npm - @gmod/cram - Versions diffs - 2.0.0 → 2.0.2 - Mend

@gmod/cram 2.0.0 → 2.0.2

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

Files changed (143) hide show

package/CHANGELOG.md +4 -0
package/dist/craiIndex.d.ts +2 -2
package/dist/craiIndex.js +5 -9
package/dist/craiIndex.js.map +1 -1
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/_base.d.ts +6 -6
package/dist/cramFile/codecs/beta.js.map +1 -1
package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
package/dist/cramFile/codecs/external.js +1 -0
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/codecs/gamma.js.map +1 -1
package/dist/cramFile/codecs/getBits.js.map +1 -1
package/dist/cramFile/codecs/huffman.d.ts +0 -1
package/dist/cramFile/codecs/huffman.js +1 -3
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/codecs/index.js.map +1 -1
package/dist/cramFile/codecs/subexp.js.map +1 -1
package/dist/cramFile/container/compressionScheme.js +1 -1
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/encoding.d.ts +20 -20
package/dist/cramFile/file.d.ts +14 -7
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/filehandle.d.ts +1 -2
package/dist/cramFile/index.d.ts +1 -2
package/dist/cramFile/index.js +3 -3
package/dist/cramFile/index.js.map +1 -1
package/dist/cramFile/record.d.ts +6 -6
package/dist/cramFile/record.js +7 -4
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.d.ts +9 -8
package/dist/cramFile/sectionParsers.js +10 -11
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +7 -11
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.js +24 -22
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.d.ts +1 -0
package/dist/cramFile/util.js +1 -1
package/dist/cramFile/util.js.map +1 -1
package/dist/index.d.ts +3 -4
package/dist/index.js +7 -30
package/dist/index.js.map +1 -1
package/dist/indexedCramFile.d.ts +6 -6
package/dist/indexedCramFile.js +13 -18
package/dist/indexedCramFile.js.map +1 -1
package/dist/io/index.d.ts +2 -1
package/dist/io/index.js +4 -3
package/dist/io/index.js.map +1 -1
package/dist/rans/d04.js.map +1 -1
package/dist/rans/d14.js.map +1 -1
package/dist/rans/decoding.js.map +1 -1
package/dist/rans/frequencies.js.map +1 -1
package/dist/rans/index.js.map +1 -1
package/dist/sam.d.ts +5 -6
package/dist/sam.js +20 -7
package/dist/sam.js.map +1 -1
package/dist/typescript.js.map +1 -1
package/dist/unzip.d.ts +2 -2
package/dist/unzip.js +1 -1
package/dist/unzip.js.map +1 -1
package/esm/craiIndex.d.ts +2 -2
package/esm/craiIndex.js +5 -9
package/esm/craiIndex.js.map +1 -1
package/esm/cramFile/codecs/_base.d.ts +6 -6
package/esm/cramFile/codecs/beta.js.map +1 -1
package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
package/esm/cramFile/codecs/external.js +1 -0
package/esm/cramFile/codecs/external.js.map +1 -1
package/esm/cramFile/codecs/gamma.js.map +1 -1
package/esm/cramFile/codecs/getBits.js.map +1 -1
package/esm/cramFile/codecs/huffman.d.ts +0 -1
package/esm/cramFile/codecs/huffman.js +1 -3
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/codecs/index.js.map +1 -1
package/esm/cramFile/codecs/subexp.js.map +1 -1
package/esm/cramFile/container/compressionScheme.js +1 -1
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/encoding.d.ts +20 -20
package/esm/cramFile/file.d.ts +14 -7
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/filehandle.d.ts +1 -2
package/esm/cramFile/index.d.ts +1 -2
package/esm/cramFile/index.js +1 -2
package/esm/cramFile/index.js.map +1 -1
package/esm/cramFile/record.d.ts +6 -6
package/esm/cramFile/record.js +7 -4
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.d.ts +9 -8
package/esm/cramFile/sectionParsers.js +10 -11
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +7 -11
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.js +24 -22
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.d.ts +1 -0
package/esm/cramFile/util.js +1 -1
package/esm/cramFile/util.js.map +1 -1
package/esm/index.d.ts +3 -4
package/esm/index.js +3 -4
package/esm/index.js.map +1 -1
package/esm/indexedCramFile.d.ts +6 -6
package/esm/indexedCramFile.js +13 -18
package/esm/indexedCramFile.js.map +1 -1
package/esm/io/index.d.ts +2 -1
package/esm/io/index.js +2 -1
package/esm/io/index.js.map +1 -1
package/esm/rans/d04.js.map +1 -1
package/esm/rans/d14.js.map +1 -1
package/esm/rans/decoding.js.map +1 -1
package/esm/rans/frequencies.js.map +1 -1
package/esm/rans/index.js.map +1 -1
package/esm/sam.d.ts +5 -6
package/esm/sam.js +20 -7
package/esm/sam.js.map +1 -1
package/esm/typescript.js.map +1 -1
package/esm/unzip.d.ts +2 -2
package/esm/unzip.js +1 -2
package/esm/unzip.js.map +1 -1
package/package.json +11 -11
package/src/craiIndex.ts +8 -13
package/src/cramFile/codecs/_base.ts +3 -3
package/src/cramFile/codecs/external.ts +1 -0
package/src/cramFile/codecs/huffman.ts +7 -8
package/src/cramFile/container/compressionScheme.ts +1 -1
package/src/cramFile/encoding.ts +10 -10
package/src/cramFile/file.ts +5 -5
package/src/cramFile/filehandle.ts +1 -3
package/src/cramFile/index.ts +1 -2
package/src/cramFile/record.ts +13 -10
package/src/cramFile/sectionParsers.ts +8 -9
package/src/cramFile/slice/decodeRecord.ts +15 -17
package/src/cramFile/slice/index.ts +26 -23
package/src/cramFile/util.ts +1 -1
package/src/index.ts +3 -5
package/src/indexedCramFile.ts +19 -23
package/src/io/index.ts +3 -1
package/src/sam.ts +28 -14
package/src/typings/binary-parser.d.ts +1 -1
package/src/unzip.ts +1 -2

package/esm/cramFile/slice/decodeRecord.js.map CHANGED Viewed

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package/esm/cramFile/slice/index.js CHANGED Viewed

@@ -136,7 +136,7 @@ export default class CramSlice {
         const containerHeader = await this.container.getHeader();
         const header = await this.file.readBlock(containerHeader._endPosition + this.containerPosition);
         if (header === undefined) {
-            throw new Error();
+            throw new Error('block header undefined');
         }
         if (header.contentType === 'MAPPED_SLICE_HEADER') {
             const content = parseItem(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
@@ -159,7 +159,7 @@ export default class CramSlice {
         for (let i = 0; i < blocks.length; i += 1) {
             const block = await this.file.readBlock(blockPosition);
             if (block === undefined) {
-                throw new Error();
+                throw new Error('block undefined');
             }
             blocks[i] = block;
             blockPosition = blocks[i]._endPosition;
@@ -191,16 +191,15 @@ export default class CramSlice {
         // read the slice header
         const sliceHeader = (await this.getHeader()).parsedContent;
         if (!isMappedSliceHeader(sliceHeader)) {
-            throw new Error();
+            throw new Error('slice header not mapped');
         }
         if (sliceHeader.refSeqId < 0) {
             return undefined;
         }
         const compressionScheme = await this.container.getCompressionScheme();
         if (compressionScheme === undefined) {
-            throw new Error();
+            throw new Error('compression scheme undefined');
         }
-        // console.log(JSON.stringify(sliceHeader, null, '  '))
         if (sliceHeader.refBaseBlockId >= 0) {
             const refBlock = await this.getBlockByContentId(sliceHeader.refBaseBlockId);
             if (!refBlock) {
@@ -243,11 +242,11 @@ export default class CramSlice {
         const { majorVersion } = await this.file.getDefinition();
         const compressionScheme = await this.container.getCompressionScheme();
         if (compressionScheme === undefined) {
-            throw new Error();
+            throw new Error('compression scheme undefined');
         }
         const sliceHeader = await this.getHeader();
         if (sliceHeader === undefined) {
-            throw new Error();
+            throw new Error('slice header undefined');
         }
         const blocksByContentId = await this._getBlocksContentIdIndex();
         // check MD5 of reference if available
@@ -354,45 +353,48 @@ export default class CramSlice {
                     : undefined;
                 const compressionScheme = await this.container.getCompressionScheme();
                 if (compressionScheme === undefined) {
-                    throw new Error();
+                    throw new Error('compression scheme undefined');
                 }
-                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) {
-                    const seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
+                const refRegions = {};
+                // iterate over the records to find the spans of the reference
+                // sequences we need to fetch
+                for (const record of records) {
+                    const seqId = singleRefId !== undefined ? singleRefId : record.sequenceId;
                     let refRegion = refRegions[seqId];
                     if (!refRegion) {
                         refRegion = {
                             id: seqId,
-                            start: records[i].alignmentStart,
+                            start: record.alignmentStart,
                             end: -Infinity,
                             seq: null,
                         };
                         refRegions[seqId] = refRegion;
                     }
-                    const end = records[i].alignmentStart +
-                        (records[i].lengthOnRef || records[i].readLength) -
+                    const end = record.alignmentStart +
+                        (record.lengthOnRef || record.readLength) -
                         1;
                     if (end > refRegion.end) {
                         refRegion.end = end;
                     }
-                    if (records[i].alignmentStart < refRegion.start) {
-                        refRegion.start = records[i].alignmentStart;
+                    if (record.alignmentStart < refRegion.start) {
+                        refRegion.start = record.alignmentStart;
                     }
                 }
                 // fetch the `seq` for all of the ref regions
                 await Promise.all(Object.values(refRegions).map(async (refRegion) => {
-                    if (refRegion.id !== -1 && refRegion.start <= refRegion.end) {
+                    if (refRegion.id !== -1 &&
+                        refRegion.start <= refRegion.end &&
+                        this.file.fetchReferenceSequenceCallback) {
                         refRegion.seq = await this.file.fetchReferenceSequenceCallback(refRegion.id, refRegion.start, refRegion.end);
                     }
                 }));
                 // now decorate all the records with them
-                for (let i = 0; i < records.length; i += 1) {
-                    const seqId = singleRefId !== undefined ? singleRefId : records[i].sequenceId;
+                for (const record of records) {
+                    const seqId = singleRefId !== undefined ? singleRefId : record.sequenceId;
                     const refRegion = refRegions[seqId];
-                    if (refRegion && refRegion.seq) {
+                    if (refRegion === null || refRegion === void 0 ? void 0 : refRegion.seq) {
                         const seq = refRegion.seq;
-                        records[i].addReferenceSequence({ ...refRegion, seq }, compressionScheme);
+                        record.addReferenceSequence({ ...refRegion, seq }, compressionScheme);
                     }
                 }
             }

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

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

@@ -1,3 +1,4 @@
+/// <reference path="../../src/typings/binary-parser.d.ts" />
 /// <reference types="node" />
 import { Parser } from '@gmod/binary-parser';
 export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;

package/esm/cramFile/util.js CHANGED Viewed

@@ -85,6 +85,6 @@ export function tinyMemoize(_class, methodName) {
     };
 }
 export function sequenceMD5(seq) {
-    return md5(seq.toUpperCase().replace(/[^\x21-\x7e]/g, ''));
+    return md5(seq.toUpperCase().replaceAll(/[^\u0021-\u007e]/g, ''));
 }
 //# sourceMappingURL=util.js.map

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

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

@@ -1,4 +1,3 @@
-import CramFile, { CramRecord } from './cramFile';
-import IndexedCramFile from './indexedCramFile';
-import CraiIndex from './craiIndex';
-export { CramFile, IndexedCramFile, CraiIndex, CramRecord };
+export { default as CramFile, CramRecord } from './cramFile';
+export { default as CraiIndex } from './craiIndex';
+export { default as IndexedCramFile } from './indexedCramFile';

package/esm/index.js CHANGED Viewed

@@ -1,5 +1,4 @@
-import CramFile, { CramRecord } from './cramFile';
-import IndexedCramFile from './indexedCramFile';
-import CraiIndex from './craiIndex';
-export { CramFile, IndexedCramFile, CraiIndex, CramRecord };
+export { default as CramFile, CramRecord } from './cramFile';
+export { default as CraiIndex } from './craiIndex';
+export { default as IndexedCramFile } from './indexedCramFile';
 //# sourceMappingURL=index.js.map

package/esm/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,QAAQ,EAAE,UAAU,EAAE,MAAM,YAAY,CAAA;AAC5D,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,eAAe,EAAE,MAAM,mBAAmB,CAAA"}

package/esm/indexedCramFile.d.ts CHANGED Viewed

@@ -3,15 +3,15 @@ import CramRecord from './cramFile/record';
 import { SeqFetch } from './cramFile/file';
 import { Filehandle } from './cramFile/filehandle';
 import { Slice } from './craiIndex';
-export type CramFileSource = {
+export interface CramFileSource {
     cramFilehandle?: Filehandle;
     cramUrl?: string;
     cramPath?: string;
-};
-export type CramIndexLike = {
+}
+export interface CramIndexLike {
     getEntriesForRange: (seqId: number, start: number, end: number) => Promise<Slice[]>;
     hasDataForReferenceSequence: (seqId: number) => Promise<boolean>;
-};
+}
 export default class IndexedCramFile {
     cram: CramFile;
     index: CramIndexLike;
@@ -33,8 +33,8 @@ export default class IndexedCramFile {
         cram: CramFile;
     } | ({
         cram?: undefined;
-        seqFetch: SeqFetch;
-        checkSequenceMD5: boolean;
+        seqFetch?: SeqFetch;
+        checkSequenceMD5?: boolean;
         cacheSize?: number;
     } & CramFileSource)));
     /**

package/esm/indexedCramFile.js CHANGED Viewed

@@ -12,12 +12,10 @@ export default class IndexedCramFile {
      * checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
      */
     constructor(args) {
+        var _a;
         // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
-        if (args.cram) {
-            this.cram = args.cram;
-        }
-        else {
-            this.cram = new CramFile({
+        this.cram =
+            (_a = args.cram) !== null && _a !== void 0 ? _a : new CramFile({
                 url: args.cramUrl,
                 path: args.cramPath,
                 filehandle: args.cramFilehandle,
@@ -25,7 +23,6 @@ export default class IndexedCramFile {
                 checkSequenceMD5: args.checkSequenceMD5,
                 cacheSize: args.cacheSize,
             });
-        }
         if (!(this.cram instanceof CramFile)) {
             throw new Error('invalid arguments: no cramfile');
         }
@@ -67,12 +64,12 @@ export default class IndexedCramFile {
         if (opts.viewAsPairs) {
             const readNames = {};
             const readIds = {};
-            for (let i = 0; i < ret.length; i += 1) {
-                const name = ret[i].readName;
+            for (const read of ret) {
+                const name = read.readName;
                 if (name === undefined) {
-                    throw new Error();
+                    throw new Error('readName undefined');
                 }
-                const id = ret[i].uniqueId;
+                const id = read.uniqueId;
                 if (!readNames[name]) {
                     readNames[name] = 0;
                 }
@@ -86,11 +83,10 @@ export default class IndexedCramFile {
                 }
             });
             const matePromises = [];
-            for (let i = 0; i < ret.length; i += 1) {
-                const cramRecord = ret[i];
+            for (const cramRecord of ret) {
                 const name = cramRecord.readName;
                 if (name === undefined) {
-                    throw new Error();
+                    throw new Error('readName undefined');
                 }
                 if (unmatedPairs[name] &&
                     cramRecord.mate &&
@@ -103,8 +99,8 @@ export default class IndexedCramFile {
             }
             const mateBlocks = await Promise.all(matePromises);
             let mateChunks = [];
-            for (let i = 0; i < mateBlocks.length; i += 1) {
-                mateChunks.push(...mateBlocks[i]);
+            for (const block of mateBlocks) {
+                mateChunks.push(...block);
             }
             // filter out duplicates
             mateChunks = mateChunks
@@ -127,10 +123,9 @@ export default class IndexedCramFile {
                 mateRecordPromises.push(recordPromise);
                 const featPromise = recordPromise.then(feats => {
                     const mateRecs = [];
-                    for (let i = 0; i < feats.length; i += 1) {
-                        const feature = feats[i];
+                    for (const feature of feats) {
                         if (feature.readName === undefined) {
-                            throw new Error();
+                            throw new Error('readName undefined');
                         }
                         if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
                             mateRecs.push(feature);

package/esm/indexedCramFile.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/io/index.d.ts CHANGED Viewed

@@ -2,4 +2,5 @@ import { Filehandle } from '../cramFile/filehandle';
 import { LocalFile, RemoteFile } from 'generic-filehandle';
 declare function fromUrl(source: string): LocalFile | RemoteFile;
 declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
-export { LocalFile, RemoteFile, fromUrl, open };
+export { fromUrl, open };
+export { LocalFile, RemoteFile } from 'generic-filehandle';

package/esm/io/index.js CHANGED Viewed

@@ -20,5 +20,6 @@ function open(maybeUrl, maybePath, maybeFilehandle) {
     }
     throw new Error('no url, path, or filehandle provided, cannot open');
 }
-export { LocalFile, RemoteFile, fromUrl, open };
+export { fromUrl, open };
+export { LocalFile, RemoteFile } from 'generic-filehandle';
 //# sourceMappingURL=index.js.map

package/esm/io/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/rans/d04.js.map CHANGED Viewed

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

@@ -1,8 +1,7 @@
-export type HeaderDataItem = {
+export declare function parseHeaderText(text: string): {
     tag: string;
-    data: Array<{
+    data: {
         tag: string;
-        value: string;
-    }>;
-};
-export declare function parseHeaderText(text: string): HeaderDataItem[];
+        value: string | undefined;
+    }[];
+}[];