@gmod/tabix 3.8.2 → 3.9.0

package/esm/tabixIndexedFile.js

@@ -8,6 +8,8 @@ const TAB = 9;
 const NEWLINE = 10;
 const CARRIAGE_RETURN = 13;
 const SEMICOLON = 59;
+const LESS_THAN = 60;
+const GREATER_THAN = 62;
 // Ceiling on how many chunk reads getLines keeps in flight ahead of the one it
 // is parsing. Six is the HTTP/1.1 per-host connection cap browsers enforce, so
 // going much above it buys nothing on the transport that matters.
@@ -181,6 +183,80 @@ function parseIntFromBytes(buffer, start, end) {
     }
     return val;
 }
+/**
+ * The GAF scan of one chunk. A read spans the lowest to the highest node id on
+ * its path, which htslib's tbx_parse1 reads the same way. Returns true once a
+ * read starts at or past `end`: records are sorted by their lowest node.
+ */
+function scanGafChunk(buffer, cpositions, dpositions, minvDataPosition, { start, end, pathCol, metaCharCode, decoder, callback }) {
+    let blockStart = 0;
+    let pos = 0;
+    while (blockStart < buffer.length) {
+        const n = buffer.indexOf(NEWLINE, blockStart);
+        if (n === -1) {
+            break;
+        }
+        const lineStart = blockStart;
+        blockStart = n + 1;
+        const target = lineStart + minvDataPosition;
+        while (pos < dpositions.length && target >= dpositions[pos]) {
+            pos++;
+        }
+        if (buffer[lineStart] === metaCharCode) {
+            continue;
+        }
+        let pathStart = lineStart;
+        for (let i = 1; i < pathCol; i++) {
+            const t = buffer.indexOf(TAB, pathStart);
+            if (t === -1 || t >= n) {
+                pathStart = n;
+                break;
+            }
+            pathStart = t + 1;
+        }
+        // A path without a leading step is a stable sequence name (or `*`), which
+        // carries no node ids. htslib parses one anyway and indexes garbage
+        // (`GRCh38#0#chr1` as nodes 0..38), so skip it rather than match that.
+        const first = buffer[pathStart];
+        if (first !== GREATER_THAN && first !== LESS_THAN) {
+            continue;
+        }
+        let pathEnd = buffer.indexOf(TAB, pathStart);
+        if (pathEnd === -1 || pathEnd > n) {
+            pathEnd = n;
+        }
+        // like htslib, skip one byte (the orientation) before each node id
+        let min = Infinity;
+        let max = -1;
+        let i = pathStart;
+        while (i < pathEnd) {
+            let id = 0;
+            let j = i + 1;
+            for (; j < pathEnd; j++) {
+                const digit = buffer[j] - 48;
+                if (digit < 0 || digit > 9) {
+                    break;
+                }
+                id = id * 10 + digit;
+            }
+            if (id < min) {
+                min = id;
+            }
+            if (id > max) {
+                max = id;
+            }
+            i = j;
+        }
+        if (min >= end) {
+            return true;
+        }
+        if (max >= start) {
+            const lineEnd = buffer[n - 1] === CARRIAGE_RETURN ? n - 1 : n;
+            callback(decoder.decode(buffer.subarray(lineStart, lineEnd)), calculateFileOffset(cpositions, dpositions, pos, lineStart, minvDataPosition), min, max + 1);
+        }
+    }
+    return false;
+}
 /**
  * Reads Tabix-indexed files (bgzipped), supporting both .tbi and .csi index formats.
  */
@@ -292,6 +368,9 @@ export default class TabixIndexedFile {
         // tabs[N] holds the byte offset of the N-th tab on the current line; with
         // the sentinel tabs[0] = blockStart - 1, column N spans tabs[N-1]+1..tabs[N]
         const tabs = new Int32Array(maxColumn + 1);
+        const gaf = metadata.format === 'GAF'
+            ? { start, end, pathCol: startCol, metaCharCode, decoder, callback }
+            : undefined;
         let totalBytes = 0;
         for (const c of chunks) {
             totalBytes += c.fetchedSize();
@@ -305,8 +384,9 @@ export default class TabixIndexedFile {
         //
         // A fixed window would be wrong, though: blocksForRange offers a chunk per
         // overlapping bin across every level, and on a sparse file the early return
-        // below stops the scan inside the first one, leaving the rest untouched
-        // (chr22_nanopore_subset offers 7 chunks and reads 1). Prefetching those
+        // below can stop the scan inside the first one, leaving the rest untouched.
+        // max_off drops only the chunks it can prove lie past the query, so the
+        // scan can still end before the last one it is offered. Prefetching those
         // would multiply the bytes such a query fetches for no gain.
         //
         // Finishing a chunk without hitting the early return proves the next chunk
@@ -333,74 +413,81 @@ export default class TabixIndexedFile {
             downloadedBytes += c.fetchedSize();
             onProgress?.(downloadedBytes, totalBytes);
             const minvDataPosition = c.minv.dataPosition;
-            let blockStart = 0;
-            let pos = 0;
-            while (blockStart < buffer.length) {
-                const n = buffer.indexOf(NEWLINE, blockStart);
-                if (n === -1) {
-                    break;
-                }
-                const target = blockStart + minvDataPosition;
-                while (pos < dpositions.length && target >= dpositions[pos]) {
-                    pos++;
-                }
-                // skip meta lines
-                if (metaCharCode !== undefined && buffer[blockStart] === metaCharCode) {
-                    blockStart = n + 1;
-                    continue;
-                }
-                // 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 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;
-                const refEnd = tabs[refCol];
-                const refLen = refEnd - refStart;
-                if (refLen !== regionRefNameBytes.length) {
-                    blockStart = n + 1;
-                    continue;
+            if (gaf) {
+                if (scanGafChunk(buffer, cpositions, dpositions, minvDataPosition, gaf)) {
+                    return;
                 }
-                let isRefMatch = true;
-                for (let i = 0; i < refLen; i++) {
-                    if (buffer[refStart + i] !== regionRefNameBytes[i]) {
-                        isRefMatch = false;
+            }
+            else {
+                let blockStart = 0;
+                let pos = 0;
+                while (blockStart < buffer.length) {
+                    const n = buffer.indexOf(NEWLINE, blockStart);
+                    if (n === -1) {
                         break;
                     }
-                }
-                if (!isRefMatch) {
+                    const target = blockStart + minvDataPosition;
+                    while (pos < dpositions.length && target >= dpositions[pos]) {
+                        pos++;
+                    }
+                    // skip meta lines
+                    if (metaCharCode !== undefined &&
+                        buffer[blockStart] === metaCharCode) {
+                        blockStart = n + 1;
+                        continue;
+                    }
+                    // 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 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;
+                    const refEnd = tabs[refCol];
+                    const refLen = refEnd - refStart;
+                    if (refLen !== regionRefNameBytes.length) {
+                        blockStart = n + 1;
+                        continue;
+                    }
+                    let isRefMatch = true;
+                    for (let i = 0; i < refLen; i++) {
+                        if (buffer[refStart + i] !== regionRefNameBytes[i]) {
+                            isRefMatch = false;
+                            break;
+                        }
+                    }
+                    if (!isRefMatch) {
+                        blockStart = n + 1;
+                        continue;
+                    }
+                    // parse start coordinate
+                    const startCoordinate = parseIntFromBytes(buffer, tabs[startCol - 1] + 1, tabs[startCol]) + coordinateOffset;
+                    if (startCoordinate >= end) {
+                        return;
+                    }
+                    // parse end coordinate
+                    let endCoordinate;
+                    if (endCol === 0 || endCol === startCol) {
+                        endCoordinate = startCoordinate + 1;
+                    }
+                    else if (isVCF) {
+                        endCoordinate = getVcfEnd(buffer, startCoordinate, tabs[3] + 1, tabs[4], tabs[endCol - 1] + 1, tabs[endCol]);
+                    }
+                    else {
+                        endCoordinate = parseIntFromBytes(buffer, tabs[endCol - 1] + 1, tabs[endCol]);
+                    }
+                    if (endCoordinate > start) {
+                        // 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;
-                    continue;
-                }
-                // parse start coordinate
-                const startCoordinate = parseIntFromBytes(buffer, tabs[startCol - 1] + 1, tabs[startCol]) +
-                    coordinateOffset;
-                if (startCoordinate >= end) {
-                    return;
-                }
-                // parse end coordinate
-                let endCoordinate;
-                if (endCol === 0 || endCol === startCol) {
-                    endCoordinate = startCoordinate + 1;
-                }
-                else if (isVCF) {
-                    endCoordinate = getVcfEnd(buffer, startCoordinate, tabs[3] + 1, tabs[4], tabs[endCol - 1] + 1, tabs[endCol]);
-                }
-                else {
-                    endCoordinate = parseIntFromBytes(buffer, tabs[endCol - 1] + 1, tabs[endCol]);
-                }
-                if (endCoordinate > start) {
-                    // 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;
             }
             // every line in this chunk was still inside the query, so the next chunk
             // has to be examined too - widen the window and start the reads for it

package/esm/tabixIndexedFile.js.map

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package/esm/util.js

@@ -196,6 +196,7 @@ const tabixFormats = {
     0: 'generic',
     1: 'SAM',
     2: 'VCF',
+    3: 'GAF',
 };
 export function parseAuxData(bytes, offset) {
     const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);

package/esm/util.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.8.2",
+  "version": "3.9.0",
   "packageManager": "pnpm@11.15.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
@@ -39,7 +39,7 @@
     "preversion": "pnpm lint && pnpm format:check && pnpm typecheck && pnpm test --run && pnpm build",
     "postversion": "git push --follow-tags",
     "build": "pnpm build:esm && pnpm build:es5",
-    "differential": "vite-node scripts/differential.mjs",
+    "differential": "node scripts/differential.mjs",
     "benchonly": "vitest bench",
     "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
     "postbuild": "webpack",

package/src/csi.ts

@@ -41,11 +41,14 @@ export default class CSI extends IndexFile {
 
     const minShift = dataView.getInt32(4, true)
     const depth = dataView.getInt32(8, true)
-    const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7
+    const maxBinNumber = (8 ** (depth + 1) - 1) / 7
     const maxRefLength = 2 ** (minShift + depth * 3)
     const auxLength = dataView.getInt32(12, true)
+    // htslib names no references in a GAF index, so its aux is the bare
+    // 28-byte header block
+    const isGaf = auxLength >= 28 && (dataView.getInt32(16, true) & 0xf) === 3
     const aux =
-      auxLength >= 30
+      auxLength >= 30 || isGaf
         ? parseAuxData(bytes, 16)
         : {
             refIdToName: [] as string[],

package/src/indexFile.ts

@@ -7,6 +7,56 @@ import type Chunk from './chunk.ts'
 import type VirtualOffset from './virtualOffset.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
+/**
+ * The virtual offset past which a coordinate-sorted file holds nothing
+ * overlapping `[.., end)`, from the binning index alone: htslib's `max_off`
+ * (`hts_itr_query` in hts.c).
+ *
+ * Walk right from the finest bin after the one holding `end - 1`, stepping up
+ * to the parent at every first child, so each bin visited begins at or past
+ * `end` and never overlaps the query. Every record in such a bin starts at or
+ * past `end`, so the first chunk of the first bin that exists is a record past
+ * the query, and in a sorted file so is every record after it.
+ *
+ * SYNC: ~/src/gmod/bam-js/src/indexFile.ts maxOffset, and see bam-js ADR 0023
+ * for why the caller drops whole merged chunks with it rather than trimming.
+ */
+export function maxOffset(
+  binIndex: Record<number, Chunk[]>,
+  end: number,
+  minShift: number,
+  depth: number,
+) {
+  if (end > 2 ** (minShift + depth * 3)) {
+    return undefined
+  }
+  const binCount = (8 ** (depth + 1) - 1) / 7
+  let bin = (8 ** depth - 1) / 7 + Math.floor((end - 1) / 2 ** minShift) + 1
+  if (bin >= binCount) {
+    bin = 0
+  }
+  for (;;) {
+    while (bin % 8 === 1) {
+      bin = (bin - 1) / 8
+    }
+    if (bin === 0) {
+      return undefined
+    }
+    const chunks = binIndex[bin]
+    if (chunks?.length) {
+      let lowest = chunks[0]!.minv
+      for (let i = 1; i < chunks.length; i++) {
+        const minv = chunks[i]!.minv
+        if (minv.compareTo(lowest) < 0) {
+          lowest = minv
+        }
+      }
+      return lowest
+    }
+    bin++
+  }
+}
+
 export interface Options {
   signal?: AbortSignal
   /**
@@ -50,6 +100,11 @@ export interface IndexData {
   maxBinNumber: number
 }
 
+// htslib files every GAF record under ref 0 and ignores a query's name
+function refIdFor(indexData: IndexData, refName: string) {
+  return indexData.format === 'GAF' ? 0 : indexData.refNameToId[refName]
+}
+
 export default abstract class IndexFile {
   public filehandle: GenericFilehandle
   /**
@@ -104,7 +159,7 @@ export default abstract class IndexFile {
   /** @internal */
   public async lineCount(refName: string, opts: Options = {}) {
     const indexData = await this.parse(opts)
-    const refId = indexData.refNameToId[refName]
+    const refId = refIdFor(indexData, refName)
     if (refId === undefined) {
       return -1
     }
@@ -121,6 +176,7 @@ export default abstract class IndexFile {
    * The chunks of the data file that may hold records overlapping the region.
    * The two index formats differ only in their binning scheme and in where
    * they keep the pruning floor, which is what the two hooks above supply.
+   * The ceiling, `maxOffset`, needs only the bins, so it serves both.
    *
    * @internal
    */
@@ -131,7 +187,7 @@ export default abstract class IndexFile {
     opts: Options = {},
   ) {
     const indexData = await this.parse(opts)
-    const refId = indexData.refNameToId[refName]
+    const refId = refIdFor(indexData, refName)
     if (refId === undefined) {
       return []
     }
@@ -139,6 +195,12 @@ export default abstract class IndexFile {
     if (!ba) {
       return []
     }
+    // htslib indexes a GAF read as [minNode, maxNode), one short of the
+    // [minNode, maxNode] that getLines matches, so look one node lower, as
+    // `tabix` does for a region's 1-based start
+    if (indexData.format === 'GAF') {
+      min = Math.max(min - 1, 0)
+    }
 
     // Find chunks in overlapping bins. Leaf bins are not pruned.
     const chunks: Chunk[] = []
@@ -153,7 +215,21 @@ export default abstract class IndexFile {
       }
     }
 
-    return optimizeChunks(chunks, this.lowestOffset(ba, min, indexData))
+    const merged = optimizeChunks(chunks, this.lowestOffset(ba, min, indexData))
+    const past = maxOffset(
+      ba.binIndex,
+      max,
+      indexData.minShift,
+      indexData.depth,
+    )
+    if (past) {
+      let n = merged.length
+      while (n > 0 && merged[n - 1]!.minv.compareTo(past) >= 0) {
+        n--
+      }
+      merged.length = n
+    }
+    return merged
   }
 
   // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same shape and the same