@gmod/cram 8.0.3 → 8.0.5

package/dist/cramFile/slice/decodeRecord.js

@@ -4,72 +4,56 @@ exports.default = decodeRecord;
 const errors_ts_1 = require("../../errors.js");
 const record_ts_1 = require("../record.js");
 const sectionParsers_ts_1 = require("../sectionParsers.js");
-// Reusable TextDecoder instance for string decoding (ASCII/Latin1)
-const textDecoder = new TextDecoder('latin1');
-/**
- * given a Buffer, read a string up to the first null character
- * @private
- */
-function readNullTerminatedString(buffer) {
-    // Find the null terminator
-    let end = 0;
-    while (end < buffer.length && buffer[end] !== 0) {
-        end++;
-    }
-    // Decode using TextDecoder (faster than char-by-char concatenation)
-    return textDecoder.decode(buffer.subarray(0, end));
-}
+const util_ts_1 = require("../util.js");
 /**
  * parse a BAM tag's array value from a binary buffer
  * @private
  */
+// Uses DataView instead of typed arrays (e.g. new Int32Array(buffer.buffer))
+// because the buffer may be a subarray of a larger ArrayBuffer. Typed array
+// constructors like Int32Array interpret .buffer as the entire underlying
+// ArrayBuffer starting at byte 0, ignoring the subarray's byteOffset. This
+// caused silent data corruption when reading tag values. DataView with explicit
+// byteOffset reads from the correct position within the parent buffer.
 function parseTagValueArray(buffer) {
     const arrayType = String.fromCharCode(buffer[0]);
-    const dataView = new DataView(buffer.buffer);
-    const littleEndian = true;
-    const length = dataView.getUint32(1, littleEndian);
+    const dv = new DataView(buffer.buffer, buffer.byteOffset, buffer.byteLength);
+    const length = dv.getUint32(1, true);
     const array = new Array(length);
-    buffer = buffer.slice(5);
+    const dataOffset = 5;
     if (arrayType === 'c') {
-        const arr = new Int8Array(buffer.buffer);
         for (let i = 0; i < length; i++) {
-            array[i] = arr[i];
+            array[i] = dv.getInt8(dataOffset + i);
         }
     }
     else if (arrayType === 'C') {
-        const arr = new Uint8Array(buffer.buffer);
         for (let i = 0; i < length; i++) {
-            array[i] = arr[i];
+            array[i] = dv.getUint8(dataOffset + i);
         }
     }
     else if (arrayType === 's') {
-        const arr = new Int16Array(buffer.buffer);
         for (let i = 0; i < length; i++) {
-            array[i] = arr[i];
+            array[i] = dv.getInt16(dataOffset + i * 2, true);
         }
     }
     else if (arrayType === 'S') {
-        const arr = new Uint16Array(buffer.buffer);
         for (let i = 0; i < length; i++) {
-            array[i] = arr[i];
+            array[i] = dv.getUint16(dataOffset + i * 2, true);
         }
     }
     else if (arrayType === 'i') {
-        const arr = new Int32Array(buffer.buffer);
         for (let i = 0; i < length; i++) {
-            array[i] = arr[i];
+            array[i] = dv.getInt32(dataOffset + i * 4, true);
         }
     }
     else if (arrayType === 'I') {
-        const arr = new Uint32Array(buffer.buffer);
         for (let i = 0; i < length; i++) {
-            array[i] = arr[i];
+            array[i] = dv.getUint32(dataOffset + i * 4, true);
         }
     }
     else if (arrayType === 'f') {
-        const arr = new Float32Array(buffer.buffer);
         for (let i = 0; i < length; i++) {
-            array[i] = arr[i];
+            array[i] = dv.getFloat32(dataOffset + i * 4, true);
         }
     }
     else {
@@ -79,55 +63,59 @@ function parseTagValueArray(buffer) {
 }
 function parseTagData(tagType, buffer) {
     if (tagType === 'Z') {
-        return readNullTerminatedString(buffer);
+        return (0, util_ts_1.readNullTerminatedStringFromBuffer)(buffer);
     }
     if (tagType === 'A') {
         return String.fromCharCode(buffer[0]);
     }
+    const dv = new DataView(buffer.buffer, buffer.byteOffset, buffer.byteLength);
     if (tagType === 'I') {
-        return new Uint32Array(buffer.buffer)[0];
+        return dv.getUint32(0, true);
     }
     if (tagType === 'i') {
-        return new Int32Array(buffer.buffer)[0];
+        return dv.getInt32(0, true);
     }
     if (tagType === 's') {
-        return new Int16Array(buffer.buffer)[0];
+        return dv.getInt16(0, true);
     }
     if (tagType === 'S') {
-        return new Uint16Array(buffer.buffer)[0];
+        return dv.getUint16(0, true);
     }
     if (tagType === 'c') {
-        return new Int8Array(buffer.buffer)[0];
+        return dv.getInt8(0);
     }
     if (tagType === 'C') {
         return buffer[0];
     }
     if (tagType === 'f') {
-        return new Float32Array(buffer.buffer)[0];
+        return dv.getFloat32(0, true);
     }
     if (tagType === 'H') {
-        return Number.parseInt(readNullTerminatedString(buffer).replace(/^0x/, ''), 16);
+        return Number.parseInt((0, util_ts_1.readNullTerminatedStringFromBuffer)(buffer).replace(/^0x/, ''), 16);
     }
     if (tagType === 'B') {
         return parseTagValueArray(buffer);
     }
     throw new errors_ts_1.CramMalformedError(`Unrecognized tag type ${tagType}`);
 }
-// Pre-defined schema lookup tables (version-independent entries)
+// Read feature schema lookup tables. Each entry maps a feature code to
+// [dataType, dataSeriesName] where dataType controls how the raw codec
+// output is converted (character→fromCharCode, string→TextDecoder,
+// numArray→Array.from, number→as-is).
 const data1SchemaBase = {
-    B: ['character', 'BA'],
-    X: ['number', 'BS'],
-    D: ['number', 'DL'],
-    I: ['string', 'IN'],
-    i: ['character', 'BA'],
-    b: ['string', 'BB'],
-    q: ['numArray', 'QQ'],
-    Q: ['number', 'QS'],
-    H: ['number', 'HC'],
-    P: ['number', 'PD'],
-    N: ['number', 'RS'],
+    B: ['character', 'BA'], // base substitution (base component)
+    X: ['number', 'BS'], // base substitution matrix index
+    D: ['number', 'DL'], // deletion length
+    I: ['string', 'IN'], // insertion bases
+    i: ['character', 'BA'], // single-base insertion
+    b: ['string', 'BB'], // stretch of bases
+    q: ['numArray', 'QQ'], // stretch of quality scores
+    Q: ['number', 'QS'], // single quality score
+    H: ['number', 'HC'], // hard clip length
+    P: ['number', 'PD'], // padding length
+    N: ['number', 'RS'], // reference skip length
 };
-// Version-specific S entry
+// Soft clip data series changed between CRAM v1 (IN) and v2+ (SC)
 const data1SchemaV1 = {
     ...data1SchemaBase,
     S: ['string', 'IN'],
@@ -136,11 +124,11 @@ const data1SchemaV2Plus = {
     ...data1SchemaBase,
     S: ['string', 'SC'],
 };
-// Second data item schema for read features that have two values
+// Features with a second data item (B has both a base and a quality score)
 const data2Schema = {
     B: ['number', 'QS'],
 };
-function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, _compressionScheme, majorVersion) {
+function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, majorVersion) {
     let currentReadPos = 0;
     let currentRefPos = alignmentStart - 1;
     const readFeatures = new Array(readFeatureCount);
@@ -152,7 +140,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
             return String.fromCharCode(data);
         }
         else if (type === 'string') {
-            return textDecoder.decode(data);
+            return (0, util_ts_1.decodeLatin1)(data);
         }
         else if (type === 'numArray') {
             return Array.from(data);
@@ -167,7 +155,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
             throw new errors_ts_1.CramMalformedError(`invalid read feature code "${code}"`);
         }
         let data = decodeRFData(schema);
-        // if this is a read feature with two data items, make the data an array
+        // if this is a read feature with two data items, make the data a tuple
         const schema2 = data2Schema[code];
         if (schema2) {
             data = [data, decodeRFData(schema2)];
@@ -190,7 +178,7 @@ function decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries,
     }
     return readFeatures;
 }
-function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber, decodeOptions, decodeBulkBytesRaw) {
+function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber, uniqueId, decodeOptions, decodeBulkBytesRaw) {
     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.
@@ -209,9 +197,9 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     }
     cursors.lastAlignmentStart = alignmentStart;
     const readGroupId = decodeDataSeries('RG');
-    let readName;
+    let readNameRaw;
     if (compressionScheme.readNamesIncluded) {
-        readName = readNullTerminatedString(decodeDataSeries('RN'));
+        readNameRaw = decodeDataSeries('RN');
     }
     let mateToUse;
     let templateSize;
@@ -223,8 +211,8 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         const mateFlags = decodeDataSeries('MF');
         let mateReadName;
         if (!compressionScheme.readNamesIncluded) {
-            mateReadName = readNullTerminatedString(decodeDataSeries('RN'));
-            readName = mateReadName;
+            readNameRaw = decodeDataSeries('RN');
+            mateReadName = (0, util_ts_1.readNullTerminatedStringFromBuffer)(readNameRaw);
         }
         const mateSequenceId = decodeDataSeries('NS');
         const mateAlignmentStart = decodeDataSeries('NP');
@@ -245,7 +233,6 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         if (record_ts_1.MateFlagsDecoder.isOnNegativeStrand(mateFlags)) {
             flags = record_ts_1.BamFlagsDecoder.setMateReverseComplemented(flags);
         }
-        // detachedCount++
     }
     else if (record_ts_1.CramFlagsDecoder.isWithMateDownstream(cramFlags)) {
         mateRecordNumber = decodeDataSeries('NF') + recordNumber + 1;
@@ -262,15 +249,12 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     const TN = compressionScheme.getTagNames(TLindex);
     const ntags = TN.length;
     const shouldDecodeTags = decodeOptions?.decodeTags !== false;
-    for (let i = 0; i < ntags; i++) {
-        const tagId = TN[i];
-        // Always decode to advance cursor position
-        const tagData = compressionScheme
-            .getCodecForTag(tagId)
-            .decode(slice, coreDataBlock, blocksByContentId, cursors);
-        // Only parse tags if requested (default: true)
-        if (shouldDecodeTags) {
-            // Use direct character access instead of slice() to avoid string allocation
+    if (shouldDecodeTags) {
+        for (let i = 0; i < ntags; i++) {
+            const tagId = TN[i];
+            const tagData = compressionScheme
+                .getCodecForTag(tagId)
+                .decode(slice, coreDataBlock, blocksByContentId, cursors);
             const tagName = tagId[0] + tagId[1];
             const tagType = tagId[2];
             tags[tagName] =
@@ -290,7 +274,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         // reading read features
         const readFeatureCount = decodeDataSeries('FN');
         if (readFeatureCount) {
-            readFeatures = decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
+            readFeatures = decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, majorVersion);
         }
         // compute the read's true span on the reference sequence, and the end
         // coordinate of the alignment on the reference
@@ -309,7 +293,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
             }
         }
         if (Number.isNaN(lengthOnRef)) {
-            console.warn(`${readName || `${sequenceId}:${alignmentStart}`} record has invalid read features`);
+            console.warn(`${sequenceId}:${alignmentStart} record has invalid read features`);
             lengthOnRef = readLength;
         }
         // mapping quality
@@ -337,7 +321,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         // Try raw bytes first for TextDecoder (most efficient)
         const rawBA = decodeBulkBytesRaw?.('BA', readLength);
         if (rawBA) {
-            readBases = textDecoder.decode(rawBA);
+            readBases = (0, util_ts_1.decodeLatin1)(rawBA);
         }
         else {
             // Fallback to single-byte decoding
@@ -369,7 +353,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         flags,
         alignmentStart,
         readGroupId,
-        readName,
+        readNameRaw,
         mateToUse,
         templateSize,
         mateRecordNumber,
@@ -379,6 +363,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         qualityScores,
         readBases,
         tags,
+        uniqueId,
     };
 }
 //# sourceMappingURL=decodeRecord.js.map

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

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package/dist/cramFile/slice/index.js

@@ -37,10 +37,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const errors_ts_1 = require("../../errors.js");
-const getBits_ts_1 = require("../codecs/getBits.js");
 const constants_ts_1 = __importDefault(require("../constants.js"));
 const decodeRecord_ts_1 = __importDefault(require("./decodeRecord.js"));
-const external_ts_1 = __importDefault(require("../codecs/external.js"));
 const record_ts_1 = __importStar(require("../record.js"));
 const sectionParsers_ts_1 = require("../sectionParsers.js");
 const util_ts_1 = require("../util.js");
@@ -64,13 +62,18 @@ function calculateMultiSegmentMatedTemplateLength(allRecords, _currentRecordNumb
     const matedRecords = getAllMatedRecords(thisRecord);
     const starts = matedRecords.map(r => r.alignmentStart);
     const ends = matedRecords.map(r => r.alignmentStart + r.readLength - 1);
-    const estimatedTemplateLength = Math.max(...ends) - Math.min(...starts) + 1;
+    const minStart = Math.min(...starts);
+    const estimatedTemplateLength = Math.max(...ends) - minStart + 1;
     if (estimatedTemplateLength >= 0) {
         matedRecords.forEach(r => {
             if (r.templateLength !== undefined) {
                 throw new errors_ts_1.CramMalformedError('mate pair group has some members that have template lengths already, this file seems malformed');
             }
-            r.templateLength = estimatedTemplateLength;
+            // sign per SAM spec: positive for leftmost, negative for rightmost
+            r.templateLength =
+                r.alignmentStart === minStart
+                    ? estimatedTemplateLength
+                    : -estimatedTemplateLength;
         });
     }
 }
@@ -85,8 +88,15 @@ function calculateIntraSliceMatePairTemplateLength(thisRecord, mateRecord) {
     const start = Math.min(thisRecord.alignmentStart, mateRecord.alignmentStart);
     const end = Math.max(thisRecord.alignmentStart + thisRecord.readLength - 1, mateRecord.alignmentStart + mateRecord.readLength - 1);
     const lengthEstimate = end - start + 1;
-    thisRecord.templateLength = lengthEstimate;
-    mateRecord.templateLength = lengthEstimate;
+    // sign per SAM spec: positive for leftmost, negative for rightmost
+    thisRecord.templateLength =
+        thisRecord.alignmentStart <= mateRecord.alignmentStart
+            ? lengthEstimate
+            : -lengthEstimate;
+    mateRecord.templateLength =
+        mateRecord.alignmentStart <= thisRecord.alignmentStart
+            ? lengthEstimate
+            : -lengthEstimate;
 }
 /**
  * establishes a mate-pair relationship between two records in the same slice.
@@ -97,10 +107,12 @@ function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, ma
     const complicatedMultiSegment = !!(mateRecord.mate ||
         (mateRecord.mateRecordNumber !== undefined &&
             mateRecord.mateRecordNumber !== currentRecordNumber));
-    // Deal with lossy read names
+    // Deal with lossy read names — assign a synthetic name from uniqueId
+    // so that paired records share the same name
     if (!thisRecord.readName) {
-        thisRecord.readName = String(thisRecord.uniqueId);
-        mateRecord.readName = thisRecord.readName;
+        const syntheticName = String(thisRecord.uniqueId);
+        thisRecord._syntheticReadName = syntheticName;
+        mateRecord._syntheticReadName = syntheticName;
     }
     thisRecord.mate = {
         sequenceId: mateRecord.sequenceId,
@@ -345,42 +357,32 @@ class CramSlice {
             }
             return codec.decode(this, coreDataBlock, blocksByContentId, cursors);
         };
-        // Create bulk byte decoder for QS and BA data series if they use External codec
+        // Bulk byte decoder for QS and BA — getBytesSubarray returns a subarray
+        // view when the codec supports it (e.g. ExternalCodec), or undefined otherwise
         const qsCodec = compressionScheme.getCodecForDataSeries('QS');
         const baCodec = compressionScheme.getCodecForDataSeries('BA');
-        const qsIsExternal = qsCodec instanceof external_ts_1.default;
-        const baIsExternal = baCodec instanceof external_ts_1.default;
-        // Create raw byte decoder for QS/BA decoding
-        const decodeBulkBytesRaw = qsIsExternal || baIsExternal
+        const decodeBulkBytesRaw = qsCodec || baCodec
             ? (dataSeriesName, length) => {
-                if (dataSeriesName === 'QS' && qsIsExternal) {
-                    return qsCodec.getBytesSubarray(blocksByContentId, cursors, length);
-                }
-                if (dataSeriesName === 'BA' && baIsExternal) {
-                    return baCodec.getBytesSubarray(blocksByContentId, cursors, length);
-                }
-                return undefined;
+                const codec = dataSeriesName === 'QS' ? qsCodec : baCodec;
+                return codec?.getBytesSubarray(blocksByContentId, cursors, length);
             }
             : undefined;
         const records = new Array(sliceHeader.parsedContent.numRecords);
         for (let i = 0; i < records.length; i += 1) {
             try {
-                const init = (0, decodeRecord_ts_1.default)(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i, decodeOptions, decodeBulkBytesRaw);
-                records[i] = new record_ts_1.default({
-                    ...init,
-                    uniqueId: sliceHeader.contentPosition +
-                        sliceHeader.parsedContent.recordCounter +
-                        i +
-                        1,
-                });
+                records[i] = new record_ts_1.default((0, decodeRecord_ts_1.default)(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i, sliceHeader.contentPosition +
+                    sliceHeader.parsedContent.recordCounter +
+                    i +
+                    1, decodeOptions, decodeBulkBytesRaw));
             }
             catch (e) {
-                if (e instanceof getBits_ts_1.CramBufferOverrunError) {
+                const err = e;
+                if (err.code === 'CRAM_BUFFER_OVERRUN') {
                     const recordsDecoded = i;
                     const recordsExpected = sliceHeader.parsedContent.numRecords;
                     throw new errors_ts_1.CramMalformedError(`Failed to decode all records in slice. Decoded ${recordsDecoded} of ${recordsExpected} expected records. ` +
                         `Buffer overrun suggests either: (1) file is truncated/corrupted, (2) compression scheme is incorrect, ` +
-                        `or (3) there's a bug in the decoder. Original error: ${e.message}`);
+                        `or (3) there's a bug in the decoder. Original error: ${err.message}`);
                 }
                 else {
                     throw e;

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

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

@@ -1,3 +1,5 @@
+export declare function readNullTerminatedStringFromBuffer(buffer: Uint8Array): string;
+export declare function decodeLatin1(buffer: Uint8Array): string;
 export declare const TWO_PWR_16_DBL: number;
 export declare const TWO_PWR_32_DBL: number;
 export declare const TWO_PWR_64_DBL: number;

package/dist/cramFile/util.js

@@ -4,6 +4,8 @@ var __importDefault = (this && this.__importDefault) || function (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.readNullTerminatedStringFromBuffer = readNullTerminatedStringFromBuffer;
+exports.decodeLatin1 = decodeLatin1;
 exports.itf8Size = itf8Size;
 exports.parseItf8 = parseItf8;
 exports.parseLtf8 = parseLtf8;
@@ -11,6 +13,17 @@ exports.parseItem = parseItem;
 exports.tinyMemoize = tinyMemoize;
 exports.sequenceMD5 = sequenceMD5;
 const md5_1 = __importDefault(require("md5"));
+const textDecoder = new TextDecoder('latin1');
+function readNullTerminatedStringFromBuffer(buffer) {
+    let end = 0;
+    while (end < buffer.length && buffer[end] !== 0) {
+        end++;
+    }
+    return textDecoder.decode(buffer.subarray(0, end));
+}
+function decodeLatin1(buffer) {
+    return textDecoder.decode(buffer);
+}
 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;

package/dist/cramFile/util.js.map

@@ -1 +1 @@
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