npm - @gmod/bam - Versions diffs - 7.3.2 → 7.3.4 - Mend

@gmod/bam 7.3.2 → 7.3.4

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 (46) hide show

package/dist/util.js.map CHANGED Viewed

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1	+ 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package/dist/virtualOffset.d.ts CHANGED Viewed

@@ -11,4 +11,4 @@ export declare class VirtualOffset {
     toString(): string;
     compareTo(b: VirtualOffset): number;
 }
-export declare function fromBytes(bytes: Uint8Array, offset?: number, bigendian?: boolean): VirtualOffset;
+export declare function fromBytes(bytes: Uint8Array, offset?: number): VirtualOffset;

package/dist/virtualOffset.js CHANGED Viewed

@@ -17,10 +17,7 @@ class VirtualOffset {
     }
 }
 exports.VirtualOffset = VirtualOffset;
-function fromBytes(bytes, offset = 0, bigendian = false) {
-    if (bigendian) {
-        throw new Error('big-endian virtual file offsets not implemented');
-    }
+function fromBytes(bytes, offset = 0) {
     return new VirtualOffset(bytes[offset + 7] * 0x10000000000 +
         bytes[offset + 6] * 0x100000000 +
         bytes[offset + 5] * 0x1000000 +

package/dist/virtualOffset.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/bai.js CHANGED Viewed

@@ -1,6 +1,6 @@
 import Chunk from "./chunk.js";
 import IndexFile, { memoizeByRefId } from "./indexFile.js";
-import { findFirstData, parsePseudoBin } from "./util.js";
+import { clampChunkEnds, findFirstData, parsePseudoBin } from "./util.js";
 import { fromBytes } from "./virtualOffset.js";
 const BAI_MAGIC = 21578050; // BAI\1
 // BAI uses a fixed 5-level binning scheme with a 14-bit (16KB) linear index
@@ -115,6 +115,7 @@ export default class BAI extends IndexFile {
                 linearIndex[j] = fromBytes(bytes, curr);
                 curr += 8;
             }
+            clampChunkEnds(Object.values(binIndex).flat(), linearIndex.map(v => v.blockPosition));
             return {
                 binIndex,
                 linearIndex,

package/esm/bai.js.map CHANGED Viewed

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

@@ -3,8 +3,8 @@ export default class Chunk {
     minv: Offset;
     maxv: Offset;
     bin: number;
-    _fetchedSize?: number | undefined;
-    constructor(minv: Offset, maxv: Offset, bin: number, _fetchedSize?: number | undefined);
+    endPosition: number;
+    constructor(minv: Offset, maxv: Offset, bin: number, endPosition?: number);
     toString(): string;
     compareTo(b: Chunk): number;
     fetchedSize(): number;

package/esm/chunk.js CHANGED Viewed

@@ -3,12 +3,16 @@ export default class Chunk {
     minv;
     maxv;
     bin;
-    _fetchedSize;
-    constructor(minv, maxv, bin, _fetchedSize) {
+    // Absolute byte offset where the fetch for this chunk ends. The compressed
+    // size of the final BGZF block (the one at maxv.blockPosition) is unknown
+    // from the index, so this defaults to a full max-size block past maxv. It can
+    // be tightened to the next known block boundary via clampChunkEnds.
+    endPosition;
+    constructor(minv, maxv, bin, endPosition = maxv.blockPosition + (1 << 16)) {
         this.minv = minv;
         this.maxv = maxv;
         this.bin = bin;
-        this._fetchedSize = _fetchedSize;
+        this.endPosition = endPosition;
     }
     toString() {
         return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
@@ -19,10 +23,7 @@ export default class Chunk {
             this.bin - b.bin);
     }
     fetchedSize() {
-        if (this._fetchedSize !== undefined) {
-            return this._fetchedSize;
-        }
-        return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition;
+        return this.endPosition - this.minv.blockPosition;
     }
 }
 //# sourceMappingURL=chunk.js.map

package/esm/chunk.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/csi.js CHANGED Viewed

@@ -1,7 +1,7 @@
 import { unzip } from '@gmod/bgzf-filehandle';
 import Chunk from "./chunk.js";
 import IndexFile, { memoizeByRefId } from "./indexFile.js";
-import { findFirstData, parseNameBytes, parsePseudoBin } from "./util.js";
+import { clampChunkEnds, findFirstData, parseNameBytes, parsePseudoBin, } from "./util.js";
 import { VirtualOffset, fromBytes } from "./virtualOffset.js";
 const CSI1_MAGIC = 21582659; // CSI\1
 const CSI2_MAGIC = 38359875; // CSI\2
@@ -133,6 +133,7 @@ export default class CSI extends IndexFile {
                     binIndex[bin] = chunks;
                 }
             }
+            clampChunkEnds(Object.values(binIndex).flat());
             return {
                 binIndex,
                 stats: pseudoBinStats,

package/esm/csi.js.map CHANGED Viewed

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

@@ -1,3 +1 @@
-export declare const TWO_PWR_16_DBL: number;
-export declare const TWO_PWR_32_DBL: number;
 export declare function longFromBytesToUnsigned(source: Uint8Array, i?: number): number;

package/esm/long.js CHANGED Viewed

@@ -1,5 +1,4 @@
-export const TWO_PWR_16_DBL = 1 << 16;
-export const TWO_PWR_32_DBL = TWO_PWR_16_DBL * TWO_PWR_16_DBL;
+const TWO_PWR_32_DBL = 2 ** 32;
 // avoids dependency on long.js
 export function longFromBytesToUnsigned(source, i = 0) {
     const low = source[i] |

package/esm/long.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"AAAA,MAAM,~~CAAC,MAAM,~~cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;~~AACrC,MAAM,CAAC,MAAM,cAAc,GAAG,cAAc,GAAG,cAAc,CAAA;AAE7D~~,+BAA+B;AAC/B,MAAM,UAAU,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}
1	+ {"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"AAAA,MAAM,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AAE9B,+BAA+B;AAC/B,MAAM,UAAU,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}

package/esm/record.d.ts CHANGED Viewed

@@ -36,7 +36,7 @@ export default class BamRecord {
     get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
     get tags(): Record<string, unknown>;
     getTag(tagName: string): unknown;
-    getTagRaw(tagName: string): string | number | Uint8Array<ArrayBufferLike> | number[] | Int8Array<ArrayBufferLike> | Int16Array<ArrayBufferLike> | Uint16Array<ArrayBufferLike> | Int32Array<ArrayBufferLike> | Uint32Array<ArrayBufferLike> | Float32Array<ArrayBufferLike> | undefined;
+    getTagRaw(tagName: string): unknown;
     private _findTag;
     private _computeTags;
     isPaired(): boolean;

package/esm/record.js CHANGED Viewed

@@ -100,6 +100,82 @@ function bArrayByteLength(Btype, limit) {
         return limit;
     }
 }
+// Cursor position just past a tag's value — i.e. the start of the next tag —
+// given the value starts at `p`. For null-terminated Z/H this steps over the
+// terminator. Returns 0 for an unknown type, whose value width is unknowable so
+// the caller must stop. Shared by _findTag and _computeTags so the two loops
+// can't drift in how they walk the tag layout. (0 is an impossible real end:
+// `p` is always past the fixed record prefix.)
+function tagValueEnd(ba, dataView, type, p, blockEnd) {
+    switch (type) {
+        case 0x41: // 'A'
+        case 0x63: // 'c'
+        case 0x43: // 'C'
+            return p + 1;
+        case 0x73: // 's'
+        case 0x53: // 'S'
+            return p + 2;
+        case 0x69: // 'i'
+        case 0x49: // 'I'
+        case 0x66: {
+            // 'f'
+            return p + 4;
+        }
+        case 0x5a: // 'Z'
+        case 0x48: {
+            // 'H'
+            let q = p;
+            while (q < blockEnd && ba[q] !== 0) {
+                q++;
+            }
+            return q + 1; // step past the null terminator
+        }
+        case 0x42: {
+            // 'B'
+            const Btype = ba[p];
+            const limit = dataView.getInt32(p + 1, true);
+            return p + 5 + bArrayByteLength(Btype, limit);
+        }
+        default:
+            console.error('Unknown BAM tag type', type);
+            return 0;
+    }
+}
+// Decode the value of a tag of `type` whose bytes start at `p`; `end` is the
+// next-tag cursor from tagValueEnd (used only to bound Z/H strings, whose bytes
+// run up to the null terminator at end-1). When `raw`, Z/H return the undecoded
+// byte subarray. Assumes `type` is a known scalar/string/B type.
+function decodeTagValue(ba, dataView, type, p, end, raw) {
+    switch (type) {
+        case 0x41: // 'A'
+            return String.fromCharCode(ba[p]);
+        case 0x69: // 'i'
+            return dataView.getInt32(p, true);
+        case 0x49: // 'I'
+            return dataView.getUint32(p, true);
+        case 0x63: // 'c'
+            return dataView.getInt8(p);
+        case 0x43: // 'C'
+            return dataView.getUint8(p);
+        case 0x73: // 's'
+            return dataView.getInt16(p, true);
+        case 0x53: // 'S'
+            return dataView.getUint16(p, true);
+        case 0x66: // 'f'
+            return dataView.getFloat32(p, true);
+        case 0x5a: // 'Z'
+        case 0x48: // 'H'
+            return raw
+                ? ba.subarray(p, end - 1)
+                : textDecoder.decode(ba.subarray(p, end - 1));
+        default: {
+            // 'B'
+            const Btype = ba[p];
+            const limit = dataView.getInt32(p + 1, true);
+            return decodeBArrayTag(ba, dataView, p + 5, Btype, limit);
+        }
+    }
+}
 export default class BamRecord {
     fileOffset;
     _byteArray;
@@ -215,165 +291,39 @@ export default class BamRecord {
     _findTag(tagName, raw) {
         const tag1 = tagName.charCodeAt(0);
         const tag2 = tagName.charCodeAt(1);
-        let p = this.tagsStart;
         const blockEnd = this._end;
         const ba = this._byteArray;
+        let p = this.tagsStart;
         while (p < blockEnd) {
-            const currentTag1 = ba[p];
-            const currentTag2 = ba[p + 1];
+            const isMatch = ba[p] === tag1 && ba[p + 1] === tag2;
             const type = ba[p + 2];
-            p += 3;
-            const isMatch = currentTag1 === tag1 && currentTag2 === tag2;
-            switch (type) {
-                case 0x41: // 'A'
-                    if (isMatch) {
-                        return String.fromCharCode(ba[p]);
-                    }
-                    p += 1;
-                    break;
-                case 0x69: // 'i'
-                    if (isMatch) {
-                        return this._dataView.getInt32(p, true);
-                    }
-                    p += 4;
-                    break;
-                case 0x49: // 'I'
-                    if (isMatch) {
-                        return this._dataView.getUint32(p, true);
-                    }
-                    p += 4;
-                    break;
-                case 0x63: // 'c'
-                    if (isMatch) {
-                        return this._dataView.getInt8(p);
-                    }
-                    p += 1;
-                    break;
-                case 0x43: // 'C'
-                    if (isMatch) {
-                        return this._dataView.getUint8(p);
-                    }
-                    p += 1;
-                    break;
-                case 0x73: // 's'
-                    if (isMatch) {
-                        return this._dataView.getInt16(p, true);
-                    }
-                    p += 2;
-                    break;
-                case 0x53: // 'S'
-                    if (isMatch) {
-                        return this._dataView.getUint16(p, true);
-                    }
-                    p += 2;
-                    break;
-                case 0x66: // 'f'
-                    if (isMatch) {
-                        return this._dataView.getFloat32(p, true);
-                    }
-                    p += 4;
-                    break;
-                case 0x5a: // 'Z'
-                case 0x48: {
-                    // 'H'
-                    const start = p;
-                    while (p < blockEnd && ba[p] !== 0) {
-                        p++;
-                    }
-                    if (isMatch) {
-                        return raw
-                            ? ba.subarray(start, p)
-                            : textDecoder.decode(ba.subarray(start, p));
-                    }
-                    p++; // advance past null terminator
-                    break;
-                }
-                case 0x42: {
-                    // 'B'
-                    const Btype = ba[p++];
-                    const limit = this._dataView.getInt32(p, true);
-                    p += 4;
-                    if (isMatch) {
-                        return decodeBArrayTag(ba, this._dataView, p, Btype, limit);
-                    }
-                    p += bArrayByteLength(Btype, limit);
-                    break;
-                }
-                default:
-                    if (type !== undefined) {
-                        console.error('Unknown BAM tag type', type);
-                    }
-                    break;
+            const valueStart = p + 3;
+            const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd);
+            if (end === 0) {
+                break; // unknown type: can't compute how far to advance
+            }
+            if (isMatch) {
+                return decodeTagValue(ba, this._dataView, type, valueStart, end, raw);
             }
+            p = end;
         }
         return undefined;
     }
     _computeTags() {
-        let p = this.tagsStart;
         const blockEnd = this._end;
         const ba = this._byteArray;
         const tags = {};
+        let p = this.tagsStart;
         while (p < blockEnd) {
             const tag = String.fromCharCode(ba[p], ba[p + 1]);
             const type = ba[p + 2];
-            p += 3;
-            switch (type) {
-                case 0x41: // 'A'
-                    tags[tag] = String.fromCharCode(ba[p]);
-                    p += 1;
-                    break;
-                case 0x69: // 'i'
-                    tags[tag] = this._dataView.getInt32(p, true);
-                    p += 4;
-                    break;
-                case 0x49: // 'I'
-                    tags[tag] = this._dataView.getUint32(p, true);
-                    p += 4;
-                    break;
-                case 0x63: // 'c'
-                    tags[tag] = this._dataView.getInt8(p);
-                    p += 1;
-                    break;
-                case 0x43: // 'C'
-                    tags[tag] = this._dataView.getUint8(p);
-                    p += 1;
-                    break;
-                case 0x73: // 's'
-                    tags[tag] = this._dataView.getInt16(p, true);
-                    p += 2;
-                    break;
-                case 0x53: // 'S'
-                    tags[tag] = this._dataView.getUint16(p, true);
-                    p += 2;
-                    break;
-                case 0x66: // 'f'
-                    tags[tag] = this._dataView.getFloat32(p, true);
-                    p += 4;
-                    break;
-                case 0x5a: // 'Z'
-                case 0x48: {
-                    // 'H'
-                    const start = p;
-                    while (p < blockEnd && ba[p] !== 0) {
-                        p++;
-                    }
-                    tags[tag] = textDecoder.decode(ba.subarray(start, p));
-                    p++; // advance past null terminator
-                    break;
-                }
-                case 0x42: {
-                    // 'B'
-                    const Btype = ba[p++];
-                    const limit = this._dataView.getInt32(p, true);
-                    p += 4;
-                    tags[tag] = decodeBArrayTag(ba, this._dataView, p, Btype, limit);
-                    p += bArrayByteLength(Btype, limit);
-                    break;
-                }
-                default:
-                    console.error('Unknown BAM tag type', type);
-                    break;
+            const valueStart = p + 3;
+            const end = tagValueEnd(ba, this._dataView, type, valueStart, blockEnd);
+            if (end === 0) {
+                break; // unknown type: can't compute how far to advance
             }
+            tags[tag] = decodeTagValue(ba, this._dataView, type, valueStart, end, false);
+            p = end;
         }
         return tags;
     }

package/esm/record.js.map CHANGED Viewed

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

@@ -38,6 +38,7 @@ export declare function optimizeChunks(chunks: Chunk[], lowest?: Offset): Chunk[
 export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
     lineCount: number;
 };
+export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
 export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRefSeq: (s: string) => string): {
     chrToIndex: Record<string, number>;
     indexToChr: {