@gmod/bam 9.0.0 → 10.0.0
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 +24 -21
- package/dist/bai.d.ts +2 -0
- package/dist/bai.js +19 -0
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.js +11 -19
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.d.ts +20 -29
- package/dist/csi.js +27 -10
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +21 -1
- package/dist/indexFile.js +60 -2
- package/dist/indexFile.js.map +1 -1
- package/dist/record.d.ts +1 -0
- package/dist/record.js +39 -22
- package/dist/record.js.map +1 -1
- package/dist/streamBam.js +2 -2
- package/dist/streamBam.js.map +1 -1
- package/dist/util.d.ts +15 -4
- package/dist/util.js +29 -4
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.d.ts +1 -0
- package/dist/virtualOffset.js +4 -0
- package/dist/virtualOffset.js.map +1 -1
- package/esm/bai.d.ts +2 -0
- package/esm/bai.js +19 -0
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.js +12 -20
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.d.ts +20 -29
- package/esm/csi.js +27 -10
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +21 -1
- package/esm/indexFile.js +59 -2
- package/esm/indexFile.js.map +1 -1
- package/esm/record.d.ts +1 -0
- package/esm/record.js +39 -22
- package/esm/record.js.map +1 -1
- package/esm/streamBam.js +3 -3
- package/esm/streamBam.js.map +1 -1
- package/esm/util.d.ts +15 -4
- package/esm/util.js +27 -4
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.d.ts +1 -0
- package/esm/virtualOffset.js +3 -0
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +7 -7
- package/src/bai.ts +21 -0
- package/src/bamFile.ts +14 -21
- package/src/csi.ts +41 -14
- package/src/indexFile.ts +72 -3
- package/src/record.ts +45 -21
- package/src/streamBam.ts +4 -4
- package/src/util.ts +33 -4
- package/src/virtualOffset.ts +4 -0
package/dist/virtualOffset.d.ts
CHANGED
package/dist/virtualOffset.js
CHANGED
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@@ -2,6 +2,7 @@
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.VirtualOffset = void 0;
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exports.fromBytes = fromBytes;
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exports.compareOffsets = compareOffsets;
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class VirtualOffset {
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blockPosition;
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dataPosition;
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@@ -22,4 +23,7 @@ function fromBytes(bytes, offset = 0) {
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bytes[offset + 3] * 0x100 +
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bytes[offset + 2], (bytes[offset + 1] << 8) | bytes[offset]);
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}
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function compareOffsets(a, b) {
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return a.blockPosition - b.blockPosition || a.dataPosition - b.dataPosition;
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}
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//# sourceMappingURL=virtualOffset.js.map
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AA0BA,8BAUC;
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{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AA0BA,8BAUC;AAED,wCAEC;AA1BD,MAAa,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;CACF;AAXD,sCAWC;AACD,SAAgB,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC;IACrD,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC;AAED,SAAgB,cAAc,CAAC,CAAe,EAAE,CAAe;IAC7D,OAAO,CAAC,CAAC,aAAa,GAAG,CAAC,CAAC,aAAa,IAAI,CAAC,CAAC,YAAY,GAAG,CAAC,CAAC,YAAY,CAAA;AAC7E,CAAC"}
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package/esm/bai.d.ts
CHANGED
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@@ -14,6 +14,8 @@ export interface IndexCovEntry {
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score: number;
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}
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export default class BAI extends IndexFile<BaiParsed> {
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protected minShift: number;
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protected depth: number;
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_parse(opts: BaseOpts): Promise<BaiParsed>;
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indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<IndexCovEntry[]>;
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protected reg2bins(min: number, max: number): readonly [readonly [0, 0], readonly [number, number], readonly [number, number], readonly [number, number], readonly [number, number], readonly [number, number]];
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package/esm/bai.js
CHANGED
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@@ -23,6 +23,22 @@ function roundUp(n, multiple) {
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const rem = n % multiple;
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return rem === 0 ? n : n - rem + multiple;
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}
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/**
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* Older samtools leaves 0:0 in linear-index windows no read overlaps. htslib
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* fills interior ones from the next entry on load (`hts.c`, "fill missing
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* values"); this also fills leading ones, which htslib leaves at 0. Either
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* way the entry stays a lower bound, since no record overlaps that window.
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* Left as 0, a leading entry scores its whole absolute file offset in
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* `indexCov`, and `getLowestChunk` falls back to the start of the file.
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*/
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function fillLinearGaps(blocks, data) {
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for (let j = blocks.length - 2; j >= 0; j--) {
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if (blocks[j] === 0 && data[j] === 0) {
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blocks[j] = blocks[j + 1];
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data[j] = data[j + 1];
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}
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}
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}
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// Compute bin ranges that overlap [beg, end). Each level's first-bin offset
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// is (8^L - 1) / 7. See SAMv1.pdf §5.1.1 for the binning derivation.
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function reg2bins(beg, end) {
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@@ -50,6 +66,8 @@ function reg2bins(beg, end) {
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];
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}
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export default class BAI extends IndexFile {
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minShift = BAI_LINEAR_SHIFT;
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depth = BAI_DEPTH;
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async _parse(opts) {
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const bytes = await this.filehandle.readFile(opts);
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const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
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@@ -146,6 +164,7 @@ export default class BAI extends IndexFile {
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linearDataPositions[j] = (bytes[curr + 1] << 8) | bytes[curr];
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curr += 8;
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}
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fillLinearGaps(linearBlockPositions, linearDataPositions);
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clampChunkEnds(Object.values(binIndex).flat(), linearBlockPositions);
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return {
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binIndex,
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package/esm/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,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC5E,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAmB9C,MAAM,eAAe,GAAG,IAAI,YAAY,CAAC,CAAC,CAAC,CAAA;AAM3C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,4EAA4E;AAC5E,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAC3B,MAAM,mBAAmB,GAAG,CAAC,IAAI,gBAAgB,CAAA,CAAC,QAAQ;AAC1D,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,wEAAwE;AACxE,8DAA8D;AAC9D,MAAM,WAAW,GAAG,CAAC,IAAI,CAAC,gBAAgB,GAAG,SAAS,GAAG,CAAC,CAAC,CAAA,CAAC,OAAO;AAEnE,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,yEAAyE;AACzE,8EAA8E;AAC9E,0CAA0C;AAC1C,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,MAAM,GAAG,GAAG,CAAC,GAAG,QAAQ,CAAA;IACxB,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,GAAG,QAAQ,CAAA;AAC3C,CAAC;AAQD,4EAA4E;AAC5E,qEAAqE;AACrE,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,yEAAyE;IACzE,wEAAwE;IACxE,sEAAsE;IACtE,2EAA2E;IAC3E,0EAA0E;IAC1E,0EAA0E;IAC1E,wEAAwE;IACxE,IAAI,GAAG,GAAG,WAAW,EAAE,CAAC;QACtB,GAAG,GAAG,WAAW,CAAA;IACnB,CAAC;IACD,IAAI,GAAG,GAAG,WAAW,EAAE,CAAC;QACtB,GAAG,GAAG,WAAW,CAAA;IACnB,CAAC;IACD,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,gBAAgB,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,gBAAgB,CAAC,CAAC;KAC5D,CAAA;AACZ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAoB;
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|
+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC5E,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAmB9C,MAAM,eAAe,GAAG,IAAI,YAAY,CAAC,CAAC,CAAC,CAAA;AAM3C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,4EAA4E;AAC5E,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAC3B,MAAM,mBAAmB,GAAG,CAAC,IAAI,gBAAgB,CAAA,CAAC,QAAQ;AAC1D,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,wEAAwE;AACxE,8DAA8D;AAC9D,MAAM,WAAW,GAAG,CAAC,IAAI,CAAC,gBAAgB,GAAG,SAAS,GAAG,CAAC,CAAC,CAAA,CAAC,OAAO;AAEnE,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,yEAAyE;AACzE,8EAA8E;AAC9E,0CAA0C;AAC1C,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,MAAM,GAAG,GAAG,CAAC,GAAG,QAAQ,CAAA;IACxB,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,GAAG,QAAQ,CAAA;AAC3C,CAAC;AAED;;;;;;;GAOG;AACH,SAAS,cAAc,CAAC,MAAoB,EAAE,IAAkB;IAC9D,KAAK,IAAI,CAAC,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC5C,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YACrC,MAAM,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;YAC1B,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;QACxB,CAAC;IACH,CAAC;AACH,CAAC;AAQD,4EAA4E;AAC5E,qEAAqE;AACrE,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,yEAAyE;IACzE,wEAAwE;IACxE,sEAAsE;IACtE,2EAA2E;IAC3E,0EAA0E;IAC1E,0EAA0E;IAC1E,wEAAwE;IACxE,IAAI,GAAG,GAAG,WAAW,EAAE,CAAC;QACtB,GAAG,GAAG,WAAW,CAAA;IACnB,CAAC;IACD,IAAI,GAAG,GAAG,WAAW,EAAE,CAAC;QACtB,GAAG,GAAG,WAAW,CAAA;IACnB,CAAC;IACD,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,gBAAgB,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,gBAAgB,CAAC,CAAC;KAC5D,CAAA;AACZ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAoB;IACzC,QAAQ,GAAG,gBAAgB,CAAA;IAC3B,KAAK,GAAG,SAAS,CAAA;IAE3B,KAAK,CAAC,MAAM,CAAC,IAAc;QACzB,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,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,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAEvD,+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,gEAAgE;oBAChE,8DAA8D;oBAC9D,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAA;gBAC7B,CAAC;YACH,CAAC;YAED,mEAAmE;YACnE,kDAAkD;YAClD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,aAAa,GAAG,gBAAgB,CAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,CAAC,CAAA;YACzE,IAAI,IAAI,CAAC,GAAG,WAAW,CAAA;QACzB,CAAC;QAED,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,cAAc,CAAC,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,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,SAAS,C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|
package/esm/bamFile.js
CHANGED
|
@@ -7,7 +7,7 @@ import NullFilehandle from "./nullFilehandle.js";
|
|
|
7
7
|
import BAMFeature from "./record.js";
|
|
8
8
|
import { packReference, referenceCovers } from "./reference.js";
|
|
9
9
|
import { parseHeaderText } from "./sam.js";
|
|
10
|
-
import { BAM_MAGIC, MAX_CONCURRENT_CHUNK_READS, appendInRange, parseRefSeqs, resolveFilehandle, throwIfAborted, } from "./util.js";
|
|
10
|
+
import { BAM_MAGIC, MAX_CONCURRENT_CHUNK_READS, appendInRange, decodeHeaderText, optimizeChunks, parseRefSeqs, readBlockSize, resolveFilehandle, throwIfAborted, } from "./util.js";
|
|
11
11
|
const blockLen = 1 << 16;
|
|
12
12
|
// Ceiling on GROWING the header read. A million contigs is roughly 10MB of
|
|
13
13
|
// compressed @SQ lines and ref-seq table, so a read that has doubled past this
|
|
@@ -198,7 +198,7 @@ export default class BamFile {
|
|
|
198
198
|
const parsed = parseRefSeqs(uncba, headLen + 8, this.renameRefSeq);
|
|
199
199
|
let samHeader;
|
|
200
200
|
if (parsed) {
|
|
201
|
-
const headerText =
|
|
201
|
+
const headerText = decodeHeaderText(uncba, headLen);
|
|
202
202
|
this.header = headerText;
|
|
203
203
|
this.chrToIndex = parsed.chrToIndex;
|
|
204
204
|
this.indexToChr = parsed.indexToChr;
|
|
@@ -260,7 +260,7 @@ export default class BamFile {
|
|
|
260
260
|
if (chrId === undefined || !this.index) {
|
|
261
261
|
return [];
|
|
262
262
|
}
|
|
263
|
-
const chunks = await this.index.blocksForRange(chrId, min
|
|
263
|
+
const chunks = await this.index.blocksForRange(chrId, min, max, opts);
|
|
264
264
|
return this._fetchChunkFeatures(chunks, chrId, chr, min, max, opts);
|
|
265
265
|
}
|
|
266
266
|
/**
|
|
@@ -495,38 +495,30 @@ export default class BamFile {
|
|
|
495
495
|
// make the count NaN.
|
|
496
496
|
const readNameCounts = new Map();
|
|
497
497
|
const readIds = new Set();
|
|
498
|
+
const names = new Array(records.length);
|
|
498
499
|
for (let i = 0, l = records.length; i < l; i++) {
|
|
499
500
|
const r = records[i];
|
|
500
501
|
const name = r.name;
|
|
502
|
+
names[i] = name;
|
|
501
503
|
readNameCounts.set(name, (readNameCounts.get(name) ?? 0) + 1);
|
|
502
504
|
readIds.add(r.fileOffset);
|
|
503
505
|
}
|
|
504
506
|
const matePromises = [];
|
|
505
507
|
for (let i = 0, l = records.length; i < l; i++) {
|
|
506
508
|
const f = records[i];
|
|
507
|
-
const name = f.name;
|
|
508
509
|
if (this.index &&
|
|
509
|
-
readNameCounts.get(
|
|
510
|
+
readNameCounts.get(names[i]) === 1 &&
|
|
510
511
|
(pairAcrossChr ||
|
|
511
512
|
(f.next_refid === chrId &&
|
|
512
513
|
Math.abs(f.start - f.next_pos) < maxInsertSize))) {
|
|
513
514
|
matePromises.push(this.index.blocksForRange(f.next_refid, f.next_pos, f.next_pos + 1, opts));
|
|
514
515
|
}
|
|
515
516
|
}
|
|
516
|
-
|
|
517
|
-
|
|
518
|
-
|
|
519
|
-
|
|
520
|
-
|
|
521
|
-
const m = chunks[j];
|
|
522
|
-
// Key on the virtual-offset span — the same key _cachedChunkFeatures
|
|
523
|
-
// uses. Chunk.toString() also folds in `bin` and fetchedSize(), which
|
|
524
|
-
// keeps two chunks covering an identical span apart here even though
|
|
525
|
-
// the cache below collapses them, so their records came back twice.
|
|
526
|
-
map.set(chunkCacheKey(m), m);
|
|
527
|
-
}
|
|
528
|
-
}
|
|
529
|
-
const mateChunks = [...map.values()];
|
|
517
|
+
// Each mate's lookup is merged on its own, so two of them can resolve to
|
|
518
|
+
// different spans over the same records. Merging the union again makes
|
|
519
|
+
// them disjoint, which is what keeps a mate in the overlap from coming
|
|
520
|
+
// back once per span.
|
|
521
|
+
const mateChunks = optimizeChunks((await Promise.all(matePromises)).flat());
|
|
530
522
|
// Bounded for the reason ADR 0008 bounds the main query path: a viewAsPairs
|
|
531
523
|
// query over a busy region resolves to many distinct mate chunks, and an
|
|
532
524
|
// unbounded fan-out inflates every one of them at once. Same inline pool
|
|
@@ -605,7 +597,7 @@ export default class BamFile {
|
|
|
605
597
|
const hasDpositions = dpositions.length > 0;
|
|
606
598
|
const hasCpositions = cpositions.length > 0;
|
|
607
599
|
while (blockStart + 4 < ba.length) {
|
|
608
|
-
const blockSize = dataView
|
|
600
|
+
const blockSize = readBlockSize(dataView, blockStart);
|
|
609
601
|
const blockEnd = blockStart + 4 + blockSize - 1;
|
|
610
602
|
if (hasDpositions) {
|
|
611
603
|
const target = blockStart + chunk.minv.dataPosition;
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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|
package/esm/csi.d.ts
CHANGED
|
@@ -1,11 +1,17 @@
|
|
|
1
|
-
import Chunk from './chunk.ts';
|
|
2
1
|
import IndexFile from './indexFile.ts';
|
|
3
2
|
import { VirtualOffset } from './virtualOffset.ts';
|
|
3
|
+
import type { ParsedIndexBase, RefIndex } from './indexFile.ts';
|
|
4
4
|
import type { BaseOpts } from './util.ts';
|
|
5
|
-
|
|
5
|
+
interface CsiRefIndex extends RefIndex {
|
|
6
|
+
loffsets: Map<number, VirtualOffset>;
|
|
7
|
+
}
|
|
8
|
+
interface CsiParsed extends ParsedIndexBase<CsiRefIndex> {
|
|
9
|
+
csi: true;
|
|
10
|
+
}
|
|
11
|
+
export default class CSI extends IndexFile<CsiParsed> {
|
|
6
12
|
private maxBinNumber;
|
|
7
|
-
|
|
8
|
-
|
|
13
|
+
protected depth: number;
|
|
14
|
+
protected minShift: number;
|
|
9
15
|
indexCov(): Promise<never[]>;
|
|
10
16
|
parseAuxData(bytes: Uint8Array, offset: number): {
|
|
11
17
|
refNameToId: Record<string, number>;
|
|
@@ -22,31 +28,15 @@ export default class CSI extends IndexFile {
|
|
|
22
28
|
format: string;
|
|
23
29
|
formatFlags: number;
|
|
24
30
|
};
|
|
25
|
-
_parse(opts: BaseOpts): Promise<
|
|
26
|
-
|
|
27
|
-
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
|
|
31
|
-
|
|
32
|
-
|
|
33
|
-
|
|
34
|
-
metaValue?: number | undefined;
|
|
35
|
-
metaChar?: string | undefined;
|
|
36
|
-
skipLines?: number | undefined;
|
|
37
|
-
format?: string | undefined;
|
|
38
|
-
formatFlags?: number | undefined;
|
|
39
|
-
firstDataLine: VirtualOffset | undefined;
|
|
40
|
-
indices: (refId: number) => {
|
|
41
|
-
binIndex: Record<number, Chunk[]>;
|
|
42
|
-
stats: {
|
|
43
|
-
lineCount: number;
|
|
44
|
-
} | undefined;
|
|
45
|
-
} | undefined;
|
|
46
|
-
refCount: number;
|
|
47
|
-
csi: boolean;
|
|
48
|
-
}>;
|
|
49
|
-
protected getLowestChunk(): VirtualOffset;
|
|
31
|
+
_parse(opts: BaseOpts): Promise<CsiParsed>;
|
|
32
|
+
/**
|
|
33
|
+
* CSI has no linear index, but each bin's `loffset` is the linear-index entry
|
|
34
|
+
* at the bin's first window (htslib's `update_loff`), so the finest bin at or
|
|
35
|
+
* left of `min` bounds the query from below the way BAI's linear index does.
|
|
36
|
+
* Walks left through siblings and then up to the parent, as `hts_itr_query`
|
|
37
|
+
* does for CSI.
|
|
38
|
+
*/
|
|
39
|
+
protected getLowestChunk(refIndex: CsiRefIndex, min: number): VirtualOffset;
|
|
50
40
|
protected getHighestChunk(): undefined;
|
|
51
41
|
/**
|
|
52
42
|
* calculate the list of bins that may overlap with region [beg,end)
|
|
@@ -55,3 +45,4 @@ export default class CSI extends IndexFile {
|
|
|
55
45
|
*/
|
|
56
46
|
protected reg2bins(beg: number, end: number): (readonly [number, number])[];
|
|
57
47
|
}
|
|
48
|
+
export {};
|
package/esm/csi.js
CHANGED
|
@@ -63,7 +63,7 @@ export default class CSI extends IndexFile {
|
|
|
63
63
|
}
|
|
64
64
|
this.minShift = dataView.getInt32(4, true);
|
|
65
65
|
this.depth = dataView.getInt32(8, true);
|
|
66
|
-
this.maxBinNumber = (
|
|
66
|
+
this.maxBinNumber = (8 ** (this.depth + 1) - 1) / 7;
|
|
67
67
|
const maxBinNumber = this.maxBinNumber;
|
|
68
68
|
const auxLength = dataView.getInt32(12, true);
|
|
69
69
|
// A tabix-only branch, which is why parseAuxData and the parseNameBytes it
|
|
@@ -98,10 +98,10 @@ export default class CSI extends IndexFile {
|
|
|
98
98
|
curr += 28 + 16;
|
|
99
99
|
}
|
|
100
100
|
else {
|
|
101
|
-
// A bin's loffset is the
|
|
102
|
-
//
|
|
103
|
-
//
|
|
104
|
-
//
|
|
101
|
+
// A bin's loffset is the linear-index entry at its first window, so
|
|
102
|
+
// the smallest over every bin is the first record's offset — one
|
|
103
|
+
// read per bin instead of one per chunk. Checked against every .csi
|
|
104
|
+
// in test/data: same answer on all 19.
|
|
105
105
|
firstDataLine = minVirtualOffset(bytes, curr, 1, firstDataLine);
|
|
106
106
|
curr += 8; // loffset
|
|
107
107
|
const chunkCount = dataView.getInt32(curr, true);
|
|
@@ -118,6 +118,7 @@ export default class CSI extends IndexFile {
|
|
|
118
118
|
const binCount = dataView.getInt32(curr, true);
|
|
119
119
|
curr += 4;
|
|
120
120
|
const binIndex = {};
|
|
121
|
+
const loffsets = new Map();
|
|
121
122
|
let pseudoBinStats;
|
|
122
123
|
for (let j = 0; j < binCount; j++) {
|
|
123
124
|
const bin = dataView.getUint32(curr, true);
|
|
@@ -127,7 +128,8 @@ export default class CSI extends IndexFile {
|
|
|
127
128
|
curr += 28 + 16;
|
|
128
129
|
}
|
|
129
130
|
else {
|
|
130
|
-
|
|
131
|
+
loffsets.set(bin, fromBytes(bytes, curr));
|
|
132
|
+
curr += 8;
|
|
131
133
|
const chunkCount = dataView.getInt32(curr, true);
|
|
132
134
|
curr += 4;
|
|
133
135
|
const chunks = new Array(chunkCount);
|
|
@@ -144,6 +146,7 @@ export default class CSI extends IndexFile {
|
|
|
144
146
|
clampChunkEnds(Object.values(binIndex).flat());
|
|
145
147
|
return {
|
|
146
148
|
binIndex,
|
|
149
|
+
loffsets,
|
|
147
150
|
stats: pseudoBinStats,
|
|
148
151
|
};
|
|
149
152
|
}
|
|
@@ -155,11 +158,25 @@ export default class CSI extends IndexFile {
|
|
|
155
158
|
...aux,
|
|
156
159
|
};
|
|
157
160
|
}
|
|
158
|
-
|
|
159
|
-
|
|
160
|
-
|
|
161
|
+
/**
|
|
162
|
+
* CSI has no linear index, but each bin's `loffset` is the linear-index entry
|
|
163
|
+
* at the bin's first window (htslib's `update_loff`), so the finest bin at or
|
|
164
|
+
* left of `min` bounds the query from below the way BAI's linear index does.
|
|
165
|
+
* Walks left through siblings and then up to the parent, as `hts_itr_query`
|
|
166
|
+
* does for CSI.
|
|
167
|
+
*/
|
|
168
|
+
getLowestChunk(refIndex, min) {
|
|
169
|
+
const { loffsets } = refIndex;
|
|
170
|
+
const leaves = 8 ** this.depth;
|
|
171
|
+
let bin = (leaves - 1) / 7 +
|
|
172
|
+
Math.min(Math.floor(min / 2 ** this.minShift), leaves - 1);
|
|
173
|
+
while (bin > 0 && !loffsets.has(bin)) {
|
|
174
|
+
const parent = Math.floor((bin - 1) / 8);
|
|
175
|
+
bin = bin > parent * 8 + 1 ? bin - 1 : parent;
|
|
176
|
+
}
|
|
177
|
+
return loffsets.get(bin) ?? ZERO_OFFSET;
|
|
161
178
|
}
|
|
162
|
-
//
|
|
179
|
+
// No linear index means nothing to forecast the far end of a query with, so
|
|
163
180
|
// estimatedBytesForRegions keeps summing every chunk on a CSI-indexed file.
|
|
164
181
|
getHighestChunk() {
|
|
165
182
|
return undefined;
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EACL,cAAc,EACd,gBAAgB,EAChB,cAAc,EACd,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EACL,cAAc,EACd,gBAAgB,EAChB,cAAc,EACd,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAK7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,WAAW,GAAG,IAAI,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAE3C,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;AAUD,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAoB;IAC3C,YAAY,GAAG,CAAC,CAAA;IACd,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEtB,uEAAuE;IACvE,iEAAiE;IACjE,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,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,GAAG,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC3D,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,cAAc,CACf,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,IAAc;QACzB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,yEAAyE;QACzE,sEAAsE;QACtE,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,KAAK,KAAK,UAAU,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACjD,oDAAoD;YACpD,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;QAC5C,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,IAAI,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,2EAA2E;QAC3E,yEAAyE;QACzE,2EAA2E;QAC3E,wEAAwE;QACxE,wEAAwE;QACxE,uEAAuE;QACvE,+DAA+D;QAC/D,EAAE;QACF,iEAAiE;QACjE,yEAAyE;QACzE,mEAAmE;QACnE,oEAAoE;QACpE,sEAAsE;QACtE,iEAAiE;QACjE,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,mEAAmE;QACnE,+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,oEAAoE;oBACpE,iEAAiE;oBACjE,oEAAoE;oBACpE,uCAAuC;oBACvC,aAAa,GAAG,gBAAgB,CAAC,KAAK,EAAE,IAAI,EAAE,CAAC,EAAE,aAAa,CAAC,CAAA;oBAC/D,IAAI,IAAI,CAAC,CAAA,CAAC,UAAU;oBACpB,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAA;gBAC7B,CAAC;YACH,CAAC;QACH,CAAC;QAED,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,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAyB,CAAA;YACjD,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,cAAc,CAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,QAAQ,CAAC,GAAG,CAAC,GAAG,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACzC,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,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,cAAc,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAC9C,OAAO;gBACL,QAAQ;gBACR,QAAQ;gBACR,KAAK,EAAE,cAAc;aACtB,CAAA;QACH,CAAC;QAED,OAAO;YACL,aAAa;YACb,OAAO,EAAE,cAAc,CAAC,UAAU,CAAC;YACnC,QAAQ;YACR,GAAG,EAAE,IAAI;YACT,GAAG,GAAG;SACP,CAAA;IACH,CAAC;IAED;;;;;;OAMG;IACO,cAAc,CAAC,QAAqB,EAAE,GAAW;QACzD,MAAM,EAAE,QAAQ,EAAE,GAAG,QAAQ,CAAA;QAC7B,MAAM,MAAM,GAAG,CAAC,IAAI,IAAI,CAAC,KAAK,CAAA;QAC9B,IAAI,GAAG,GACL,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC;YAChB,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,QAAQ,CAAC,EAAE,MAAM,GAAG,CAAC,CAAC,CAAA;QAC5D,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACrC,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;YACxC,GAAG,GAAG,GAAG,GAAG,MAAM,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;QAC/C,CAAC;QACD,OAAO,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,WAAW,CAAA;IACzC,CAAC;IAED,4EAA4E;IAC5E,4EAA4E;IAClE,eAAe;QACvB,OAAO,SAAS,CAAA;IAClB,CAAC;IAED;;;;OAIG;IACH,gDAAgD;IACtC,QAAQ,CAAC,GAAW,EAAE,GAAW;QACzC,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,MAAM,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QACpD,IAAI,GAAG,GAAG,MAAM,EAAE,CAAC;YACjB,GAAG,GAAG,MAAM,CAAA;QACd,CAAC;QACD,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,uEAAuE;YACvE,oEAAoE;YACpE,uEAAuE;YACvE,4EAA4E;YAC5E,sEAAsE;YACtE,gEAAgE;YAChE,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;CACF"}
|
package/esm/indexFile.d.ts
CHANGED
|
@@ -19,6 +19,23 @@ export interface ParsedIndexBase<R extends RefIndex = RefIndex> {
|
|
|
19
19
|
indices: (refId: number) => R | undefined;
|
|
20
20
|
}
|
|
21
21
|
export declare function memoizeByRefId<T>(getIndices: (refId: number) => T | undefined, maxSize?: number): (refId: number) => T | undefined;
|
|
22
|
+
/**
|
|
23
|
+
* The virtual offset past which a coordinate-sorted file holds nothing
|
|
24
|
+
* overlapping `[.., end)`, from the binning index alone: htslib's `max_off`
|
|
25
|
+
* (`hts_itr_query` in hts.c).
|
|
26
|
+
*
|
|
27
|
+
* Walk right from the finest bin after the one holding `end - 1`, stepping up
|
|
28
|
+
* to the parent at every first child, so each bin visited begins at or past
|
|
29
|
+
* `end` and never overlaps the query. Every record in such a bin starts at or
|
|
30
|
+
* past `end`, so the first chunk of the first bin that exists is a record past
|
|
31
|
+
* the query, and in a sorted file so is every record after it.
|
|
32
|
+
*
|
|
33
|
+
* A bound, unlike the linear-index forecast in `chunksLikelyRead`: it rests on
|
|
34
|
+
* the same sort order `appendInRange` and the early stop already assume, and
|
|
35
|
+
* cannot drop a record they would keep. See ADR 0023 for why the caller drops
|
|
36
|
+
* whole merged chunks with it rather than trimming them.
|
|
37
|
+
*/
|
|
38
|
+
export declare function maxOffset(binIndex: Record<number, Chunk[]>, end: number, minShift: number, depth: number): import("./virtualOffset.ts").Offset | undefined;
|
|
22
39
|
export default abstract class IndexFile<TParsed extends ParsedIndexBase = ParsedIndexBase> {
|
|
23
40
|
filehandle: GenericFilehandle;
|
|
24
41
|
renameRefSeq: (s: string) => string;
|
|
@@ -37,6 +54,8 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
|
|
|
37
54
|
end: number;
|
|
38
55
|
score: number;
|
|
39
56
|
}[]>;
|
|
57
|
+
protected abstract minShift: number;
|
|
58
|
+
protected abstract depth: number;
|
|
40
59
|
protected abstract reg2bins(min: number, max: number): readonly (readonly [number, number])[];
|
|
41
60
|
protected abstract getLowestChunk(refIndex: RefIndex, min: number): OffsetCoords | undefined;
|
|
42
61
|
protected abstract getHighestChunk(refIndex: RefIndex, max: number): number | undefined;
|
|
@@ -87,7 +106,8 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
|
|
|
87
106
|
* exists — was being told 5.6x the truth on exactly the windows a reader
|
|
88
107
|
* spends their time in, and cannot answer it by zooming: every window narrower
|
|
89
108
|
* than a linear-index interval resolves to the same chunks and so to the same
|
|
90
|
-
* number.
|
|
109
|
+
* number. The table predates `max_off` (ADR 0023), which now drops most of
|
|
110
|
+
* the gap between the first two columns from `blocksForRange` itself.
|
|
91
111
|
*
|
|
92
112
|
* Still summed over merged chunks rather than per region, so two regions
|
|
93
113
|
* sharing a chunk are charged for it once.
|
package/esm/indexFile.js
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import { SharedReadCache } from '@gmod/shared-read-cache';
|
|
2
2
|
import QuickLRU from '@jbrowse/quick-lru';
|
|
3
3
|
import { chunksLikelyRead, optimizeChunks } from "./util.js";
|
|
4
|
+
import { compareOffsets } from "./virtualOffset.js";
|
|
4
5
|
// SYNC: ~/src/gmod/tabix-js/src/util.ts memoizeByRefId
|
|
5
6
|
// LRU-cache the result of getIndices(refId) so repeated lookups for the same
|
|
6
7
|
// reference don't re-walk the index bytes.
|
|
@@ -20,6 +21,52 @@ export function memoizeByRefId(getIndices, maxSize = 5) {
|
|
|
20
21
|
return result;
|
|
21
22
|
};
|
|
22
23
|
}
|
|
24
|
+
/**
|
|
25
|
+
* The virtual offset past which a coordinate-sorted file holds nothing
|
|
26
|
+
* overlapping `[.., end)`, from the binning index alone: htslib's `max_off`
|
|
27
|
+
* (`hts_itr_query` in hts.c).
|
|
28
|
+
*
|
|
29
|
+
* Walk right from the finest bin after the one holding `end - 1`, stepping up
|
|
30
|
+
* to the parent at every first child, so each bin visited begins at or past
|
|
31
|
+
* `end` and never overlaps the query. Every record in such a bin starts at or
|
|
32
|
+
* past `end`, so the first chunk of the first bin that exists is a record past
|
|
33
|
+
* the query, and in a sorted file so is every record after it.
|
|
34
|
+
*
|
|
35
|
+
* A bound, unlike the linear-index forecast in `chunksLikelyRead`: it rests on
|
|
36
|
+
* the same sort order `appendInRange` and the early stop already assume, and
|
|
37
|
+
* cannot drop a record they would keep. See ADR 0023 for why the caller drops
|
|
38
|
+
* whole merged chunks with it rather than trimming them.
|
|
39
|
+
*/
|
|
40
|
+
export function maxOffset(binIndex, end, minShift, depth) {
|
|
41
|
+
if (end > 2 ** (minShift + depth * 3)) {
|
|
42
|
+
return undefined;
|
|
43
|
+
}
|
|
44
|
+
const binCount = (8 ** (depth + 1) - 1) / 7;
|
|
45
|
+
let bin = (8 ** depth - 1) / 7 + Math.floor((end - 1) / 2 ** minShift) + 1;
|
|
46
|
+
if (bin >= binCount) {
|
|
47
|
+
bin = 0;
|
|
48
|
+
}
|
|
49
|
+
for (;;) {
|
|
50
|
+
while (bin % 8 === 1) {
|
|
51
|
+
bin = (bin - 1) / 8;
|
|
52
|
+
}
|
|
53
|
+
if (bin === 0) {
|
|
54
|
+
return undefined;
|
|
55
|
+
}
|
|
56
|
+
const chunks = binIndex[bin];
|
|
57
|
+
if (chunks?.length) {
|
|
58
|
+
let lowest = chunks[0].minv;
|
|
59
|
+
for (let i = 1; i < chunks.length; i++) {
|
|
60
|
+
const minv = chunks[i].minv;
|
|
61
|
+
if (compareOffsets(minv, lowest) < 0) {
|
|
62
|
+
lowest = minv;
|
|
63
|
+
}
|
|
64
|
+
}
|
|
65
|
+
return lowest;
|
|
66
|
+
}
|
|
67
|
+
bin++;
|
|
68
|
+
}
|
|
69
|
+
}
|
|
23
70
|
export default class IndexFile {
|
|
24
71
|
filehandle;
|
|
25
72
|
renameRefSeq;
|
|
@@ -57,7 +104,16 @@ export default class IndexFile {
|
|
|
57
104
|
}
|
|
58
105
|
}
|
|
59
106
|
}
|
|
60
|
-
|
|
107
|
+
const merged = optimizeChunks(chunks, this.getLowestChunk(ba, min));
|
|
108
|
+
const past = maxOffset(binIndex, max, this.minShift, this.depth);
|
|
109
|
+
if (past) {
|
|
110
|
+
let n = merged.length;
|
|
111
|
+
while (n > 0 && compareOffsets(merged[n - 1].minv, past) >= 0) {
|
|
112
|
+
n--;
|
|
113
|
+
}
|
|
114
|
+
merged.length = n;
|
|
115
|
+
}
|
|
116
|
+
return merged;
|
|
61
117
|
}
|
|
62
118
|
// SYNC: ~/src/gmod/tabix-js/src/indexFile.ts parse — same shape and the same
|
|
63
119
|
// reasoning below.
|
|
@@ -115,7 +171,8 @@ export default class IndexFile {
|
|
|
115
171
|
* exists — was being told 5.6x the truth on exactly the windows a reader
|
|
116
172
|
* spends their time in, and cannot answer it by zooming: every window narrower
|
|
117
173
|
* than a linear-index interval resolves to the same chunks and so to the same
|
|
118
|
-
* number.
|
|
174
|
+
* number. The table predates `max_off` (ADR 0023), which now drops most of
|
|
175
|
+
* the gap between the first two columns from `blocksForRange` itself.
|
|
119
176
|
*
|
|
120
177
|
* Still summed over merged chunks rather than per region, so two regions
|
|
121
178
|
* sharing a chunk are charged for it once.
|