@gmod/bam 7.1.0 → 7.1.2
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/CHANGELOG.md +8 -0
- package/dist/bai.js +10 -14
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +14 -0
- package/dist/bamFile.js +73 -7
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +5 -4
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +6 -0
- package/dist/indexFile.js +11 -0
- package/dist/indexFile.js.map +1 -1
- package/dist/util.js +50 -21
- package/dist/util.js.map +1 -1
- package/esm/bai.js +10 -14
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +14 -0
- package/esm/bamFile.js +73 -7
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +5 -4
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +6 -0
- package/esm/indexFile.js +11 -0
- package/esm/indexFile.js.map +1 -1
- package/esm/util.js +50 -21
- package/esm/util.js.map +1 -1
- package/package.json +3 -3
- package/src/bai.ts +10 -15
- package/src/bamFile.ts +98 -12
- package/src/csi.ts +5 -4
- package/src/indexFile.ts +22 -1
- package/src/util.ts +55 -20
package/CHANGELOG.md
CHANGED
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@@ -1,3 +1,11 @@
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## [7.1.2](https://github.com/GMOD/bam-js/compare/v7.1.1...v7.1.2) (2025-12-12)
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## [7.1.1](https://github.com/GMOD/bam-js/compare/v7.1.0...v7.1.1) (2025-12-12)
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# [7.1.0](https://github.com/GMOD/bam-js/compare/v7.0.6...v7.1.0) (2025-12-11)
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package/dist/bai.js
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@@ -206,28 +206,24 @@ class BAI extends indexFile_ts_1.default {
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const overlappingBins = reg2bins(min, max);
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const chunks = [];
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// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
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const { binIndex } = ba;
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for (const [start, end] of overlappingBins) {
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for (let bin = start; bin <= end; bin++) {
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for (
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chunks.push(
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const binChunks = binIndex[bin];
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if (binChunks) {
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for (let i = 0, l = binChunks.length; i < l; i++) {
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chunks.push(binChunks[i]);
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}
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}
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}
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}
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// Use the linear index to find minimum file position of chunks that could
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// contain alignments in the region
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// contain alignments in the region. Linear index entries are monotonically
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// non-decreasing, so the first entry at minLin is the minimum.
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const { linearIndex } = ba;
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const nintv = linearIndex.length;
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const minLin = Math.min(min >> 14, nintv - 1);
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const
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for (let i = minLin; i <= maxLin; ++i) {
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const vp = ba.linearIndex[i];
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if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
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lowest = vp;
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}
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}
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const lowest = linearIndex[minLin];
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return (0, util_ts_1.optimizeChunks)(chunks, lowest);
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}
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async parse(opts = {}) {
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package/dist/bai.js.map
CHANGED
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@@ -1 +1 @@
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+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;AAAA,0DAAgC;AAEhC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAKkB;AAClB,yDAA6D;AAE7D,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAQD,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KAChC,CAAA;AACZ,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAGxC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,KAAgB;QAC3B,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAE3C,0BAA0B;QAC1B,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC3C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,aAAwC,CAAA;QAE5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAE9C,IAAI,IAAI,CAAC,CAAA;YAET,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;oBACX,CAAC;gBACH,CAAC;YACH,CAAC;YAED,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,mEAAmE;YACnE,qEAAqE;YACrE,OAAO;YACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,MAAM,MAAM,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI,CAAC,CAAA;gBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;gBACpD,WAAW,CAAC,CAAC,CAAC,GAAG,MAAM,CAAA;YACzB,CAAC;QACH,CAAC;QACD,MAAM,YAAY,GAAG,IAAI,mBAAQ,CAAwC;YACvE,OAAO,EAAE,CAAC;SACX,CAAC,CAAA;QAEF,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,KAAK,CAAA;YAET,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBAC/C,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,mEAAmE;YACnE,qEAAqE;YACrE,OAAO;YACP,MAAM,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,MAAM,MAAM,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACrC,IAAI,IAAI,CAAC,CAAA;gBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;gBACpD,WAAW,CAAC,CAAC,CAAC,GAAG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|
package/dist/bamFile.d.ts
CHANGED
|
@@ -23,6 +23,11 @@ export default class BamFile {
|
|
|
23
23
|
buffer: Uint8Array;
|
|
24
24
|
nextIn: number;
|
|
25
25
|
}>;
|
|
26
|
+
chunkFeatureCache: QuickLRU<string, {
|
|
27
|
+
minBlock: number;
|
|
28
|
+
maxBlock: number;
|
|
29
|
+
features: BAMFeature[];
|
|
30
|
+
}>;
|
|
26
31
|
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, }: {
|
|
27
32
|
bamFilehandle?: GenericFilehandle;
|
|
28
33
|
bamPath?: string;
|
|
@@ -60,6 +65,9 @@ export default class BamFile {
|
|
|
60
65
|
};
|
|
61
66
|
getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<BAMFeature[]>;
|
|
62
67
|
streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
|
|
68
|
+
private chunkCacheKey;
|
|
69
|
+
private blocksOverlap;
|
|
70
|
+
private evictOverlappingChunks;
|
|
63
71
|
_fetchChunkFeatures(chunks: Chunk[], chrId: number, min: number, max: number, opts?: BamOpts): AsyncGenerator<BAMFeature[], void, unknown>;
|
|
64
72
|
fetchPairs(chrId: number, feats: BAMFeature[][], opts: BamOpts): Promise<BAMFeature[]>;
|
|
65
73
|
_readChunk({ chunk, opts }: {
|
|
@@ -77,4 +85,10 @@ export default class BamFile {
|
|
|
77
85
|
lineCount(seqName: string): Promise<number>;
|
|
78
86
|
indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;
|
|
79
87
|
blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
|
|
88
|
+
clearFeatureCache(): void;
|
|
89
|
+
estimatedBytesForRegions(regions: {
|
|
90
|
+
refName: string;
|
|
91
|
+
start: number;
|
|
92
|
+
end: number;
|
|
93
|
+
}[], opts?: BaseOpts): Promise<number>;
|
|
80
94
|
}
|
package/dist/bamFile.js
CHANGED
|
@@ -22,6 +22,9 @@ class BamFile {
|
|
|
22
22
|
this.cache = new quick_lru_1.default({
|
|
23
23
|
maxSize: 1000,
|
|
24
24
|
});
|
|
25
|
+
// Cache for parsed features by chunk
|
|
26
|
+
// When a new chunk overlaps a cached chunk, we evict the cached one
|
|
27
|
+
this.chunkFeatureCache = new quick_lru_1.default({ maxSize: 100 });
|
|
25
28
|
this.renameRefSeq = renameRefSeqs;
|
|
26
29
|
if (bamFilehandle) {
|
|
27
30
|
this.bam = bamFilehandle;
|
|
@@ -144,26 +147,62 @@ class BamFile {
|
|
|
144
147
|
const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
|
|
145
148
|
yield* this._fetchChunkFeatures(chunks, chrId, min, max, opts);
|
|
146
149
|
}
|
|
150
|
+
chunkCacheKey(chunk) {
|
|
151
|
+
const { minv, maxv } = chunk;
|
|
152
|
+
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
|
|
153
|
+
}
|
|
154
|
+
blocksOverlap(minBlock1, maxBlock1, minBlock2, maxBlock2) {
|
|
155
|
+
return minBlock1 <= maxBlock2 && maxBlock1 >= minBlock2;
|
|
156
|
+
}
|
|
157
|
+
// Evict any cached chunks that overlap with the given block range
|
|
158
|
+
evictOverlappingChunks(minBlock, maxBlock) {
|
|
159
|
+
for (const [key, entry] of this.chunkFeatureCache) {
|
|
160
|
+
if (this.blocksOverlap(minBlock, maxBlock, entry.minBlock, entry.maxBlock)) {
|
|
161
|
+
// console.log(
|
|
162
|
+
// `[BAM Cache] Evicting overlapping chunk: ${key} (${entry.features.length} features, blocks ${entry.minBlock}-${entry.maxBlock})`,
|
|
163
|
+
// )
|
|
164
|
+
this.chunkFeatureCache.delete(key);
|
|
165
|
+
}
|
|
166
|
+
}
|
|
167
|
+
}
|
|
147
168
|
async *_fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
|
|
148
169
|
const { viewAsPairs } = opts;
|
|
149
170
|
const feats = [];
|
|
150
171
|
let done = false;
|
|
172
|
+
// let cacheHits = 0
|
|
173
|
+
// let cacheMisses = 0
|
|
151
174
|
for (const chunk of chunks) {
|
|
152
|
-
const
|
|
153
|
-
|
|
154
|
-
|
|
155
|
-
|
|
156
|
-
const
|
|
175
|
+
const cacheKey = this.chunkCacheKey(chunk);
|
|
176
|
+
const minBlock = chunk.minv.blockPosition;
|
|
177
|
+
const maxBlock = chunk.maxv.blockPosition;
|
|
178
|
+
let records;
|
|
179
|
+
const cached = this.chunkFeatureCache.get(cacheKey);
|
|
180
|
+
if (cached) {
|
|
181
|
+
records = cached.features;
|
|
182
|
+
// cacheHits++
|
|
183
|
+
}
|
|
184
|
+
else {
|
|
185
|
+
this.evictOverlappingChunks(minBlock, maxBlock);
|
|
186
|
+
const { data, cpositions, dpositions } = await this._readChunk({
|
|
187
|
+
chunk,
|
|
188
|
+
opts,
|
|
189
|
+
});
|
|
190
|
+
records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
|
|
191
|
+
this.chunkFeatureCache.set(cacheKey, {
|
|
192
|
+
minBlock,
|
|
193
|
+
maxBlock,
|
|
194
|
+
features: records,
|
|
195
|
+
});
|
|
196
|
+
// cacheMisses++
|
|
197
|
+
}
|
|
157
198
|
const recs = [];
|
|
158
199
|
for (const feature of records) {
|
|
159
200
|
if (feature.ref_id === chrId) {
|
|
160
201
|
if (feature.start >= max) {
|
|
161
|
-
// past end of range, can stop iterating
|
|
162
202
|
done = true;
|
|
163
203
|
break;
|
|
164
204
|
}
|
|
165
205
|
else if (feature.end >= min) {
|
|
166
|
-
// must be in range
|
|
167
206
|
recs.push(feature);
|
|
168
207
|
}
|
|
169
208
|
}
|
|
@@ -174,6 +213,13 @@ class BamFile {
|
|
|
174
213
|
break;
|
|
175
214
|
}
|
|
176
215
|
}
|
|
216
|
+
// const total = cacheHits + cacheMisses
|
|
217
|
+
// if (total > 0) {
|
|
218
|
+
// const hitRate = (cacheHits / total) * 100
|
|
219
|
+
// console.log(
|
|
220
|
+
// `[BAM Cache] chunks: ${total}, hits: ${cacheHits}, misses: ${cacheMisses}, rate: ${hitRate.toFixed(1)}%, cacheSize: ${this.chunkFeatureCache.size}`,
|
|
221
|
+
// )
|
|
222
|
+
// }
|
|
177
223
|
if (viewAsPairs) {
|
|
178
224
|
yield this.fetchPairs(chrId, feats, opts);
|
|
179
225
|
}
|
|
@@ -308,6 +354,26 @@ class BamFile {
|
|
|
308
354
|
? []
|
|
309
355
|
: this.index.blocksForRange(seqId, start, end, opts);
|
|
310
356
|
}
|
|
357
|
+
clearFeatureCache() {
|
|
358
|
+
this.chunkFeatureCache.clear();
|
|
359
|
+
}
|
|
360
|
+
async estimatedBytesForRegions(regions, opts) {
|
|
361
|
+
if (!this.index) {
|
|
362
|
+
return 0;
|
|
363
|
+
}
|
|
364
|
+
await this.getHeader(opts);
|
|
365
|
+
if (!this.chrToIndex) {
|
|
366
|
+
throw new Error('Header not yet parsed');
|
|
367
|
+
}
|
|
368
|
+
const regionsWithIds = regions.map(r => {
|
|
369
|
+
const refId = this.chrToIndex[r.refName];
|
|
370
|
+
if (refId === undefined) {
|
|
371
|
+
throw new Error(`Unknown reference name: ${r.refName}`);
|
|
372
|
+
}
|
|
373
|
+
return { refId, start: r.start, end: r.end };
|
|
374
|
+
});
|
|
375
|
+
return this.index.estimatedBytesForRegions(regionsWithIds, opts);
|
|
376
|
+
}
|
|
311
377
|
}
|
|
312
378
|
exports.default = BamFile;
|
|
313
379
|
//# sourceMappingURL=bamFile.js.map
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
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+
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|
package/dist/csi.js
CHANGED
|
@@ -185,12 +185,13 @@ class CSI extends indexFile_ts_1.default {
|
|
|
185
185
|
}
|
|
186
186
|
const chunks = [];
|
|
187
187
|
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
|
|
188
|
+
const { binIndex } = ba;
|
|
188
189
|
for (const [start, end] of overlappingBins) {
|
|
189
190
|
for (let bin = start; bin <= end; bin++) {
|
|
190
|
-
|
|
191
|
-
|
|
192
|
-
for (
|
|
193
|
-
chunks.push(
|
|
191
|
+
const binChunks = binIndex[bin];
|
|
192
|
+
if (binChunks) {
|
|
193
|
+
for (let i = 0, l = binChunks.length; i < l; i++) {
|
|
194
|
+
chunks.push(binChunks[i]);
|
|
194
195
|
}
|
|
195
196
|
}
|
|
196
197
|
}
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,0DAAgC;AAEhC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,0DAAgC;AAEhC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;IAwPtB,CAAC;IApPC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GACV,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EACnC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,IAAA,wBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;oBACjD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,mBAAQ,CAAwC;YACvE,OAAO,EAAE,CAAC;SACX,CAAC,CAAA;QAEF,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,cAAc,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,cAAc,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACpE,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,OAAO;gBACL,QAAQ;gBACR,KAAK,EAAE,cAAc;aACtB,CAAA;QACH,CAAC;QAED,OAAO;YACL,UAAU;YACV,aAAa;YACb,OAAO,EAAE,CAAC,KAAa,EAAE,EAAE;gBACzB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;oBAC7B,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBAChC,IAAI,MAAM,EAAE,CAAC;wBACX,YAAY,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;oBACjC,CAAC;oBACD,OAAO,MAAM,CAAA;gBACf,CAAC;gBACD,OAAO,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAChC,CAAC;YACD,QAAQ;YACR,GAAG,EAAE,IAAI;YACT,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,GAAG,GAAG;SACP,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAEnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAE/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,MAAM,GAAG,EAAE,CAAA;QACjB,sEAAsE;QACtE,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;QACvB,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAC/B,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;wBACjD,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxD,CAAC;IAED;;;OAGG;IACH,QAAQ,CAAC,GAAW,EAAE,GAAW;QAC/B,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;QACvC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC;YAClB,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;QACf,CAAC,CAAC,wCAAwC;QAC1C,GAAG,IAAI,CAAC,CAAA;QACR,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,OAAO,CAAC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC5C,MAAM,IAAI,KAAK,CACb,SAAS,GAAG,IAAI,GAAG,mDAAmD,IAAI,CAAC,QAAQ,WAAW,IAAI,CAAC,KAAK,0DAA0D,CACnK,CAAA;YACH,CAAC;YACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAU,CAAC,CAAA;QAC5B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE;QAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACrC,OAAO,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IAC1C,CAAC;CACF;AA3PD,sBA2PC"}
|
package/dist/indexFile.d.ts
CHANGED
|
@@ -1,6 +1,11 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
2
|
import { BaseOpts } from './util.ts';
|
|
3
3
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
4
|
+
export interface Region {
|
|
5
|
+
refId: number;
|
|
6
|
+
start: number;
|
|
7
|
+
end: number;
|
|
8
|
+
}
|
|
4
9
|
export default abstract class IndexFile {
|
|
5
10
|
filehandle: GenericFilehandle;
|
|
6
11
|
renameRefSeq: (s: string) => string;
|
|
@@ -15,4 +20,5 @@ export default abstract class IndexFile {
|
|
|
15
20
|
score: number;
|
|
16
21
|
}[]>;
|
|
17
22
|
abstract blocksForRange(chrId: number, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
|
|
23
|
+
estimatedBytesForRegions(regions: Region[], opts?: BaseOpts): Promise<number>;
|
|
18
24
|
}
|
package/dist/indexFile.js
CHANGED
|
@@ -1,10 +1,21 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
+
const util_ts_1 = require("./util.js");
|
|
3
4
|
class IndexFile {
|
|
4
5
|
constructor({ filehandle, renameRefSeq = (n) => n, }) {
|
|
5
6
|
this.filehandle = filehandle;
|
|
6
7
|
this.renameRefSeq = renameRefSeq;
|
|
7
8
|
}
|
|
9
|
+
async estimatedBytesForRegions(regions, opts) {
|
|
10
|
+
const blockResults = await Promise.all(regions.map(r => this.blocksForRange(r.refId, r.start, r.end, opts)));
|
|
11
|
+
// Deduplicate and merge overlapping blocks across all regions
|
|
12
|
+
const mergedBlocks = (0, util_ts_1.optimizeChunks)(blockResults.flat());
|
|
13
|
+
let total = 0;
|
|
14
|
+
for (const block of mergedBlocks) {
|
|
15
|
+
total += block.fetchedSize();
|
|
16
|
+
}
|
|
17
|
+
return total;
|
|
18
|
+
}
|
|
8
19
|
}
|
|
9
20
|
exports.default = IndexFile;
|
|
10
21
|
//# sourceMappingURL=indexFile.js.map
|
package/dist/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":";;AACA,uCAAoD;AAUpD,MAA8B,SAAS;IAIrC,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;IAeD,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,IAAA,wBAAc,EAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AA1CD,4BA0CC"}
|
package/dist/util.js
CHANGED
|
@@ -17,33 +17,62 @@ function makeOpts(obj = {}) {
|
|
|
17
17
|
return 'aborted' in obj ? { signal: obj } : obj;
|
|
18
18
|
}
|
|
19
19
|
function optimizeChunks(chunks, lowest) {
|
|
20
|
-
const
|
|
21
|
-
|
|
22
|
-
if (chunks.length === 0) {
|
|
20
|
+
const n = chunks.length;
|
|
21
|
+
if (n === 0) {
|
|
23
22
|
return chunks;
|
|
24
23
|
}
|
|
25
|
-
chunks
|
|
24
|
+
// Pre-filter chunks below lowest threshold before sorting
|
|
25
|
+
let filtered;
|
|
26
|
+
if (lowest) {
|
|
27
|
+
const lowestBlock = lowest.blockPosition;
|
|
28
|
+
const lowestData = lowest.dataPosition;
|
|
29
|
+
filtered = [];
|
|
30
|
+
for (let i = 0; i < n; i++) {
|
|
31
|
+
const chunk = chunks[i];
|
|
32
|
+
const maxv = chunk.maxv;
|
|
33
|
+
const cmp = maxv.blockPosition - lowestBlock || maxv.dataPosition - lowestData;
|
|
34
|
+
if (cmp > 0) {
|
|
35
|
+
filtered.push(chunk);
|
|
36
|
+
}
|
|
37
|
+
}
|
|
38
|
+
if (filtered.length === 0) {
|
|
39
|
+
return filtered;
|
|
40
|
+
}
|
|
41
|
+
}
|
|
42
|
+
else {
|
|
43
|
+
filtered = chunks;
|
|
44
|
+
}
|
|
45
|
+
filtered.sort((c0, c1) => {
|
|
26
46
|
const dif = c0.minv.blockPosition - c1.minv.blockPosition;
|
|
27
|
-
return dif
|
|
47
|
+
return dif !== 0 ? dif : c0.minv.dataPosition - c1.minv.dataPosition;
|
|
28
48
|
});
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
|
|
35
|
-
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
|
|
39
|
-
|
|
40
|
-
|
|
41
|
-
|
|
42
|
-
|
|
43
|
-
|
|
44
|
-
|
|
49
|
+
const mergedChunks = [];
|
|
50
|
+
let lastChunk = filtered[0];
|
|
51
|
+
mergedChunks.push(lastChunk);
|
|
52
|
+
let lastMinBlock = lastChunk.minv.blockPosition;
|
|
53
|
+
let lastMaxBlock = lastChunk.maxv.blockPosition;
|
|
54
|
+
for (let i = 1; i < filtered.length; i++) {
|
|
55
|
+
const chunk = filtered[i];
|
|
56
|
+
const chunkMinBlock = chunk.minv.blockPosition;
|
|
57
|
+
const chunkMaxBlock = chunk.maxv.blockPosition;
|
|
58
|
+
// Inlined canMergeBlocks: check if chunks are close enough to merge
|
|
59
|
+
if (chunkMinBlock - lastMaxBlock < 65000 &&
|
|
60
|
+
chunkMaxBlock - lastMinBlock < 5000000) {
|
|
61
|
+
const chunkMaxv = chunk.maxv;
|
|
62
|
+
const lastMaxv = lastChunk.maxv;
|
|
63
|
+
const cmp = chunkMaxBlock - lastMaxBlock ||
|
|
64
|
+
chunkMaxv.dataPosition - lastMaxv.dataPosition;
|
|
65
|
+
if (cmp > 0) {
|
|
66
|
+
lastChunk.maxv = chunkMaxv;
|
|
67
|
+
lastMaxBlock = chunkMaxBlock;
|
|
45
68
|
}
|
|
46
69
|
}
|
|
70
|
+
else {
|
|
71
|
+
mergedChunks.push(chunk);
|
|
72
|
+
lastChunk = chunk;
|
|
73
|
+
lastMinBlock = chunkMinBlock;
|
|
74
|
+
lastMaxBlock = chunkMaxBlock;
|
|
75
|
+
}
|
|
47
76
|
}
|
|
48
77
|
return mergedChunks;
|
|
49
78
|
}
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAIA,wCAKC;AAaD,4BAEC;AAED,
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAIA,wCAKC;AAaD,4BAEC;AAED,wCAmEC;AAED,wCAIC;AAED,sCASC;AAED,wCAwBC;AAED,4CAYC;AAED,8BAQC;AA/JD,uCAAmD;AAGnD,SAAgB,cAAc,CAAC,MAAa,EAAE,MAAa;IACzD,OAAO,CACL,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,KAAK;QAC7D,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,IAAI,CAAC,aAAa,GAAG,OAAO,CAChE,CAAA;AACH,CAAC;AAaD,SAAgB,QAAQ,CAAC,MAA8B,EAAE;IACvD,OAAO,SAAS,IAAI,GAAG,CAAC,CAAC,CAAE,EAAE,MAAM,EAAE,GAAG,EAAe,CAAC,CAAC,CAAC,GAAG,CAAA;AAC/D,CAAC;AAED,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAe;IAC7D,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;IACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,MAAM,CAAA;IACf,CAAC;IAED,0DAA0D;IAC1D,IAAI,QAAiB,CAAA;IACrB,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,WAAW,GAAG,MAAM,CAAC,aAAa,CAAA;QACxC,MAAM,UAAU,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,QAAQ,GAAG,EAAE,CAAA;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;YACxB,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;YACvB,MAAM,GAAG,GACP,IAAI,CAAC,aAAa,GAAG,WAAW,IAAI,IAAI,CAAC,YAAY,GAAG,UAAU,CAAA;YACpE,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACtB,CAAC;QACH,CAAC;QACD,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,QAAQ,CAAA;QACjB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,QAAQ,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,MAAM,YAAY,GAAY,EAAE,CAAA;IAChC,IAAI,SAAS,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;IAC5B,YAAY,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;IAE5B,IAAI,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,aAAa,CAAA;IAC/C,IAAI,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,aAAa,CAAA;IAE/C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,oEAAoE;QACpE,IACE,aAAa,GAAG,YAAY,GAAG,KAAK;YACpC,aAAa,GAAG,YAAY,GAAG,OAAO,EACtC,CAAC;YACD,MAAM,SAAS,GAAG,KAAK,CAAC,IAAI,CAAA;YAC5B,MAAM,QAAQ,GAAG,SAAS,CAAC,IAAI,CAAA;YAC/B,MAAM,GAAG,GACP,aAAa,GAAG,YAAY;gBAC5B,SAAS,CAAC,YAAY,GAAG,QAAQ,CAAC,YAAY,CAAA;YAChD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,SAAS,CAAC,IAAI,GAAG,SAAS,CAAA;gBAC1B,YAAY,GAAG,aAAa,CAAA;YAC9B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACxB,SAAS,GAAG,KAAK,CAAA;YACjB,YAAY,GAAG,aAAa,CAAA;YAC5B,YAAY,GAAG,aAAa,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,SAAgB,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO;QACL,SAAS,EAAE,IAAA,iCAAuB,EAAC,KAAK,EAAE,MAAM,CAAC;KAClD,CAAA;AACH,CAAC;AAED,SAAgB,aAAa,CAC3B,aAAwC,EACxC,aAA4B;IAE5B,OAAO,aAAa;QAClB,CAAC,CAAC,aAAa,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;YAC1C,CAAC,CAAC,aAAa;YACf,CAAC,CAAC,aAAa;QACjB,CAAC,CAAC,aAAa,CAAA;AACnB,CAAC;AAED,SAAgB,cAAc,CAC5B,UAAsB,EACtB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAG,EAAE,CAAA;IACtB,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC9C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,IAAI,OAAO,GAAG,EAAE,CAAA;gBAChB,KAAK,IAAI,CAAC,GAAG,aAAa,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;oBACvC,OAAO,IAAI,MAAM,CAAC,YAAY,CAAC,UAAU,CAAC,CAAC,CAAE,CAAC,CAAA;gBAChD,CAAC;gBACD,OAAO,GAAG,YAAY,CAAC,OAAO,CAAC,CAAA;gBAC/B,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;YAClC,CAAC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,SAAgB,gBAAgB,CAAC,IAAkB;IACjD,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,IAAI,KAAK,CAAC,MAAM,CAAA;IAC7B,CAAC;IACD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;IAC/C,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAEM,KAAK,UAAU,SAAS,CAAI,GAAuB;IACxD,MAAM,GAAG,GAAQ,EAAE,CAAA;IACnB,IAAI,KAAK,EAAE,MAAM,CAAC,IAAI,GAAG,EAAE,CAAC;QAC1B,KAAK,MAAM,IAAI,IAAI,CAAC,EAAE,CAAC;YACrB,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QAChB,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
|
package/esm/bai.js
CHANGED
|
@@ -201,28 +201,24 @@ export default class BAI extends IndexFile {
|
|
|
201
201
|
const overlappingBins = reg2bins(min, max);
|
|
202
202
|
const chunks = [];
|
|
203
203
|
// Find chunks in overlapping bins. Leaf bins (< 4681) are not pruned
|
|
204
|
+
const { binIndex } = ba;
|
|
204
205
|
for (const [start, end] of overlappingBins) {
|
|
205
206
|
for (let bin = start; bin <= end; bin++) {
|
|
206
|
-
|
|
207
|
-
|
|
208
|
-
for (
|
|
209
|
-
chunks.push(
|
|
207
|
+
const binChunks = binIndex[bin];
|
|
208
|
+
if (binChunks) {
|
|
209
|
+
for (let i = 0, l = binChunks.length; i < l; i++) {
|
|
210
|
+
chunks.push(binChunks[i]);
|
|
210
211
|
}
|
|
211
212
|
}
|
|
212
213
|
}
|
|
213
214
|
}
|
|
214
215
|
// Use the linear index to find minimum file position of chunks that could
|
|
215
|
-
// contain alignments in the region
|
|
216
|
-
|
|
217
|
-
|
|
216
|
+
// contain alignments in the region. Linear index entries are monotonically
|
|
217
|
+
// non-decreasing, so the first entry at minLin is the minimum.
|
|
218
|
+
const { linearIndex } = ba;
|
|
219
|
+
const nintv = linearIndex.length;
|
|
218
220
|
const minLin = Math.min(min >> 14, nintv - 1);
|
|
219
|
-
const
|
|
220
|
-
for (let i = minLin; i <= maxLin; ++i) {
|
|
221
|
-
const vp = ba.linearIndex[i];
|
|
222
|
-
if (vp && (!lowest || vp.compareTo(lowest) < 0)) {
|
|
223
|
-
lowest = vp;
|
|
224
|
-
}
|
|
225
|
-
}
|
|
221
|
+
const lowest = linearIndex[minLin];
|
|
226
222
|
return optimizeChunks(chunks, lowest);
|
|
227
223
|
}
|
|
228
224
|
async parse(opts = {}) {
|
package/esm/bai.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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