@gmod/cram 8.0.2 → 8.0.4

package/esm/cramFile/codecs/_base.d.ts

@@ -24,4 +24,5 @@ export default abstract class CramCodec<TResult extends DataType = DataType, TPa
     dataType: DataType;
     constructor(parameters: TParameters, dataType: TResult);
     abstract decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): DataTypeMapping[TResult] | undefined;
+    getBytesSubarray(_blocksByContentId: Record<number, CramFileBlock>, _cursors: Cursors, _length: number): Uint8Array | undefined;
 }

package/esm/cramFile/codecs/_base.js

@@ -4,5 +4,8 @@ export default class CramCodec {
         this.parameters = parameters;
         this.dataType = dataType;
     }
+    getBytesSubarray(_blocksByContentId, _cursors, _length) {
+        return undefined;
+    }
 }
 //# sourceMappingURL=_base.js.map

package/esm/cramFile/codecs/_base.js.map

@@ -1 +1 @@
-{"version":3,"file":"_base.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/_base.ts"],"names":[],"mappings":"AAyBA,mBAAmB;AACnB,MAAM,CAAC,OAAO,OAAgB,SAAS;IAOrC,YAAY,UAAuB,EAAE,QAAiB;QACpD,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;CAQF"}
+{"version":3,"file":"_base.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/_base.ts"],"names":[],"mappings":"AAyBA,mBAAmB;AACnB,MAAM,CAAC,OAAO,OAAgB,SAAS;IAOrC,YAAY,UAAuB,EAAE,QAAiB;QACpD,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;IASD,gBAAgB,CACd,kBAAiD,EACjD,QAAiB,EACjB,OAAe;QAEf,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}

package/esm/cramFile/codecs/byteArrayLength.d.ts

@@ -7,7 +7,7 @@ type CramCodecFactory = <TData extends DataType = DataType>(encodingData: CramEn
 export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayLengthEncoding['parameters']> {
     private instantiateCodec;
     constructor(parameters: ByteArrayLengthEncoding['parameters'], dataType: 'byteArray', instantiateCodec: CramCodecFactory);
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBuffer>;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Uint8Array<ArrayBufferLike>;
     _getLengthCodec(): CramCodec<"int", unknown>;
     _getDataCodec(): CramCodec<"byte", unknown>;
 }

package/esm/cramFile/codecs/byteArrayLength.js

@@ -8,17 +8,24 @@ export default class ByteArrayStopCodec extends CramCodec {
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         const lengthCodec = this._getLengthCodec();
         const arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) || 0;
-        const data = new Uint8Array(arrayLength);
         if (arrayLength > 0) {
             const dataCodec = this._getDataCodec();
-            // Call decode directly on codec to avoid repeated lookups
-            for (let i = 0; i < arrayLength; i += 1) {
-                data[i] =
-                    dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) ||
-                        0;
+            const subarray = dataCodec.getBytesSubarray(blocksByContentId, cursors, arrayLength);
+            if (subarray) {
+                return subarray;
             }
+            else {
+                const data = new Uint8Array(arrayLength);
+                for (let i = 0; i < arrayLength; i += 1) {
+                    data[i] =
+                        dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) || 0;
+                }
+                return data;
+            }
+        }
+        else {
+            return new Uint8Array(0);
         }
-        return data;
     }
     // memoize
     _getLengthCodec() {

package/esm/cramFile/codecs/byteArrayLength.js.map

@@ -1 +1 @@
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+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,YAAY,CAAA;AAK/C,OAAO,EAAE,WAAW,EAAE,MAAM,YAAY,CAAA;AAOxC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;IAC1C,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO,CAAC,IAAI,CAAC,CAAA;QAE3E,IAAI,WAAW,GAAG,CAAC,EAAE,CAAC;YACpB,MAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;YACtC,MAAM,QAAQ,GAAG,SAAS,CAAC,gBAAgB,CACzC,iBAAiB,EACjB,OAAO,EACP,WAAW,CACZ,CAAA;YACD,IAAI,QAAQ,EAAE,CAAC;gBACb,OAAO,QAAQ,CAAA;YACjB,CAAC;iBAAM,CAAC;gBACN,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;gBACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;oBACxC,IAAI,CAAC,CAAC,CAAC;wBACL,SAAS,CAAC,MAAM,CACd,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,IAAI,CAAC,CAAA;gBACV,CAAC;gBACD,OAAO,IAAI,CAAA;YACb,CAAC;QACH,CAAC;aAAM,CAAC;YACN,OAAO,IAAI,UAAU,CAAC,CAAC,CAAC,CAAA;QAC1B,CAAC;IACH,CAAC;IAED,UAAU;IACV,eAAe;QACb,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,aAAa;QACX,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QACrD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AAED,+BAA+B,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IAC1D,WAAW,CAAC,kBAAkB,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC,CAAC,CAAA"}

package/esm/cramFile/codecs/external.d.ts

@@ -1,7 +1,7 @@
 import CramCodec, { Cursors } from './_base.ts';
+import { ExternalCramEncoding } from '../encoding.ts';
 import { CramFileBlock } from '../file.ts';
 import CramSlice from '../slice/index.ts';
-import { ExternalCramEncoding } from '../encoding.ts';
 export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
     constructor(parameters: ExternalCramEncoding['parameters'], dataType: 'int' | 'byte');
     decode(_slice: CramSlice, _coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number | undefined;

package/esm/cramFile/codecs/external.js

@@ -1,7 +1,37 @@
 import CramCodec from "./_base.js";
 import { CramUnimplementedError } from "../../errors.js";
-import { parseItf8 } from "../util.js";
 import { CramBufferOverrunError } from "./getBits.js";
+function parseItf8Inline(buffer, cursor) {
+    const offset = cursor.bytePosition;
+    const countFlags = buffer[offset];
+    if (countFlags < 0x80) {
+        cursor.bytePosition = offset + 1;
+        return countFlags;
+    }
+    if (countFlags < 0xc0) {
+        cursor.bytePosition = offset + 2;
+        return ((countFlags & 0x3f) << 8) | buffer[offset + 1];
+    }
+    if (countFlags < 0xe0) {
+        cursor.bytePosition = offset + 3;
+        return (((countFlags & 0x1f) << 16) |
+            (buffer[offset + 1] << 8) |
+            buffer[offset + 2]);
+    }
+    if (countFlags < 0xf0) {
+        cursor.bytePosition = offset + 4;
+        return (((countFlags & 0x0f) << 24) |
+            (buffer[offset + 1] << 16) |
+            (buffer[offset + 2] << 8) |
+            buffer[offset + 3]);
+    }
+    cursor.bytePosition = offset + 5;
+    return (((countFlags & 0x0f) << 28) |
+        (buffer[offset + 1] << 20) |
+        (buffer[offset + 2] << 12) |
+        (buffer[offset + 3] << 4) |
+        (buffer[offset + 4] & 0x0f));
+}
 export default class ExternalCodec extends CramCodec {
     constructor(parameters, dataType) {
         super(parameters, dataType);
@@ -17,9 +47,7 @@ export default class ExternalCodec extends CramCodec {
         }
         const cursor = cursors.externalBlocks.getCursor(blockContentId);
         if (this.dataType === 'int') {
-            const [result, bytesRead] = parseItf8(contentBlock.content, cursor.bytePosition);
-            cursor.bytePosition += bytesRead;
-            return result;
+            return parseItf8Inline(contentBlock.content, cursor);
         }
         else {
             if (cursor.bytePosition >= contentBlock.content.length) {

package/esm/cramFile/codecs/external.js.map

@@ -1 +1 @@
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+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,YAAY,CAAA;AAC/C,OAAO,EAAE,sBAAsB,EAAE,MAAM,iBAAiB,CAAA;AAGxD,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGrD,SAAS,eAAe,CAAC,MAAkB,EAAE,MAAgC;IAC3E,MAAM,MAAM,GAAG,MAAM,CAAC,YAAY,CAAA;IAClC,MAAM,UAAU,GAAG,MAAM,CAAC,MAAM,CAAE,CAAA;IAClC,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QACtB,MAAM,CAAC,YAAY,GAAG,MAAM,GAAG,CAAC,CAAA;QAChC,OAAO,UAAU,CAAA;IACnB,CAAC;IACD,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QACtB,MAAM,CAAC,YAAY,GAAG,MAAM,GAAG,CAAC,CAAA;QAChC,OAAO,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,CAAA;IACzD,CAAC;IACD,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QACtB,MAAM,CAAC,YAAY,GAAG,MAAM,GAAG,CAAC,CAAA;QAChC,OAAO,CACL,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;YAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;YAC1B,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,CACpB,CAAA;IACH,CAAC;IACD,IAAI,UAAU,GAAG,IAAI,EAAE,CAAC;QACtB,MAAM,CAAC,YAAY,GAAG,MAAM,GAAG,CAAC,CAAA;QAChC,OAAO,CACL,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;YAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;YAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;YAC1B,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,CACpB,CAAA;IACH,CAAC;IACD,MAAM,CAAC,YAAY,GAAG,MAAM,GAAG,CAAC,CAAA;IAChC,OAAO,CACL,CAAC,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC;QAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QAC3B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QAC1B,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,IAAI,CAAC,CAC7B,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;IACC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACxD,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,MAAiB,EACjB,cAA6B,EAC7B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAE/D,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,OAAO,eAAe,CAAC,YAAY,CAAC,OAAO,EAAE,MAAM,CAAC,CAAA;QACtD,CAAC;aAAM,CAAC;YACN,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;gBACvD,MAAM,IAAI,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;YACH,CAAC;YACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;QACrD,CAAC;IACH,CAAC;IAED,gBAAgB,CACd,iBAAgD,EAChD,OAAgB,EAChB,MAAc;QAEd,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,MAAM,KAAK,GAAG,MAAM,CAAC,YAAY,CAAA;QACjC,MAAM,GAAG,GAAG,KAAK,GAAG,MAAM,CAAA;QAE1B,IAAI,GAAG,GAAG,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACtC,MAAM,IAAI,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QAED,MAAM,CAAC,YAAY,GAAG,GAAG,CAAA;QACzB,OAAO,YAAY,CAAC,OAAO,CAAC,QAAQ,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;IAClD,CAAC;CACF"}

package/esm/cramFile/codecs/getBits.d.ts

@@ -1,4 +1,5 @@
 export declare class CramBufferOverrunError extends Error {
+    readonly code: "CRAM_BUFFER_OVERRUN";
 }
 export declare function getBits(data: Uint8Array, cursor: {
     bytePosition: number;

package/esm/cramFile/codecs/getBits.js

@@ -1,4 +1,8 @@
 export class CramBufferOverrunError extends Error {
+    constructor() {
+        super(...arguments);
+        this.code = 'CRAM_BUFFER_OVERRUN';
+    }
 }
 export function getBits(data, cursor, numBits) {
     if (cursor.bytePosition + (7 - cursor.bitPosition + numBits) / 8 >

package/esm/cramFile/codecs/getBits.js.map

@@ -1 +1 @@
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package/esm/cramFile/record.d.ts

@@ -5,14 +5,43 @@ export interface RefRegion {
     end: number;
     seq: string;
 }
-export interface ReadFeature {
-    code: string;
+interface ReadFeatureBase {
     pos: number;
     refPos: number;
-    data: any;
+}
+/**
+ * Read features describe differences between a read and the reference sequence.
+ * Each feature has a code indicating the type of difference, a position in the
+ * read (pos), and a position on the reference (refPos).
+ */
+export type ReadFeature = 
+/** I=insertion, S=soft clip, b=bases, i=single-base insertion — all carry a sequence string */
+(ReadFeatureBase & {
+    code: 'I' | 'S' | 'b' | 'i';
+    data: string;
+})
+/** B=base and quality pair — [substituted base, quality score] */
+ | (ReadFeatureBase & {
+    code: 'B';
+    data: [string, number];
+})
+/** X=base substitution — data is the substitution matrix index, ref/sub filled in by addReferenceSequence */
+ | (ReadFeatureBase & {
+    code: 'X';
+    data: number;
     ref?: string;
     sub?: string;
-}
+})
+/** D=deletion, N=reference skip, H=hard clip, P=padding, Q=single quality score */
+ | (ReadFeatureBase & {
+    code: 'D' | 'N' | 'H' | 'P' | 'Q';
+    data: number;
+})
+/** q=quality scores for a stretch of bases */
+ | (ReadFeatureBase & {
+    code: 'q';
+    data: number[];
+});
 export interface DecodeOptions {
     /** Whether to parse tags. If false, raw tag data is stored for lazy parsing. Default true. */
     decodeTags?: boolean;
@@ -41,7 +70,7 @@ export declare const MateFlagsDecoder: FlagsDecoder<"OnNegativeStrand" | "Unmapp
  * Class of each CRAM record returned by this API.
  */
 export default class CramRecord {
-    tags: Record<string, string>;
+    tags: Record<string, string | number | number[] | undefined>;
     flags: number;
     cramFlags: number;
     readBases?: string | null;
@@ -52,7 +81,9 @@ export default class CramRecord {
     readLength: number;
     templateLength?: number;
     templateSize?: number;
-    readName?: string;
+    private _readName?;
+    private _readNameRaw?;
+    _syntheticReadName?: string;
     mateRecordNumber?: number;
     mate?: MateRecord;
     uniqueId: number;
@@ -60,9 +91,8 @@ export default class CramRecord {
     readGroupId: number;
     mappingQuality: number | undefined;
     qualityScores: Uint8Array | null | undefined;
-    constructor({ flags, cramFlags, readLength, mappingQuality, lengthOnRef, qualityScores, mateRecordNumber, readBases, readFeatures, mateToUse, readGroupId, readName, sequenceId, uniqueId, templateSize, alignmentStart, tags, }: ReturnType<typeof decodeRecord> & {
-        uniqueId: number;
-    });
+    get readName(): string | undefined;
+    constructor({ flags, cramFlags, readLength, mappingQuality, lengthOnRef, qualityScores, mateRecordNumber, readBases, readFeatures, mateToUse, readGroupId, readNameRaw, sequenceId, uniqueId, templateSize, alignmentStart, tags, }: ReturnType<typeof decodeRecord>);
     /**
      * Get a single quality score at the given index.
      * @param index 0-based index into the quality scores

package/esm/cramFile/record.js

@@ -1,4 +1,15 @@
 import Constants from "./constants.js";
+import { readNullTerminatedStringFromBuffer } from "./util.js";
+// precomputed pair orientation strings indexed by ((flags >> 4) & 0xF) | (isize > 0 ? 16 : 0)
+// bits 0-3 encode flag bits 0x10(reverse),0x20(mate reverse),0x40(read1),0x80(read2)
+// bit 4 encodes whether isize > 0
+// prettier-ignore
+const PAIR_ORIENTATION_TABLE = [
+    'F F ', 'F R ', 'R F ', 'R R ', 'F2F1', 'F2R1', 'R2F1', 'R2R1',
+    'F1F2', 'F1R2', 'R1F2', 'R1R2', 'F2F1', 'F2R1', 'R2F1', 'R2R1',
+    'F F ', 'R F ', 'F R ', 'R R ', 'F1F2', 'R1F2', 'F1R2', 'R1R2',
+    'F2F1', 'R2F1', 'F2R1', 'R2R1', 'F1F2', 'R1F2', 'F1R2', 'R1R2',
+];
 export const defaultDecodeOptions = {
     decodeTags: true,
 };
@@ -30,48 +41,37 @@ function decodeReadSequence(cramRecord, refRegion) {
                 // process the read feature
                 currentReadFeature += 1;
                 if (feature.code === 'b') {
-                    // specify a base pair for some reason
                     const added = feature.data;
                     bases += added;
                     regionPos += added.length;
                 }
                 else if (feature.code === 'B') {
-                    // base pair and associated quality
-                    // TODO: do we need to set the quality in the qual scores?
                     bases += feature.data[0];
                     regionPos += 1;
                 }
                 else if (feature.code === 'X') {
-                    // base substitution
                     bases += feature.sub;
                     regionPos += 1;
                 }
                 else if (feature.code === 'I') {
-                    // insertion
                     bases += feature.data;
                 }
                 else if (feature.code === 'D') {
-                    // deletion
                     regionPos += feature.data;
                 }
                 else if (feature.code === 'i') {
-                    // insert single base
                     bases += feature.data;
                 }
                 else if (feature.code === 'N') {
-                    // reference skip. delete some bases
-                    // do nothing
-                    // seqBases.splice(feature.pos - 1, feature.data)
                     regionPos += feature.data;
                 }
                 else if (feature.code === 'S') {
-                    // soft clipped bases that should be present in the read seq
-                    // seqBases.splice(feature.pos - 1, 0, ...feature.data.split(''))
                     bases += feature.data;
                 }
                 else if (feature.code === 'P') {
                     // padding, do nothing
                 }
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                 else if (feature.code === 'H') {
                     // hard clip, do nothing
                 }
@@ -167,24 +167,37 @@ export const MateFlagsDecoder = makeFlagsHelper(MateFlags);
  * Class of each CRAM record returned by this API.
  */
 export default class CramRecord {
-    constructor({ flags, cramFlags, readLength, mappingQuality, lengthOnRef, qualityScores, mateRecordNumber, readBases, readFeatures, mateToUse, readGroupId, readName, sequenceId, uniqueId, templateSize, alignmentStart, tags, }) {
+    get readName() {
+        if (this._readName === undefined) {
+            if (this._readNameRaw) {
+                this._readName = readNullTerminatedStringFromBuffer(this._readNameRaw);
+                this._readNameRaw = undefined;
+            }
+            else {
+                return this._syntheticReadName;
+            }
+        }
+        return this._readName;
+    }
+    constructor({ flags, cramFlags, readLength, mappingQuality, lengthOnRef, qualityScores, mateRecordNumber, readBases, readFeatures, mateToUse, readGroupId, readNameRaw, sequenceId, uniqueId, templateSize, alignmentStart, tags, }) {
         this.flags = flags;
         this.cramFlags = cramFlags;
         this.readLength = readLength;
         this.mappingQuality = mappingQuality;
         this.lengthOnRef = lengthOnRef;
         this.qualityScores = qualityScores;
-        if (readBases) {
-            this.readBases = readBases;
-        }
         this.readGroupId = readGroupId;
-        this.readName = readName;
         this.sequenceId = sequenceId;
         this.uniqueId = uniqueId;
-        this.templateSize = templateSize;
         this.alignmentStart = alignmentStart;
         this.tags = tags;
-        // backwards compatibility
+        if (readNameRaw) {
+            this._readNameRaw = readNameRaw;
+        }
+        if (readBases) {
+            this.readBases = readBases;
+        }
+        this.templateSize = templateSize;
         if (readFeatures) {
             this.readFeatures = readFeatures;
         }
@@ -290,29 +303,15 @@ export default class CramRecord {
         return this.readBases;
     }
     // adapted from igv.js
-    // inlines flag checks and uses template literal instead of array+join
+    // uses precomputed lookup table indexed by flag bits + isize sign
     getPairOrientation() {
         const f = this.flags;
         // combined check: paired (0x1) set, unmapped (0x4) clear, mate unmapped (0x8) clear
         if ((f & 0xd) !== 0x1 || this.sequenceId !== this.mate?.sequenceId) {
             return undefined;
         }
-        const s1 = f & 0x10 ? 'R' : 'F';
-        const s2 = f & 0x20 ? 'R' : 'F';
-        let o1 = ' ';
-        let o2 = ' ';
-        if (f & 0x40) {
-            o1 = '1';
-            o2 = '2';
-        }
-        else if (f & 0x80) {
-            o1 = '2';
-            o2 = '1';
-        }
         const isize = this.templateLength || this.templateSize || 0;
-        return isize > 0
-            ? `${s1}${o1}${s2}${o2}`
-            : `${s2}${o2}${s1}${o1}`;
+        return PAIR_ORIENTATION_TABLE[((f >> 4) & 0xf) | (isize > 0 ? 16 : 0)];
     }
     /**
      * Annotates this feature with the given reference sequence basepair
@@ -354,6 +353,7 @@ export default class CramRecord {
             }
             data[k] = this[k];
         });
+        data.readName = this.readName;
         data.readBases = this.getReadBases();
         data.qualityScores = this.qualityScores
             ? Array.from(this.qualityScores)

package/esm/cramFile/record.js.map

@@ -1 +1 @@
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package/esm/cramFile/slice/decodeRecord.d.ts

@@ -6,14 +6,14 @@ import CramSlice, { SliceHeader } from './index.ts';
 import { CramFileBlock } from '../file.ts';
 export type DataSeriesDecoder = <T extends DataSeriesEncodingKey>(dataSeriesName: T) => DataTypeMapping[DataSeriesTypes[T]] | undefined;
 export type BulkByteRawDecoder = (dataSeriesName: 'QS' | 'BA', length: number) => Uint8Array | 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, decodeOptions?: Required<DecodeOptions>, decodeBulkBytesRaw?: BulkByteRawDecoder): {
+export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSeriesDecoder, compressionScheme: CramContainerCompressionScheme, sliceHeader: SliceHeader, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors, majorVersion: number, recordNumber: number, uniqueId: number, decodeOptions?: Required<DecodeOptions>, decodeBulkBytesRaw?: BulkByteRawDecoder): {
     readLength: number;
     sequenceId: number | undefined;
     cramFlags: number;
     flags: number;
     alignmentStart: number;
     readGroupId: number;
-    readName: string | undefined;
+    readNameRaw: Uint8Array<ArrayBufferLike> | undefined;
     mateToUse: {
         mateFlags: number;
         mateSequenceId: number;
@@ -27,5 +27,6 @@ export default function decodeRecord(slice: CramSlice, decodeDataSeries: DataSer
     mappingQuality: number | undefined;
     qualityScores: Uint8Array<ArrayBufferLike> | null | undefined;
     readBases: string | null | undefined;
-    tags: Record<string, any>;
+    tags: Record<string, string | number | number[] | undefined>;
+    uniqueId: number;
 };