@gmod/cram 4.0.9 → 5.0.0

package/dist/cramFile/container/index.js

@@ -3,12 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const errors_1 = require("../../errors");
-// locals
-const slice_1 = __importDefault(require("../slice"));
-const util_1 = require("../util");
-const compressionScheme_1 = __importDefault(require("./compressionScheme"));
-const sectionParsers_1 = require("../sectionParsers");
+const errors_ts_1 = require("../../errors.js");
+const index_ts_1 = __importDefault(require("../slice/index.js"));
+const util_ts_1 = require("../util.js");
+const compressionScheme_ts_1 = __importDefault(require("./compressionScheme.js"));
+const sectionParsers_ts_1 = require("../sectionParsers.js");
 class CramContainer {
     constructor(file, filePosition) {
         this.file = file;
@@ -25,12 +24,12 @@ class CramContainer {
             return null;
         }
         const { majorVersion } = await this.file.getDefinition();
-        const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
+        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
         const block = await this.getFirstBlock();
         if (block.contentType !== 'COMPRESSION_HEADER') {
-            throw new errors_1.CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
+            throw new errors_ts_1.CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
         }
-        const content = (0, util_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
+        const content = (0, util_ts_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
         return {
             ...block,
             parsedContent: content,
@@ -47,24 +46,24 @@ class CramContainer {
         if (!header) {
             return undefined;
         }
-        return new compressionScheme_1.default(header.parsedContent);
+        return new compressionScheme_ts_1.default(header.parsedContent);
     }
     getSlice(slicePosition, sliceSize) {
         // note: slicePosition is relative to the end of the container header
         // TODO: perhaps we should cache slices?
-        return new slice_1.default(this, slicePosition, sliceSize);
+        return new index_ts_1.default(this, slicePosition, sliceSize);
     }
     async _readContainerHeader(position) {
         const { majorVersion } = await this.file.getDefinition();
-        const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
+        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
         const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
         // parse the container header. do it in 2 pieces because you cannot tell
         // how much to buffer until you read numLandmarks
         const bytes1 = await this.file.read(cramContainerHeader1.maxLength, position);
-        const header1 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
-        const numLandmarksSize = (0, util_1.itf8Size)(header1.numLandmarks);
+        const header1 = (0, util_ts_1.parseItem)(bytes1, cramContainerHeader1.parser);
+        const numLandmarksSize = (0, util_ts_1.itf8Size)(header1.numLandmarks);
         const bytes2 = await this.file.read(cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
-        const header2 = (0, util_1.parseItem)(bytes2, cramContainerHeader2.parser);
+        const header2 = (0, util_ts_1.parseItem)(bytes2, cramContainerHeader2.parser);
         if (this.file.validateChecksums && header2.crc32 !== undefined) {
             await this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, `container header beginning at position ${position}`);
         }
@@ -80,6 +79,6 @@ exports.default = CramContainer;
 'getHeader getCompressionHeaderBlock getCompressionScheme'
     .split(' ')
     .forEach(method => {
-    (0, util_1.tinyMemoize)(CramContainer, method);
+    (0, util_ts_1.tinyMemoize)(CramContainer, method);
 });
 //# sourceMappingURL=index.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":";;;;;AAAA,+CAAoD;AACpD,iEAAyC;AACzC,wCAA6D;AAC7D,kFAAmE;AAEnE,4DAAwD;AAExD,MAAqB,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,IAAA,qCAAiB,EAAC,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,8BAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,8BAA8B,CACxE,CAAA;QACH,CAAC;QAED,MAAM,OAAO,GAAG,IAAA,mBAAS,EACvB,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,kBAAS,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,IAAA,qCAAiB,EAAC,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,IAAA,mBAAS,EAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAC9D,MAAM,gBAAgB,GAAG,IAAA,kBAAQ,EAAC,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,IAAA,mBAAS,EAAC,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;AAlGD,gCAkGC;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE;IAChB,IAAA,qBAAW,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;AACpC,CAAC,CAAC,CAAA"}

package/dist/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/dist/cramFile/file.js

@@ -1,7 +1,4 @@
 "use strict";
-// import bzip2 from 'bzip2'
-// import BZip2 from 'bzip2-wasm'
-// import { decompress } from 'bz2'
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
     var desc = Object.getOwnPropertyDescriptor(m, k);
@@ -41,17 +38,17 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
-const seek_bzip_1 = __importDefault(require("seek-bzip"));
 const xz_decompress_1 = require("xz-decompress");
-const errors_1 = require("../errors");
-const htscodecs = __importStar(require("../htscodecs"));
-const io_1 = require("../io");
-const rans_1 = __importDefault(require("../rans"));
-const sam_1 = require("../sam");
-const unzip_1 = require("../unzip");
-const container_1 = __importDefault(require("./container"));
-const sectionParsers_1 = require("./sectionParsers");
-const util_1 = require("./util");
+const errors_ts_1 = require("../errors.js");
+const htscodecs = __importStar(require("../htscodecs/index.js"));
+const io_ts_1 = require("../io.js");
+const index_ts_1 = __importDefault(require("../rans/index.js"));
+const sam_ts_1 = require("../sam.js");
+const index_ts_2 = require("../seek-bzip/index.js");
+const unzip_ts_1 = require("../unzip.js");
+const index_ts_3 = __importDefault(require("./container/index.js"));
+const sectionParsers_ts_1 = require("./sectionParsers.js");
+const util_ts_1 = require("./util.js");
 function bufferToStream(buf) {
     return new ReadableStream({
         start(controller) {
@@ -76,7 +73,7 @@ function getEndianness() {
 }
 class CramFile {
     constructor(args) {
-        this.file = (0, io_1.open)(args.url, args.path, args.filehandle);
+        this.file = (0, io_ts_1.open)(args.url, args.path, args.filehandle);
         this.validateChecksums = true;
         this.fetchReferenceSequenceCallback = args.seqFetch;
         this.options = {
@@ -98,11 +95,11 @@ class CramFile {
     }
     // memoized
     async getDefinition() {
-        const { maxLength, parser } = (0, sectionParsers_1.cramFileDefinition)();
+        const { maxLength, parser } = (0, sectionParsers_ts_1.cramFileDefinition)();
         const headbytes = await this.file.read(maxLength, 0);
         const definition = parser(headbytes).value;
         if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
-            throw new errors_1.CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
+            throw new errors_ts_1.CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
         }
         return definition;
     }
@@ -110,7 +107,7 @@ class CramFile {
     async getSamHeader() {
         const firstContainer = await this.getContainerById(0);
         if (!firstContainer) {
-            throw new errors_1.CramMalformedError('file contains no containers');
+            throw new errors_ts_1.CramMalformedError('file contains no containers');
         }
         const firstBlock = await firstContainer.getFirstBlock();
         const content = firstBlock.content;
@@ -120,7 +117,7 @@ class CramFile {
         const decoder = new TextDecoder('utf8');
         const text = decoder.decode(content.subarray(textStart, textStart + headerLength));
         this.header = text;
-        return (0, sam_1.parseHeaderText)(text);
+        return (0, sam_ts_1.parseHeaderText)(text);
     }
     async getHeaderText() {
         await this.getSamHeader();
@@ -128,7 +125,7 @@ class CramFile {
     }
     async getContainerById(containerNumber) {
         const { majorVersion } = await this.getDefinition();
-        const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
+        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
         let position = sectionParsers.cramFileDefinition.maxLength;
         // skip with a series of reads to the proper container
         let currentContainer;
@@ -165,7 +162,7 @@ class CramFile {
         // https://github.com/alexgorbatchev/crc/blob/31fc3853e417b5fb5ec83335428805842575f699/src/define_crc.ts#L5
         const calculatedCrc32 = (0, crc32_1.default)(b) >>> 0;
         if (calculatedCrc32 !== recordedCrc32) {
-            throw new errors_1.CramMalformedError(`crc mismatch in ${description}: recorded CRC32 = ${recordedCrc32}, but calculated CRC32 = ${calculatedCrc32}`);
+            throw new errors_ts_1.CramMalformedError(`crc mismatch in ${description}: recorded CRC32 = ${recordedCrc32}, but calculated CRC32 = ${calculatedCrc32}`);
         }
     }
     /**
@@ -176,7 +173,7 @@ class CramFile {
      */
     async containerCount() {
         const { majorVersion } = await this.getDefinition();
-        const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
+        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
         let containerCount = 0;
         let position = sectionParsers.cramFileDefinition.maxLength;
         try {
@@ -208,34 +205,30 @@ class CramFile {
         return containerCount;
     }
     getContainerAtPosition(position) {
-        return new container_1.default(this, position);
+        return new index_ts_3.default(this, position);
     }
     async readBlockHeader(position) {
         const { majorVersion } = await this.getDefinition();
-        const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
+        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
         const { cramBlockHeader } = sectionParsers;
         const buffer = await this.file.read(cramBlockHeader.maxLength, position);
-        return (0, util_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
+        return (0, util_ts_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
     }
     async _parseSection(section, position, size = section.maxLength, preReadBuffer) {
         const buffer = preReadBuffer ?? (await this.file.read(size, position));
-        const data = (0, util_1.parseItem)(buffer, section.parser, 0, position);
+        const data = (0, util_ts_1.parseItem)(buffer, section.parser, 0, position);
         if (data._size !== size) {
-            throw new errors_1.CramMalformedError(`section read error: requested size ${size} does not equal parsed size ${data._size}`);
+            throw new errors_ts_1.CramMalformedError(`section read error: requested size ${size} does not equal parsed size ${data._size}`);
         }
         return data;
     }
     async _uncompressPre(compressionMethod, inputBuffer, uncompressedSize) {
         // console.log({ compressionMethod })
         if (compressionMethod === 'gzip') {
-            const ret = (0, unzip_1.unzip)(inputBuffer);
-            if (ret[0] === 24) {
-                // console.log(ret.slice(0, 500).join(','))
-            }
-            return ret;
+            return (0, unzip_ts_1.unzip)(inputBuffer);
         }
         else if (compressionMethod === 'bzip2') {
-            return seek_bzip_1.default.decode(inputBuffer);
+            return (0, index_ts_2.decode)(inputBuffer);
         }
         else if (compressionMethod === 'lzma') {
             const decompressedResponse = new Response(new xz_decompress_1.XzReadableStream(bufferToStream(inputBuffer)));
@@ -243,10 +236,8 @@ class CramFile {
         }
         else if (compressionMethod === 'rans') {
             const outputBuffer = new Uint8Array(uncompressedSize);
-            (0, rans_1.default)(inputBuffer, outputBuffer);
+            (0, index_ts_1.default)(inputBuffer, outputBuffer);
             return outputBuffer;
-            // htscodecs r4x8 is slower, but compatible.
-            // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
         }
         else if (compressionMethod === 'rans4x16') {
             return htscodecs.r4x16_uncompress(inputBuffer);
@@ -261,7 +252,7 @@ class CramFile {
             return htscodecs.tok3_uncompress(inputBuffer);
         }
         else {
-            throw new errors_1.CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
+            throw new errors_ts_1.CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
         }
     }
     async _uncompress(compressionMethod, inputBuffer, uncompressedSize) {
@@ -275,7 +266,7 @@ class CramFile {
     }
     async readBlock(position) {
         const { majorVersion } = await this.getDefinition();
-        const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
+        const sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
         const blockHeader = await this.readBlockHeader(position);
         const blockContentPosition = blockHeader._endPosition;
         const d = await this.file.read(blockHeader.compressedSize, blockContentPosition);
@@ -310,6 +301,6 @@ class CramFile {
 }
 exports.default = CramFile;
 'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
-    (0, util_1.tinyMemoize)(CramFile, method);
+    (0, util_ts_1.tinyMemoize)(CramFile, method);
 });
 //# sourceMappingURL=file.js.map

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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package/dist/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/dist/cramFile/index.js

@@ -4,8 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = exports.CramRecord = void 0;
-var record_1 = require("./record");
-Object.defineProperty(exports, "CramRecord", { enumerable: true, get: function () { return __importDefault(record_1).default; } });
-var file_1 = require("./file");
-Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(file_1).default; } });
+var record_ts_1 = require("./record.js");
+Object.defineProperty(exports, "CramRecord", { enumerable: true, get: function () { return __importDefault(record_ts_1).default; } });
+var file_ts_1 = require("./file.js");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(file_ts_1).default; } });
 //# sourceMappingURL=index.js.map

package/dist/cramFile/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAgD;AAAvC,qHAAA,OAAO,OAAc;AAE9B,+BAAgC;AAAvB,gHAAA,OAAO,OAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":";;;;;;AAAA,yCAAmD;AAA1C,wHAAA,OAAO,OAAc;AAE9B,qCAAmC;AAA1B,mHAAA,OAAO,OAAA"}

package/dist/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/dist/cramFile/record.js

@@ -4,7 +4,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MateFlagsDecoder = exports.CramFlagsDecoder = exports.BamFlagsDecoder = exports.MateFlags = exports.CramFlags = exports.BamFlags = void 0;
-const constants_1 = __importDefault(require("./constants"));
+const constants_ts_1 = __importDefault(require("./constants.js"));
 function decodeReadSequence(cramRecord, refRegion) {
     // if it has no length, it has no sequence
     if (!cramRecord.lengthOnRef && !cramRecord.readLength) {
@@ -207,69 +207,69 @@ class CramRecord {
      * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
      */
     isPaired() {
-        return !!(this.flags & constants_1.default.BAM_FPAIRED);
+        return !!(this.flags & constants_ts_1.default.BAM_FPAIRED);
     }
     /** @returns {boolean} true if the read is paired, and both segments are mapped */
     isProperlyPaired() {
-        return !!(this.flags & constants_1.default.BAM_FPROPER_PAIR);
+        return !!(this.flags & constants_ts_1.default.BAM_FPROPER_PAIR);
     }
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
     isSegmentUnmapped() {
-        return !!(this.flags & constants_1.default.BAM_FUNMAP);
+        return !!(this.flags & constants_ts_1.default.BAM_FUNMAP);
     }
     /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
     isMateUnmapped() {
-        return !!(this.flags & constants_1.default.BAM_FMUNMAP);
+        return !!(this.flags & constants_ts_1.default.BAM_FMUNMAP);
     }
     /** @returns {boolean} true if the read is mapped to the reverse strand */
     isReverseComplemented() {
-        return !!(this.flags & constants_1.default.BAM_FREVERSE);
+        return !!(this.flags & constants_ts_1.default.BAM_FREVERSE);
     }
     /** @returns {boolean} true if the mate is mapped to the reverse strand */
     isMateReverseComplemented() {
-        return !!(this.flags & constants_1.default.BAM_FMREVERSE);
+        return !!(this.flags & constants_ts_1.default.BAM_FMREVERSE);
     }
     /** @returns {boolean} true if this is read number 1 in a pair */
     isRead1() {
-        return !!(this.flags & constants_1.default.BAM_FREAD1);
+        return !!(this.flags & constants_ts_1.default.BAM_FREAD1);
     }
     /** @returns {boolean} true if this is read number 2 in a pair */
     isRead2() {
-        return !!(this.flags & constants_1.default.BAM_FREAD2);
+        return !!(this.flags & constants_ts_1.default.BAM_FREAD2);
     }
     /** @returns {boolean} true if this is a secondary alignment */
     isSecondary() {
-        return !!(this.flags & constants_1.default.BAM_FSECONDARY);
+        return !!(this.flags & constants_ts_1.default.BAM_FSECONDARY);
     }
     /** @returns {boolean} true if this read has failed QC checks */
     isFailedQc() {
-        return !!(this.flags & constants_1.default.BAM_FQCFAIL);
+        return !!(this.flags & constants_ts_1.default.BAM_FQCFAIL);
     }
     /** @returns {boolean} true if the read is an optical or PCR duplicate */
     isDuplicate() {
-        return !!(this.flags & constants_1.default.BAM_FDUP);
+        return !!(this.flags & constants_ts_1.default.BAM_FDUP);
     }
     /** @returns {boolean} true if this is a supplementary alignment */
     isSupplementary() {
-        return !!(this.flags & constants_1.default.BAM_FSUPPLEMENTARY);
+        return !!(this.flags & constants_ts_1.default.BAM_FSUPPLEMENTARY);
     }
     /**
      * @returns {boolean} true if the read is detached
      */
     isDetached() {
-        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_DETACHED);
+        return !!(this.cramFlags & constants_ts_1.default.CRAM_FLAG_DETACHED);
     }
     /** @returns {boolean} true if the read has a mate in this same CRAM segment */
     hasMateDownStream() {
-        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_MATE_DOWNSTREAM);
+        return !!(this.cramFlags & constants_ts_1.default.CRAM_FLAG_MATE_DOWNSTREAM);
     }
     /** @returns {boolean} true if the read contains qual scores */
     isPreservingQualityScores() {
-        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_PRESERVE_QUAL_SCORES);
+        return !!(this.cramFlags & constants_ts_1.default.CRAM_FLAG_PRESERVE_QUAL_SCORES);
     }
     /** @returns {boolean} true if the read has no sequence bases */
     isUnknownBases() {
-        return !!(this.cramFlags & constants_1.default.CRAM_FLAG_NO_SEQ);
+        return !!(this.cramFlags & constants_ts_1.default.CRAM_FLAG_NO_SEQ);
     }
     /**
      * Get the original sequence of this read.

package/dist/cramFile/record.js.map

@@ -1 +1 @@
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package/dist/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: {