@gmod/cram 4.0.3 → 4.0.5

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

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

@@ -3,14 +3,15 @@ import crc32 from 'crc/calculators/crc32';
 import QuickLRU from 'quick-lru';
 import { XzReadableStream } from 'xz-decompress';
 import { CramMalformedError, CramUnimplementedError } from '../errors';
-import htscodecs from '../htscodecs';
+import * as htscodecs from '../htscodecs';
 import { open } from '../io';
 import ransuncompress from '../rans';
 import { parseHeaderText } from '../sam';
 import { unzip } from '../unzip';
+import { concatUint8Array } from '../util';
 import CramContainer from './container';
 import { cramFileDefinition, getSectionParsers, } from './sectionParsers';
-import { concatUint8Array, parseItem, tinyMemoize } from './util';
+import { parseItem, tinyMemoize } from './util';
 function bufferToStream(buf) {
     return new ReadableStream({
         start(controller) {
@@ -52,11 +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);
     }
@@ -77,19 +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();
@@ -99,21 +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
@@ -121,9 +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;
                 }
             }
@@ -147,38 +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;
     }
@@ -189,25 +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}`);
@@ -263,9 +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'
@@ -280,9 +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);

package/esm/cramFile/sectionParsers.js.map

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

@@ -4,10 +4,10 @@ import CramContainerCompressionScheme, { DataSeriesTypes } from '../container/co
 import { ReadFeature } from '../record';
 import CramSlice, { SliceHeader } from './index';
 import { CramFileBlock } from '../file';
-export type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]];
+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;
-    sequenceId: number;
+    sequenceId: number | undefined;
     cramFlags: number;
     flags: number;
     alignmentStart: number;

package/esm/cramFile/slice/decodeRecord.js

@@ -115,15 +115,15 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
         if (type === 'character') {
             return String.fromCharCode(data);
         }
-        if (type === 'string') {
+        else if (type === 'string') {
             let r = '';
             for (let i = 0; i < data.byteLength; i++) {
                 r += String.fromCharCode(data[i]);
             }
             return r;
         }
-        if (type === 'numArray') {
-            return data.toArray();
+        else if (type === 'numArray') {
+            return Array.from(data);
         }
         // else if (type === 'number') {
         //   return data[0]
@@ -177,9 +177,8 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
 }
 export default function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
     let flags = decodeDataSeries('BF');
-    // 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.
+    // 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 (!isMappedSliceHeader(sliceHeader.parsedContent)) {
         throw new Error('slice header not mapped');
@@ -255,7 +254,11 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
             .getCodecForTag(tagId)
             .decode(slice, coreDataBlock, blocksByContentId, cursors);
         tags[tagName] =
-            typeof tagData === 'number' ? tagData : parseTagData(tagType, tagData);
+            tagData === undefined
+                ? undefined
+                : typeof tagData === 'number'
+                    ? tagData
+                    : parseTagData(tagType, tagData);
     }
     let readFeatures;
     let lengthOnRef;