@gmod/cram 4.0.4 → 4.0.6

package/esm/cramFile/codecs/byteArrayLength.js.map

@@ -1 +1 @@
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+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAK5C,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAOrC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;IAC1C,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO,CAAC,IAAI,CAAC,CAAA;QAE3E,MAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;QACtC,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;QACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,CAAC,CAAC;gBACL,SAAS,CAAC,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO,CAAC,IAAI,CAAC,CAAA;QAC3E,CAAC;QAED,OAAO,IAAI,CAAA;IACb,CAAC;IAED,UAAU;IACV,eAAe;QACb,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,aAAa;QACX,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QACrD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AAED,+BAA+B,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IAC1D,WAAW,CAAC,kBAAkB,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC,CAAC,CAAA"}

package/esm/cramFile/codecs/external.d.ts

@@ -5,7 +5,7 @@ import { ExternalCramEncoding } from '../encoding';
 export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
     private readonly _decodeData;
     constructor(parameters: ExternalCramEncoding['parameters'], dataType: 'int' | 'byte');
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number | undefined;
     _decodeInt(contentBlock: CramFileBlock, cursor: Cursor): number;
     _decodeByte(contentBlock: CramFileBlock, cursor: Cursor): number;
 }

package/esm/cramFile/codecs/external.js

@@ -1,5 +1,5 @@
 import CramCodec from './_base';
-import { CramMalformedError, CramUnimplementedError } from '../../errors';
+import { CramUnimplementedError } from '../../errors';
 import { parseItf8 } from '../util';
 import { CramBufferOverrunError } from './getBits';
 export default class ExternalCodec extends CramCodec {
@@ -18,11 +18,8 @@ export default class ExternalCodec extends CramCodec {
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];
-        if (!contentBlock) {
-            throw new CramMalformedError(`no block found with content ID ${blockContentId}}`);
-        }
         const cursor = cursors.externalBlocks.getCursor(blockContentId);
-        return this._decodeData(contentBlock, cursor);
+        return contentBlock ? this._decodeData(contentBlock, cursor) : undefined;
     }
     _decodeInt(contentBlock, cursor) {
         const [result, bytesRead] = parseItf8(contentBlock.content, cursor.bytePosition);

package/esm/cramFile/codecs/external.js.map

@@ -1 +1 @@
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+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGrD,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QAEtD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,YAAY,CAAC,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAC1E,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,SAAS,CACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF"}

package/esm/cramFile/container/index.d.ts

@@ -5,30 +5,21 @@ export default class CramContainer {
     file: CramFile;
     filePosition: number;
     constructor(file: CramFile, filePosition: number);
-    getHeader(): Promise<({
+    getHeader(): Promise<{
+        _size: number;
+        _endPosition: number;
+        numLandmarks: number;
+        landmarks: number[];
+        crc32?: number | undefined;
         length: number;
         refSeqId: number;
         refSeqStart: number;
         alignmentSpan: number;
         numBlocks: number;
-        numLandmarks: number;
         numBases: number | undefined;
         recordCounter: number;
         numRecords: number;
-    } & {
-        _endPosition: number;
-        _size: number;
-    } & {
-        numLandmarks: number;
-        landmarks: number[];
-        crc32?: number | undefined;
-    } & {
-        _endPosition: number;
-        _size: number;
-    } & {
-        _size: number;
-        _endPosition: number;
-    }) | undefined>;
+    }>;
     getCompressionHeaderBlock(): Promise<{
         parsedContent: {
             dataSeriesEncoding: import("../codecs/dataSeriesTypes").DataSeriesEncodingMap;
@@ -48,32 +39,23 @@ export default class CramContainer {
         _size: number;
         content: Uint8Array;
         crc32?: number;
-    } | null | undefined>;
-    getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;
+    } | null>;
+    getFirstBlock(): Promise<import("../file").CramFileBlock>;
     getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
     getSlice(slicePosition: number, sliceSize: number): CramSlice;
-    _readContainerHeader(position: number): Promise<({
+    _readContainerHeader(position: number): Promise<{
+        _size: number;
+        _endPosition: number;
+        numLandmarks: number;
+        landmarks: number[];
+        crc32?: number | undefined;
         length: number;
         refSeqId: number;
         refSeqStart: number;
         alignmentSpan: number;
         numBlocks: number;
-        numLandmarks: number;
         numBases: number | undefined;
         recordCounter: number;
         numRecords: number;
-    } & {
-        _endPosition: number;
-        _size: number;
-    } & {
-        numLandmarks: number;
-        landmarks: number[];
-        crc32?: number | undefined;
-    } & {
-        _endPosition: number;
-        _size: number;
-    } & {
-        _size: number;
-        _endPosition: number;
-    }) | undefined>;
+    }>;
 }

package/esm/cramFile/container/index.js

@@ -16,15 +16,12 @@ export default class CramContainer {
         const containerHeader = await this.getHeader();
         // if there are no records in the container, there will be no compression
         // header
-        if (!containerHeader?.numRecords) {
+        if (!containerHeader.numRecords) {
             return null;
         }
         const { majorVersion } = await this.file.getDefinition();
         const sectionParsers = getSectionParsers(majorVersion);
         const block = await this.getFirstBlock();
-        if (block === undefined) {
-            return undefined;
-        }
         if (block.contentType !== 'COMPRESSION_HEADER') {
             throw new CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
         }
@@ -36,9 +33,6 @@ export default class CramContainer {
     }
     async getFirstBlock() {
         const containerHeader = await this.getHeader();
-        if (!containerHeader) {
-            return undefined;
-        }
         return this.file.readBlock(containerHeader._endPosition);
     }
     // parses the compression header data into a CramContainerCompressionScheme
@@ -59,31 +53,22 @@ export default class CramContainer {
         const { majorVersion } = await this.file.getDefinition();
         const sectionParsers = getSectionParsers(majorVersion);
         const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
-        const { size: fileSize } = await this.file.stat();
-        if (position >= fileSize) {
-            console.warn(`pos:${position}>=fileSize:${fileSize} in cram container`);
-            return undefined;
-        }
         // 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 = parseItem(bytes1, cramContainerHeader1.parser);
         const numLandmarksSize = itf8Size(header1.numLandmarks);
-        if (position + header1.length >= fileSize) {
-            // header indicates container goes beyond fileSize
-            console.warn(`container at ${position} is beyond fileSize:${fileSize}, skipping`);
-            return undefined;
-        }
         const bytes2 = await this.file.read(cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
         const header2 = 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}`);
         }
-        const completeHeader = Object.assign(header1, header2, {
+        return {
+            ...header1,
+            ...header2,
             _size: header1._size + header2._size - numLandmarksSize,
             _endPosition: header1._size + header2._size - numLandmarksSize + position,
-        });
-        return completeHeader;
+        };
     }
 }
 'getHeader getCompressionHeaderBlock getCompressionScheme'

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

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

@@ -32,7 +32,6 @@ export default class CramFile {
     featureCache: QuickLRU<string, Promise<CramRecord[]>>;
     private header;
     constructor(args: CramFileArgs);
-    stat(): Promise<import("generic-filehandle2").Stats>;
     read(length: number, position: number): Promise<Uint8Array<ArrayBuffer>>;
     getDefinition(): Promise<{
         magic: string;
@@ -52,10 +51,13 @@ export default class CramFile {
     checkCrc32(position: number, length: number, recordedCrc32: number, description: string): Promise<void>;
     /**
      * @returns {Promise[number]} the number of containers in the file
+     *
+     * note: this is currently used only in unit tests, and after removing file
+     * length check, relies on a try catch to read return an error to break
      */
     containerCount(): Promise<number | undefined>;
     getContainerAtPosition(position: number): CramContainer;
-    readBlockHeader(position: number): Promise<({
+    readBlockHeader(position: number): Promise<{
         uncompressedSize: number;
         compressedSize: number;
         contentId: number;
@@ -64,17 +66,17 @@ export default class CramFile {
     } & {
         _endPosition: number;
         _size: number;
-    }) | undefined>;
+    }>;
     _parseSection<T>(section: {
         maxLength: number;
         parser: (buffer: Uint8Array, offset: number) => {
             offset: number;
             value: T;
         };
-    }, position: number, size?: number, preReadBuffer?: Uint8Array): Promise<(T & {
+    }, position: number, size?: number, preReadBuffer?: Uint8Array): Promise<T & {
         _endPosition: number;
         _size: number;
-    }) | undefined>;
+    }>;
     _uncompress(compressionMethod: CompressionMethod, inputBuffer: Uint8Array, uncompressedSize: number): Promise<any>;
-    readBlock(position: number): Promise<CramFileBlock | undefined>;
+    readBlock(position: number): Promise<CramFileBlock>;
 }

package/esm/cramFile/file.js

@@ -53,11 +53,6 @@ export default class CramFile {
             throw new Error('Detected big-endian machine, may be unable to run');
         }
     }
-    // can just stat this object like a filehandle
-    stat() {
-        return this.file.stat();
-    }
-    // can just stat this object like a filehandle
     read(length, position) {
         return this.file.read(length, position);
     }
@@ -78,19 +73,14 @@ export default class CramFile {
             throw new CramMalformedError('file contains no containers');
         }
         const firstBlock = await firstContainer.getFirstBlock();
-        if (firstBlock === undefined) {
-            return parseHeaderText('');
-        }
-        else {
-            const content = firstBlock.content;
-            const dataView = new DataView(content.buffer);
-            const headerLength = dataView.getInt32(0, true);
-            const textStart = 4;
-            const decoder = new TextDecoder('utf8');
-            const text = decoder.decode(content.subarray(textStart, textStart + headerLength));
-            this.header = text;
-            return parseHeaderText(text);
-        }
+        const content = firstBlock.content;
+        const dataView = new DataView(content.buffer);
+        const headerLength = dataView.getInt32(0, true);
+        const textStart = 4;
+        const decoder = new TextDecoder('utf8');
+        const text = decoder.decode(content.subarray(textStart, textStart + headerLength));
+        this.header = text;
+        return parseHeaderText(text);
     }
     async getHeaderText() {
         await this.getSamHeader();
@@ -100,21 +90,16 @@ export default class CramFile {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = getSectionParsers(majorVersion);
         let position = sectionParsers.cramFileDefinition.maxLength;
-        const { size: fileSize } = await this.file.stat();
-        const { cramContainerHeader1 } = sectionParsers;
         // skip with a series of reads to the proper container
         let currentContainer;
         for (let i = 0; i <= containerNumber; i++) {
             // if we are about to go off the end of the file
             // and have not found that container, it does not exist
-            if (position + cramContainerHeader1.maxLength + 8 >= fileSize) {
-                return undefined;
-            }
+            // if (position + cramContainerHeader1.maxLength + 8 >= fileSize) {
+            //   return undefined
+            // }
             currentContainer = this.getContainerAtPosition(position);
             const currentHeader = await currentContainer.getHeader();
-            if (!currentHeader) {
-                throw new CramMalformedError(`container ${containerNumber} not found in file`);
-            }
             // if this is the first container, read all the blocks in the container
             // to determine its length, because we cannot trust the container
             // header's given length due to a bug somewhere in htslib
@@ -122,9 +107,6 @@ export default class CramFile {
                 position = currentHeader._endPosition;
                 for (let j = 0; j < currentHeader.numBlocks; j++) {
                     const block = await this.readBlock(position);
-                    if (block === undefined) {
-                        return undefined;
-                    }
                     position = block._endPosition;
                 }
             }
@@ -148,38 +130,40 @@ export default class CramFile {
     }
     /**
      * @returns {Promise[number]} the number of containers in the file
+     *
+     * note: this is currently used only in unit tests, and after removing file
+     * length check, relies on a try catch to read return an error to break
      */
     async containerCount() {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = getSectionParsers(majorVersion);
-        const { size: fileSize } = await this.file.stat();
-        const { cramContainerHeader1 } = sectionParsers;
         let containerCount = 0;
         let position = sectionParsers.cramFileDefinition.maxLength;
-        while (position + cramContainerHeader1.maxLength + 8 < fileSize) {
-            const currentHeader = await this.getContainerAtPosition(position).getHeader();
-            if (!currentHeader) {
-                break;
-            }
-            // if this is the first container, read all the blocks in the container,
-            // because we cannot trust the container header's given length due to a
-            // bug somewhere in htslib
-            if (containerCount === 0) {
-                position = currentHeader._endPosition;
-                for (let j = 0; j < currentHeader.numBlocks; j++) {
-                    const block = await this.readBlock(position);
-                    if (block === undefined) {
-                        return undefined;
+        try {
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+            while (true) {
+                const currentHeader = await this.getContainerAtPosition(position).getHeader();
+                // if this is the first container, read all the blocks in the container,
+                // because we cannot trust the container header's given length due to a
+                // bug somewhere in htslib
+                if (containerCount === 0) {
+                    position = currentHeader._endPosition;
+                    for (let j = 0; j < currentHeader.numBlocks; j++) {
+                        const block = await this.readBlock(position);
+                        position = block._endPosition;
                     }
-                    position = block._endPosition;
                 }
+                else {
+                    // otherwise, just traverse to the next container using the container's
+                    // length
+                    position += currentHeader._size + currentHeader.length;
+                }
+                containerCount += 1;
             }
-            else {
-                // otherwise, just traverse to the next container using the container's
-                // length
-                position += currentHeader._size + currentHeader.length;
-            }
-            containerCount += 1;
+        }
+        catch (e) {
+            containerCount--;
+            /* do nothing */
         }
         return containerCount;
     }
@@ -190,25 +174,11 @@ export default class CramFile {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = getSectionParsers(majorVersion);
         const { cramBlockHeader } = sectionParsers;
-        const { size: fileSize } = await this.file.stat();
-        if (position + cramBlockHeader.maxLength >= fileSize) {
-            return undefined;
-        }
         const buffer = await this.file.read(cramBlockHeader.maxLength, position);
         return parseItem(buffer, cramBlockHeader.parser, 0, position);
     }
     async _parseSection(section, position, size = section.maxLength, preReadBuffer) {
-        let buffer;
-        if (preReadBuffer) {
-            buffer = preReadBuffer;
-        }
-        else {
-            const { size: fileSize } = await this.file.stat();
-            if (position + size >= fileSize) {
-                return undefined;
-            }
-            buffer = await this.file.read(size, position);
-        }
+        const buffer = preReadBuffer ?? (await this.file.read(size, position));
         const data = parseItem(buffer, section.parser, 0, position);
         if (data._size !== size) {
             throw new CramMalformedError(`section read error: requested size ${size} does not equal parsed size ${data._size}`);
@@ -264,9 +234,6 @@ export default class CramFile {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = getSectionParsers(majorVersion);
         const blockHeader = await this.readBlockHeader(position);
-        if (blockHeader === undefined) {
-            return undefined;
-        }
         const blockContentPosition = blockHeader._endPosition;
         const d = await this.file.read(blockHeader.compressedSize, blockContentPosition);
         const uncompressedData = blockHeader.compressionMethod !== 'raw'
@@ -281,9 +248,6 @@ export default class CramFile {
         if (majorVersion >= 3) {
             // parse the crc32
             const crc = await this._parseSection(sectionParsers.cramBlockCrc32, blockContentPosition + blockHeader.compressedSize);
-            if (crc === undefined) {
-                return undefined;
-            }
             block.crc32 = crc.crc32;
             // check the block data crc32
             if (this.validateChecksums) {

package/esm/cramFile/file.js.map

@@ -1 +1 @@
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package/esm/cramFile/record.js.map

@@ -1 +1 @@
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package/esm/cramFile/sectionParsers.js

@@ -554,8 +554,9 @@ function cramContainerHeader1(majorVersion) {
             // byte size of the container data (blocks)
             const length = dataView.getInt32(offset, true);
             offset += 4;
-            // reference sequence identifier, -1 for unmapped reads, -2 for multiple
-            // reference sequences
+            // reference sequence identifier:
+            // -1 for unmapped reads,
+            // -2 for multiple reference sequences
             const [refSeqId, newOffset1] = parseItf8(buffer, offset);
             offset += newOffset1;
             const [refSeqStart, newOffset2] = parseItf8(buffer, offset);