@gmod/tabix 3.4.3 → 3.5.1
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.
- package/README.md +31 -20
- package/dist/csi.d.ts +8 -0
- package/dist/csi.js +29 -3
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +2 -0
- package/dist/indexFile.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tabixIndexedFile.js +43 -5
- package/dist/tabixIndexedFile.js.map +1 -1
- package/esm/csi.d.ts +8 -0
- package/esm/csi.js +29 -3
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +2 -0
- package/esm/indexFile.js.map +1 -1
- package/esm/tabixIndexedFile.js +43 -5
- package/esm/tabixIndexedFile.js.map +1 -1
- package/package.json +15 -14
- package/src/csi.ts +33 -3
- package/src/indexFile.ts +2 -0
- package/src/tabixIndexedFile.ts +46 -9
package/dist/tabixIndexedFile.js
CHANGED
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@@ -14,6 +14,10 @@ const TAB = 9;
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14
14
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const NEWLINE = 10;
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15
15
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const CARRIAGE_RETURN = 13;
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16
16
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const SEMICOLON = 59;
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17
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+
// Ceiling on how many chunk reads getLines keeps in flight ahead of the one it
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18
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// is parsing. Six is the HTTP/1.1 per-host connection cap browsers enforce, so
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19
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// going much above it buys nothing on the transport that matters.
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20
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+
const MAX_READ_AHEAD_CHUNKS = 6;
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21
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function resolveFilehandle(filehandle, path, url) {
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if (filehandle) {
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return filehandle;
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@@ -207,8 +211,38 @@ class TabixIndexedFile {
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}
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let downloadedBytes = 0;
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onProgress?.(0, totalBytes);
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-
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211
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-
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214
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+
// Read ahead, but only as far as the scan has earned. Every chunk is its
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215
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// own range request, so a query spanning many of them pays a network round
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216
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// trip apiece, serially — for a remote file that dominates, well ahead of
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217
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// decompression (1kg.chr1 over a 1Mb window reads 22 chunks in a row).
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218
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//
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// A fixed window would be wrong, though: blocksForRange offers a chunk per
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220
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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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// 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
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// has to be examined, so the window starts at one and doubles per chunk
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// consumed. A query that stops in its first chunk issues exactly the reads
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// a sequential scan did; a long scan reaches full concurrency after three.
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let readAhead = 1;
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const reads = [];
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const ensureReadsStarted = (count) => {
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while (reads.length < Math.min(count, chunks.length)) {
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const c = chunks[reads.length];
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const read = this.chunkCache.get(c.toString(), c, signal);
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void read.catch(() => {
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// a prefetch the early return skips is never awaited, so swallow its
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// rejection here rather than let it surface unhandled
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});
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reads.push(read);
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}
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};
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ensureReadsStarted(1);
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for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
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const c = chunks[ci];
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const { buffer, cpositions, dpositions } = await reads[ci];
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downloadedBytes += c.fetchedSize();
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onProgress?.(downloadedBytes, totalBytes);
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const minvDataPosition = c.minv.dataPosition;
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@@ -245,14 +279,14 @@ class TabixIndexedFile {
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blockStart = n + 1;
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continue;
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}
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-
let
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+
let isRefMatch = true;
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for (let i = 0; i < refLen; i++) {
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if (buffer[refStart + i] !== regionRefNameBytes[i]) {
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-
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285
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+
isRefMatch = false;
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break;
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}
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}
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-
if (!
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+
if (!isRefMatch) {
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blockStart = n + 1;
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continue;
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}
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@@ -281,6 +315,10 @@ class TabixIndexedFile {
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}
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blockStart = n + 1;
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}
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// every line in this chunk was still inside the query, so the next chunk
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319
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// has to be examined too - widen the window and start the reads for it
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readAhead = Math.min(readAhead * 2, MAX_READ_AHEAD_CHUNKS);
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ensureReadsStarted(ci + 1 + readAhead);
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}
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}
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/** @internal */
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@@ -1 +1 @@
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1
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-
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|
|
1
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G,EAAE,CAAC;oBAC3B,OAAM;gBACR,CAAC;gBAED,uBAAuB;gBACvB,IAAI,aAAqB,CAAA;gBACzB,IAAI,MAAM,KAAK,CAAC,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;oBACxC,aAAa,GAAG,eAAe,GAAG,CAAC,CAAA;gBACrC,CAAC;qBAAM,IAAI,KAAK,EAAE,CAAC;oBACjB,aAAa,GAAG,SAAS,CACvB,MAAM,EACN,eAAe,EACf,IAAI,CAAC,CAAC,CAAE,GAAG,CAAC,EACZ,IAAI,CAAC,CAAC,CAAE,EACR,IAAI,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,CAAC,EACrB,IAAI,CAAC,MAAM,CAAE,CACd,CAAA;gBACH,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,iBAAiB,CAC/B,MAAM,EACN,IAAI,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,CAAC,EACrB,IAAI,CAAC,MAAM,CAAE,CACd,CAAA;gBACH,CAAC;gBAED,IAAI,aAAa,GAAG,KAAK,EAAE,CAAC;oBAC1B,wDAAwD;oBACxD,MAAM,OAAO,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,eAAe,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC7D,MAAM,IAAI,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC,CAAA;oBACjE,QAAQ,CACN,IAAI,EACJ,mBAAmB,CACjB,UAAU,EACV,UAAU,EACV,GAAG,EACH,UAAU,EACV,gBAAgB,CACjB,EACD,eAAe,EACf,aAAa,CACd,CAAA;gBACH,CAAC;gBACD,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;YACpB,CAAC;YAED,yEAAyE;YACzE,uEAAuE;YACvE,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,SAAS,GAAG,CAAC,EAAE,qBAAqB,CAAC,CAAA;YAC1D,kBAAkB,CAAC,EAAE,GAAG,CAAC,GAAG,SAAS,CAAC,CAAA;QACxC,CAAC;IACH,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QAClC,OAAO,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,OAAgB,EAAE;QACtC,MAAM,EAAE,aAAa,EAAE,QAAQ,EAAE,YAAY,EAAE,GAC7C,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAE9B,MAAM,QAAQ,GAAG,CAAC,aAAa,EAAE,aAAa,IAAI,CAAC,CAAC,GAAG,YAAY,CAAA;QACnE,uEAAuE;QACvE,8DAA8D;QAE9D,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,QAAQ,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;QACzD,MAAM,KAAK,GAAG,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAe,CAAA;QAE9C,0CAA0C;QAC1C,IAAI,QAAQ,EAAE,CAAC;YACb,IAAI,WAAW,GAAG,CAAC,CAAC,CAAA;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YAEvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC7C,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBACrB,IAAI,CAAC,KAAK,WAAW,GAAG,CAAC,IAAI,IAAI,KAAK,QAAQ,EAAE,CAAC;oBAC/C,MAAK;gBACP,CAAC;gBACD,IAAI,IAAI,KAAK,OAAO,EAAE,CAAC;oBACrB,WAAW,GAAG,CAAC,CAAA;gBACjB,CAAC;YACH,CAAC;YACD,OAAO,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;QAC3C,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAgB,EAAE;QAChC,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9C,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;IACxC,CAAC;IAED,KAAK,CAAC,yBAAyB,CAAC,OAAgB,EAAE;QAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAC7C,OAAO,QAAQ,CAAC,WAAW,CAAA;IAC7B,CAAC;IAED,6CAA6C;IAC7C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,OAAO,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,SAAS,CAAC,CAAQ,EAAE,OAAgB,EAAE;QAC1C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,IAAI,CACpC,CAAC,CAAC,WAAW,EAAE,EACf,CAAC,CAAC,IAAI,CAAC,aAAa,EACpB,IAAI,CACL,CAAA;QACD,OAAO,IAAA,iCAAe,EAAC,GAAG,EAAE,CAAC,CAAC,CAAA;IAChC,CAAC;CACF;AAhVD,mCAgVC"}
|
package/esm/csi.d.ts
CHANGED
|
@@ -50,6 +50,14 @@ export default class CSI extends IndexFile {
|
|
|
50
50
|
format: string;
|
|
51
51
|
}>;
|
|
52
52
|
blocksForRange(refName: string, min: number, max: number, opts?: Options): Promise<Chunk[]>;
|
|
53
|
+
/**
|
|
54
|
+
* CSI's equivalent of the BAI/TBI linear index: the loffset of the deepest
|
|
55
|
+
* indexed bin covering `beg` is the earliest virtual offset any record
|
|
56
|
+
* overlapping `beg` can have, so chunks ending at or before it are dead.
|
|
57
|
+
* Walks leaf -> previous sibling -> parent until an indexed bin is found.
|
|
58
|
+
* SYNC: htslib hts_itr_query min_off computation
|
|
59
|
+
*/
|
|
60
|
+
private minOffset;
|
|
53
61
|
/** @internal */
|
|
54
62
|
reg2bins(beg: number, end: number): (readonly [number, number])[];
|
|
55
63
|
}
|
package/esm/csi.js
CHANGED
|
@@ -85,6 +85,7 @@ export default class CSI extends IndexFile {
|
|
|
85
85
|
const binCount = dataView.getInt32(pos, true);
|
|
86
86
|
pos += 4;
|
|
87
87
|
const binIndex = {};
|
|
88
|
+
const loffsets = {};
|
|
88
89
|
let stats;
|
|
89
90
|
for (let j = 0; j < binCount; j++) {
|
|
90
91
|
const bin = dataView.getUint32(pos, true);
|
|
@@ -94,7 +95,8 @@ export default class CSI extends IndexFile {
|
|
|
94
95
|
pos += 28 + 16;
|
|
95
96
|
}
|
|
96
97
|
else {
|
|
97
|
-
|
|
98
|
+
loffsets[bin] = fromBytes(bytes, pos);
|
|
99
|
+
pos += 8;
|
|
98
100
|
const chunkCount = dataView.getInt32(pos, true);
|
|
99
101
|
pos += 4;
|
|
100
102
|
const chunks = Array.from({ length: chunkCount });
|
|
@@ -106,7 +108,7 @@ export default class CSI extends IndexFile {
|
|
|
106
108
|
}
|
|
107
109
|
}
|
|
108
110
|
clampChunkEnds(Object.values(binIndex).flat());
|
|
109
|
-
return { binIndex, stats };
|
|
111
|
+
return { binIndex, loffsets, stats };
|
|
110
112
|
}
|
|
111
113
|
return {
|
|
112
114
|
...aux,
|
|
@@ -148,7 +150,31 @@ export default class CSI extends IndexFile {
|
|
|
148
150
|
}
|
|
149
151
|
}
|
|
150
152
|
}
|
|
151
|
-
return optimizeChunks(chunks);
|
|
153
|
+
return optimizeChunks(chunks, this.minOffset(ba.loffsets, min));
|
|
154
|
+
}
|
|
155
|
+
/**
|
|
156
|
+
* CSI's equivalent of the BAI/TBI linear index: the loffset of the deepest
|
|
157
|
+
* indexed bin covering `beg` is the earliest virtual offset any record
|
|
158
|
+
* overlapping `beg` can have, so chunks ending at or before it are dead.
|
|
159
|
+
* Walks leaf -> previous sibling -> parent until an indexed bin is found.
|
|
160
|
+
* SYNC: htslib hts_itr_query min_off computation
|
|
161
|
+
*/
|
|
162
|
+
minOffset(loffsets, beg) {
|
|
163
|
+
let found;
|
|
164
|
+
if (loffsets) {
|
|
165
|
+
// first bin of the deepest level, i.e. (8**depth - 1) / 7
|
|
166
|
+
let bin = (lshift(1, 3 * this.depth) - 1) / 7 + rshift(beg, this.minShift);
|
|
167
|
+
while (found === undefined && bin > 0) {
|
|
168
|
+
found = loffsets[bin];
|
|
169
|
+
if (found === undefined) {
|
|
170
|
+
const parent = Math.floor((bin - 1) / 8);
|
|
171
|
+
const firstChild = parent * 8 + 1;
|
|
172
|
+
bin = bin > firstChild ? bin - 1 : parent;
|
|
173
|
+
}
|
|
174
|
+
}
|
|
175
|
+
found ??= loffsets[0];
|
|
176
|
+
}
|
|
177
|
+
return found;
|
|
152
178
|
}
|
|
153
179
|
/** @internal */
|
|
154
180
|
reg2bins(beg, end) {
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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|
package/esm/indexFile.d.ts
CHANGED
|
@@ -16,6 +16,8 @@ export interface RefIndex {
|
|
|
16
16
|
lineCount: number;
|
|
17
17
|
};
|
|
18
18
|
linearIndex?: VirtualOffset[];
|
|
19
|
+
/** CSI only: per-bin loffset, the linear index's equivalent for pruning */
|
|
20
|
+
loffsets?: Record<number, VirtualOffset>;
|
|
19
21
|
}
|
|
20
22
|
export interface IndexData {
|
|
21
23
|
refNameToId: Record<string, number>;
|
package/esm/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAyCA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAC9B,UAAU,CAAmB;IAC5B,MAAM,CAAqB;IAEnC,YAAY,EAAE,UAAU,EAAqC;QAC3D,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;IAC9B,CAAC;IAID,gBAAgB;IACT,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACxD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;QACD,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAC,CAAA;IACzD,CAAC;IAED,gBAAgB;IACT,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QACzC,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAC7D,OAAO,IAAI,CAAA;IACb,CAAC;IAUD,gBAAgB;IAChB,KAAK,CAAC,KAAK,CAAC,OAAgB,EAAE;QAC5B,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,KAAc,EAAE,EAAE;YACzD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,MAAM,KAAK,CAAA;QACb,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;QAC/C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QAClC,OAAO,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IACvC,CAAC;CACF"}
|
package/esm/tabixIndexedFile.js
CHANGED
|
@@ -9,6 +9,10 @@ const TAB = 9;
|
|
|
9
9
|
const NEWLINE = 10;
|
|
10
10
|
const CARRIAGE_RETURN = 13;
|
|
11
11
|
const SEMICOLON = 59;
|
|
12
|
+
// Ceiling on how many chunk reads getLines keeps in flight ahead of the one it
|
|
13
|
+
// is parsing. Six is the HTTP/1.1 per-host connection cap browsers enforce, so
|
|
14
|
+
// going much above it buys nothing on the transport that matters.
|
|
15
|
+
const MAX_READ_AHEAD_CHUNKS = 6;
|
|
12
16
|
function resolveFilehandle(filehandle, path, url) {
|
|
13
17
|
if (filehandle) {
|
|
14
18
|
return filehandle;
|
|
@@ -202,8 +206,38 @@ export default class TabixIndexedFile {
|
|
|
202
206
|
}
|
|
203
207
|
let downloadedBytes = 0;
|
|
204
208
|
onProgress?.(0, totalBytes);
|
|
205
|
-
|
|
206
|
-
|
|
209
|
+
// Read ahead, but only as far as the scan has earned. Every chunk is its
|
|
210
|
+
// own range request, so a query spanning many of them pays a network round
|
|
211
|
+
// trip apiece, serially — for a remote file that dominates, well ahead of
|
|
212
|
+
// decompression (1kg.chr1 over a 1Mb window reads 22 chunks in a row).
|
|
213
|
+
//
|
|
214
|
+
// A fixed window would be wrong, though: blocksForRange offers a chunk per
|
|
215
|
+
// overlapping bin across every level, and on a sparse file the early return
|
|
216
|
+
// below stops the scan inside the first one, leaving the rest untouched
|
|
217
|
+
// (chr22_nanopore_subset offers 7 chunks and reads 1). Prefetching those
|
|
218
|
+
// would multiply the bytes such a query fetches for no gain.
|
|
219
|
+
//
|
|
220
|
+
// Finishing a chunk without hitting the early return proves the next chunk
|
|
221
|
+
// has to be examined, so the window starts at one and doubles per chunk
|
|
222
|
+
// consumed. A query that stops in its first chunk issues exactly the reads
|
|
223
|
+
// a sequential scan did; a long scan reaches full concurrency after three.
|
|
224
|
+
let readAhead = 1;
|
|
225
|
+
const reads = [];
|
|
226
|
+
const ensureReadsStarted = (count) => {
|
|
227
|
+
while (reads.length < Math.min(count, chunks.length)) {
|
|
228
|
+
const c = chunks[reads.length];
|
|
229
|
+
const read = this.chunkCache.get(c.toString(), c, signal);
|
|
230
|
+
void read.catch(() => {
|
|
231
|
+
// a prefetch the early return skips is never awaited, so swallow its
|
|
232
|
+
// rejection here rather than let it surface unhandled
|
|
233
|
+
});
|
|
234
|
+
reads.push(read);
|
|
235
|
+
}
|
|
236
|
+
};
|
|
237
|
+
ensureReadsStarted(1);
|
|
238
|
+
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
239
|
+
const c = chunks[ci];
|
|
240
|
+
const { buffer, cpositions, dpositions } = await reads[ci];
|
|
207
241
|
downloadedBytes += c.fetchedSize();
|
|
208
242
|
onProgress?.(downloadedBytes, totalBytes);
|
|
209
243
|
const minvDataPosition = c.minv.dataPosition;
|
|
@@ -240,14 +274,14 @@ export default class TabixIndexedFile {
|
|
|
240
274
|
blockStart = n + 1;
|
|
241
275
|
continue;
|
|
242
276
|
}
|
|
243
|
-
let
|
|
277
|
+
let isRefMatch = true;
|
|
244
278
|
for (let i = 0; i < refLen; i++) {
|
|
245
279
|
if (buffer[refStart + i] !== regionRefNameBytes[i]) {
|
|
246
|
-
|
|
280
|
+
isRefMatch = false;
|
|
247
281
|
break;
|
|
248
282
|
}
|
|
249
283
|
}
|
|
250
|
-
if (!
|
|
284
|
+
if (!isRefMatch) {
|
|
251
285
|
blockStart = n + 1;
|
|
252
286
|
continue;
|
|
253
287
|
}
|
|
@@ -276,6 +310,10 @@ export default class TabixIndexedFile {
|
|
|
276
310
|
}
|
|
277
311
|
blockStart = n + 1;
|
|
278
312
|
}
|
|
313
|
+
// every line in this chunk was still inside the query, so the next chunk
|
|
314
|
+
// has to be examined too - widen the window and start the reads for it
|
|
315
|
+
readAhead = Math.min(readAhead * 2, MAX_READ_AHEAD_CHUNKS);
|
|
316
|
+
ensureReadsStarted(ci + 1 + readAhead);
|
|
279
317
|
}
|
|
280
318
|
}
|
|
281
319
|
/** @internal */
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
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|
package/package.json
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/tabix",
|
|
3
|
-
"version": "3.
|
|
3
|
+
"version": "3.5.1",
|
|
4
|
+
"packageManager": "pnpm@11.15.1",
|
|
4
5
|
"description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
|
|
5
6
|
"type": "module",
|
|
6
7
|
"sideEffects": false,
|
|
@@ -56,21 +57,21 @@
|
|
|
56
57
|
},
|
|
57
58
|
"devDependencies": {
|
|
58
59
|
"@eslint/js": "^10.0.1",
|
|
59
|
-
"@types/node": "^
|
|
60
|
-
"@vitest/coverage-v8": "^4.1.
|
|
61
|
-
"eslint": "^10.
|
|
62
|
-
"eslint-plugin-import-x": "^4.
|
|
63
|
-
"eslint-plugin-unicorn": "^
|
|
64
|
-
"prettier": "^3.
|
|
60
|
+
"@types/node": "^26.1.1",
|
|
61
|
+
"@vitest/coverage-v8": "^4.1.10",
|
|
62
|
+
"eslint": "^10.7.0",
|
|
63
|
+
"eslint-plugin-import-x": "^4.17.1",
|
|
64
|
+
"eslint-plugin-unicorn": "^72.0.0",
|
|
65
|
+
"prettier": "^3.9.6",
|
|
65
66
|
"rimraf": "^6.1.3",
|
|
66
|
-
"standard-changelog": "^
|
|
67
|
-
"typedoc": "^0.28.
|
|
67
|
+
"standard-changelog": "^8.1.0",
|
|
68
|
+
"typedoc": "^0.28.20",
|
|
68
69
|
"typedoc-plugin-markdown": "^4.12.0",
|
|
69
|
-
"typescript": "^6.0.
|
|
70
|
-
"typescript-eslint": "^8.
|
|
71
|
-
"vitest": "^4.1.
|
|
72
|
-
"webpack": "^5.
|
|
73
|
-
"webpack-cli": "^7.
|
|
70
|
+
"typescript": "^6.0.0",
|
|
71
|
+
"typescript-eslint": "^8.65.0",
|
|
72
|
+
"vitest": "^4.1.10",
|
|
73
|
+
"webpack": "^5.108.4",
|
|
74
|
+
"webpack-cli": "^7.2.1"
|
|
74
75
|
},
|
|
75
76
|
"publishConfig": {
|
|
76
77
|
"access": "public"
|
package/src/csi.ts
CHANGED
|
@@ -107,6 +107,7 @@ export default class CSI extends IndexFile {
|
|
|
107
107
|
const binCount = dataView.getInt32(pos, true)
|
|
108
108
|
pos += 4
|
|
109
109
|
const binIndex: Record<number, Chunk[]> = {}
|
|
110
|
+
const loffsets: Record<number, VirtualOffset> = {}
|
|
110
111
|
let stats
|
|
111
112
|
for (let j = 0; j < binCount; j++) {
|
|
112
113
|
const bin = dataView.getUint32(pos, true)
|
|
@@ -115,7 +116,8 @@ export default class CSI extends IndexFile {
|
|
|
115
116
|
stats = parsePseudoBin(bytes, pos + 28)
|
|
116
117
|
pos += 28 + 16
|
|
117
118
|
} else {
|
|
118
|
-
|
|
119
|
+
loffsets[bin] = fromBytes(bytes, pos)
|
|
120
|
+
pos += 8
|
|
119
121
|
const chunkCount = dataView.getInt32(pos, true)
|
|
120
122
|
pos += 4
|
|
121
123
|
const chunks = Array.from<Chunk>({ length: chunkCount })
|
|
@@ -131,7 +133,7 @@ export default class CSI extends IndexFile {
|
|
|
131
133
|
}
|
|
132
134
|
}
|
|
133
135
|
clampChunkEnds(Object.values(binIndex).flat())
|
|
134
|
-
return { binIndex, stats }
|
|
136
|
+
return { binIndex, loffsets, stats }
|
|
135
137
|
}
|
|
136
138
|
|
|
137
139
|
return {
|
|
@@ -184,7 +186,35 @@ export default class CSI extends IndexFile {
|
|
|
184
186
|
}
|
|
185
187
|
}
|
|
186
188
|
|
|
187
|
-
return optimizeChunks(chunks)
|
|
189
|
+
return optimizeChunks(chunks, this.minOffset(ba.loffsets, min))
|
|
190
|
+
}
|
|
191
|
+
|
|
192
|
+
/**
|
|
193
|
+
* CSI's equivalent of the BAI/TBI linear index: the loffset of the deepest
|
|
194
|
+
* indexed bin covering `beg` is the earliest virtual offset any record
|
|
195
|
+
* overlapping `beg` can have, so chunks ending at or before it are dead.
|
|
196
|
+
* Walks leaf -> previous sibling -> parent until an indexed bin is found.
|
|
197
|
+
* SYNC: htslib hts_itr_query min_off computation
|
|
198
|
+
*/
|
|
199
|
+
private minOffset(
|
|
200
|
+
loffsets: Record<number, VirtualOffset> | undefined,
|
|
201
|
+
beg: number,
|
|
202
|
+
) {
|
|
203
|
+
let found: VirtualOffset | undefined
|
|
204
|
+
if (loffsets) {
|
|
205
|
+
// first bin of the deepest level, i.e. (8**depth - 1) / 7
|
|
206
|
+
let bin = (lshift(1, 3 * this.depth) - 1) / 7 + rshift(beg, this.minShift)
|
|
207
|
+
while (found === undefined && bin > 0) {
|
|
208
|
+
found = loffsets[bin]
|
|
209
|
+
if (found === undefined) {
|
|
210
|
+
const parent = Math.floor((bin - 1) / 8)
|
|
211
|
+
const firstChild = parent * 8 + 1
|
|
212
|
+
bin = bin > firstChild ? bin - 1 : parent
|
|
213
|
+
}
|
|
214
|
+
}
|
|
215
|
+
found ??= loffsets[0]
|
|
216
|
+
}
|
|
217
|
+
return found
|
|
188
218
|
}
|
|
189
219
|
|
|
190
220
|
/** @internal */
|
package/src/indexFile.ts
CHANGED
|
@@ -16,6 +16,8 @@ export interface RefIndex {
|
|
|
16
16
|
binIndex: Record<number, Chunk[]>
|
|
17
17
|
stats?: { lineCount: number }
|
|
18
18
|
linearIndex?: VirtualOffset[]
|
|
19
|
+
/** CSI only: per-bin loffset, the linear index's equivalent for pruning */
|
|
20
|
+
loffsets?: Record<number, VirtualOffset>
|
|
19
21
|
}
|
|
20
22
|
|
|
21
23
|
export interface IndexData {
|
package/src/tabixIndexedFile.ts
CHANGED
|
@@ -17,6 +17,11 @@ const NEWLINE = 10
|
|
|
17
17
|
const CARRIAGE_RETURN = 13
|
|
18
18
|
const SEMICOLON = 59
|
|
19
19
|
|
|
20
|
+
// Ceiling on how many chunk reads getLines keeps in flight ahead of the one it
|
|
21
|
+
// is parsing. Six is the HTTP/1.1 per-host connection cap browsers enforce, so
|
|
22
|
+
// going much above it buys nothing on the transport that matters.
|
|
23
|
+
const MAX_READ_AHEAD_CHUNKS = 6
|
|
24
|
+
|
|
20
25
|
type GetLinesCallback = (
|
|
21
26
|
line: string,
|
|
22
27
|
fileOffset: number,
|
|
@@ -327,12 +332,39 @@ export default class TabixIndexedFile {
|
|
|
327
332
|
let downloadedBytes = 0
|
|
328
333
|
onProgress?.(0, totalBytes)
|
|
329
334
|
|
|
330
|
-
|
|
331
|
-
|
|
332
|
-
|
|
333
|
-
|
|
334
|
-
|
|
335
|
-
|
|
335
|
+
// Read ahead, but only as far as the scan has earned. Every chunk is its
|
|
336
|
+
// own range request, so a query spanning many of them pays a network round
|
|
337
|
+
// trip apiece, serially — for a remote file that dominates, well ahead of
|
|
338
|
+
// decompression (1kg.chr1 over a 1Mb window reads 22 chunks in a row).
|
|
339
|
+
//
|
|
340
|
+
// A fixed window would be wrong, though: blocksForRange offers a chunk per
|
|
341
|
+
// overlapping bin across every level, and on a sparse file the early return
|
|
342
|
+
// below stops the scan inside the first one, leaving the rest untouched
|
|
343
|
+
// (chr22_nanopore_subset offers 7 chunks and reads 1). Prefetching those
|
|
344
|
+
// would multiply the bytes such a query fetches for no gain.
|
|
345
|
+
//
|
|
346
|
+
// Finishing a chunk without hitting the early return proves the next chunk
|
|
347
|
+
// has to be examined, so the window starts at one and doubles per chunk
|
|
348
|
+
// consumed. A query that stops in its first chunk issues exactly the reads
|
|
349
|
+
// a sequential scan did; a long scan reaches full concurrency after three.
|
|
350
|
+
let readAhead = 1
|
|
351
|
+
const reads: Promise<ReadChunk>[] = []
|
|
352
|
+
const ensureReadsStarted = (count: number) => {
|
|
353
|
+
while (reads.length < Math.min(count, chunks.length)) {
|
|
354
|
+
const c = chunks[reads.length]!
|
|
355
|
+
const read = this.chunkCache.get(c.toString(), c, signal)
|
|
356
|
+
void read.catch(() => {
|
|
357
|
+
// a prefetch the early return skips is never awaited, so swallow its
|
|
358
|
+
// rejection here rather than let it surface unhandled
|
|
359
|
+
})
|
|
360
|
+
reads.push(read)
|
|
361
|
+
}
|
|
362
|
+
}
|
|
363
|
+
ensureReadsStarted(1)
|
|
364
|
+
|
|
365
|
+
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
366
|
+
const c = chunks[ci]!
|
|
367
|
+
const { buffer, cpositions, dpositions } = await reads[ci]!
|
|
336
368
|
downloadedBytes += c.fetchedSize()
|
|
337
369
|
onProgress?.(downloadedBytes, totalBytes)
|
|
338
370
|
const minvDataPosition = c.minv.dataPosition
|
|
@@ -375,14 +407,14 @@ export default class TabixIndexedFile {
|
|
|
375
407
|
blockStart = n + 1
|
|
376
408
|
continue
|
|
377
409
|
}
|
|
378
|
-
let
|
|
410
|
+
let isRefMatch = true
|
|
379
411
|
for (let i = 0; i < refLen; i++) {
|
|
380
412
|
if (buffer[refStart + i] !== regionRefNameBytes[i]) {
|
|
381
|
-
|
|
413
|
+
isRefMatch = false
|
|
382
414
|
break
|
|
383
415
|
}
|
|
384
416
|
}
|
|
385
|
-
if (!
|
|
417
|
+
if (!isRefMatch) {
|
|
386
418
|
blockStart = n + 1
|
|
387
419
|
continue
|
|
388
420
|
}
|
|
@@ -436,6 +468,11 @@ export default class TabixIndexedFile {
|
|
|
436
468
|
}
|
|
437
469
|
blockStart = n + 1
|
|
438
470
|
}
|
|
471
|
+
|
|
472
|
+
// every line in this chunk was still inside the query, so the next chunk
|
|
473
|
+
// has to be examined too - widen the window and start the reads for it
|
|
474
|
+
readAhead = Math.min(readAhead * 2, MAX_READ_AHEAD_CHUNKS)
|
|
475
|
+
ensureReadsStarted(ci + 1 + readAhead)
|
|
439
476
|
}
|
|
440
477
|
}
|
|
441
478
|
|