@gmod/cram 4.0.3 → 4.0.5

package/dist/cramFile/codecs/_base.d.ts

@@ -23,5 +23,5 @@ export default abstract class CramCodec<TResult extends DataType = DataType, TPa
     parameters: TParameters;
     dataType: DataType;
     constructor(parameters: TParameters, dataType: TResult);
-    abstract decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): DataTypeMapping[TResult];
+    abstract decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): DataTypeMapping[TResult] | undefined;
 }

package/dist/cramFile/codecs/byteArrayLength.js

@@ -12,11 +12,12 @@ class ByteArrayStopCodec extends _base_1.default {
     }
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         const lengthCodec = this._getLengthCodec();
-        const arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+        const arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) || 0;
         const dataCodec = this._getDataCodec();
         const data = new Uint8Array(arrayLength);
         for (let i = 0; i < arrayLength; i += 1) {
-            data[i] = dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+            data[i] =
+                dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) || 0;
         }
         return data;
     }

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

@@ -1 +1 @@
-{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,oDAA4C;AAK5C,kCAAqC;AAOrC,MAAqB,kBAAmB,SAAQ,eAG/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,GAAG,WAAW,CAAC,MAAM,CACpC,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QAED,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,GAAG,SAAS,CAAC,MAAM,CACxB,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QACH,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;AAtDD,qCAsDC;AAED,+BAA+B,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IAC1D,IAAA,kBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC,CAAC,CAAA"}
+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,oDAA4C;AAK5C,kCAAqC;AAOrC,MAAqB,kBAAmB,SAAQ,eAG/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;AA9CD,qCA8CC;AAED,+BAA+B,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IAC1D,IAAA,kBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC,CAAC,CAAA"}

package/dist/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/dist/cramFile/codecs/external.js

@@ -23,11 +23,8 @@ class ExternalCodec extends _base_1.default {
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];
-        if (!contentBlock) {
-            throw new errors_1.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] = (0, util_1.parseItf8)(contentBlock.content, cursor.bytePosition);

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

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,oDAAoD;AACpD,yCAAyE;AAGzE,kCAAmC;AACnC,uCAAkD;AAGlD,MAAqB,aAAc,SAAQ,eAG1C;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,+BAAsB,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;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,GAAG,CACpD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAS,EACnC,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,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF;AA3DD,gCA2DC"}
+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,oDAAoD;AACpD,yCAAqD;AAGrD,kCAAmC;AACnC,uCAAkD;AAGlD,MAAqB,aAAc,SAAQ,eAG1C;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,+BAAsB,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,IAAA,gBAAS,EACnC,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,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF;AAvDD,gCAuDC"}

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

@@ -21,15 +21,12 @@ 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 = (0, sectionParsers_1.getSectionParsers)(majorVersion);
         const block = await this.getFirstBlock();
-        if (block === undefined) {
-            return undefined;
-        }
         if (block.contentType !== 'COMPRESSION_HEADER') {
             throw new errors_1.CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
         }
@@ -41,9 +38,6 @@ class CramContainer {
     }
     async getFirstBlock() {
         const containerHeader = await this.getHeader();
-        if (!containerHeader) {
-            return undefined;
-        }
         return this.file.readBlock(containerHeader._endPosition);
     }
     // parses the compression header data into a CramContainerCompressionScheme
@@ -64,31 +58,22 @@ class CramContainer {
         const { majorVersion } = await this.file.getDefinition();
         const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
         const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
-        const { size: fileSize } = await this.file.stat();
-        if (position >= fileSize) {
-            console.warn(`pos:${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 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
         const numLandmarksSize = (0, util_1.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 = (0, util_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}`);
         }
-        const completeHeader = Object.assign(header1, header2, {
+        return {
+            ...header1,
+            ...header2,
             _size: header1._size + header2._size - numLandmarksSize,
             _endPosition: header1._size + header2._size - numLandmarksSize + position,
-        });
-        return completeHeader;
+        };
     }
 }
 exports.default = CramContainer;

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,yCAAiD;AACjD,SAAS;AACT,qDAAgC;AAChC,kCAA0D;AAC1D,4EAAgE;AAEhE,sDAAqD;AAErD,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,kCAAiB,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,2BAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,8BAA8B,CACxE,CAAA;QACH,CAAC;QAED,MAAM,OAAO,GAAG,IAAA,gBAAS,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,2BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IACjE,CAAC;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,eAAS,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,kCAAiB,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,gBAAS,EAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAC9D,MAAM,gBAAgB,GAAG,IAAA,eAAQ,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,gBAAS,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,kBAAW,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;AACpC,CAAC,CAAC,CAAA"}

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

@@ -1,4 +1,37 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -8,14 +41,15 @@ const crc32_1 = __importDefault(require("crc/calculators/crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
 const xz_decompress_1 = require("xz-decompress");
 const errors_1 = require("../errors");
-const htscodecs_1 = __importDefault(require("../htscodecs"));
+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 util_1 = require("../util");
 const container_1 = __importDefault(require("./container"));
 const sectionParsers_1 = require("./sectionParsers");
-const util_1 = require("./util");
+const util_2 = require("./util");
 function bufferToStream(buf) {
     return new ReadableStream({
         start(controller) {
@@ -57,11 +91,6 @@ 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);
     }
@@ -82,19 +111,14 @@ class CramFile {
             throw new errors_1.CramMalformedError('file contains no containers');
         }
         const firstBlock = await firstContainer.getFirstBlock();
-        if (firstBlock === undefined) {
-            return (0, sam_1.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 (0, sam_1.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 (0, sam_1.parseHeaderText)(text);
     }
     async getHeaderText() {
         await this.getSamHeader();
@@ -104,21 +128,16 @@ class CramFile {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = (0, sectionParsers_1.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 errors_1.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
@@ -126,9 +145,6 @@ 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;
                 }
             }
@@ -152,38 +168,40 @@ 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 = (0, sectionParsers_1.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;
     }
@@ -194,26 +212,12 @@ class CramFile {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = (0, sectionParsers_1.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 (0, util_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
+        return (0, util_2.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 data = (0, util_1.parseItem)(buffer, section.parser, 0, position);
+        const buffer = preReadBuffer ?? (await this.file.read(size, position));
+        const data = (0, util_2.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 ${data._size}`);
         }
@@ -249,16 +253,16 @@ class CramFile {
             // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
         }
         else if (compressionMethod === 'rans4x16') {
-            return htscodecs_1.default.r4x16_uncompress(inputBuffer);
+            return htscodecs.r4x16_uncompress(inputBuffer);
         }
         else if (compressionMethod === 'arith') {
-            return htscodecs_1.default.arith_uncompress(inputBuffer);
+            return htscodecs.arith_uncompress(inputBuffer);
         }
         else if (compressionMethod === 'fqzcomp') {
-            return htscodecs_1.default.fqzcomp_uncompress(inputBuffer);
+            return htscodecs.fqzcomp_uncompress(inputBuffer);
         }
         else if (compressionMethod === 'tok3') {
-            return htscodecs_1.default.tok3_uncompress(inputBuffer);
+            return htscodecs.tok3_uncompress(inputBuffer);
         }
         else {
             throw new errors_1.CramUnimplementedError(`${compressionMethod} decompression not yet implemented`);
@@ -268,9 +272,6 @@ class CramFile {
         const { majorVersion } = await this.getDefinition();
         const sectionParsers = (0, sectionParsers_1.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'
@@ -285,9 +286,6 @@ 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) {
@@ -307,6 +305,6 @@ class CramFile {
 }
 exports.default = CramFile;
 'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
-    (0, util_1.tinyMemoize)(CramFile, method);
+    (0, util_2.tinyMemoize)(CramFile, method);
 });
 //# sourceMappingURL=file.js.map

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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