@gmod/tabix 3.4.1 → 3.4.3

package/esm/tabixIndexedFile.js

@@ -7,6 +7,7 @@ import TBI from "./tbi.js";
 import { optimizeChunks } from "./util.js";
 const TAB = 9;
 const NEWLINE = 10;
+const CARRIAGE_RETURN = 13;
 const SEMICOLON = 59;
 function resolveFilehandle(filehandle, path, url) {
     if (filehandle) {
@@ -20,6 +21,35 @@ function resolveFilehandle(filehandle, path, url) {
     }
     throw new TypeError('must provide either filehandle, path, or url');
 }
+// An explicitly supplied index always wins over the `<path>.tbi` /
+// `<url>.tbi` names derived from the data file, whichever kind it is.
+function resolveIndex({ tbiFilehandle, csiFilehandle, tbiPath, csiPath, tbiUrl, csiUrl, path, url, }) {
+    if (tbiFilehandle) {
+        return new TBI({ filehandle: tbiFilehandle });
+    }
+    if (csiFilehandle) {
+        return new CSI({ filehandle: csiFilehandle });
+    }
+    if (tbiPath) {
+        return new TBI({ filehandle: new LocalFile(tbiPath) });
+    }
+    if (csiPath) {
+        return new CSI({ filehandle: new LocalFile(csiPath) });
+    }
+    if (csiUrl) {
+        return new CSI({ filehandle: new RemoteFile(csiUrl) });
+    }
+    if (tbiUrl) {
+        return new TBI({ filehandle: new RemoteFile(tbiUrl) });
+    }
+    if (path) {
+        return new TBI({ filehandle: new LocalFile(`${path}.tbi`) });
+    }
+    if (url) {
+        return new TBI({ filehandle: new RemoteFile(`${url}.tbi`) });
+    }
+    throw new TypeError('must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl');
+}
 function calculateFileOffset(cpositions, dpositions, pos, blockStart, minvDataPosition) {
     return (cpositions[pos] * (1 << 8) +
         (blockStart - dpositions[pos]) +
@@ -89,33 +119,16 @@ export default class TabixIndexedFile {
     chunkCache;
     constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = 5 * 2 ** 20, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
-        if (tbiFilehandle) {
-            this.index = new TBI({ filehandle: tbiFilehandle });
-        }
-        else if (csiFilehandle) {
-            this.index = new CSI({ filehandle: csiFilehandle });
-        }
-        else if (tbiPath) {
-            this.index = new TBI({ filehandle: new LocalFile(tbiPath) });
-        }
-        else if (csiPath) {
-            this.index = new CSI({ filehandle: new LocalFile(csiPath) });
-        }
-        else if (path) {
-            this.index = new TBI({ filehandle: new LocalFile(`${path}.tbi`) });
-        }
-        else if (csiUrl) {
-            this.index = new CSI({ filehandle: new RemoteFile(csiUrl) });
-        }
-        else if (tbiUrl) {
-            this.index = new TBI({ filehandle: new RemoteFile(tbiUrl) });
-        }
-        else if (url) {
-            this.index = new TBI({ filehandle: new RemoteFile(`${url}.tbi`) });
-        }
-        else {
-            throw new TypeError('must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl');
-        }
+        this.index = resolveIndex({
+            tbiFilehandle,
+            csiFilehandle,
+            tbiPath,
+            csiPath,
+            tbiUrl,
+            csiUrl,
+            path,
+            url,
+        });
         this.chunkCache = new AbortablePromiseCache({
             cache: new LRU({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
             fill: (args, signal) => this.readChunk(args, { signal }),
@@ -210,15 +223,14 @@ export default class TabixIndexedFile {
                     blockStart = n + 1;
                     continue;
                 }
-                // find tab positions
+                // find tab positions. Columns past the end of the line all get `n`
+                // rather than breaking out, which would leave stale offsets from the
+                // previous line in the tail of the array.
                 tabs[0] = blockStart - 1;
                 for (let i = 0; i < maxColumn; i++) {
-                    const tabPos = buffer.indexOf(TAB, tabs[i] + 1);
-                    if (tabPos === -1 || tabPos >= n) {
-                        tabs[i + 1] = n;
-                        break;
-                    }
-                    tabs[i + 1] = tabPos;
+                    const prev = tabs[i];
+                    const tabPos = prev < n ? buffer.indexOf(TAB, prev + 1) : -1;
+                    tabs[i + 1] = tabPos === -1 || tabPos >= n ? n : tabPos;
                 }
                 // compare ref name bytes directly
                 const refStart = tabs[refCol - 1] + 1;
@@ -257,7 +269,9 @@ export default class TabixIndexedFile {
                     endCoordinate = parseIntFromBytes(buffer, tabs[endCol - 1] + 1, tabs[endCol]);
                 }
                 if (endCoordinate > start) {
-                    const line = decoder.decode(buffer.subarray(blockStart, n));
+                    // trim a CRLF terminator, matching htslib's line reader
+                    const lineEnd = buffer[n - 1] === CARRIAGE_RETURN ? n - 1 : n;
+                    const line = decoder.decode(buffer.subarray(blockStart, lineEnd));
                     callback(line, calculateFileOffset(cpositions, dpositions, pos, blockStart, minvDataPosition), startCoordinate, endCoordinate);
                 }
                 blockStart = n + 1;

package/esm/tabixIndexedFile.js.map

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package/esm/tbi.js

@@ -1,24 +1,26 @@
 import { unzip } from '@gmod/bgzf-filehandle';
 import Chunk from "./chunk.js";
 import IndexFile from "./indexFile.js";
-import { findFirstData, memoizeByRefId, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
+import { clampChunkEnds, findFirstData, memoizeByRefId, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
 import { fromBytes } from "./virtualOffset.js";
 const TBI_MAGIC = 21_578_324; // TBI\1
+// TBI is always the fixed depth-5, 14-bit-leaf binning scheme
+const TBI_DEPTH = 5;
+const TBI_MAX_REF_LENGTH = 2 ** (14 + TBI_DEPTH * 3);
 /**
  * calculate the list of bins that may overlap with region [beg,end)
  * (zero-based half-open)
  */
 function reg2bins(beg, end) {
-    beg += 1; // < convert to 1-based closed
-    end -= 1;
-    return [
-        [0, 0],
-        [1 + (beg >> 26), 1 + (end >> 26)],
-        [9 + (beg >> 23), 9 + (end >> 23)],
-        [73 + (beg >> 20), 73 + (end >> 20)],
-        [585 + (beg >> 17), 585 + (end >> 17)],
-        [4681 + (beg >> 14), 4681 + (end >> 14)],
-    ];
+    // Clamp into the binning scheme's range. Past 2**31 the shifts below
+    // truncate to int32 and go negative, which would silently yield no bins.
+    const b = Math.min(Math.max(beg, 0), TBI_MAX_REF_LENGTH);
+    const e = Math.min(end, TBI_MAX_REF_LENGTH) - 1;
+    const bins = [];
+    if (b <= e) {
+        bins.push([0, 0], [1 + (b >> 26), 1 + (e >> 26)], [9 + (b >> 23), 9 + (e >> 23)], [73 + (b >> 20), 73 + (e >> 20)], [585 + (b >> 17), 585 + (e >> 17)], [4681 + (b >> 14), 4681 + (e >> 14)]);
+    }
+    return bins;
 }
 export default class TabixIndex extends IndexFile {
     /** @internal */
@@ -28,14 +30,12 @@ export default class TabixIndex extends IndexFile {
             onProgress: opts.onProgress,
         });
         const bytes = (await unzip(buf));
-        const dataView = new DataView(bytes.buffer);
+        const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
         if (dataView.getUint32(0, true) !== TBI_MAGIC) {
             throw new Error('Not a TBI file');
         }
         const refCount = dataView.getUint32(4, true);
-        const depth = 5;
-        const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
-        const maxRefLength = 2 ** (14 + depth * 3);
+        const maxBinNumber = ((1 << ((TBI_DEPTH + 1) * 3)) - 1) / 7;
         // TBI header layout matches CSI aux data; parseAuxData handles both
         const { refNameToId, refIdToName, coordinateType, format, columnNumbers, metaChar, skipLines, } = parseAuxData(bytes, 8);
         // nameSectionLength is at TBI offset 32; re-read to find where bin data starts
@@ -116,13 +116,14 @@ export default class TabixIndex extends IndexFile {
                 linearIndex[k] = fromBytes(bytes, pos);
                 pos += 8;
             }
+            clampChunkEnds(Object.values(binIndex).flat(), linearIndex.map(v => v.blockPosition));
             return { binIndex, linearIndex, stats };
         }
         return {
             indices: memoizeByRefId(getIndices),
             metaChar,
             maxBinNumber,
-            maxRefLength,
+            maxRefLength: TBI_MAX_REF_LENGTH,
             skipLines,
             firstDataLine,
             columnNumbers,
@@ -134,9 +135,6 @@ export default class TabixIndex extends IndexFile {
         };
     }
     async blocksForRange(refName, min, max, opts = {}) {
-        if (min < 0) {
-            min = 0;
-        }
         const indexData = await this.parse(opts);
         const refId = indexData.refNameToId[refName];
         if (refId === undefined) {
@@ -146,12 +144,12 @@ export default class TabixIndex extends IndexFile {
         if (!ba) {
             return [];
         }
-        const linearIndex = ba.linearIndex ?? [];
-        // min >= 2**31 overflows int32 and produces a negative >> 14 result —
-        // query is well beyond the indexed range
-        if (linearIndex.length > 0 && min >= 2 ** 31) {
+        if (min > TBI_MAX_REF_LENGTH) {
             console.warn('querying outside of possible tabix range');
         }
+        // clamp before the >> 14 below, which would truncate to int32 and go
+        // negative past 2**31
+        const beg = Math.min(Math.max(min, 0), TBI_MAX_REF_LENGTH);
         const overlappingBins = reg2bins(min, max); // List of bin #s that overlap min, max
         const chunks = [];
         // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
@@ -168,7 +166,8 @@ export default class TabixIndex extends IndexFile {
         // The linear index is monotonically non-decreasing, so the minimum virtual
         // offset for chunks that could overlap [min, ...) is at index minLin.
         // SYNC: ~/src/gmod/bam-js/src/bai.ts getLowestChunk
-        const lowest = linearIndex[Math.min(min >> 14, linearIndex.length - 1)];
+        const linearIndex = ba.linearIndex;
+        const lowest = linearIndex?.[Math.min(beg >> 14, linearIndex.length - 1)];
         return optimizeChunks(chunks, lowest);
     }
 }

package/esm/tbi.js.map

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

@@ -1,6 +1,7 @@
 import Chunk from './chunk.ts';
 import type VirtualOffset from './virtualOffset.ts';
 export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
+export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
 export declare function findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
 export declare function parseNameBytes(namesBytes: Uint8Array): {
     refNameToId: Record<string, number>;

package/esm/util.js

@@ -50,7 +50,7 @@ export function optimizeChunks(chunks, lowest) {
             const cmp = chunkMaxBlock - lastMaxBlock ||
                 chunk.maxv.dataPosition - lastChunk.maxv.dataPosition;
             if (cmp > 0) {
-                mergedChunks[mergedChunks.length - 1] = new Chunk(lastChunk.minv, chunk.maxv, lastChunk.bin);
+                mergedChunks[mergedChunks.length - 1] = new Chunk(lastChunk.minv, chunk.maxv, lastChunk.bin, chunk.endPosition);
                 lastMaxBlock = chunkMaxBlock;
             }
         }
@@ -62,6 +62,41 @@ export function optimizeChunks(chunks, lowest) {
     }
     return mergedChunks;
 }
+// Tighten each chunk's endPosition (default: a full max-size BGZF block past
+// maxv) down to the next known block boundary. Every chunk min/maxv blockPosition
+// and every extraBoundary (e.g. linear-index entries) is a real BGZF block start;
+// since blocks don't overlap, the first boundary strictly greater than a chunk's
+// maxv.blockPosition is an upper bound on where that final block ends — always at
+// least the true block end, so the clamped fetch still contains the whole block.
+// Shrinks both the byte estimate and the actual fetch with no extra I/O.
+export function clampChunkEnds(chunks, extraBoundaries = []) {
+    // Array#sort with a comparator beats a Float64Array numeric sort here:
+    // extraBoundaries (the linear index) arrives already sorted and TimSort
+    // exploits the existing run, which introsort cannot.
+    const boundaries = [...extraBoundaries];
+    for (const c of chunks) {
+        boundaries.push(c.minv.blockPosition, c.maxv.blockPosition);
+    }
+    boundaries.sort((a, b) => a - b);
+    for (const c of chunks) {
+        const max = c.maxv.blockPosition;
+        // first boundary strictly greater than max
+        let lo = 0;
+        let hi = boundaries.length;
+        while (lo < hi) {
+            const mid = (lo + hi) >>> 1;
+            if (boundaries[mid] > max) {
+                hi = mid;
+            }
+            else {
+                lo = mid + 1;
+            }
+        }
+        if (lo < boundaries.length) {
+            c.endPosition = Math.min(c.endPosition, boundaries[lo]);
+        }
+    }
+}
 export function findFirstData(currentFdl, virtualOffset) {
     return !currentFdl || currentFdl.compareTo(virtualOffset) > 0
         ? virtualOffset
@@ -94,7 +129,7 @@ const tabixFormats = {
     2: 'VCF',
 };
 export function parseAuxData(bytes, offset) {
-    const dataView = new DataView(bytes.buffer);
+    const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
     const formatFlags = dataView.getInt32(offset, true);
     const coordinateType = formatFlags & 0x1_00_00 ? 'zero-based-half-open' : '1-based-closed';
     const format = tabixFormats[formatFlags & 0xf];

package/esm/util.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,8 +1,9 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.4.1",
+  "version": "3.4.3",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
+  "sideEffects": false,
   "main": "dist/index.js",
   "exports": {
     "import": "./esm/index.js",

package/src/chunk.ts

@@ -5,11 +5,22 @@ export default class Chunk {
   public minv: VirtualOffset
   public maxv: VirtualOffset
   public bin: number
+  // 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.
+  public endPosition: number
 
-  constructor(minv: VirtualOffset, maxv: VirtualOffset, bin: number) {
+  constructor(
+    minv: VirtualOffset,
+    maxv: VirtualOffset,
+    bin: number,
+    endPosition = maxv.blockPosition + (1 << 16),
+  ) {
     this.minv = minv
     this.maxv = maxv
     this.bin = bin
+    this.endPosition = endPosition
   }
 
   toString() {
@@ -19,6 +30,6 @@ export default class Chunk {
   }
 
   fetchedSize() {
-    return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition
+    return this.endPosition - this.minv.blockPosition
   }
 }

package/src/csi.ts

@@ -3,6 +3,7 @@ import { unzip } from '@gmod/bgzf-filehandle'
 import Chunk from './chunk.ts'
 import IndexFile from './indexFile.ts'
 import {
+  clampChunkEnds,
   findFirstData,
   memoizeByRefId,
   optimizeChunks,
@@ -13,7 +14,6 @@ import { fromBytes } from './virtualOffset.ts'
 
 import type { Options, RefIndex } from './indexFile.ts'
 import type VirtualOffset from './virtualOffset.ts'
-import type { GenericFilehandle } from 'generic-filehandle2'
 
 const CSI1_MAGIC = 21_582_659 // CSI\1
 const CSI2_MAGIC = 38_359_875 // CSI\2
@@ -28,19 +28,9 @@ function rshift(num: number, bits: number) {
 }
 
 export default class CSI extends IndexFile {
-  private maxBinNumber: number
-  private depth: number
-  private minShift: number
-  constructor(args: { filehandle: GenericFilehandle }) {
-    super(args)
-    this.maxBinNumber = 0
-    this.depth = 0
-    this.minShift = 0
-  }
-  /** @internal */
-  indexCov() {
-    throw new Error('CSI indexes do not support indexcov')
-  }
+  private maxBinNumber = 0
+  private depth = 0
+  private minShift = 0
 
   /** @internal */
   async _parse(opts: Options = {}) {
@@ -49,7 +39,11 @@ export default class CSI extends IndexFile {
       onProgress: opts.onProgress,
     })
     const bytes = (await unzip(buf)) as Uint8Array
-    const dataView = new DataView(bytes.buffer)
+    const dataView = new DataView(
+      bytes.buffer,
+      bytes.byteOffset,
+      bytes.byteLength,
+    )
 
     const magic = dataView.getUint32(0, true)
     let csiVersion
@@ -136,6 +130,7 @@ export default class CSI extends IndexFile {
           binIndex[bin] = chunks
         }
       }
+      clampChunkEnds(Object.values(binIndex).flat())
       return { binIndex, stats }
     }
 

package/src/long.ts

@@ -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
 
 export function longFromBytesToUnsigned(source: Uint8Array, i = 0) {
   const low =