@gmod/bam 7.6.2 → 7.7.1
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/dist/bai.d.ts +6 -3
- package/dist/bai.js +37 -16
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +3 -3
- package/dist/bamFile.js +39 -12
- package/dist/bamFile.js.map +1 -1
- package/dist/chunk.d.ts +0 -1
- package/dist/chunk.js +0 -5
- package/dist/chunk.js.map +1 -1
- package/dist/csi.d.ts +0 -2
- package/dist/csi.js +4 -11
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +2 -3
- package/dist/indexFile.js.map +1 -1
- package/dist/sam.js +8 -3
- package/dist/sam.js.map +1 -1
- package/dist/util.d.ts +3 -3
- package/dist/util.js +35 -4
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.d.ts +8 -3
- package/dist/virtualOffset.js +0 -3
- package/dist/virtualOffset.js.map +1 -1
- package/esm/bai.d.ts +6 -3
- package/esm/bai.js +37 -16
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +3 -3
- package/esm/bamFile.js +39 -12
- package/esm/bamFile.js.map +1 -1
- package/esm/chunk.d.ts +0 -1
- package/esm/chunk.js +0 -5
- package/esm/chunk.js.map +1 -1
- package/esm/csi.d.ts +0 -2
- package/esm/csi.js +4 -11
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +2 -3
- package/esm/indexFile.js.map +1 -1
- package/esm/sam.js +8 -3
- package/esm/sam.js.map +1 -1
- package/esm/util.d.ts +3 -3
- package/esm/util.js +35 -4
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.d.ts +8 -3
- package/esm/virtualOffset.js +0 -3
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +1 -1
- package/src/bai.ts +50 -20
- package/src/bamFile.ts +38 -11
- package/src/chunk.ts +0 -8
- package/src/csi.ts +4 -10
- package/src/indexFile.ts +2 -3
- package/src/sam.ts +8 -3
- package/src/util.ts +42 -7
- package/src/virtualOffset.ts +9 -8
- package/dist/long.d.ts +0 -1
- package/dist/long.js +0 -17
- package/dist/long.js.map +0 -1
- package/esm/long.d.ts +0 -1
- package/esm/long.js +0 -14
- package/esm/long.js.map +0 -1
- package/src/long.ts +0 -16
package/dist/bai.d.ts
CHANGED
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@@ -1,9 +1,9 @@
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1
1
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import IndexFile from './indexFile.ts';
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import type { ParsedIndexBase, RefIndex } from './indexFile.ts';
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import type { BaseOpts } from './util.ts';
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4
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-
import type { VirtualOffset } from './virtualOffset.ts';
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interface BaiRefIndex extends RefIndex {
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-
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5
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+
linearBlockPositions: Float64Array;
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linearDataPositions: Float64Array;
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}
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interface BaiParsed extends ParsedIndexBase<BaiRefIndex> {
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bai: true;
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@@ -17,6 +17,9 @@ export default class BAI extends IndexFile<BaiParsed> {
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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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-
protected getLowestChunk(refIndex: BaiRefIndex, min: number):
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protected getLowestChunk(refIndex: BaiRefIndex, min: number): {
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blockPosition: number;
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dataPosition: number;
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} | undefined;
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}
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export {};
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package/dist/bai.js
CHANGED
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@@ -40,6 +40,7 @@ const chunk_ts_1 = __importDefault(require("./chunk.js"));
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const indexFile_ts_1 = __importStar(require("./indexFile.js"));
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const util_ts_1 = require("./util.js");
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const virtualOffset_ts_1 = require("./virtualOffset.js");
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+
const EMPTY_POSITIONS = new Float64Array(0);
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const BAI_MAGIC = 21578050; // BAI\1
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// BAI uses a fixed 5-level binning scheme with a 14-bit (16KB) linear index
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// resolution. See SAMv1.pdf §5.1.3 (hts-specs).
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@@ -146,22 +147,36 @@ class BAI extends indexFile_ts_1.default {
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}
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const linearCount = dataView.getInt32(curr, true);
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curr += 4;
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-
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// Share one empty array rather than allocating a pair per reference. An
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// assembly with tens of thousands of unplaced scaffolds (cho.bam.bai:
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// 28751 references, 205 linear entries between them) reaches here once
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// per reference, and almost every one of those has an empty linear index.
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const linearBlockPositions = linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount);
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const linearDataPositions = linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount);
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for (let j = 0; j < linearCount; j++) {
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-
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// a virtual offset is a 48-bit block position in the high bytes and a
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// 16-bit data position in the low two
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linearBlockPositions[j] =
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bytes[curr + 7] * 0x10000000000 +
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bytes[curr + 6] * 0x100000000 +
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bytes[curr + 5] * 0x1000000 +
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bytes[curr + 4] * 0x10000 +
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bytes[curr + 3] * 0x100 +
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bytes[curr + 2];
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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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-
(0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat(),
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+
(0, util_ts_1.clampChunkEnds)(Object.values(binIndex).flat(), linearBlockPositions);
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return {
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binIndex,
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-
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+
linearBlockPositions,
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linearDataPositions,
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stats,
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};
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}
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return {
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bai: true,
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firstDataLine,
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-
maxBlockSize: 1 << 16,
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indices: (0, indexFile_ts_1.memoizeByRefId)(getIndices),
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refCount,
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};
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@@ -174,17 +189,18 @@ class BAI extends indexFile_ts_1.default {
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if (!seqIdx) {
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return [];
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}
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const {
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-
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const { linearBlockPositions, stats } = seqIdx;
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const nintv = linearBlockPositions.length;
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if (nintv === 0) {
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return [];
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}
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-
const e = end === undefined ? (
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const e = end === undefined ? (nintv - 1) * v : roundUp(end, v);
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const s = start === undefined ? 0 : roundDown(start, v);
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const depths = range
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? new Array((e - s) / v)
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: new Array(
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const totalSize =
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if (e > (
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: new Array(nintv - 1);
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const totalSize = linearBlockPositions[nintv - 1];
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if (e > (nintv - 1) * v) {
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throw new Error('query outside of range of linear index');
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}
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// Scale the block-delta into a read count as we go, rather than building the
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@@ -192,9 +208,9 @@ class BAI extends indexFile_ts_1.default {
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// multiply-then-divide order: hoisting lineCount/totalSize into a factor
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// reassociates the arithmetic and shifts scores by an ulp.
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const lineCount = stats?.lineCount ?? 0;
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-
let currentPos =
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let currentPos = linearBlockPositions[s / v];
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for (let i = s / v, j = 0; i < e / v; i++, j++) {
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const nextPos =
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const nextPos = linearBlockPositions[i + 1];
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depths[j] = {
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score: ((nextPos - currentPos) * lineCount) / totalSize,
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start: i * v,
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@@ -211,9 +227,14 @@ class BAI extends indexFile_ts_1.default {
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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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getLowestChunk(refIndex, min) {
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const {
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const
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return
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const { linearBlockPositions, linearDataPositions } = refIndex;
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const i = Math.min(min >> BAI_LINEAR_SHIFT, linearBlockPositions.length - 1);
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return i < 0
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? undefined
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: {
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blockPosition: linearBlockPositions[i],
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dataPosition: linearDataPositions[i],
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};
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}
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}
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exports.default = BAI;
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package/dist/bai.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAA4E;AAC5E,yDAA8C;
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|
+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAA4E;AAC5E,yDAA8C;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;AAE1D,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,4EAA4E;AAC5E,qEAAqE;AACrE,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,gBAAgB,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,gBAAgB,CAAC,CAAC;KAC5D,CAAA;AACZ,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAoB;IACnD,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,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,mEAAmE;YACnE,kDAAkD;YAClD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,aAAa,GAAG,IAAA,0BAAgB,EAAC,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,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,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,wEAAwE;YACxE,sEAAsE;YACtE,uEAAuE;YACvE,0EAA0E;YAC1E,MAAM,oBAAoB,GACxB,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YACrE,MAAM,mBAAmB,GACvB,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YACrE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,sEAAsE;gBACtE,sCAAsC;gBACtC,oBAAoB,CAAC,CAAC,CAAC;oBACrB,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,aAAa;wBAChC,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,WAAW;wBAC9B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,SAAS;wBAC5B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,OAAO;wBAC1B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,KAAK;wBACxB,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,CAAA;gBAClB,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,IAAI,CAAE,CAAA;gBAC/D,IAAI,IAAI,CAAC,CAAA;YACX,CAAC;YAED,IAAA,wBAAc,EAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,EAAE,oBAAoB,CAAC,CAAA;YACpE,OAAO;gBACL,QAAQ;gBACR,oBAAoB;gBACpB,mBAAmB;gBACnB,KAAK;aACN,CAAA;QACH,CAAC;QAED,OAAO;YACL,GAAG,EAAE,IAAI;YACT,aAAa;YACb,OAAO,EAAE,IAAA,6BAAc,EAAC,UAAU,CAAC;YACnC,QAAQ;SACT,CAAA;IACH,CAAC;IAED,KAAK,CAAC,QAAQ,CACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,IAAe;QAEf,MAAM,CAAC,GAAG,mBAAmB,CAAA;QAC7B,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;QACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAEvC,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,oBAAoB,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;QAC9C,MAAM,KAAK,GAAG,oBAAoB,CAAC,MAAM,CAAA;QACzC,IAAI,KAAK,KAAK,CAAC,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;QAC/D,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QACvD,MAAM,MAAM,GAAoB,KAAK;YACnC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;YACxB,CAAC,CAAC,IAAI,KAAK,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QACxB,MAAM,SAAS,GAAG,oBAAoB,CAAC,KAAK,GAAG,CAAC,CAAE,CAAA;QAClD,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;QAC3D,CAAC;QACD,6EAA6E;QAC7E,6EAA6E;QAC7E,yEAAyE;QACzE,2DAA2D;QAC3D,MAAM,SAAS,GAAG,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;QACvC,IAAI,UAAU,GAAG,oBAAoB,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;QAC7C,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC/C,MAAM,OAAO,GAAG,oBAAoB,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;YAC5C,MAAM,CAAC,CAAC,CAAC,GAAG;gBACV,KAAK,EAAE,CAAC,CAAC,OAAO,GAAG,UAAU,CAAC,GAAG,SAAS,CAAC,GAAG,SAAS;gBACvD,KAAK,EAAE,CAAC,GAAG,CAAC;gBACZ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC;aACf,CAAA;YACD,UAAU,GAAG,OAAO,CAAA;QACtB,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAES,QAAQ,CAAC,GAAW,EAAE,GAAW;QACzC,OAAO,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IAC3B,CAAC;IAED,0EAA0E;IAC1E,2EAA2E;IAC3E,+DAA+D;IACrD,cAAc,CAAC,QAAqB,EAAE,GAAW;QACzD,MAAM,EAAE,oBAAoB,EAAE,mBAAmB,EAAE,GAAG,QAAQ,CAAA;QAC9D,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,gBAAgB,EAAE,oBAAoB,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QAC5E,OAAO,CAAC,GAAG,CAAC;YACV,CAAC,CAAC,SAAS;YACX,CAAC,CAAC;gBACE,aAAa,EAAE,oBAAoB,CAAC,CAAC,CAAE;gBACvC,YAAY,EAAE,mBAAmB,CAAC,CAAC,CAAE;aACtC,CAAA;IACP,CAAC;CACF;AAlMD,sBAkMC"}
|
package/dist/bamFile.d.ts
CHANGED
|
@@ -72,7 +72,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
72
72
|
tag: string;
|
|
73
73
|
value: string;
|
|
74
74
|
}[];
|
|
75
|
-
}[]
|
|
75
|
+
}[]>;
|
|
76
76
|
/**
|
|
77
77
|
* Installs the header text and ref name/id maps from the start of a
|
|
78
78
|
* decompressed BAM stream, returning the parsed SAM header lines. Returns
|
|
@@ -92,7 +92,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
92
92
|
tag: string;
|
|
93
93
|
value: string;
|
|
94
94
|
}[];
|
|
95
|
-
}[]
|
|
95
|
+
}[]>;
|
|
96
96
|
getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
|
|
97
97
|
private getSeqId;
|
|
98
98
|
/**
|
|
@@ -113,7 +113,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
113
113
|
features: T[];
|
|
114
114
|
bytes: number;
|
|
115
115
|
}>;
|
|
116
|
-
readBamFeatures(ba: Uint8Array, cpositions: number
|
|
116
|
+
readBamFeatures(ba: Uint8Array, cpositions: ArrayLike<number>, dpositions: ArrayLike<number>, chunk: Chunk): T[];
|
|
117
117
|
hasRefSeq(seqName: string, opts?: BaseOpts): Promise<boolean>;
|
|
118
118
|
lineCount(seqName: string, opts?: BaseOpts): Promise<number>;
|
|
119
119
|
indexCov(seqName: string, start?: number, end?: number): Promise<never[] | import("./bai.ts").IndexCovEntry[]>;
|
package/dist/bamFile.js
CHANGED
|
@@ -136,7 +136,12 @@ class BamFile {
|
|
|
136
136
|
}
|
|
137
137
|
async getHeaderPre(opts = {}) {
|
|
138
138
|
if (!this.index) {
|
|
139
|
-
|
|
139
|
+
// Only reachable via `new BamFile({htsget: true})` used directly rather
|
|
140
|
+
// than through HtsgetFile, which overrides this. Throwing rather than
|
|
141
|
+
// returning undefined keeps `| undefined` off getHeader()'s public type,
|
|
142
|
+
// and makes that misuse loud instead of silently answering every query
|
|
143
|
+
// with zero records (getSeqId would find no chrToIndex).
|
|
144
|
+
throw new Error('no index to read a header from: use HtsgetFile for htsget sources');
|
|
140
145
|
}
|
|
141
146
|
const indexData = await this.index.parse(opts);
|
|
142
147
|
// The records start at firstDataLine, so reading up to it plus the bgzf
|
|
@@ -367,21 +372,38 @@ class BamFile {
|
|
|
367
372
|
const chunks = res[i];
|
|
368
373
|
for (let j = 0, jl = chunks.length; j < jl; j++) {
|
|
369
374
|
const m = chunks[j];
|
|
370
|
-
|
|
375
|
+
// Key on the virtual-offset span — the same key _cachedChunkFeatures
|
|
376
|
+
// uses. Chunk.toString() also folds in `bin` and fetchedSize(), which
|
|
377
|
+
// keeps two chunks covering an identical span apart here even though
|
|
378
|
+
// the cache below collapses them, so their records came back twice.
|
|
379
|
+
map.set(chunkCacheKey(m), m);
|
|
371
380
|
}
|
|
372
381
|
}
|
|
373
|
-
const
|
|
374
|
-
|
|
375
|
-
|
|
376
|
-
|
|
377
|
-
|
|
378
|
-
|
|
379
|
-
|
|
380
|
-
|
|
382
|
+
const mateChunks = [...map.values()];
|
|
383
|
+
// Bounded for the reason ADR 0008 bounds the main query path: a viewAsPairs
|
|
384
|
+
// query over a busy region resolves to many distinct mate chunks, and an
|
|
385
|
+
// unbounded fan-out inflates every one of them at once. Same inline pool
|
|
386
|
+
// shape as _fetchChunkFeatures — ADR 0009 measured extracting a shared
|
|
387
|
+
// mapConcurrent helper at ~11% on the hot path, so it stays inline.
|
|
388
|
+
const mateFeatLists = new Array(mateChunks.length);
|
|
389
|
+
let next = 0;
|
|
390
|
+
const readNext = async () => {
|
|
391
|
+
while (next < mateChunks.length) {
|
|
392
|
+
const ci = next++;
|
|
393
|
+
const features = await this._cachedChunkFeatures(mateChunks[ci], opts);
|
|
394
|
+
const mateRecs = [];
|
|
395
|
+
for (let i = 0, l = features.length; i < l; i++) {
|
|
396
|
+
const feature = features[i];
|
|
397
|
+
if (readNameCounts.get(feature.name) === 1 &&
|
|
398
|
+
!readIds.has(feature.fileOffset)) {
|
|
399
|
+
mateRecs.push(feature);
|
|
400
|
+
}
|
|
381
401
|
}
|
|
402
|
+
mateFeatLists[ci] = mateRecs;
|
|
382
403
|
}
|
|
383
|
-
|
|
384
|
-
|
|
404
|
+
};
|
|
405
|
+
const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, mateChunks.length);
|
|
406
|
+
await Promise.all(Array.from({ length: workers }, () => readNext()));
|
|
385
407
|
return mateFeatLists.flat();
|
|
386
408
|
}
|
|
387
409
|
async _readChunkFeatures(chunk, opts) {
|
|
@@ -399,6 +421,11 @@ class BamFile {
|
|
|
399
421
|
bytes: data.byteLength,
|
|
400
422
|
};
|
|
401
423
|
}
|
|
424
|
+
// cpositions/dpositions are `ArrayLike`, not `number[]`, because the wasm
|
|
425
|
+
// decompressor produces them as Float64Arrays — @gmod/bgzf-filehandle spreads
|
|
426
|
+
// them into plain arrays on the way out, and this signature is what lets that
|
|
427
|
+
// copy be dropped there without a change here. Only indexed reads and
|
|
428
|
+
// `.length` are used below either way.
|
|
402
429
|
readBamFeatures(ba, cpositions, dpositions, chunk) {
|
|
403
430
|
let blockStart = 0;
|
|
404
431
|
const sink = [];
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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3B,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAE,CAAC;wBAC/B,KAAK,CAAC,IAAI,CAAC,YAAY;wBACvB,CAAC;oBACH,CAAC,CAAC,IAAA,eAAK,EAAC,EAAE,CAAC,QAAQ,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC,KAAK,CAAC,EAClD,QAAQ,CACT,CAAA;gBAED,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACpB,CAAC;YAED,UAAU,GAAG,QAAQ,GAAG,CAAC,CAAA;QAC3B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,IAAe;QAC9C,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,KAAK;YACP,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IACjC,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,IAAe;QAC9C,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IAC7E,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,OAAe,EAAE,KAAc,EAAE,GAAY;QAC1D,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAA;QAC1C,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,KAAa,EACb,GAAW,EACX,IAAe;QAEf,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,iBAAiB;QACf,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,CAAA;IAChC,CAAC;IAED,KAAK,CAAC,wBAAwB,CAC5B,OAA0D,EAC1D,IAAe;QAEf,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,CAAC,CAAA;QACV,CAAC;QACD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACjC,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;YAC1C,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QAC3E,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,KAAK,CAAC,wBAAwB,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAC1D,CAAC;CACF;AA1hBD,0BA0hBC"}
|
package/dist/chunk.d.ts
CHANGED
package/dist/chunk.js
CHANGED
|
@@ -19,11 +19,6 @@ class Chunk {
|
|
|
19
19
|
toString() {
|
|
20
20
|
return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
|
|
21
21
|
}
|
|
22
|
-
compareTo(b) {
|
|
23
|
-
return (this.minv.compareTo(b.minv) ||
|
|
24
|
-
this.maxv.compareTo(b.maxv) ||
|
|
25
|
-
this.bin - b.bin);
|
|
26
|
-
}
|
|
27
22
|
fetchedSize() {
|
|
28
23
|
return this.endPosition - this.minv.blockPosition;
|
|
29
24
|
}
|
package/dist/chunk.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IACjB,IAAI,CAAQ;IACZ,IAAI,CAAQ;IACZ,GAAG,CAAQ;IAClB,2EAA2E;IAC3E,0EAA0E;IAC1E,8EAA8E;IAC9E,oEAAoE;IAC7D,WAAW,CAAQ;IAE1B,YACE,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,WAAW,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;QAE5C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IACjB,IAAI,CAAQ;IACZ,IAAI,CAAQ;IACZ,GAAG,CAAQ;IAClB,2EAA2E;IAC3E,0EAA0E;IAC1E,8EAA8E;IAC9E,oEAAoE;IAC7D,WAAW,CAAQ;IAE1B,YACE,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,WAAW,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;QAE5C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,KAAK,IAAI,CAAC,IAAI,CAAC,QAAQ,EAAE,SACrD,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,WAAW;QACT,OAAO,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACnD,CAAC;CACF;AA/BD,wBA+BC"}
|
package/dist/csi.d.ts
CHANGED
|
@@ -36,7 +36,6 @@ export default class CSI extends IndexFile {
|
|
|
36
36
|
skipLines?: number | undefined;
|
|
37
37
|
format?: string | undefined;
|
|
38
38
|
formatFlags?: number | undefined;
|
|
39
|
-
csiVersion: number;
|
|
40
39
|
firstDataLine: VirtualOffset | undefined;
|
|
41
40
|
indices: (refId: number) => {
|
|
42
41
|
binIndex: Record<number, Chunk[]>;
|
|
@@ -46,7 +45,6 @@ export default class CSI extends IndexFile {
|
|
|
46
45
|
} | undefined;
|
|
47
46
|
refCount: number;
|
|
48
47
|
csi: boolean;
|
|
49
|
-
maxBlockSize: number;
|
|
50
48
|
}>;
|
|
51
49
|
protected getLowestChunk(): VirtualOffset;
|
|
52
50
|
/**
|
package/dist/csi.js
CHANGED
|
@@ -92,17 +92,12 @@ class CSI extends indexFile_ts_1.default {
|
|
|
92
92
|
const buffer = await this.filehandle.readFile(opts);
|
|
93
93
|
const bytes = await (0, bgzf_filehandle_1.unzip)(buffer);
|
|
94
94
|
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
95
|
-
|
|
95
|
+
// CSI\1 and CSI\2 are parsed identically here — v2 only adds fields this
|
|
96
|
+
// reader doesn't consume — so the version is validated, not retained.
|
|
96
97
|
const magic = dataView.getUint32(0, true);
|
|
97
|
-
if (magic
|
|
98
|
-
csiVersion = 1;
|
|
99
|
-
}
|
|
100
|
-
else if (magic === CSI2_MAGIC) {
|
|
101
|
-
csiVersion = 2;
|
|
102
|
-
}
|
|
103
|
-
else {
|
|
104
|
-
throw new Error(`Not a CSI file ${magic}`);
|
|
98
|
+
if (magic !== CSI1_MAGIC && magic !== CSI2_MAGIC) {
|
|
105
99
|
// TODO: do we need to support big-endian CSI files?
|
|
100
|
+
throw new Error(`Not a CSI file ${magic}`);
|
|
106
101
|
}
|
|
107
102
|
this.minShift = dataView.getInt32(4, true);
|
|
108
103
|
this.depth = dataView.getInt32(8, true);
|
|
@@ -177,12 +172,10 @@ class CSI extends indexFile_ts_1.default {
|
|
|
177
172
|
};
|
|
178
173
|
}
|
|
179
174
|
return {
|
|
180
|
-
csiVersion,
|
|
181
175
|
firstDataLine,
|
|
182
176
|
indices: (0, indexFile_ts_1.memoizeByRefId)(getIndices),
|
|
183
177
|
refCount,
|
|
184
178
|
csi: true,
|
|
185
|
-
maxBlockSize: 1 << 16,
|
|
186
179
|
...aux,
|
|
187
180
|
};
|
|
188
181
|
}
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,WAAW,GAAG,IAAI,gCAAa,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;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAChC,YAAY,GAAG,CAAC,CAAA;IAChB,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEpB,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,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,IAAc;QACzB,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,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,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,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,sEAAsE;oBACtE,qEAAqE;oBACrE,sEAAsE;oBACtE,kDAAkD;oBAClD,aAAa,GAAG,IAAA,0BAAgB,EAAC,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,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,IAAI,IAAI,CAAC,CAAA,CAAC,6DAA6D;oBACvE,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,KAA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|
package/dist/indexFile.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import type Chunk from './chunk.ts';
|
|
2
2
|
import type { BaseOpts } from './util.ts';
|
|
3
|
-
import type {
|
|
3
|
+
import type { OffsetCoords, VirtualOffset } from './virtualOffset.ts';
|
|
4
4
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
5
5
|
export interface Region {
|
|
6
6
|
refId: number;
|
|
@@ -16,7 +16,6 @@ export interface RefIndex {
|
|
|
16
16
|
export interface ParsedIndexBase<R extends RefIndex = RefIndex> {
|
|
17
17
|
firstDataLine: VirtualOffset | undefined;
|
|
18
18
|
refCount: number;
|
|
19
|
-
maxBlockSize: number;
|
|
20
19
|
indices: (refId: number) => R | undefined;
|
|
21
20
|
}
|
|
22
21
|
export declare function memoizeByRefId<T>(getIndices: (refId: number) => T | undefined, maxSize?: number): (refId: number) => T | undefined;
|
|
@@ -35,7 +34,7 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
|
|
|
35
34
|
score: number;
|
|
36
35
|
}[]>;
|
|
37
36
|
protected abstract reg2bins(min: number, max: number): readonly (readonly [number, number])[];
|
|
38
|
-
protected abstract getLowestChunk(refIndex: RefIndex, min: number):
|
|
37
|
+
protected abstract getLowestChunk(refIndex: RefIndex, min: number): OffsetCoords | undefined;
|
|
39
38
|
blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
|
|
40
39
|
parse(opts?: BaseOpts): Promise<TParsed>;
|
|
41
40
|
lineCount(refId: number, opts?: BaseOpts): Promise<number>;
|
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":";;;;;AA6BA,wCAeC;AA5CD,mEAAyC;AAEzC,uCAA0C;AAwB1C,uDAAuD;AACvD,6EAA6E;AAC7E,2CAA2C;AAC3C,SAAgB,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,KAAK,GAAG,IAAI,mBAAQ,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAClD,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,IAAI,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;YACrB,OAAO,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QACzB,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,EAAE,CAAC;YACX,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC1B,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC;AAED,MAA8B,SAAS;IAG9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAElC,MAAM,CAAmB;IAEjC,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;IAwBD,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;QACD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAY,EAAE,CAAA;QAC1B,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;QACD,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,IAAI,CAAC,cAAc,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,CAAA;IAC7D,CAAC;IAED,KAAK,CAAC,OAAiB,EAAE;QACvB,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,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,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IACnC,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;AA5GD,4BA4GC"}
|
package/dist/sam.js
CHANGED
|
@@ -11,9 +11,14 @@ function parseHeaderText(text) {
|
|
|
11
11
|
tag: tag.slice(1),
|
|
12
12
|
data: fields.map(f => {
|
|
13
13
|
const r = f.indexOf(':');
|
|
14
|
-
|
|
15
|
-
|
|
16
|
-
|
|
14
|
+
// A field with no colon is not a TAG:VALUE pair — @CO lines are free
|
|
15
|
+
// text, one comment per line (`samtools view -H c2#pad.3.0.cram`).
|
|
16
|
+
// Without this branch `slice(0, -1)` silently drops the comment's last
|
|
17
|
+
// character into the tag. Same shape @gmod/cram's parseHeaderText
|
|
18
|
+
// returns, so both feed a consumer's header parser identically.
|
|
19
|
+
return r === -1
|
|
20
|
+
? { tag: f, value: '' }
|
|
21
|
+
: { tag: f.slice(0, r), value: f.slice(r + 1) };
|
|
17
22
|
}),
|
|
18
23
|
});
|
|
19
24
|
}
|
package/dist/sam.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;AAAA,
|
|
1
|
+
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;AAAA,0CAuBC;AAvBD,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,qEAAqE;oBACrE,mEAAmE;oBACnE,uEAAuE;oBACvE,kEAAkE;oBAClE,gEAAgE;oBAChE,OAAO,CAAC,KAAK,CAAC,CAAC;wBACb,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE;wBACvB,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAA;gBACnD,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
|
package/dist/util.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
2
|
import { VirtualOffset } from './virtualOffset.ts';
|
|
3
|
-
import type {
|
|
3
|
+
import type { OffsetCoords } from './virtualOffset.ts';
|
|
4
4
|
export interface BamOpts {
|
|
5
5
|
viewAsPairs?: boolean;
|
|
6
6
|
pairAcrossChr?: boolean;
|
|
@@ -25,11 +25,11 @@ export interface BaseOpts {
|
|
|
25
25
|
*/
|
|
26
26
|
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
|
|
27
27
|
}
|
|
28
|
-
export declare function optimizeChunks(chunks: Chunk[], lowest?:
|
|
28
|
+
export declare function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords): Chunk[];
|
|
29
29
|
export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
|
|
30
30
|
lineCount: number;
|
|
31
31
|
};
|
|
32
|
-
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number
|
|
32
|
+
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: ArrayLike<number>): void;
|
|
33
33
|
export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRefSeq: (s: string) => string): {
|
|
34
34
|
chrToIndex: Record<string, number>;
|
|
35
35
|
indexToChr: {
|
package/dist/util.js
CHANGED
|
@@ -12,7 +12,6 @@ exports.parseNameBytes = parseNameBytes;
|
|
|
12
12
|
exports.concatUint8Array = concatUint8Array;
|
|
13
13
|
exports.appendInRange = appendInRange;
|
|
14
14
|
const chunk_ts_1 = __importDefault(require("./chunk.js"));
|
|
15
|
-
const long_ts_1 = require("./long.js");
|
|
16
15
|
const virtualOffset_ts_1 = require("./virtualOffset.js");
|
|
17
16
|
function optimizeChunks(chunks, lowest) {
|
|
18
17
|
const n = chunks.length;
|
|
@@ -73,9 +72,20 @@ function optimizeChunks(chunks, lowest) {
|
|
|
73
72
|
}
|
|
74
73
|
return mergedChunks;
|
|
75
74
|
}
|
|
75
|
+
// The pseudo-bin's mapped-record count, a little-endian uint64. Read as two
|
|
76
|
+
// 32-bit halves rather than via BigInt: exact up to Number.MAX_SAFE_INTEGER,
|
|
77
|
+
// which is far past any real record count, and allocates nothing.
|
|
76
78
|
function parsePseudoBin(bytes, offset) {
|
|
79
|
+
const low = bytes[offset] |
|
|
80
|
+
(bytes[offset + 1] << 8) |
|
|
81
|
+
(bytes[offset + 2] << 16) |
|
|
82
|
+
(bytes[offset + 3] << 24);
|
|
83
|
+
const high = bytes[offset + 4] |
|
|
84
|
+
(bytes[offset + 5] << 8) |
|
|
85
|
+
(bytes[offset + 6] << 16) |
|
|
86
|
+
(bytes[offset + 7] << 24);
|
|
77
87
|
return {
|
|
78
|
-
lineCount: (0
|
|
88
|
+
lineCount: (high >>> 0) * 2 ** 32 + (low >>> 0),
|
|
79
89
|
};
|
|
80
90
|
}
|
|
81
91
|
// Tighten each chunk's endPosition (default: a full max-size BGZF block past
|
|
@@ -86,9 +96,30 @@ function parsePseudoBin(bytes, offset) {
|
|
|
86
96
|
// least the true block end, so the clamped fetch still contains the whole block.
|
|
87
97
|
// Shrinks both the byte estimate and the actual fetch with no extra I/O.
|
|
88
98
|
function clampChunkEnds(chunks, extraBoundaries = []) {
|
|
89
|
-
|
|
99
|
+
if (chunks.length === 0) {
|
|
100
|
+
return;
|
|
101
|
+
}
|
|
102
|
+
// A plain array, sized once and filled by index. Not a Float64Array: this
|
|
103
|
+
// runs once per reference, and an assembly with tens of thousands of unplaced
|
|
104
|
+
// scaffolds (cho.bam.bai has 28751 references) pays the allocation that many
|
|
105
|
+
// times over, where each individual boundary list is a handful of entries.
|
|
106
|
+
// The small-allocation cost dominates the faster typed sort by a wide margin
|
|
107
|
+
// at that shape. Filling by index still avoids the intermediate array that
|
|
108
|
+
// mapping the linear index to block positions used to build.
|
|
109
|
+
// Pre-sized and filled by index. Measured against both alternatives on five
|
|
110
|
+
// real .bai shapes (min of 21, interleaved, sign-stable over 3 runs):
|
|
111
|
+
// building with push instead is 5-8% slower here, and a Float64Array is
|
|
112
|
+
// faster to sort but allocates per reference, which costs 1.7x on an
|
|
113
|
+
// assembly with 28751 scaffolds. Filling by index also avoids the
|
|
114
|
+
// intermediate array that mapping the linear index used to build.
|
|
115
|
+
const boundaries = new Array(extraBoundaries.length + chunks.length * 2);
|
|
116
|
+
let n = 0;
|
|
117
|
+
for (let i = 0, l = extraBoundaries.length; i < l; i++) {
|
|
118
|
+
boundaries[n++] = extraBoundaries[i];
|
|
119
|
+
}
|
|
90
120
|
for (const c of chunks) {
|
|
91
|
-
boundaries
|
|
121
|
+
boundaries[n++] = c.minv.blockPosition;
|
|
122
|
+
boundaries[n++] = c.maxv.blockPosition;
|
|
92
123
|
}
|
|
93
124
|
boundaries.sort((a, b) => a - b);
|
|
94
125
|
for (const c of chunks) {
|