npm - @gmod/cram - Versions diffs - 8.0.0 → 8.0.2 - Mend

@gmod/cram 8.0.0 → 8.0.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (26) hide show

package/dist/cram-bundle.js +1 -1
package/dist/cramFile/file.d.ts +1 -0
package/dist/cramFile/file.js +43 -0
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.d.ts +1 -5
package/dist/cramFile/record.js +22 -42
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/slice/index.js +19 -1
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/wasm/htscodecs.js +0 -0
package/dist/wasm/htscodecs.js.map +1 -1
package/esm/cramFile/file.d.ts +1 -0
package/esm/cramFile/file.js +43 -0
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.d.ts +1 -5
package/esm/cramFile/record.js +22 -42
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/slice/index.js +19 -1
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/wasm/htscodecs.js +0 -0
package/esm/wasm/htscodecs.js.map +1 -1
package/package.json +6 -6
package/src/cramFile/file.ts +82 -0
package/src/cramFile/record.ts +28 -44
package/src/cramFile/slice/index.ts +31 -2
package/src/wasm/htscodecs.js +0 -0

package/dist/cramFile/file.d.ts CHANGED Viewed

@@ -75,4 +75,5 @@ export default class CramFile {
     _uncompressPre(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<Uint8Array<ArrayBufferLike>>;
     _uncompress(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<Uint8Array<ArrayBufferLike>>;
     readBlock(position: number): Promise<CramFileBlock>;
+    readBlockFromBuffer(buffer: Uint8Array, bufferOffset: number, filePosition: number): Promise<CramFileBlock>;
 }

package/dist/cramFile/file.js CHANGED Viewed

@@ -299,6 +299,49 @@ class CramFile {
         }
         return block;
     }
+    async readBlockFromBuffer(buffer, bufferOffset, filePosition) {
+        const { majorVersion } = await this.getDefinition();
+        if (!this._sectionParsers) {
+            this._sectionParsers = (0, sectionParsers_ts_1.getSectionParsers)(majorVersion);
+        }
+        const sectionParsers = this._sectionParsers;
+        const { cramBlockHeader } = sectionParsers;
+        const headerBytes = buffer.subarray(bufferOffset, bufferOffset + cramBlockHeader.maxLength);
+        const blockHeader = (0, util_ts_1.parseItem)(headerBytes, cramBlockHeader.parser, 0, filePosition);
+        const blockContentPosition = blockHeader._endPosition;
+        const contentOffset = bufferOffset + blockHeader._size;
+        const d = buffer.subarray(contentOffset, contentOffset + blockHeader.compressedSize);
+        const uncompressedData = blockHeader.compressionMethod !== 'raw'
+            ? await this._uncompress(blockHeader.compressionMethod, d, blockHeader.uncompressedSize)
+            : d;
+        const block = {
+            ...blockHeader,
+            _endPosition: blockContentPosition,
+            contentPosition: blockContentPosition,
+            content: uncompressedData,
+        };
+        if (majorVersion >= 3) {
+            const crcOffset = contentOffset + blockHeader.compressedSize;
+            const crcBytes = buffer.subarray(crcOffset, crcOffset + sectionParsers.cramBlockCrc32.maxLength);
+            const crc = (0, util_ts_1.parseItem)(crcBytes, sectionParsers.cramBlockCrc32.parser, 0, blockContentPosition + blockHeader.compressedSize);
+            block.crc32 = crc.crc32;
+            if (this.validateChecksums) {
+                const blockData = buffer.subarray(bufferOffset, bufferOffset + blockHeader._size + blockHeader.compressedSize);
+                const calculatedCrc32 = (0, crc32_1.default)(blockData) >>> 0;
+                if (calculatedCrc32 !== crc.crc32) {
+                    throw new errors_ts_1.CramMalformedError(`crc mismatch in block data: recorded CRC32 = ${crc.crc32}, but calculated CRC32 = ${calculatedCrc32}`);
+                }
+            }
+            block._endPosition = crc._endPosition;
+            block._size =
+                block.compressedSize + sectionParsers.cramBlockCrc32.maxLength;
+        }
+        else {
+            block._endPosition = blockContentPosition + block.compressedSize;
+            block._size = block.compressedSize;
+        }
+        return block;
+    }
 }
 exports.default = CramFile;
 'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {

package/dist/cramFile/file.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/cramFile/record.d.ts CHANGED Viewed

@@ -110,11 +110,7 @@ export default class CramRecord {
      * @returns {String} sequence basepairs
      */
     getReadBases(): string | null | undefined;
-    /**
-     * Get the pair orientation of a paired read. Adapted from igv.js
-     * @returns {String} of paired orientatin
-     */
-    getPairOrientation(): string | null;
+    getPairOrientation(): string | undefined;
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base

package/dist/cramFile/record.js CHANGED Viewed

@@ -295,50 +295,30 @@ class CramRecord {
         }
         return this.readBases;
     }
-    /**
-     * Get the pair orientation of a paired read. Adapted from igv.js
-     * @returns {String} of paired orientatin
-     */
+    // adapted from igv.js
+    // inlines flag checks and uses template literal instead of array+join
     getPairOrientation() {
-        if (!this.isSegmentUnmapped() &&
-            this.isPaired() &&
-            !this.isMateUnmapped() &&
-            this.sequenceId === this.mate?.sequenceId) {
-            const s1 = this.isReverseComplemented() ? 'R' : 'F';
-            const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-            let o1 = ' ';
-            let o2 = ' ';
-            if (this.isRead1()) {
-                o1 = '1';
-                o2 = '2';
-            }
-            else if (this.isRead2()) {
-                o1 = '2';
-                o2 = '1';
-            }
-            const tmp = [];
-            let isize = this.templateLength || this.templateSize;
-            if (isize === undefined) {
-                throw new Error('One of templateSize and templateLength must be set');
-            }
-            if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
-                isize = -isize;
-            }
-            if (isize > 0) {
-                tmp[0] = s1;
-                tmp[1] = o1;
-                tmp[2] = s2;
-                tmp[3] = o2;
-            }
-            else {
-                tmp[2] = s1;
-                tmp[3] = o1;
-                tmp[0] = s2;
-                tmp[1] = o2;
-            }
-            return tmp.join('');
+        const f = this.flags;
+        // combined check: paired (0x1) set, unmapped (0x4) clear, mate unmapped (0x8) clear
+        if ((f & 0xd) !== 0x1 || this.sequenceId !== this.mate?.sequenceId) {
+            return undefined;
         }
-        return null;
+        const s1 = f & 0x10 ? 'R' : 'F';
+        const s2 = f & 0x20 ? 'R' : 'F';
+        let o1 = ' ';
+        let o2 = ' ';
+        if (f & 0x40) {
+            o1 = '1';
+            o2 = '2';
+        }
+        else if (f & 0x80) {
+            o1 = '2';
+            o2 = '1';
+        }
+        const isize = this.templateLength || this.templateSize || 0;
+        return isize > 0
+            ? `${s1}${o1}${s2}${o2}`
+            : `${s2}${o2}${s1}${o1}`;
     }
     /**
      * Annotates this feature with the given reference sequence basepair

package/dist/cramFile/record.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/cramFile/slice/index.js CHANGED Viewed

@@ -183,7 +183,25 @@ class CramSlice {
     // memoize
     async getBlocks() {
         const header = await this.getHeader();
-        // read all the blocks into memory and store them
+        if (this.sliceSize) {
+            // if we know the slice size (from the index), do one big read for all
+            // blocks and parse from the in-memory buffer
+            const containerHeader = await this.container.getHeader();
+            const sliceFilePosition = containerHeader._endPosition + this.containerPosition;
+            const blocksFilePosition = header._endPosition;
+            const headerSize = blocksFilePosition - sliceFilePosition;
+            const remainingBytes = this.sliceSize - headerSize;
+            const allBlocksBuffer = await this.file.read(remainingBytes, blocksFilePosition);
+            const blocks = new Array(header.parsedContent.numBlocks);
+            let bufferOffset = 0;
+            for (let i = 0; i < blocks.length; i++) {
+                const block = await this.file.readBlockFromBuffer(allBlocksBuffer, bufferOffset, blocksFilePosition + bufferOffset);
+                blocks[i] = block;
+                bufferOffset = block._endPosition - blocksFilePosition;
+            }
+            return blocks;
+        }
+        // fallback: read blocks one at a time (non-indexed access)
         let blockPosition = header._endPosition;
         const blocks = new Array(header.parsedContent.numBlocks);
         for (let i = 0; i < blocks.length; i++) {

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

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"htscodecs.js","sourceRoot":"","sources":["../../src/wasm/htscodecs.js"],"names":[],"mappings":";;AAAA,KAAK,UAAU,qBAAqB,CAAC,SAAS,GAAC,EAAE;IAAE,IAAI,SAAS,CAAC;IAAA,IAAI,CAAC,GAAC,SAAS,EAAC,CAAC,GAAC,CAAC,CAAC,UAAU,CAAC,iBAAiB,EAAC,CAAC,GAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC;IAAA,IAAG,UAAU,CAAC,MAAM,IAAE,CAAC;QAAC,IAAG,CAAC;YAAA,IAAI,GAAG,CAAC,GAAG,EAAC,CAAC,CAAC,CAAA;QAAA,CAAC;QAAA,MAAK,CAAC,CAAA,CAAC;IAAA,IAAI,CAAC,GAAC,OAAO,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,EAAC,CAAC,GAAC,OAAO,CAAC,KAAK,CAAC,IAAI,CAAC,OAAO,CAAC,EAAC,CAAC,GAAC,CAAC,CAAC,EAAC,CAAC,CAAC;IAAA,SAAS,CAAC,CAAC,CAAC,IAAE,KAAI,IAAI,CAAC,GAAC,CAAC,EAAC,CAAC,GAAC,CAAC,CAAC,MAAM,EAAC,CAAC,GAAC,IAAI,UAAU,CAAC,CAAC,CAAC,EAAC,CAAC,EAAC,CAAC,GAAC,CAAC,EAAC,EAAE,CAAC;QAAC,CAAC,GAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,EAAC,CAAC,CAAC,CAAC,CAAC,GAAC,CAAC,CAAC,IAAE,CAAC,GAAC,CAAC,CAAC,CAAA,OAAO,CAAC,CAAA,CAAA,CAAC;IAAA,IAAI,CAAC,EAAC,CAAC,EAAC,CAAC,EAAC,CAAC,EAAC,CAAC,EAAC,CAAC,EAAC,CAAC,EAAC,CAAC,EAAC,CAAC,EAAC,CAAC,EAAC,CAAC,GAAC,CAAC,CAAC,CAAC;IACnY,SAAS,CAAC,KAAG,IAAI,CAAC,GAAC,CAAC,CAAC,MAAM,CAAC,CAAA,CAAC,GAAC,IAAI,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,GAAC,IAAI,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,CAAC,MAAM,GAAC,CAAC,GAAC,IAAI,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA,IAAI,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,GAAC,IAAI,UAAU,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,GAAC,IAAI,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,GAAC,IAAI,YAAY,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,GAAC,IAAI,YAAY,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,GAAC,IAAI,aAAa,CAAC,CAAC,CAAC,CAAC,CAAA,IAAI,cAAc,CAAC,CAAC,CAAC,CAAA,CAAA,CAAC;IAAA,SAAS,CAAC,CAAC,CAAC,IAAE,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,GAAC,UAAU,GAAC,CAAC,GAAC,GAAG,CAAC,CAAA,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,GAAC,CAAC,CAAC,CAAC,CAAA,CAAC,GAAC,IAAI,WAAW,CAAC,YAAY,CAAC,CAAC,GAAC,0CAA0C,CAAC,CAAC,CAAA,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA,MAAM,CAAC,CAAC,CAAA,CAAC;IAAA,IAAI,CAAC,CAAC;IAAA,KAAK,UAAU,CAAC,CAAC,CAAC,IAAE,OAAO,CAAC,CAAA,CAAA,CAAC;IAC/a,KAAK,UAAU,EAAE,CAAC,CAAC,IAAE,IAAI,CAAC,GAAC,CAAC,CAAC,CAAA,IAAG,CAAC;QAAA,IAAI,CAAC,GAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;QAAA,OAAO,MAAM,WAAW,CAAC,WAAW,CAAC,CAAC,EAAC,CAAC,CAAC,CAAA;IAAA,CAAC;IAAA,OAAM,CAAC,EAAC,CAAC;QAAA,CAAC,CAAC,0CAA0C,CAAC,EAAE,CAAC,EAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAAA,CAAC,CAAA,CAAC;IAAA,KAAK,UAAU,EAAE,CAAC,CAAC,IAAE,OAAO,EAAE,CAAC,CAAC,CAAC,CAAA,CAAA,CAAC;IAAA,MAAM,CAAC;QAAmB,YAAY,CAAC;YAA/B,SAAI,GAAC,YAAY,CAAC;YAAe,IAAI,CAAC,OAAO,GAAC,gCAAgC,CAAC,GAAG,CAAC;YAAA,IAAI,CAAC,MAAM,GAAC,CAAC,CAAA;QAAA,CAAC;KAAC;IACxS,KAAI,IAAI,CAAC,GAAC,CAAC,CAAA,EAAE,GAAC,OAAK,CAAC,GAAC,CAAC,CAAC,MAAM;QAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,CAAC,CAAA,CAAA,CAAC,EAAC,CAAC,GAAC,EAAE,EAAC,CAAC,GAAC,EAAE,EAAC,EAAE,GAAC,GAAE,EAAE,GAAC,IAAI,CAAC,GAAC,CAAC,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,CAAA,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAA,CAAC,EAAC,CAAC,GAAC,CAAC,CAAC,EAAC,CAAC,GAAC,CAAC,EAAC,CAAC,GAAC,EAAE,EAAC,CAAC,GAAC,CAAC,CAAA,EAAE,GAAC,IAAG,CAAC,CAAC,CAAC,YAAY,CAAC,IAAE,QAAQ,IAAE,CAAC,CAAC;QAAC,MAAM,CAAC,CAAC,CAAA,CAAC,EAAC,CAAC,GAAC,CAAC,CAAA,EAAE,GAAC,CAAC,GAAC,CAAC,CAAC,CAAA,CAAC,IAAE,CAAC,GAAC,CAAC,IAAE,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,CAAC,EAAC,CAAC,GAAC,CAAC,CAAC,CAAC,CAAC,CAAA,MAAM,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,EAAC,EAAE,GAAC,CAAC,CAAA,EAAE,GAAC,IAAG,CAAC,CAAC;QAAC,IAAG,CAAC;YAAA,CAAC,EAAE,CAAA;QAAA,CAAC;QAAA,OAAM,CAAC,EAAC,CAAC;YAAA,CAAC,CAAC,CAAC,CAAC,CAAA;QAAA,CAAC;gBAAO,CAAC;YAAA,IAAG,CAAC,CAAC,CAAC,IAAE,CAAC,GAAC,CAAC,CAAC;gBAAC,IAAG,CAAC;oBAAA,CAAC,GAAC,CAAC,GAAC,CAAC,EAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBAAA,CAAC;gBAAA,OAAM,CAAC,EAAC,CAAC;oBAAA,CAAC,CAAC,CAAC,CAAC,CAAA;gBAAA,CAAC;QAAA,CAAC,CAAA,CAAC,EAAC,EAAE,GAAC,CAAC,IAAI,EAAC,EAAE,EAAC,EAAE,CAAC,EAAC,EAAE,GAAC,IAAI,WAAW,EAAC,CAAC,GAAC,IAAI,UAAU,CAAC,GAAG,CAAC,EAAC,CAAC,GAAC,EAAE,EAAC,CAAC,IAAE,CAAC,EAAC,EAAE,CAAC;QAAC,CAAC,CAAC,EAAE,GAAC,CAAC,CAAC,GAAC,EAAE,GAAC,CAAC,EAAC,CAAC,CAAC,EAAE,GAAC,CAAC,CAAC,GAAC,CAAC,EAAC,CAAC,CAAC,EAAE,GAAC,CAAC,CAAC,GAAC,EAAE,GAAC,CAAC,CAAC;IAAA,CAAC,CAAC,EAAE,CAAC,GAAC,EAAE,CAAC;IAAA,CAAC,CAAC,EAAE,CAAC,GAAC,EAAE,CAAC;IAAA,CAAC,CAAC,aAAa,IAAE,CAAC,CAAC,GAAC,CAAC,CAAC,aAAa,CAAC,CAAC;IAAA,CAAC,CAAC,KAAK,IAAE,CAAC,CAAC,GAAC,CAAC,CAAC,KAAK,CAAC,CAAC;IACxe,CAAC,CAAC,QAAQ,IAAE,CAAC,CAAC,GAAC,CAAC,CAAC,QAAQ,CAAC,CAAC;IAAA,IAAG,CAAC,CAAC,OAAO;QAAC,KAAI,UAAU,IAAE,OAAO,CAAC,CAAC,OAAO,IAAE,CAAC,CAAC,CAAC,OAAO,GAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,EAAC,CAAC,GAAC,CAAC,CAAC,OAAO,CAAC,MAAM;YAAE,CAAC,CAAC,OAAO,CAAC,KAAK,EAAE,EAAE,CAAC;IAAA,CAAC,CAAC,QAAQ,GAAC,UAAS,CAAC,EAAC,CAAC,GAAC,IAAI,IAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAE,CAAC,CAAC,GAAC,GAAG,CAAC,CAAC,CAAA,QAAO,CAAC,EAAC,CAAC;QAAA,KAAK,IAAI,CAAC,CAAA,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC;QAAA,KAAK,IAAI,CAAC,CAAA,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC;QAAA,KAAK,KAAK,CAAC,CAAA,OAAO,CAAC,CAAC,CAAC,IAAE,CAAC,CAAC,CAAC;QAAA,KAAK,KAAK,CAAC,CAAA,OAAO,CAAC,CAAC,CAAC,IAAE,CAAC,CAAC,CAAC;QAAA,KAAK,KAAK,CAAC,CAAA,OAAO,CAAC,CAAC,CAAC,IAAE,CAAC,CAAC,CAAC;QAAA,KAAK,OAAO,CAAC,CAAA,OAAO,CAAC,CAAC,CAAC,IAAE,CAAC,CAAC,CAAC;QAAA,KAAK,QAAQ,CAAC,CAAA,OAAO,CAAC,CAAC,CAAC,IAAE,CAAC,CAAC,CAAC;QAAA,KAAK,GAAG,CAAC,CAAA,OAAO,CAAC,CAAC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package/esm/cramFile/file.d.ts CHANGED Viewed

@@ -75,4 +75,5 @@ export default class CramFile {
     _uncompressPre(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<Uint8Array<ArrayBufferLike>>;
     _uncompress(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<Uint8Array<ArrayBufferLike>>;
     readBlock(position: number): Promise<CramFileBlock>;
+    readBlockFromBuffer(buffer: Uint8Array, bufferOffset: number, filePosition: number): Promise<CramFileBlock>;
 }

package/esm/cramFile/file.js CHANGED Viewed

@@ -261,6 +261,49 @@ export default class CramFile {
         }
         return block;
     }
+    async readBlockFromBuffer(buffer, bufferOffset, filePosition) {
+        const { majorVersion } = await this.getDefinition();
+        if (!this._sectionParsers) {
+            this._sectionParsers = getSectionParsers(majorVersion);
+        }
+        const sectionParsers = this._sectionParsers;
+        const { cramBlockHeader } = sectionParsers;
+        const headerBytes = buffer.subarray(bufferOffset, bufferOffset + cramBlockHeader.maxLength);
+        const blockHeader = parseItem(headerBytes, cramBlockHeader.parser, 0, filePosition);
+        const blockContentPosition = blockHeader._endPosition;
+        const contentOffset = bufferOffset + blockHeader._size;
+        const d = buffer.subarray(contentOffset, contentOffset + blockHeader.compressedSize);
+        const uncompressedData = blockHeader.compressionMethod !== 'raw'
+            ? await this._uncompress(blockHeader.compressionMethod, d, blockHeader.uncompressedSize)
+            : d;
+        const block = {
+            ...blockHeader,
+            _endPosition: blockContentPosition,
+            contentPosition: blockContentPosition,
+            content: uncompressedData,
+        };
+        if (majorVersion >= 3) {
+            const crcOffset = contentOffset + blockHeader.compressedSize;
+            const crcBytes = buffer.subarray(crcOffset, crcOffset + sectionParsers.cramBlockCrc32.maxLength);
+            const crc = parseItem(crcBytes, sectionParsers.cramBlockCrc32.parser, 0, blockContentPosition + blockHeader.compressedSize);
+            block.crc32 = crc.crc32;
+            if (this.validateChecksums) {
+                const blockData = buffer.subarray(bufferOffset, bufferOffset + blockHeader._size + blockHeader.compressedSize);
+                const calculatedCrc32 = crc32(blockData) >>> 0;
+                if (calculatedCrc32 !== crc.crc32) {
+                    throw new CramMalformedError(`crc mismatch in block data: recorded CRC32 = ${crc.crc32}, but calculated CRC32 = ${calculatedCrc32}`);
+                }
+            }
+            block._endPosition = crc._endPosition;
+            block._size =
+                block.compressedSize + sectionParsers.cramBlockCrc32.maxLength;
+        }
+        else {
+            block._endPosition = blockContentPosition + block.compressedSize;
+            block._size = block.compressedSize;
+        }
+        return block;
+    }
 }
 'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
     tinyMemoize(CramFile, method);

package/esm/cramFile/file.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/cramFile/record.d.ts CHANGED Viewed

@@ -110,11 +110,7 @@ export default class CramRecord {
      * @returns {String} sequence basepairs
      */
     getReadBases(): string | null | undefined;
-    /**
-     * Get the pair orientation of a paired read. Adapted from igv.js
-     * @returns {String} of paired orientatin
-     */
-    getPairOrientation(): string | null;
+    getPairOrientation(): string | undefined;
     /**
      * Annotates this feature with the given reference sequence basepair
      * information. This will add a `sub` and a `ref` item to base

package/esm/cramFile/record.js CHANGED Viewed

@@ -289,50 +289,30 @@ export default class CramRecord {
         }
         return this.readBases;
     }
-    /**
-     * Get the pair orientation of a paired read. Adapted from igv.js
-     * @returns {String} of paired orientatin
-     */
+    // adapted from igv.js
+    // inlines flag checks and uses template literal instead of array+join
     getPairOrientation() {
-        if (!this.isSegmentUnmapped() &&
-            this.isPaired() &&
-            !this.isMateUnmapped() &&
-            this.sequenceId === this.mate?.sequenceId) {
-            const s1 = this.isReverseComplemented() ? 'R' : 'F';
-            const s2 = this.isMateReverseComplemented() ? 'R' : 'F';
-            let o1 = ' ';
-            let o2 = ' ';
-            if (this.isRead1()) {
-                o1 = '1';
-                o2 = '2';
-            }
-            else if (this.isRead2()) {
-                o1 = '2';
-                o2 = '1';
-            }
-            const tmp = [];
-            let isize = this.templateLength || this.templateSize;
-            if (isize === undefined) {
-                throw new Error('One of templateSize and templateLength must be set');
-            }
-            if (this.alignmentStart > this.mate.alignmentStart && isize > 0) {
-                isize = -isize;
-            }
-            if (isize > 0) {
-                tmp[0] = s1;
-                tmp[1] = o1;
-                tmp[2] = s2;
-                tmp[3] = o2;
-            }
-            else {
-                tmp[2] = s1;
-                tmp[3] = o1;
-                tmp[0] = s2;
-                tmp[1] = o2;
-            }
-            return tmp.join('');
+        const f = this.flags;
+        // combined check: paired (0x1) set, unmapped (0x4) clear, mate unmapped (0x8) clear
+        if ((f & 0xd) !== 0x1 || this.sequenceId !== this.mate?.sequenceId) {
+            return undefined;
         }
-        return null;
+        const s1 = f & 0x10 ? 'R' : 'F';
+        const s2 = f & 0x20 ? 'R' : 'F';
+        let o1 = ' ';
+        let o2 = ' ';
+        if (f & 0x40) {
+            o1 = '1';
+            o2 = '2';
+        }
+        else if (f & 0x80) {
+            o1 = '2';
+            o2 = '1';
+        }
+        const isize = this.templateLength || this.templateSize || 0;
+        return isize > 0
+            ? `${s1}${o1}${s2}${o2}`
+            : `${s2}${o2}${s1}${o1}`;
     }
     /**
      * Annotates this feature with the given reference sequence basepair