`Unrecognized tag type ${tagType}`);
+    throw new errors_ts_1.CramMalformedError(`Unrecognized tag type ${tagType}`);
 }
 function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion) {
     let currentReadPos = 0;
@@ -152,7 +152,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
             N: ['number', 'RS'],
         }[code];
         if (!data1Schema) {
-            throw new errors_1.CramMalformedError(`invalid read feature code "${code}"`);
+            throw new errors_ts_1.CramMalformedError(`invalid read feature code "${code}"`);
         }
         let data = decodeRFData(data1Schema);
         // if this is a tag with two data items, make the data an array and add the second item
@@ -183,7 +183,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     // note: the C data type of compressionFlags is byte in cram v1 and int32 in
     // cram v2+, but that does not matter for us here in javascript land.
     const cramFlags = decodeDataSeries('CF');
-    if (!(0, sectionParsers_1.isMappedSliceHeader)(sliceHeader.parsedContent)) {
+    if (!(0, sectionParsers_ts_1.isMappedSliceHeader)(sliceHeader.parsedContent)) {
         throw new Error('slice header not mapped');
     }
     const sequenceId = majorVersion > 1 && sliceHeader.parsedContent.refSeqId === -2
@@ -205,7 +205,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     let templateSize;
     let mateRecordNumber;
     // mate record
-    if (record_1.CramFlagsDecoder.isDetached(cramFlags)) {
+    if (record_ts_1.CramFlagsDecoder.isDetached(cramFlags)) {
         // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't
         // matter for javascript
         const mateFlags = decodeDataSeries('MF');
@@ -226,16 +226,16 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         }
         templateSize = decodeDataSeries('TS');
         // set mate unmapped if needed
-        if (record_1.MateFlagsDecoder.isUnmapped(mateFlags)) {
-            flags = record_1.BamFlagsDecoder.setMateUnmapped(flags);
+        if (record_ts_1.MateFlagsDecoder.isUnmapped(mateFlags)) {
+            flags = record_ts_1.BamFlagsDecoder.setMateUnmapped(flags);
         }
         // set mate reversed if needed
-        if (record_1.MateFlagsDecoder.isOnNegativeStrand(mateFlags)) {
-            flags = record_1.BamFlagsDecoder.setMateReverseComplemented(flags);
+        if (record_ts_1.MateFlagsDecoder.isOnNegativeStrand(mateFlags)) {
+            flags = record_ts_1.BamFlagsDecoder.setMateReverseComplemented(flags);
         }
         // detachedCount++
     }
-    else if (record_1.CramFlagsDecoder.isWithMateDownstream(cramFlags)) {
+    else if (record_ts_1.CramFlagsDecoder.isWithMateDownstream(cramFlags)) {
         mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
     }
     // TODO: the aux tag parsing will have to be refactored if we want to support
@@ -243,7 +243,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     const TLindex = decodeDataSeries('TL');
     if (TLindex < 0) {
         /* TODO: check nTL: TLindex >= compressionHeader.tagEncoding.size */
-        throw new errors_1.CramMalformedError('invalid TL index');
+        throw new errors_ts_1.CramMalformedError('invalid TL index');
     }
     const tags = {};
     // TN = tag names
@@ -268,7 +268,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     let mappingQuality;
     let qualityScores;
     let readBases = undefined;
-    if (!record_1.BamFlagsDecoder.isSegmentUnmapped(flags)) {
+    if (!record_ts_1.BamFlagsDecoder.isSegmentUnmapped(flags)) {
         // reading read features
         const readFeatureCount = decodeDataSeries('FN');
         if (readFeatureCount) {
@@ -296,14 +296,14 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         }
         // mapping quality
         mappingQuality = decodeDataSeries('MQ');
-        if (record_1.CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
+        if (record_ts_1.CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
             qualityScores = new Array(readLength);
             for (let i = 0; i < qualityScores.length; i++) {
                 qualityScores[i] = decodeDataSeries('QS');
             }
         }
     }
-    else if (record_1.CramFlagsDecoder.isDecodeSequenceAsStar(cramFlags)) {
+    else if (record_ts_1.CramFlagsDecoder.isDecodeSequenceAsStar(cramFlags)) {
         readBases = null;
         qualityScores = null;
     }
@@ -313,7 +313,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
             bases[i] = decodeDataSeries('BA');
         }
         readBases = String.fromCharCode(...bases);
-        if (record_1.CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
+        if (record_ts_1.CramFlagsDecoder.isPreservingQualityScores(cramFlags)) {
             qualityScores = new Array(readLength);
             for (let i = 0; i < bases.length; i++) {
                 qualityScores[i] = decodeDataSeries('QS');

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

@@ -1 +1 @@
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package/dist/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;