npm - @gmod/cram - Versions diffs - 4.0.4 → 4.0.6 - Mend

@gmod/cram 4.0.4 → 4.0.6

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 (60) 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 +37 -73
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 +7 -4
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 -0
package/dist/cramFile/util.js +75 -51
package/dist/cramFile/util.js.map +1 -1
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 +37 -73
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 +7 -4
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 -0
package/esm/cramFile/util.js +74 -51
package/esm/cramFile/util.js.map +1 -1
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 +41 -77
package/src/cramFile/record.ts +1 -1
package/src/cramFile/sectionParsers.ts +5 -2
package/src/cramFile/slice/decodeRecord.ts +26 -23
package/src/cramFile/slice/index.ts +25 -31
package/src/cramFile/util.ts +107 -73
package/errors.js +0 -27

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

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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

@@ -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];

package/dist/cramFile/util.js CHANGED Viewed

@@ -3,15 +3,19 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+exports.TWO_PWR_56_DBL = exports.TWO_PWR_24_DBL = exports.TWO_PWR_64_DBL = exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL = void 0;
 exports.itf8Size = itf8Size;
 exports.parseItf8 = parseItf8;
 exports.parseLtf8 = parseLtf8;
 exports.parseItem = parseItem;
 exports.tinyMemoize = tinyMemoize;
 exports.sequenceMD5 = sequenceMD5;
-const longfn_1 = require("longfn");
 const md5_1 = __importDefault(require("md5"));
-const getBits_1 = require("./codecs/getBits");
+exports.TWO_PWR_16_DBL = 1 << 16;
+exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL * exports.TWO_PWR_16_DBL;
+exports.TWO_PWR_64_DBL = exports.TWO_PWR_32_DBL * exports.TWO_PWR_32_DBL;
+exports.TWO_PWR_24_DBL = 1 << 24;
+exports.TWO_PWR_56_DBL = exports.TWO_PWR_24_DBL * exports.TWO_PWR_32_DBL;
 function itf8Size(v) {
     if (!(v & ~0x7f)) {
         return 1;
@@ -31,29 +35,34 @@ function parseItf8(buffer, initialOffset) {
     let offset = initialOffset;
     const countFlags = buffer[offset];
     let result;
+    // Single byte value (0xxxxxxx)
     if (countFlags < 0x80) {
         result = countFlags;
-        offset = offset + 1;
+        offset += 1;
     }
+    // Two byte value (10xxxxxx)
     else if (countFlags < 0xc0) {
-        result = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff;
-        offset = offset + 2;
+        result = ((countFlags & 0x3f) << 8) | buffer[offset + 1];
+        offset += 2;
     }
+    // Three byte value (110xxxxx)
     else if (countFlags < 0xe0) {
         result =
-            ((countFlags << 16) | (buffer[offset + 1] << 8) | buffer[offset + 2]) &
-                0x1fffff;
-        offset = offset + 3;
+            ((countFlags & 0x1f) << 16) |
+                (buffer[offset + 1] << 8) |
+                buffer[offset + 2];
+        offset += 3;
     }
+    // Four byte value (1110xxxx)
     else if (countFlags < 0xf0) {
         result =
-            ((countFlags << 24) |
+            ((countFlags & 0x0f) << 24) |
                 (buffer[offset + 1] << 16) |
                 (buffer[offset + 2] << 8) |
-                buffer[offset + 3]) &
-                0x0fffffff;
-        offset = offset + 4;
+                buffer[offset + 3];
+        offset += 4;
     }
+    // Five byte value (11110xxx)
     else {
         result =
             ((countFlags & 0x0f) << 28) |
@@ -61,85 +70,104 @@ function parseItf8(buffer, initialOffset) {
                 (buffer[offset + 2] << 12) |
                 (buffer[offset + 3] << 4) |
                 (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 = offset + 5;
-    }
-    if (offset > buffer.length) {
-        throw new getBits_1.CramBufferOverrunError('Attempted to read beyond end of buffer; this file seems truncated.');
+        offset += 5;
     }
     return [result, offset - initialOffset];
 }
 function parseLtf8(buffer, initialOffset) {
-    const dataView = new DataView(buffer.buffer);
     let offset = initialOffset;
     const countFlags = buffer[offset];
-    let n;
+    let value;
+    // Single byte value < 0x80
     if (countFlags < 0x80) {
-        n = countFlags;
+        value = countFlags;
         offset += 1;
     }
+    // Two byte value < 0xC0
     else if (countFlags < 0xc0) {
-        n = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff;
+        value = ((countFlags << 8) | buffer[offset + 1]) & 0x3fff;
         offset += 2;
     }
+    // Three byte value < 0xE0
     else if (countFlags < 0xe0) {
-        n =
-            ((buffer[offset] << 16) |
+        value =
+            ((countFlags & 0x3f) << 16) |
                 (buffer[offset + 1] << 8) |
-                buffer[offset + 2]) &
-                0x1fffff;
-        n = ((countFlags & 63) << 16) | dataView.getUint16(offset + 1, true);
+                buffer[offset + 2];
         offset += 3;
     }
+    // Four byte value < 0xF0
     else if (countFlags < 0xf0) {
-        n =
-            ((buffer[offset] << 24) |
+        value =
+            ((countFlags & 0x1f) << 24) |
                 (buffer[offset + 1] << 16) |
                 (buffer[offset + 2] << 8) |
-                buffer[offset + 3]) &
-                0x0fffffff;
+                buffer[offset + 3];
         offset += 4;
     }
+    // Five byte value < 0xF8
     else if (countFlags < 0xf8) {
-        n =
-            ((buffer[offset] & 15) * 2 ** 32 + (buffer[offset + 1] << 24)) |
-                ((buffer[offset + 2] << 16) |
+        value =
+            (buffer[offset] & 0x0f) * exports.TWO_PWR_32_DBL +
+                ((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;
     }
+    // Six byte value < 0xFC
     else if (countFlags < 0xfc) {
-        n =
-            ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * 2 ** 32 +
-                (buffer[offset + 2] << 24)) |
-                ((buffer[offset + 3] << 16) |
+        value =
+            (((buffer[offset] & 0x07) << 8) | buffer[offset + 1]) * exports.TWO_PWR_32_DBL +
+                ((buffer[offset + 2] << 24) |
+                    (buffer[offset + 3] << 16) |
                     (buffer[offset + 4] << 8) |
                     buffer[offset + 5]);
         offset += 6;
     }
+    // Seven byte value < 0xFE
     else if (countFlags < 0xfe) {
-        n =
-            ((((buffer[offset] & 3) << 16) |
+        value =
+            (((buffer[offset] & 0x03) << 16) |
                 (buffer[offset + 1] << 8) |
                 buffer[offset + 2]) *
-                2 ** 32 +
-                (buffer[offset + 3] << 24)) |
-                ((buffer[offset + 4] << 16) |
+                exports.TWO_PWR_32_DBL +
+                ((buffer[offset + 3] << 24) |
+                    (buffer[offset + 4] << 16) |
                     (buffer[offset + 5] << 8) |
                     buffer[offset + 6]);
         offset += 7;
     }
+    // Eight byte value < 0xFF
     else if (countFlags < 0xff) {
-        n = (0, longfn_1.toNumber)((0, longfn_1.fromBytesBE)(buffer.slice(offset + 1, offset + 8), false));
+        value =
+            ((buffer[offset + 1] << 24) |
+                (buffer[offset + 2] << 16) |
+                (buffer[offset + 3] << 8) |
+                buffer[offset + 4]) *
+                exports.TWO_PWR_32_DBL +
+                ((buffer[offset + 5] << 24) |
+                    (buffer[offset + 6] << 16) |
+                    (buffer[offset + 7] << 8) |
+                    buffer[offset + 8]);
         offset += 8;
     }
+    // Nine byte value
     else {
-        n = (0, longfn_1.toNumber)((0, longfn_1.fromBytesBE)(buffer.subarray(offset + 1, offset + 9), false));
+        value =
+            buffer[offset + 1] * exports.TWO_PWR_56_DBL +
+                ((buffer[offset + 2] << 24) |
+                    (buffer[offset + 3] << 16) |
+                    (buffer[offset + 4] << 8) |
+                    buffer[offset + 5]) *
+                    exports.TWO_PWR_32_DBL +
+                ((buffer[offset + 6] << 24) |
+                    (buffer[offset + 7] << 16) |
+                    (buffer[offset + 8] << 8) |
+                    buffer[offset + 9]);
         offset += 9;
     }
-    return [n, offset - initialOffset];
+    return [value, offset - initialOffset];
 }
 function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition = 0) {
     const { offset, value } = parser(buffer, startBufferPosition);
@@ -149,10 +177,6 @@ function parseItem(buffer, parser, startBufferPosition = 0, 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. memoizes a method in the stupidest
-// possible way, with no regard for the arguments.  actually, this only works
-// on methods that take no arguments
 function tinyMemoize(_class, methodName) {
     const method = _class.prototype[methodName];
     const memoAttrName = `_memo_${methodName}`;

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

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

@@ -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/esm/cramFile/codecs/byteArrayLength.js CHANGED Viewed

@@ -7,11 +7,12 @@ export default class ByteArrayStopCodec extends CramCodec {
     }
     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;
     }