npm - @gmod/cram - Versions diffs - 4.0.3 → 4.0.5 - Mend

@gmod/cram 4.0.3 → 4.0.5

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 (132) hide show

package/README.md +53 -51
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/_base.d.ts +1 -1
package/dist/cramFile/codecs/byteArrayLength.js +3 -2
package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
package/dist/cramFile/codecs/external.d.ts +1 -1
package/dist/cramFile/codecs/external.js +1 -4
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/container/index.d.ts +16 -34
package/dist/cramFile/container/index.js +5 -20
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +8 -6
package/dist/cramFile/file.js +80 -82
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.js +3 -2
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.d.ts +2 -2
package/dist/cramFile/slice/decodeRecord.js +10 -7
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.js +14 -16
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.d.ts +5 -2
package/dist/cramFile/util.js +75 -79
package/dist/cramFile/util.js.map +1 -1
package/dist/htscodecs/arith_gen.d.ts +5 -7
package/dist/htscodecs/arith_gen.js +122 -105
package/dist/htscodecs/arith_gen.js.map +1 -1
package/dist/htscodecs/arith_sh.d.ts +1 -8
package/dist/htscodecs/arith_sh.js +16 -10
package/dist/htscodecs/arith_sh.js.map +1 -1
package/dist/htscodecs/byte_model.d.ts +1 -6
package/dist/htscodecs/byte_model.js +25 -17
package/dist/htscodecs/byte_model.js.map +1 -1
package/dist/htscodecs/fqzcomp.d.ts +1 -1
package/dist/htscodecs/fqzcomp.js +98 -77
package/dist/htscodecs/fqzcomp.js.map +1 -1
package/dist/htscodecs/index.d.ts +5 -5
package/dist/htscodecs/index.js +53 -16
package/dist/htscodecs/index.js.map +1 -1
package/dist/htscodecs/iostream.d.ts +9 -20
package/dist/htscodecs/iostream.js +21 -116
package/dist/htscodecs/iostream.js.map +1 -1
package/dist/htscodecs/rans.d.ts +1 -1
package/dist/htscodecs/rans.js +65 -54
package/dist/htscodecs/rans.js.map +1 -1
package/dist/htscodecs/rans4x16.d.ts +1 -1
package/dist/htscodecs/rans4x16.js +151 -111
package/dist/htscodecs/rans4x16.js.map +1 -1
package/dist/htscodecs/tok3.d.ts +1 -2
package/dist/htscodecs/tok3.js +82 -239
package/dist/htscodecs/tok3.js.map +1 -1
package/dist/util.d.ts +1 -0
package/dist/util.js +20 -0
package/dist/util.js.map +1 -0
package/esm/cramFile/codecs/_base.d.ts +1 -1
package/esm/cramFile/codecs/byteArrayLength.js +3 -2
package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
package/esm/cramFile/codecs/external.d.ts +1 -1
package/esm/cramFile/codecs/external.js +2 -5
package/esm/cramFile/codecs/external.js.map +1 -1
package/esm/cramFile/container/index.d.ts +16 -34
package/esm/cramFile/container/index.js +5 -20
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +8 -6
package/esm/cramFile/file.js +40 -75
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.js +3 -2
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.d.ts +2 -2
package/esm/cramFile/slice/decodeRecord.js +10 -7
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.js +14 -16
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.d.ts +5 -2
package/esm/cramFile/util.js +74 -77
package/esm/cramFile/util.js.map +1 -1
package/esm/htscodecs/arith_gen.d.ts +5 -7
package/esm/htscodecs/arith_gen.js +108 -97
package/esm/htscodecs/arith_gen.js.map +1 -1
package/esm/htscodecs/arith_sh.d.ts +1 -8
package/esm/htscodecs/arith_sh.js +14 -11
package/esm/htscodecs/arith_sh.js.map +1 -1
package/esm/htscodecs/byte_model.d.ts +1 -6
package/esm/htscodecs/byte_model.js +23 -18
package/esm/htscodecs/byte_model.js.map +1 -1
package/esm/htscodecs/fqzcomp.d.ts +1 -1
package/esm/htscodecs/fqzcomp.js +91 -76
package/esm/htscodecs/fqzcomp.js.map +1 -1
package/esm/htscodecs/index.d.ts +5 -5
package/esm/htscodecs/index.js +14 -20
package/esm/htscodecs/index.js.map +1 -1
package/esm/htscodecs/iostream.d.ts +9 -20
package/esm/htscodecs/iostream.js +19 -117
package/esm/htscodecs/iostream.js.map +1 -1
package/esm/htscodecs/rans.d.ts +1 -1
package/esm/htscodecs/rans.js +61 -56
package/esm/htscodecs/rans.js.map +1 -1
package/esm/htscodecs/rans4x16.d.ts +1 -1
package/esm/htscodecs/rans4x16.js +143 -109
package/esm/htscodecs/rans4x16.js.map +1 -1
package/esm/htscodecs/tok3.d.ts +1 -2
package/esm/htscodecs/tok3.js +41 -237
package/esm/htscodecs/tok3.js.map +1 -1
package/esm/util.d.ts +1 -0
package/esm/util.js +17 -0
package/esm/util.js.map +1 -0
package/package.json +3 -6
package/src/cramFile/codecs/_base.ts +1 -1
package/src/cramFile/codecs/byteArrayLength.ts +4 -12
package/src/cramFile/codecs/external.ts +3 -7
package/src/cramFile/container/index.ts +5 -24
package/src/cramFile/file.ts +44 -79
package/src/cramFile/record.ts +1 -1
package/src/cramFile/sectionParsers.ts +5 -2
package/src/cramFile/slice/decodeRecord.ts +29 -28
package/src/cramFile/slice/index.ts +25 -31
package/src/cramFile/util.ts +107 -106
package/src/htscodecs/{arith_gen.js → arith_gen.ts} +133 -95
package/src/htscodecs/{arith_sh.js → arith_sh.ts} +17 -9
package/src/htscodecs/{byte_model.js → byte_model.ts} +26 -16
package/src/htscodecs/{fqzcomp.js → fqzcomp.ts} +108 -74
package/src/htscodecs/{index.js → index.ts} +14 -20
package/src/htscodecs/iostream.ts +159 -0
package/src/htscodecs/{rans.js → rans.ts} +73 -56
package/src/htscodecs/{rans4x16.js → rans4x16.ts} +180 -111
package/src/htscodecs/tok3.ts +197 -0
package/src/util.ts +16 -0
package/errors.js +0 -27
package/src/htscodecs/iostream.js +0 -257
package/src/htscodecs/tok3.js +0 -413

package/dist/cramFile/record.js.map CHANGED Viewed

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package/dist/cramFile/sectionParsers.js CHANGED Viewed

@@ -563,8 +563,9 @@ 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] = (0, util_1.parseItf8)(buffer, offset);
             offset += newOffset1;
             const [refSeqStart, newOffset2] = (0, util_1.parseItf8)(buffer, offset);

package/dist/cramFile/sectionParsers.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/cramFile/slice/decodeRecord.d.ts CHANGED Viewed

@@ -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/dist/cramFile/slice/decodeRecord.js CHANGED Viewed

@@ -118,15 +118,15 @@ 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]
@@ -180,9 +180,8 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
 }
 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 (!(0, sectionParsers_1.isMappedSliceHeader)(sliceHeader.parsedContent)) {
         throw new Error('slice header not mapped');
@@ -258,7 +257,11 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
             .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;

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

	@@ -1 +1 @@
1	- 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package/dist/cramFile/slice/index.js CHANGED Viewed

@@ -139,13 +139,7 @@ class CramSlice {
         const { majorVersion } = await this.file.getDefinition();
         const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
         const containerHeader = await this.container.getHeader();
-        if (!containerHeader) {
-            throw new Error('no container header detected');
-        }
         const header = await this.file.readBlock(containerHeader._endPosition + this.containerPosition);
-        if (header === undefined) {
-            throw new Error('block header undefined');
-        }
         if (header.contentType === 'MAPPED_SLICE_HEADER') {
             const content = (0, util_1.parseItem)(header.content, sectionParsers.cramMappedSliceHeader.parser, 0, containerHeader._endPosition);
             return { ...header, parsedContent: content };
@@ -166,9 +160,6 @@ class CramSlice {
         const blocks = new Array(header.parsedContent.numBlocks);
         for (let i = 0; i < blocks.length; i++) {
             const block = await this.file.readBlock(blockPosition);
-            if (block === undefined) {
-                throw new Error('block undefined');
-            }
             blocks[i] = block;
             blockPosition = blocks[i]._endPosition;
         }
@@ -300,9 +291,7 @@ class CramSlice {
             if (!codec) {
                 throw new errors_1.CramMalformedError(`no codec defined for ${dataSeriesName} data series`);
             }
-            // console.log(dataSeriesName, Object.getPrototypeOf(codec))
-            const decoded = codec.decode(this, coreDataBlock, blocksByContentId, cursors);
-            return decoded;
+            return codec.decode(this, coreDataBlock, blocksByContentId, cursors);
         };
         const records = new Array(sliceHeader.parsedContent.numRecords);
         for (let i = 0; i < records.length; i += 1) {
@@ -327,11 +316,20 @@ class CramSlice {
             }
         }
         // interpret `recordsToNextFragment` attributes to make standard `mate`
-        // objects Resolve mate pair cross-references between records in this slice
+        // 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 !== undefined && mateRecordNumber >= 0) {
-                associateIntraSliceMate(records, i, records[i], records[mateRecordNumber]);
+            const r = records[i];
+            // check for !!r added after removal  of "stat" file size check: found
+            // some undefined entries
+            if (r) {
+                const { mateRecordNumber } = r;
+                if (mateRecordNumber !== undefined &&
+                    mateRecordNumber >= 0 &&
+                    records[mateRecordNumber]) {
+                    associateIntraSliceMate(records, i, r, records[mateRecordNumber]);
+                }
             }
         }
         return records;

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

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

@@ -1,3 +1,8 @@
+export declare const TWO_PWR_16_DBL: number;
+export declare const TWO_PWR_32_DBL: number;
+export declare const TWO_PWR_64_DBL: number;
+export declare const TWO_PWR_24_DBL: number;
+export declare const TWO_PWR_56_DBL: number;
 export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
 export declare function parseItf8(buffer: Uint8Array, initialOffset: number): readonly [number, number];
 export declare function parseLtf8(buffer: Uint8Array, initialOffset: number): readonly [number, number];
@@ -10,5 +15,3 @@ export declare function parseItem<T>(buffer: Uint8Array, parser: (buffer: Uint8A
 };
 export declare function tinyMemoize(_class: any, methodName: any): void;
 export declare function sequenceMD5(seq: string): string;
-export declare function sum(array: Uint8Array[]): number;
-export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;