@gmod/cram 1.6.3 → 1.7.0

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

@@ -1,20 +1,27 @@
+import CramRecord from '../record';
+import CramContainer from '../container';
+import { CramFileBlock } from '../file';
+import { MappedSliceHeader, UnmappedSliceHeader } from '../sectionParsers';
+export declare type SliceHeader = CramFileBlock & {
+    parsedContent: MappedSliceHeader | UnmappedSliceHeader;
+};
 export default class CramSlice {
-    constructor(container: any, position: any);
-    container: any;
-    file: any;
-    containerPosition: any;
-    getHeader(): Promise<any>;
-    getBlocks(): Promise<any[]>;
-    getCoreDataBlock(): Promise<any>;
-    _getBlocksContentIdIndex(): Promise<{}>;
-    getBlockByContentId(id: any): Promise<any>;
+    container: CramContainer;
+    containerPosition: number;
+    private file;
+    constructor(container: CramContainer, containerPosition: number, _unused: number);
+    getHeader(): Promise<SliceHeader>;
+    getBlocks(): Promise<CramFileBlock[]>;
+    getCoreDataBlock(): Promise<CramFileBlock>;
+    _getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;
+    getBlockByContentId(id: number): Promise<CramFileBlock>;
     getReferenceRegion(): Promise<{
         seq: any;
-        start: any;
+        start: number;
         end: number;
-        span: any;
+        span: number;
     } | undefined>;
-    getAllRecords(): Promise<any>;
-    _fetchRecords(): Promise<any[]>;
-    getRecords(filterFunction: any): Promise<any>;
+    getAllRecords(): Promise<CramRecord[]>;
+    _fetchRecords(): Promise<CramRecord[]>;
+    getRecords(filterFunction: (r: CramRecord) => boolean): Promise<CramRecord[]>;
 }

package/esm/cramFile/slice/index.js

@@ -1,7 +1,10 @@
-import { CramMalformedError, CramBufferOverrunError, CramArgumentError, } from '../../errors';
-import { parseItem, tinyMemoize, sequenceMD5 } from '../util';
+import { CramArgumentError, CramMalformedError } from '../../errors';
+import { parseItem, sequenceMD5, tinyMemoize } from '../util';
 import Constants from '../constants';
 import decodeRecord from './decodeRecord';
+import CramRecord from '../record';
+import { isMappedSliceHeader, } from '../sectionParsers';
+import { CramBufferOverrunError } from '../codecs/getBits';
 /**
  * @private
  * Try to estimate the template length from a bunch of interrelated multi-segment reads.
@@ -12,7 +15,8 @@ import decodeRecord from './decodeRecord';
 function calculateMultiSegmentMatedTemplateLength(allRecords, currentRecordNumber, thisRecord) {
     function getAllMatedRecords(startRecord) {
         const records = [startRecord];
-        if (startRecord.mateRecordNumber >= 0) {
+        if (startRecord.mateRecordNumber !== undefined &&
+            startRecord.mateRecordNumber >= 0) {
             const mateRecord = allRecords[startRecord.mateRecordNumber];
             if (!mateRecord) {
                 throw new CramMalformedError('intra-slice mate record not found, this file seems malformed');
@@ -120,10 +124,10 @@ function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, ma
     delete thisRecord.mateRecordNumber;
 }
 export default class CramSlice {
-    constructor(container, position) {
+    constructor(container, containerPosition, _unused) {
         this.container = container;
+        this.containerPosition = containerPosition;
         this.file = container.file;
-        this.containerPosition = position;
     }
     // memoize
     async getHeader() {
@@ -131,25 +135,33 @@ export default class CramSlice {
         const sectionParsers = await this.file.getSectionParsers();
         const containerHeader = await this.container.getHeader();
         const header = await this.file.readBlock(containerHeader._endPosition + this.containerPosition);
+        if (header === undefined) {
+            throw new Error();
+        }
         if (header.contentType === 'MAPPED_SLICE_HEADER') {
-            header.content = parseItem(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
+            const content = parseItem(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
+            return { ...header, parsedContent: content };
         }
         else if (header.contentType === 'UNMAPPED_SLICE_HEADER') {
-            header.content = parseItem(header.content, sectionParsers.cramUnmappedSliceHeader.parser, 0, containerHeader._endPosition);
+            const content = parseItem(header.content, sectionParsers.cramUnmappedSliceHeader.parser, 0, containerHeader._endPosition);
+            return { ...header, parsedContent: content };
         }
         else {
-            throw new CramMalformedError(`error reading slice header block, invalid content type ${header._contentType}`);
+            throw new CramMalformedError(`error reading slice header block, invalid content type ${header.contentType}`);
         }
-        return header;
     }
     // memoize
     async getBlocks() {
         const header = await this.getHeader();
         // read all the blocks into memory and store them
         let blockPosition = header._endPosition;
-        const blocks = new Array(header.content.numBlocks);
+        const blocks = new Array(header.parsedContent.numBlocks);
         for (let i = 0; i < blocks.length; i += 1) {
-            blocks[i] = await this.file.readBlock(blockPosition);
+            const block = await this.file.readBlock(blockPosition);
+            if (block === undefined) {
+                throw new Error();
+            }
+            blocks[i] = block;
             blockPosition = blocks[i]._endPosition;
         }
         return blocks;
@@ -177,20 +189,28 @@ export default class CramSlice {
     }
     async getReferenceRegion() {
         // read the slice header
-        const sliceHeader = (await this.getHeader()).content;
+        const sliceHeader = (await this.getHeader()).parsedContent;
+        if (!isMappedSliceHeader(sliceHeader)) {
+            throw new Error();
+        }
         if (sliceHeader.refSeqId < 0) {
             return undefined;
         }
         const compressionScheme = await this.container.getCompressionScheme();
+        if (compressionScheme === undefined) {
+            throw new Error();
+        }
         // console.log(JSON.stringify(sliceHeader, null, '  '))
         if (sliceHeader.refBaseBlockId >= 0) {
-            const refBlock = this.getBlockByContentId(sliceHeader.refBaseBlockId);
+            const refBlock = await this.getBlockByContentId(sliceHeader.refBaseBlockId);
             if (!refBlock) {
                 throw new CramMalformedError('embedded reference specified, but reference block does not exist');
             }
-            if (sliceHeader.span > refBlock.uncompressedSize) {
-                throw new CramMalformedError('Embedded reference is too small');
-            }
+            // TODO: we do not read anything named 'span'
+            // if (sliceHeader.span > refBlock.uncompressedSize) {
+            //   throw new CramMalformedError('Embedded reference is too small')
+            // }
+            // TODO verify
             return {
                 seq: refBlock.data.toString('utf8'),
                 start: sliceHeader.refSeqStart,
@@ -222,22 +242,29 @@ export default class CramSlice {
     async _fetchRecords() {
         const { majorVersion } = await this.file.getDefinition();
         const compressionScheme = await this.container.getCompressionScheme();
+        if (compressionScheme === undefined) {
+            throw new Error();
+        }
         const sliceHeader = await this.getHeader();
+        if (sliceHeader === undefined) {
+            throw new Error();
+        }
         const blocksByContentId = await this._getBlocksContentIdIndex();
         // check MD5 of reference if available
         if (majorVersion > 1 &&
             this.file.options.checkSequenceMD5 &&
-            sliceHeader.content.refSeqId >= 0 &&
-            sliceHeader.content.md5.join('') !== '0000000000000000') {
+            isMappedSliceHeader(sliceHeader.parsedContent) &&
+            sliceHeader.parsedContent.refSeqId >= 0 &&
+            sliceHeader.parsedContent.md5.join('') !== '0000000000000000') {
             const refRegion = await this.getReferenceRegion();
             if (refRegion) {
                 const { seq, start, end } = refRegion;
                 const seqMd5 = sequenceMD5(seq);
-                const storedMd5 = sliceHeader.content.md5
+                const storedMd5 = sliceHeader.parsedContent.md5
                     .map(byte => (byte < 16 ? '0' : '') + byte.toString(16))
                     .join('');
                 if (seqMd5 !== storedMd5) {
-                    throw new CramMalformedError(`MD5 checksum reference mismatch for ref ${sliceHeader.content.refSeqId} pos ${start}..${end}. recorded MD5: ${storedMd5}, calculated MD5: ${seqMd5}`);
+                    throw new CramMalformedError(`MD5 checksum reference mismatch for ref ${sliceHeader.parsedContent.refSeqId} pos ${start}..${end}. recorded MD5: ${storedMd5}, calculated MD5: ${seqMd5}`);
                 }
             }
         }
@@ -247,7 +274,9 @@ export default class CramSlice {
         // data block
         const coreDataBlock = await this.getCoreDataBlock();
         const cursors = {
-            lastAlignmentStart: sliceHeader.content.refSeqStart || 0,
+            lastAlignmentStart: isMappedSliceHeader(sliceHeader.parsedContent)
+                ? sliceHeader.parsedContent.refSeqStart
+                : 0,
             coreBlock: { bitPosition: 7, bytePosition: 0 },
             externalBlocks: {
                 map: new Map(),
@@ -261,23 +290,26 @@ export default class CramSlice {
                 },
             },
         };
-        const decodeDataSeries = dataSeriesName => {
+        const decodeDataSeries = (dataSeriesName) => {
             const codec = compressionScheme.getCodecForDataSeries(dataSeriesName);
             if (!codec) {
                 throw new CramMalformedError(`no codec defined for ${dataSeriesName} data series`);
             }
             // console.log(dataSeriesName, Object.getPrototypeOf(codec))
-            return codec.decode(this, coreDataBlock, blocksByContentId, cursors);
+            const decoded = codec.decode(this, coreDataBlock, blocksByContentId, cursors);
+            return decoded;
         };
-        let records = new Array(sliceHeader.content.numRecords);
+        let records = new Array(sliceHeader.parsedContent.numRecords);
         for (let i = 0; i < records.length; i += 1) {
             try {
-                records[i] = decodeRecord(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
-                records[i].uniqueId =
-                    sliceHeader.contentPosition +
-                        sliceHeader.content.recordCounter +
+                const init = decodeRecord(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
+                records[i] = new CramRecord({
+                    ...init,
+                    uniqueId: sliceHeader.contentPosition +
+                        sliceHeader.parsedContent.recordCounter +
                         i +
-                        1;
+                        1,
+                });
             }
             catch (e) {
                 if (e instanceof CramBufferOverrunError) {
@@ -294,7 +326,7 @@ export default class CramSlice {
         // objects Resolve mate pair cross-references between records in this slice
         for (let i = 0; i < records.length; i += 1) {
             const { mateRecordNumber } = records[i];
-            if (mateRecordNumber >= 0) {
+            if (mateRecordNumber !== undefined && mateRecordNumber >= 0) {
                 associateIntraSliceMate(records, i, records[i], records[mateRecordNumber]);
             }
         }
@@ -303,22 +335,27 @@ export default class CramSlice {
     async getRecords(filterFunction) {
         // fetch the features if necessary, using the file-level feature cache
         const cacheKey = this.container.filePosition + this.containerPosition;
-        let recordsPromise = this.file.featureCache.get(cacheKey);
+        let recordsPromise = this.file.featureCache.get(cacheKey.toString());
         if (!recordsPromise) {
             recordsPromise = this._fetchRecords();
-            this.file.featureCache.set(cacheKey, recordsPromise);
+            this.file.featureCache.set(cacheKey.toString(), recordsPromise);
         }
-        const records = (await recordsPromise).filter(filterFunction);
+        const unfiltered = await recordsPromise;
+        const records = unfiltered.filter(filterFunction);
         // if we can fetch reference sequence, add the reference sequence to the records
         if (records.length && this.file.fetchReferenceSequenceCallback) {
             const sliceHeader = await this.getHeader();
-            if (sliceHeader.content.refSeqId >= 0 || // single-ref slice
-                sliceHeader.content.refSeqId === -2 // multi-ref slice
+            if (isMappedSliceHeader(sliceHeader.parsedContent) &&
+                (sliceHeader.parsedContent.refSeqId >= 0 || // single-ref slice
+                    sliceHeader.parsedContent.refSeqId === -2) // multi-ref slice
             ) {
-                const singleRefId = sliceHeader.content.refSeqId >= 0
-                    ? sliceHeader.content.refSeqId
+                const singleRefId = sliceHeader.parsedContent.refSeqId >= 0
+                    ? sliceHeader.parsedContent.refSeqId
                     : undefined;
                 const compressionScheme = await this.container.getCompressionScheme();
+                if (compressionScheme === undefined) {
+                    throw new Error();
+                }
                 const refRegions = {}; // seqId => { start, end, seq }
                 // iterate over the records to find the spans of the reference sequences we need to fetch
                 for (let i = 0; i < records.length; i += 1) {
@@ -329,6 +366,7 @@ export default class CramSlice {
                             id: seqId,
                             start: records[i].alignmentStart,
                             end: -Infinity,
+                            seq: null,
                         };
                         refRegions[seqId] = refRegion;
                     }
@@ -353,7 +391,8 @@ export default class CramSlice {
                     const seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
                     const refRegion = refRegions[seqId];
                     if (refRegion && refRegion.seq) {
-                        records[i].addReferenceSequence(refRegion, compressionScheme);
+                        const seq = refRegion.seq;
+                        records[i].addReferenceSequence({ ...refRegion, seq }, compressionScheme);
                     }
                 }
             }

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

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package/esm/cramFile/util.d.ts

@@ -1,5 +1,11 @@
-export function itf8Size(v: any): 1 | 2 | 3 | 4 | 5;
-export function parseItf8(buffer: any, initialOffset: any): any[];
-export function parseItem(buffer: any, parser: any, startBufferPosition?: number, startFilePosition?: number): any;
-export function tinyMemoize(_class: any, methodName: any): void;
-export function sequenceMD5(seq: any): any;
+/// <reference types="node" />
+import { Parser } from '@gmod/binary-parser';
+export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
+export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
+export declare type ParsedItem<T> = T & {
+    _endPosition: number;
+    _size: number;
+};
+export declare function parseItem<T>(buffer: Buffer, parser: Parser<T>, startBufferPosition?: number, startFilePosition?: number): ParsedItem<T>;
+export declare function tinyMemoize(_class: any, methodName: any): void;
+export declare function sequenceMD5(seq: string): string;

package/esm/cramFile/util.js

@@ -1,5 +1,5 @@
 import md5 from 'md5';
-import { CramBufferOverrunError } from '../errors';
+import { CramBufferOverrunError } from './codecs/getBits';
 export function itf8Size(v) {
     if (!(v & ~0x7f)) {
         return 1;
@@ -21,17 +21,17 @@ export function parseItf8(buffer, initialOffset) {
     let result;
     if (countFlags < 0x80) {
         result = countFlags;
-        offset += 1;
+        offset = offset + 1;
     }
     else if (countFlags < 0xc0) {
         result = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff;
-        offset += 2;
+        offset = offset + 2;
     }
     else if (countFlags < 0xe0) {
         result =
             ((countFlags << 16) | (buffer[offset + 1] << 8) | buffer[offset + 2]) &
                 0x1fffff;
-        offset += 3;
+        offset = offset + 3;
     }
     else if (countFlags < 0xf0) {
         result =
@@ -40,7 +40,7 @@ export function parseItf8(buffer, initialOffset) {
                 (buffer[offset + 2] << 8) |
                 buffer[offset + 3]) &
                 0x0fffffff;
-        offset += 4;
+        offset = offset + 4;
     }
     else {
         result =
@@ -51,91 +51,20 @@ export function parseItf8(buffer, initialOffset) {
                 (buffer[offset + 4] & 0x0f);
         // x=((0xff & 0x0f)<<28) | (0xff<<20) | (0xff<<12) | (0xff<<4) | (0x0f & 0x0f);
         // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
-        offset += 5;
+        offset = offset + 5;
     }
     if (offset > buffer.length) {
         throw new CramBufferOverrunError('Attempted to read beyond end of buffer; this file seems truncated.');
     }
     return [result, offset - initialOffset];
 }
-// parseLtf8(buffer, initialOffset) {
-//   let offset = initialOffset
-//   const countFlags = buffer[offset]
-//   let result
-//   if (countFlags < 0x80) {
-//     result = countFlags
-//     offset += 1
-//   } else if (countFlags < 0xc0) {
-//     result = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff
-//     offset += 2
-//   } else if (countFlags < 0xe0) {
-//     result =
-//       ((buffer[offset] << 16) |
-//         (buffer[offset + 1] << 8) |
-//         buffer[offset + 2]) &
-//       0x1fffff
-//     offset += 3
-//   } else if (countFlags < 0xf0) {
-//     result =
-//       ((buffer[offset] << 24) |
-//         (buffer[offset + 1] << 16) |
-//         (buffer[offset + 2] << 8) |
-//         buffer[offset + 3]) &
-//       0x0fffffff
-//     offset += 4
-//   } else if (countFlags < 0xf8) {
-//     result =
-//       ((buffer[offset] & 15) * Math.pow(2,32) + (buffer[offset + 1] << 24)) |
-//       ((buffer[offset + 2] << 16) |
-//         (buffer[offset + 3] << 8) |
-//         buffer[offset + 4])
-//     // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
-//     offset += 5
-//   } else if (countFlags < 0xfc) {
-//     result =
-//       ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2,32) +
-//         (buffer[offset + 2] << 24)) |
-//       ((buffer[offset + 3] << 16) |
-//         (buffer[offset + 4] << 8) |
-//         buffer[offset + 5])
-//     offset += 6
-//   } else if (countFlags < 0xfe) {
-//     result =
-//       ((((buffer[offset] & 3) << 16) |
-//         (buffer[offset + 1] << 8) |
-//         buffer[offset + 2]) *
-//         Math.pow(2,32) +
-//         (buffer[offset + 3] << 24)) |
-//       ((buffer[offset + 4] << 16) |
-//         (buffer[offset + 5] << 8) |
-//         buffer[offset + 6])
-//     offset += 7
-//   } else if (countFlags < 0xff) {
-//     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 8))
-//     if (
-//       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
-//       result.lessThan(Number.MIN_SAFE_INTEGER)
-//     )
-//       throw new CramUnimplementedError('integer overflow')
-//     result = result.toNumber()
-//     offset += 8
-//   } else {
-//     result = Long.fromBytesBE(buffer.slice(offset + 1, offset + 9))
-//     if (
-//       result.greaterThan(Number.MAX_SAFE_INTEGER) ||
-//       result.lessThan(Number.MIN_SAFE_INTEGER)
-//     )
-//       throw new CramUnimplementedError('integer overflow')
-//     result = result.toNumber()
-//     offset += 9
-//   }
-//   return [result, offset - initialOffset]
-// },
 export function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition = 0) {
     const { offset, result } = parser.parse(buffer);
-    result._endPosition = offset + startFilePosition;
-    result._size = offset - startBufferPosition;
-    return result;
+    return {
+        ...result,
+        _endPosition: offset + startFilePosition,
+        _size: offset - startBufferPosition,
+    };
 }
 // this would be nice as a decorator, but i'm a little worried about
 // babel support for it going away or changing.

package/esm/cramFile/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/cramFile/util.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,KAAK,CAAA;AAErB,OAAO,EAAE,sBAAsB,EAAE,MAAM,kBAAkB,CAAA;AAEzD,MAAM,UAAU,QAAQ,CAAC,CAAS;IAChC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,EAAE;QAChB,OAAO,CAAC,CAAA;KACT;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE;QAClB,OAAO,CAAC,CAAA;KACT;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE;QACpB,OAAO,CAAC,CAAA;KACT;IACD,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE;QACrB,OAAO,CAAC,CAAA;KACT;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,MAAM,UAAU,SAAS,CACvB,MAAkB,EAClB,aAAqB;IAErB,IAAI,MAAM,GAAG,aAAa,CAAA;IAC1B,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,CAAC,CAAA;IACjC,IAAI,MAAM,CAAA;IACV,IAAI,UAAU,GAAG,IAAI,EAAE;QACrB,MAAM,GAAG,UAAU,CAAA;QACnB,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE;QAC5B,MAAM,GAAG,CAAC,CAAC,UAAU,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;QAC1D,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE;QAC5B,MAAM;YACJ,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC,GAAG,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrE,QAAQ,CAAA;QACV,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;SAAM,IAAI,UAAU,GAAG,IAAI,EAAE;QAC5B,MAAM;YACJ,CAAC,CAAC,UAAU,IAAI,EAAE,CAAC;gBACjB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;gBACrB,UAAU,CAAA;QACZ,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;SAAM;QACL,MAAM;YACJ,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;gBAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;gBACzB,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,CAAA;QAC7B,+EAA+E;QAC/E,+EAA+E;QAC/E,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;KACpB;IACD,IAAI,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE;QAC1B,MAAM,IAAI,sBAAsB,CAC9B,oEAAoE,CACrE,CAAA;KACF;IACD,OAAO,CAAC,MAAM,EAAE,MAAM,GAAG,aAAa,CAAC,CAAA;AACzC,CAAC;AAiFD,MAAM,UAAU,SAAS,CACvB,MAAc,EACd,MAAiB,EACjB,mBAAmB,GAAG,CAAC,EACvB,iBAAiB,GAAG,CAAC;IAErB,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAC/C,OAAO;QACL,GAAG,MAAM;QACT,YAAY,EAAE,MAAM,GAAG,iBAAiB;QACxC,KAAK,EAAE,MAAM,GAAG,mBAAmB;KACpC,CAAA;AACH,CAAC;AAED,oEAAoE;AACpE,+CAA+C;AAC/C,0EAA0E;AAC1E,0EAA0E;AAC1E,MAAM,UAAU,WAAW,CAAC,MAAW,EAAE,UAAe;IACtD,MAAM,MAAM,GAAG,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,CAAA;IAC3C,MAAM,YAAY,GAAG,SAAS,UAAU,EAAE,CAAA;IAC1C,MAAM,CAAC,SAAS,CAAC,UAAU,CAAC,GAAG,SAAS,aAAa;QACnD,IAAI,CAAC,CAAC,YAAY,IAAI,IAAI,CAAC,EAAE;YAC3B,MAAM,GAAG,GAAG,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAC7B,IAAI,CAAC,YAAY,CAAC,GAAG,GAAG,CAAA;YACxB,OAAO,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE;gBAC9B,OAAO,IAAI,CAAC,YAAY,CAAC,CAAA;YAC3B,CAAC,CAAC,CAAA;SACH;QACD,OAAO,IAAI,CAAC,YAAY,CAAC,CAAA;IAC3B,CAAC,CAAA;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,GAAW;IACrC,OAAO,GAAG,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,OAAO,CAAC,eAAe,EAAE,EAAE,CAAC,CAAC,CAAA;AAC5D,CAAC"}

package/esm/errors.d.ts

@@ -1,23 +1,18 @@
-export class CramError extends Error {
+export declare class CramError extends Error {
 }
 /** Error caused by encountering a part of the CRAM spec that has not yet been implemented */
-export class CramUnimplementedError extends Error {
+export declare class CramUnimplementedError extends Error {
 }
 /** An error caused by malformed data.  */
-export class CramMalformedError extends CramError {
-}
-/**
- * An error caused by attempting to read beyond the end of the defined data.
- */
-export class CramBufferOverrunError extends CramMalformedError {
+export declare class CramMalformedError extends CramError {
 }
 /**
  * An error caused by data being too big, exceeding a size limit.
  */
-export class CramSizeLimitError extends CramError {
+export declare class CramSizeLimitError extends CramError {
 }
 /**
  * An invalid argument was supplied to a cram-js method or object.
  */
-export class CramArgumentError extends CramError {
+export declare class CramArgumentError extends CramError {
 }

package/esm/errors.js

@@ -6,11 +6,6 @@ export class CramUnimplementedError extends Error {
 /** An error caused by malformed data.  */
 export class CramMalformedError extends CramError {
 }
-/**
- * An error caused by attempting to read beyond the end of the defined data.
- */
-export class CramBufferOverrunError extends CramMalformedError {
-}
 /**
  * An error caused by data being too big, exceeding a size limit.
  */

package/esm/errors.js.map

@@ -1 +1 @@
-{"version":3,"file":"errors.js","sourceRoot":"","sources":["../src/errors.js"],"names":[],"mappings":"AAAA,MAAM,OAAO,SAAU,SAAQ,KAAK;CAAG;AAEvC,6FAA6F;AAC7F,MAAM,OAAO,sBAAuB,SAAQ,KAAK;CAAG;AAEpD,0CAA0C;AAC1C,MAAM,OAAO,kBAAmB,SAAQ,SAAS;CAAG;AAEpD;;GAEG;AACH,MAAM,OAAO,sBAAuB,SAAQ,kBAAkB;CAAG;AAEjE;;GAEG;AACH,MAAM,OAAO,kBAAmB,SAAQ,SAAS;CAAG;AAEpD;;GAEG;AACH,MAAM,OAAO,iBAAkB,SAAQ,SAAS;CAAG"}
+{"version":3,"file":"errors.js","sourceRoot":"","sources":["../src/errors.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,SAAU,SAAQ,KAAK;CAAG;AAEvC,6FAA6F;AAC7F,MAAM,OAAO,sBAAuB,SAAQ,KAAK;CAAG;AAEpD,0CAA0C;AAC1C,MAAM,OAAO,kBAAmB,SAAQ,SAAS;CAAG;AAEpD;;GAEG;AACH,MAAM,OAAO,kBAAmB,SAAQ,SAAS;CAAG;AAEpD;;GAEG;AACH,MAAM,OAAO,iBAAkB,SAAQ,SAAS;CAAG"}

package/esm/index.d.ts

@@ -1,4 +1,4 @@
-import CramFile from "./cramFile";
-import IndexedCramFile from "./indexedCramFile";
-import CraiIndex from "./craiIndex";
+import CramFile from './cramFile';
+import IndexedCramFile from './indexedCramFile';
+import CraiIndex from './craiIndex';
 export { CramFile, IndexedCramFile, CraiIndex };

package/esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.js"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,QAAQ,EAAE,eAAe,EAAE,SAAS,EAAE,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,eAAe,MAAM,mBAAmB,CAAA;AAC/C,OAAO,SAAS,MAAM,aAAa,CAAA;AAEnC,OAAO,EAAE,QAAQ,EAAE,eAAe,EAAE,SAAS,EAAE,CAAA"}