@gmod/tabix 3.8.1 → 3.8.3

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Files changed (22) hide show
  1. package/README.md +86 -83
  2. package/dist/csi.js +1 -1
  3. package/dist/csi.js.map +1 -1
  4. package/dist/indexFile.d.ts +16 -0
  5. package/dist/indexFile.js +56 -1
  6. package/dist/indexFile.js.map +1 -1
  7. package/dist/tabix-bundle.js +1 -1
  8. package/dist/tabixIndexedFile.d.ts +12 -8
  9. package/dist/tabixIndexedFile.js +3 -2
  10. package/dist/tabixIndexedFile.js.map +1 -1
  11. package/esm/csi.js +1 -1
  12. package/esm/csi.js.map +1 -1
  13. package/esm/indexFile.d.ts +16 -0
  14. package/esm/indexFile.js +55 -1
  15. package/esm/indexFile.js.map +1 -1
  16. package/esm/tabixIndexedFile.d.ts +12 -8
  17. package/esm/tabixIndexedFile.js +3 -2
  18. package/esm/tabixIndexedFile.js.map +1 -1
  19. package/package.json +2 -2
  20. package/src/csi.ts +1 -1
  21. package/src/indexFile.ts +66 -1
  22. package/src/tabixIndexedFile.ts +15 -10
package/dist/tabixIndexedFile.d.ts CHANGED
@@ -9,11 +9,12 @@ interface GetLinesOpts {
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  signal?: AbortSignal;
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  lineCallback: GetLinesCallback;
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  /**
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- * Called as the compressed data blocks covering the query are fetched, with
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- * cumulative downloaded bytes and the total bytes to fetch. Reported at block
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- * granularity (one tick per chunk, including instant ticks for cache hits),
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- * which is the natural unit since chunk byte sizes are known up front from
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- * the index. Lets callers render a determinate download progress bar.
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+ * Called as the chunks covering the query are fetched, with cumulative
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+ * downloaded bytes and the total bytes to fetch. One tick per chunk — the run
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+ * of BGZF blocks the index resolves a query to — including instant ticks for
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+ * chunks already cached. That is the natural unit here, since chunk byte
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+ * sizes are known up front from the index, which is what lets a caller render
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+ * a determinate progress bar rather than a spinner.
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  */
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  onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
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  }
@@ -78,9 +79,12 @@ export default class TabixIndexedFile {
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  */
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  chunkCacheIdleTimeoutMs?: number;
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  /**
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- * A budget shared with other files — any `@gmod/shared-read-cache`
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- * consumer, so `@gmod/bam` and `@gmod/cram` can join the same one — so
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- * that the ceiling applies to their sum rather than to each of them.
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+ * A budget shared with other files, so that the ceiling applies to their
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+ * sum rather than to each of them. Any `@gmod/shared-read-cache` consumer
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+ * that weighs in the same unit can join it: `@gmod/bam` also weighs
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+ * decompressed bytes, while `@gmod/cram` weighs decoded records and
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+ * `@gmod/bbi` weighs entries, and a budget mixing those adds bytes to
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+ * records and bounds neither.
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  *
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  * {@link chunkCacheSize} is per file, which is not a bound on a consumer
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  * that opens one file per track. @gmod/bam measured the shape: six tracks
package/dist/tabixIndexedFile.js CHANGED
@@ -310,8 +310,9 @@ class TabixIndexedFile {
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  //
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  // A fixed window would be wrong, though: blocksForRange offers a chunk per
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  // overlapping bin across every level, and on a sparse file the early return
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- // below stops the scan inside the first one, leaving the rest untouched
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- // (chr22_nanopore_subset offers 7 chunks and reads 1). Prefetching those
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+ // below can stop the scan inside the first one, leaving the rest untouched.
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+ // max_off drops only the chunks it can prove lie past the query, so the
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+ // scan can still end before the last one it is offered. Prefetching those
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  // would multiply the bytes such a query fetches for no gain.
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  //
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  // Finishing a chunk without hitting the early return proves the next chunk
package/dist/tabixIndexedFile.js.map CHANGED
@@ -1 +1 @@
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package/esm/csi.js CHANGED
@@ -29,7 +29,7 @@ export default class CSI extends IndexFile {
29
29
  }
30
30
  const minShift = dataView.getInt32(4, true);
31
31
  const depth = dataView.getInt32(8, true);
32
- const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7;
32
+ const maxBinNumber = (8 ** (depth + 1) - 1) / 7;
33
33
  const maxRefLength = 2 ** (minShift + depth * 3);
34
34
  const auxLength = dataView.getInt32(12, true);
35
35
  const aux = auxLength >= 30
package/esm/csi.js.map CHANGED
@@ -1 +1 @@
1
- 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package/esm/indexFile.d.ts CHANGED
@@ -1,6 +1,21 @@
1
1
  import type Chunk from './chunk.ts';
2
2
  import type VirtualOffset from './virtualOffset.ts';
3
3
  import type { GenericFilehandle } from 'generic-filehandle2';
4
+ /**
5
+ * The virtual offset past which a coordinate-sorted file holds nothing
6
+ * overlapping `[.., end)`, from the binning index alone: htslib's `max_off`
7
+ * (`hts_itr_query` in hts.c).
8
+ *
9
+ * Walk right from the finest bin after the one holding `end - 1`, stepping up
10
+ * to the parent at every first child, so each bin visited begins at or past
11
+ * `end` and never overlaps the query. Every record in such a bin starts at or
12
+ * past `end`, so the first chunk of the first bin that exists is a record past
13
+ * the query, and in a sorted file so is every record after it.
14
+ *
15
+ * SYNC: ~/src/gmod/bam-js/src/indexFile.ts maxOffset, and see bam-js ADR 0023
16
+ * for why the caller drops whole merged chunks with it rather than trimming.
17
+ */
18
+ export declare function maxOffset(binIndex: Record<number, Chunk[]>, end: number, minShift: number, depth: number): VirtualOffset | undefined;
4
19
  export interface Options {
5
20
  signal?: AbortSignal;
6
21
  /**
@@ -111,6 +126,7 @@ export default abstract class IndexFile {
111
126
  * The chunks of the data file that may hold records overlapping the region.
112
127
  * The two index formats differ only in their binning scheme and in where
113
128
  * they keep the pruning floor, which is what the two hooks above supply.
129
+ * The ceiling, `maxOffset`, needs only the bins, so it serves both.
114
130
  *
115
131
  * @internal
116
132
  */
package/esm/indexFile.js CHANGED
@@ -1,6 +1,50 @@
1
1
  import { unzip } from '@gmod/bgzf-filehandle';
2
2
  import { SharedReadCache } from '@gmod/shared-read-cache';
3
3
  import { optimizeChunks } from "./util.js";
4
+ /**
5
+ * The virtual offset past which a coordinate-sorted file holds nothing
6
+ * overlapping `[.., end)`, from the binning index alone: htslib's `max_off`
7
+ * (`hts_itr_query` in hts.c).
8
+ *
9
+ * Walk right from the finest bin after the one holding `end - 1`, stepping up
10
+ * to the parent at every first child, so each bin visited begins at or past
11
+ * `end` and never overlaps the query. Every record in such a bin starts at or
12
+ * past `end`, so the first chunk of the first bin that exists is a record past
13
+ * the query, and in a sorted file so is every record after it.
14
+ *
15
+ * SYNC: ~/src/gmod/bam-js/src/indexFile.ts maxOffset, and see bam-js ADR 0023
16
+ * for why the caller drops whole merged chunks with it rather than trimming.
17
+ */
18
+ export function maxOffset(binIndex, end, minShift, depth) {
19
+ if (end > 2 ** (minShift + depth * 3)) {
20
+ return undefined;
21
+ }
22
+ const binCount = (8 ** (depth + 1) - 1) / 7;
23
+ let bin = (8 ** depth - 1) / 7 + Math.floor((end - 1) / 2 ** minShift) + 1;
24
+ if (bin >= binCount) {
25
+ bin = 0;
26
+ }
27
+ for (;;) {
28
+ while (bin % 8 === 1) {
29
+ bin = (bin - 1) / 8;
30
+ }
31
+ if (bin === 0) {
32
+ return undefined;
33
+ }
34
+ const chunks = binIndex[bin];
35
+ if (chunks?.length) {
36
+ let lowest = chunks[0].minv;
37
+ for (let i = 1; i < chunks.length; i++) {
38
+ const minv = chunks[i].minv;
39
+ if (minv.compareTo(lowest) < 0) {
40
+ lowest = minv;
41
+ }
42
+ }
43
+ return lowest;
44
+ }
45
+ bin++;
46
+ }
47
+ }
4
48
  export default class IndexFile {
5
49
  filehandle;
6
50
  /**
@@ -44,6 +88,7 @@ export default class IndexFile {
44
88
  * The chunks of the data file that may hold records overlapping the region.
45
89
  * The two index formats differ only in their binning scheme and in where
46
90
  * they keep the pruning floor, which is what the two hooks above supply.
91
+ * The ceiling, `maxOffset`, needs only the bins, so it serves both.
47
92
  *
48
93
  * @internal
49
94
  */
@@ -69,7 +114,16 @@ export default class IndexFile {
69
114
  }
70
115
  }
71
116
  }
72
- return optimizeChunks(chunks, this.lowestOffset(ba, min, indexData));
117
+ const merged = optimizeChunks(chunks, this.lowestOffset(ba, min, indexData));
118
+ const past = maxOffset(ba.binIndex, max, indexData.minShift, indexData.depth);
119
+ if (past) {
120
+ let n = merged.length;
121
+ while (n > 0 && merged[n - 1].minv.compareTo(past) >= 0) {
122
+ n--;
123
+ }
124
+ merged.length = n;
125
+ }
126
+ return merged;
73
127
  }
74
128
  // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same shape and the same
75
129
  // reasoning below.
package/esm/indexFile.js.map CHANGED
@@ -1 +1 @@
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package/esm/tabixIndexedFile.d.ts CHANGED
@@ -9,11 +9,12 @@ interface GetLinesOpts {
9
9
  signal?: AbortSignal;
10
10
  lineCallback: GetLinesCallback;
11
11
  /**
12
- * Called as the compressed data blocks covering the query are fetched, with
13
- * cumulative downloaded bytes and the total bytes to fetch. Reported at block
14
- * granularity (one tick per chunk, including instant ticks for cache hits),
15
- * which is the natural unit since chunk byte sizes are known up front from
16
- * the index. Lets callers render a determinate download progress bar.
12
+ * Called as the chunks covering the query are fetched, with cumulative
13
+ * downloaded bytes and the total bytes to fetch. One tick per chunk — the run
14
+ * of BGZF blocks the index resolves a query to — including instant ticks for
15
+ * chunks already cached. That is the natural unit here, since chunk byte
16
+ * sizes are known up front from the index, which is what lets a caller render
17
+ * a determinate progress bar rather than a spinner.
17
18
  */
18
19
  onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
19
20
  }
@@ -78,9 +79,12 @@ export default class TabixIndexedFile {
78
79
  */
79
80
  chunkCacheIdleTimeoutMs?: number;
80
81
  /**
81
- * A budget shared with other files — any `@gmod/shared-read-cache`
82
- * consumer, so `@gmod/bam` and `@gmod/cram` can join the same one — so
83
- * that the ceiling applies to their sum rather than to each of them.
82
+ * A budget shared with other files, so that the ceiling applies to their
83
+ * sum rather than to each of them. Any `@gmod/shared-read-cache` consumer
84
+ * that weighs in the same unit can join it: `@gmod/bam` also weighs
85
+ * decompressed bytes, while `@gmod/cram` weighs decoded records and
86
+ * `@gmod/bbi` weighs entries, and a budget mixing those adds bytes to
87
+ * records and bounds neither.
84
88
  *
85
89
  * {@link chunkCacheSize} is per file, which is not a bound on a consumer
86
90
  * that opens one file per track. @gmod/bam measured the shape: six tracks
package/esm/tabixIndexedFile.js CHANGED
@@ -305,8 +305,9 @@ export default class TabixIndexedFile {
305
305
  //
306
306
  // A fixed window would be wrong, though: blocksForRange offers a chunk per
307
307
  // overlapping bin across every level, and on a sparse file the early return
308
- // below stops the scan inside the first one, leaving the rest untouched
309
- // (chr22_nanopore_subset offers 7 chunks and reads 1). Prefetching those
308
+ // below can stop the scan inside the first one, leaving the rest untouched.
309
+ // max_off drops only the chunks it can prove lie past the query, so the
310
+ // scan can still end before the last one it is offered. Prefetching those
310
311
  // would multiply the bytes such a query fetches for no gain.
311
312
  //
312
313
  // Finishing a chunk without hitting the early return proves the next chunk
package/esm/tabixIndexedFile.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/tabix",
3
- "version": "3.8.1",
3
+ "version": "3.8.3",
4
4
  "packageManager": "pnpm@11.15.1",
5
5
  "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
6
6
  "type": "module",
@@ -52,7 +52,7 @@
52
52
  ],
53
53
  "dependencies": {
54
54
  "@gmod/bgzf-filehandle": "^6.6.0",
55
- "@gmod/shared-read-cache": "^1.5.1",
55
+ "@gmod/shared-read-cache": "^1.7.2",
56
56
  "@jbrowse/quick-lru": "^7.3.5",
57
57
  "generic-filehandle2": "^2.2.1"
58
58
  },
package/src/csi.ts CHANGED
@@ -41,7 +41,7 @@ export default class CSI extends IndexFile {
41
41
 
42
42
  const minShift = dataView.getInt32(4, true)
43
43
  const depth = dataView.getInt32(8, true)
44
- const maxBinNumber = ((1 << ((depth + 1) * 3)) - 1) / 7
44
+ const maxBinNumber = (8 ** (depth + 1) - 1) / 7
45
45
  const maxRefLength = 2 ** (minShift + depth * 3)
46
46
  const auxLength = dataView.getInt32(12, true)
47
47
  const aux =
package/src/indexFile.ts CHANGED
@@ -7,6 +7,56 @@ import type Chunk from './chunk.ts'
7
7
  import type VirtualOffset from './virtualOffset.ts'
8
8
  import type { GenericFilehandle } from 'generic-filehandle2'
9
9
 
10
+ /**
11
+ * The virtual offset past which a coordinate-sorted file holds nothing
12
+ * overlapping `[.., end)`, from the binning index alone: htslib's `max_off`
13
+ * (`hts_itr_query` in hts.c).
14
+ *
15
+ * Walk right from the finest bin after the one holding `end - 1`, stepping up
16
+ * to the parent at every first child, so each bin visited begins at or past
17
+ * `end` and never overlaps the query. Every record in such a bin starts at or
18
+ * past `end`, so the first chunk of the first bin that exists is a record past
19
+ * the query, and in a sorted file so is every record after it.
20
+ *
21
+ * SYNC: ~/src/gmod/bam-js/src/indexFile.ts maxOffset, and see bam-js ADR 0023
22
+ * for why the caller drops whole merged chunks with it rather than trimming.
23
+ */
24
+ export function maxOffset(
25
+ binIndex: Record<number, Chunk[]>,
26
+ end: number,
27
+ minShift: number,
28
+ depth: number,
29
+ ) {
30
+ if (end > 2 ** (minShift + depth * 3)) {
31
+ return undefined
32
+ }
33
+ const binCount = (8 ** (depth + 1) - 1) / 7
34
+ let bin = (8 ** depth - 1) / 7 + Math.floor((end - 1) / 2 ** minShift) + 1
35
+ if (bin >= binCount) {
36
+ bin = 0
37
+ }
38
+ for (;;) {
39
+ while (bin % 8 === 1) {
40
+ bin = (bin - 1) / 8
41
+ }
42
+ if (bin === 0) {
43
+ return undefined
44
+ }
45
+ const chunks = binIndex[bin]
46
+ if (chunks?.length) {
47
+ let lowest = chunks[0]!.minv
48
+ for (let i = 1; i < chunks.length; i++) {
49
+ const minv = chunks[i]!.minv
50
+ if (minv.compareTo(lowest) < 0) {
51
+ lowest = minv
52
+ }
53
+ }
54
+ return lowest
55
+ }
56
+ bin++
57
+ }
58
+ }
59
+
10
60
  export interface Options {
11
61
  signal?: AbortSignal
12
62
  /**
@@ -121,6 +171,7 @@ export default abstract class IndexFile {
121
171
  * The chunks of the data file that may hold records overlapping the region.
122
172
  * The two index formats differ only in their binning scheme and in where
123
173
  * they keep the pruning floor, which is what the two hooks above supply.
174
+ * The ceiling, `maxOffset`, needs only the bins, so it serves both.
124
175
  *
125
176
  * @internal
126
177
  */
@@ -153,7 +204,21 @@ export default abstract class IndexFile {
153
204
  }
154
205
  }
155
206
 
156
- return optimizeChunks(chunks, this.lowestOffset(ba, min, indexData))
207
+ const merged = optimizeChunks(chunks, this.lowestOffset(ba, min, indexData))
208
+ const past = maxOffset(
209
+ ba.binIndex,
210
+ max,
211
+ indexData.minShift,
212
+ indexData.depth,
213
+ )
214
+ if (past) {
215
+ let n = merged.length
216
+ while (n > 0 && merged[n - 1]!.minv.compareTo(past) >= 0) {
217
+ n--
218
+ }
219
+ merged.length = n
220
+ }
221
+ return merged
157
222
  }
158
223
 
159
224
  // SYNC: ~/src/gmod/bam-js/src/indexFile.ts parse — same shape and the same
package/src/tabixIndexedFile.ts CHANGED
@@ -64,11 +64,12 @@ interface GetLinesOpts {
64
64
  signal?: AbortSignal
65
65
  lineCallback: GetLinesCallback
66
66
  /**
67
- * Called as the compressed data blocks covering the query are fetched, with
68
- * cumulative downloaded bytes and the total bytes to fetch. Reported at block
69
- * granularity (one tick per chunk, including instant ticks for cache hits),
70
- * which is the natural unit since chunk byte sizes are known up front from
71
- * the index. Lets callers render a determinate download progress bar.
67
+ * Called as the chunks covering the query are fetched, with cumulative
68
+ * downloaded bytes and the total bytes to fetch. One tick per chunk — the run
69
+ * of BGZF blocks the index resolves a query to — including instant ticks for
70
+ * chunks already cached. That is the natural unit here, since chunk byte
71
+ * sizes are known up front from the index, which is what lets a caller render
72
+ * a determinate progress bar rather than a spinner.
72
73
  */
73
74
  onProgress?: (bytesDownloaded: number, totalBytes?: number) => void
74
75
  }
@@ -351,9 +352,12 @@ export default class TabixIndexedFile {
351
352
  */
352
353
  chunkCacheIdleTimeoutMs?: number
353
354
  /**
354
- * A budget shared with other files — any `@gmod/shared-read-cache`
355
- * consumer, so `@gmod/bam` and `@gmod/cram` can join the same one — so
356
- * that the ceiling applies to their sum rather than to each of them.
355
+ * A budget shared with other files, so that the ceiling applies to their
356
+ * sum rather than to each of them. Any `@gmod/shared-read-cache` consumer
357
+ * that weighs in the same unit can join it: `@gmod/bam` also weighs
358
+ * decompressed bytes, while `@gmod/cram` weighs decoded records and
359
+ * `@gmod/bbi` weighs entries, and a budget mixing those adds bytes to
360
+ * records and bounds neither.
357
361
  *
358
362
  * {@link chunkCacheSize} is per file, which is not a bound on a consumer
359
363
  * that opens one file per track. @gmod/bam measured the shape: six tracks
@@ -517,8 +521,9 @@ export default class TabixIndexedFile {
517
521
  //
518
522
  // A fixed window would be wrong, though: blocksForRange offers a chunk per
519
523
  // overlapping bin across every level, and on a sparse file the early return
520
- // below stops the scan inside the first one, leaving the rest untouched
521
- // (chr22_nanopore_subset offers 7 chunks and reads 1). Prefetching those
524
+ // below can stop the scan inside the first one, leaving the rest untouched.
525
+ // max_off drops only the chunks it can prove lie past the query, so the
526
+ // scan can still end before the last one it is offered. Prefetching those
522
527
  // would multiply the bytes such a query fetches for no gain.
523
528
  //
524
529
  // Finishing a chunk without hitting the early return proves the next chunk