npm - @gmod/tabix - Versions diffs - 3.8.2 → 3.8.3 - Mend

@gmod/tabix 3.8.2 → 3.8.3

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 (20) hide show

package/README.md +13 -11
package/dist/csi.js +1 -1
package/dist/csi.js.map +1 -1
package/dist/indexFile.d.ts +16 -0
package/dist/indexFile.js +56 -1
package/dist/indexFile.js.map +1 -1
package/dist/tabix-bundle.js +1 -1
package/dist/tabixIndexedFile.js +3 -2
package/dist/tabixIndexedFile.js.map +1 -1
package/esm/csi.js +1 -1
package/esm/csi.js.map +1 -1
package/esm/indexFile.d.ts +16 -0
package/esm/indexFile.js +55 -1
package/esm/indexFile.js.map +1 -1
package/esm/tabixIndexedFile.js +3 -2
package/esm/tabixIndexedFile.js.map +1 -1
package/package.json +1 -1
package/src/csi.ts +1 -1
package/src/indexFile.ts +66 -1
package/src/tabixIndexedFile.ts +3 -2

package/dist/tabixIndexedFile.js CHANGED Viewed

@@ -310,8 +310,9 @@ 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

package/dist/tabixIndexedFile.js.map CHANGED Viewed

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

@@ -29,7 +29,7 @@ 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);
         const aux = auxLength >= 30

package/esm/csi.js.map CHANGED Viewed

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

@@ -1,6 +1,21 @@
 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 declare function maxOffset(binIndex: Record<number, Chunk[]>, end: number, minShift: number, depth: number): VirtualOffset | undefined;
 export interface Options {
     signal?: AbortSignal;
     /**
@@ -111,6 +126,7 @@ 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
      */

package/esm/indexFile.js CHANGED Viewed

@@ -1,6 +1,50 @@
 import { unzip } from '@gmod/bgzf-filehandle';
 import { SharedReadCache } from '@gmod/shared-read-cache';
 import { optimizeChunks } from "./util.js";
+/**
+ * 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, end, minShift, depth) {
+    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 default class IndexFile {
     filehandle;
     /**
@@ -44,6 +88,7 @@ export default 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
      */
@@ -69,7 +114,16 @@ export default 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
     // reasoning below.

package/esm/indexFile.js.map CHANGED Viewed

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package/esm/tabixIndexedFile.js CHANGED Viewed

@@ -305,8 +305,9 @@ 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

package/esm/tabixIndexedFile.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.8.2",
+  "version": "3.8.3",
   "packageManager": "pnpm@11.15.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",

package/src/csi.ts CHANGED Viewed

@@ -41,7 +41,7 @@ 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)
     const aux =

package/src/indexFile.ts CHANGED Viewed

@@ -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
   /**
@@ -121,6 +171,7 @@ 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
    */
@@ -153,7 +204,21 @@ 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

package/src/tabixIndexedFile.ts CHANGED Viewed

@@ -521,8 +521,9 @@ 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