@gmod/bam 5.0.7 → 6.0.1
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/CHANGELOG.md +6 -2
- package/dist/bai.d.ts +4 -4
- package/dist/bai.js +16 -17
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +6 -7
- package/dist/bamFile.js +27 -46
- package/dist/bamFile.js.map +1 -1
- package/dist/chunk.d.ts +1 -1
- package/dist/chunk.js +0 -5
- package/dist/chunk.js.map +1 -1
- package/dist/csi.d.ts +4 -4
- package/dist/csi.js +20 -18
- package/dist/csi.js.map +1 -1
- package/dist/htsget.d.ts +4 -4
- package/dist/htsget.js +7 -9
- package/dist/htsget.js.map +1 -1
- package/dist/index.d.ts +5 -5
- package/dist/index.js +10 -10
- package/dist/index.js.map +1 -1
- package/dist/indexFile.d.ts +2 -6
- package/dist/indexFile.js +0 -6
- package/dist/indexFile.js.map +1 -1
- package/dist/nullIndex.d.ts +1 -1
- package/dist/nullIndex.js +2 -2
- package/dist/nullIndex.js.map +1 -1
- package/dist/record.js +57 -46
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +2 -2
- package/dist/util.js +2 -2
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.js +0 -2
- package/dist/virtualOffset.js.map +1 -1
- package/esm/bai.d.ts +4 -4
- package/esm/bai.js +4 -5
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +6 -7
- package/esm/bamFile.js +12 -31
- package/esm/bamFile.js.map +1 -1
- package/esm/chunk.d.ts +1 -1
- package/esm/chunk.js +0 -5
- package/esm/chunk.js.map +1 -1
- package/esm/csi.d.ts +4 -4
- package/esm/csi.js +10 -8
- package/esm/csi.js.map +1 -1
- package/esm/htsget.d.ts +4 -4
- package/esm/htsget.js +3 -5
- package/esm/htsget.js.map +1 -1
- package/esm/index.d.ts +5 -5
- package/esm/index.js +5 -5
- package/esm/index.js.map +1 -1
- package/esm/indexFile.d.ts +2 -6
- package/esm/indexFile.js +0 -6
- package/esm/indexFile.js.map +1 -1
- package/esm/nullIndex.d.ts +1 -1
- package/esm/nullIndex.js +1 -1
- package/esm/nullIndex.js.map +1 -1
- package/esm/record.js +47 -35
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +2 -2
- package/esm/util.js +1 -1
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.js +0 -2
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +18 -12
- package/src/bai.ts +9 -4
- package/src/bamFile.ts +18 -39
- package/src/chunk.ts +1 -1
- package/src/csi.ts +6 -5
- package/src/htsget.ts +7 -4
- package/src/index.ts +5 -5
- package/src/indexFile.ts +2 -6
- package/src/nullIndex.ts +1 -1
- package/src/record.ts +1 -1
- package/src/util.ts +3 -3
package/CHANGELOG.md
CHANGED
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@@ -1,10 +1,14 @@
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## [
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## [6.0.1](https://github.com/GMOD/bam-js/compare/v6.0.0...v6.0.1) (2025-04-30)
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# [6.0.0](https://github.com/GMOD/bam-js/compare/v5.0.7...v6.0.0) (2025-04-30)
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## [5.0.7](https://github.com/GMOD/bam-js/compare/v5.0.6...v5.0.7) (2025-03-11)
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## [5.0.6](https://github.com/GMOD/bam-js/compare/v5.0.5...v5.0.6) (2025-02-28)
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## [5.0.5](https://github.com/GMOD/bam-js/compare/v5.0.4...v5.0.5) (2024-12-18)
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package/dist/bai.d.ts
CHANGED
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@@ -1,7 +1,7 @@
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import Chunk from './chunk';
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import IndexFile from './indexFile';
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import { BaseOpts } from './util';
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import { VirtualOffset } from './virtualOffset';
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import Chunk from './chunk.ts';
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import IndexFile from './indexFile.ts';
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import { BaseOpts } from './util.ts';
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import { VirtualOffset } from './virtualOffset.ts';
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export interface IndexCovEntry {
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start: number;
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end: number;
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package/dist/bai.js
CHANGED
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@@ -4,10 +4,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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const quick_lru_1 = __importDefault(require("quick-lru"));
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const
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const
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const
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const
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const chunk_ts_1 = __importDefault(require("./chunk.js"));
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const indexFile_ts_1 = __importDefault(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 BAI_MAGIC = 21578050; // BAI\1
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function roundDown(n, multiple) {
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return n - (n % multiple);
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[4681 + (beg >> 14), 4681 + (end >> 14)],
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];
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}
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class BAI extends
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setupP;
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class BAI extends indexFile_ts_1.default {
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async lineCount(refId, opts) {
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const indexData = await this.parse(opts);
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return indexData.indices(refId)?.stats?.lineCount || 0;
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// ends
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const linearIndex = new Array(linearCount);
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for (let j = 0; j < linearCount; j++) {
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const offset = (0,
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const offset = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
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curr += 8;
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firstDataLine = (0,
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firstDataLine = (0, util_ts_1.findFirstData)(firstDataLine, offset);
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linearIndex[j] = offset;
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}
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}
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curr += 4;
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if (bin === binLimit + 1) {
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curr += 4;
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stats = (0,
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stats = (0, util_ts_1.parsePseudoBin)(bytes, curr + 16);
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curr += 32;
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}
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else if (bin > binLimit + 1) {
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curr += 4;
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const chunks = new Array(chunkCount);
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for (let k = 0; k < chunkCount; k++) {
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const u = (0,
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const u = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
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curr += 8;
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const v = (0,
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const v = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
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curr += 8;
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firstDataLine = (0,
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chunks[k] = new
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firstDataLine = (0, util_ts_1.findFirstData)(firstDataLine, u);
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chunks[k] = new chunk_ts_1.default(u, v, bin);
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}
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binIndex[bin] = chunks;
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}
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// ends
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const linearIndex = new Array(linearCount);
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for (let j = 0; j < linearCount; j++) {
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const offset = (0,
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const offset = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
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curr += 8;
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firstDataLine = (0,
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firstDataLine = (0, util_ts_1.findFirstData)(firstDataLine, offset);
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linearIndex[j] = offset;
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}
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return {
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if (ba.binIndex[bin]) {
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const binChunks = ba.binIndex[bin];
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for (const binChunk of binChunks) {
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chunks.push(new
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chunks.push(new chunk_ts_1.default(binChunk.minv, binChunk.maxv, bin));
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}
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}
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}
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}
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}
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return (0,
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return (0, util_ts_1.optimizeChunks)(chunks, lowest);
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}
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async parse(opts = {}) {
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if (!this.setupP) {
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package/dist/bai.js.map
CHANGED
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{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;AAAA,0DAAgC;AAEhC,
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+
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|
package/dist/bamFile.d.ts
CHANGED
|
@@ -1,8 +1,8 @@
|
|
|
1
|
-
import BAI from './bai';
|
|
2
|
-
import Chunk from './chunk';
|
|
3
|
-
import CSI from './csi';
|
|
4
|
-
import BAMFeature from './record';
|
|
5
|
-
import { BamOpts, BaseOpts } from './util';
|
|
1
|
+
import BAI from './bai.ts';
|
|
2
|
+
import Chunk from './chunk.ts';
|
|
3
|
+
import CSI from './csi.ts';
|
|
4
|
+
import BAMFeature from './record.ts';
|
|
5
|
+
import type { BamOpts, BaseOpts } from './util.ts';
|
|
6
6
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
7
7
|
export declare const BAM_MAGIC = 21840194;
|
|
8
8
|
export default class BamFile {
|
|
@@ -18,7 +18,6 @@ export default class BamFile {
|
|
|
18
18
|
index?: BAI | CSI;
|
|
19
19
|
htsget: boolean;
|
|
20
20
|
headerP?: ReturnType<BamFile['getHeaderPre']>;
|
|
21
|
-
private featureCache;
|
|
22
21
|
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime, renameRefSeqs, }: {
|
|
23
22
|
bamFilehandle?: GenericFilehandle;
|
|
24
23
|
bamPath?: string;
|
|
@@ -71,6 +70,6 @@ export default class BamFile {
|
|
|
71
70
|
readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): Promise<BAMFeature[]>;
|
|
72
71
|
hasRefSeq(seqName: string): Promise<boolean | undefined>;
|
|
73
72
|
lineCount(seqName: string): Promise<number>;
|
|
74
|
-
indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai").IndexCovEntry[]>;
|
|
73
|
+
indexCov(seqName: string, start?: number, end?: number): Promise<import("./bai.ts").IndexCovEntry[]>;
|
|
75
74
|
blocksForRange(seqName: string, start: number, end: number, opts?: BaseOpts): Promise<Chunk[]>;
|
|
76
75
|
}
|
package/dist/bamFile.js
CHANGED
|
@@ -4,43 +4,20 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
exports.BAM_MAGIC = void 0;
|
|
7
|
-
const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
|
|
8
7
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
9
8
|
const crc32_1 = __importDefault(require("crc/calculators/crc32"));
|
|
10
9
|
const generic_filehandle2_1 = require("generic-filehandle2");
|
|
11
|
-
const
|
|
12
|
-
const
|
|
13
|
-
const
|
|
14
|
-
const
|
|
15
|
-
const
|
|
16
|
-
const
|
|
17
|
-
const util_1 = require("./util");
|
|
10
|
+
const bai_ts_1 = __importDefault(require("./bai.js"));
|
|
11
|
+
const csi_ts_1 = __importDefault(require("./csi.js"));
|
|
12
|
+
const nullFilehandle_ts_1 = __importDefault(require("./nullFilehandle.js"));
|
|
13
|
+
const record_ts_1 = __importDefault(require("./record.js"));
|
|
14
|
+
const sam_ts_1 = require("./sam.js");
|
|
15
|
+
const util_ts_1 = require("./util.js");
|
|
18
16
|
exports.BAM_MAGIC = 21840194;
|
|
19
17
|
const blockLen = 1 << 16;
|
|
20
18
|
class BamFile {
|
|
21
|
-
renameRefSeq;
|
|
22
|
-
bam;
|
|
23
|
-
header;
|
|
24
|
-
chrToIndex;
|
|
25
|
-
indexToChr;
|
|
26
|
-
yieldThreadTime;
|
|
27
|
-
index;
|
|
28
|
-
htsget = false;
|
|
29
|
-
headerP;
|
|
30
|
-
featureCache = new abortable_promise_cache_1.default({
|
|
31
|
-
cache: new quick_lru_1.default({
|
|
32
|
-
maxSize: 50,
|
|
33
|
-
}),
|
|
34
|
-
fill: async (args, signal) => {
|
|
35
|
-
const { chunk, opts } = args;
|
|
36
|
-
const { data, cpositions, dpositions } = await this._readChunk({
|
|
37
|
-
chunk,
|
|
38
|
-
opts: { ...opts, signal },
|
|
39
|
-
});
|
|
40
|
-
return this.readBamFeatures(data, cpositions, dpositions, chunk);
|
|
41
|
-
},
|
|
42
|
-
});
|
|
43
19
|
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
|
|
20
|
+
this.htsget = false;
|
|
44
21
|
this.renameRefSeq = renameRefSeqs;
|
|
45
22
|
if (bamFilehandle) {
|
|
46
23
|
this.bam = bamFilehandle;
|
|
@@ -53,34 +30,34 @@ class BamFile {
|
|
|
53
30
|
}
|
|
54
31
|
else if (htsget) {
|
|
55
32
|
this.htsget = true;
|
|
56
|
-
this.bam = new
|
|
33
|
+
this.bam = new nullFilehandle_ts_1.default();
|
|
57
34
|
}
|
|
58
35
|
else {
|
|
59
36
|
throw new Error('unable to initialize bam');
|
|
60
37
|
}
|
|
61
38
|
if (csiFilehandle) {
|
|
62
|
-
this.index = new
|
|
39
|
+
this.index = new csi_ts_1.default({ filehandle: csiFilehandle });
|
|
63
40
|
}
|
|
64
41
|
else if (csiPath) {
|
|
65
|
-
this.index = new
|
|
42
|
+
this.index = new csi_ts_1.default({ filehandle: new generic_filehandle2_1.LocalFile(csiPath) });
|
|
66
43
|
}
|
|
67
44
|
else if (csiUrl) {
|
|
68
|
-
this.index = new
|
|
45
|
+
this.index = new csi_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(csiUrl) });
|
|
69
46
|
}
|
|
70
47
|
else if (baiFilehandle) {
|
|
71
|
-
this.index = new
|
|
48
|
+
this.index = new bai_ts_1.default({ filehandle: baiFilehandle });
|
|
72
49
|
}
|
|
73
50
|
else if (baiPath) {
|
|
74
|
-
this.index = new
|
|
51
|
+
this.index = new bai_ts_1.default({ filehandle: new generic_filehandle2_1.LocalFile(baiPath) });
|
|
75
52
|
}
|
|
76
53
|
else if (baiUrl) {
|
|
77
|
-
this.index = new
|
|
54
|
+
this.index = new bai_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(baiUrl) });
|
|
78
55
|
}
|
|
79
56
|
else if (bamPath) {
|
|
80
|
-
this.index = new
|
|
57
|
+
this.index = new bai_ts_1.default({ filehandle: new generic_filehandle2_1.LocalFile(`${bamPath}.bai`) });
|
|
81
58
|
}
|
|
82
59
|
else if (bamUrl) {
|
|
83
|
-
this.index = new
|
|
60
|
+
this.index = new bai_ts_1.default({ filehandle: new generic_filehandle2_1.RemoteFile(`${bamUrl}.bai`) });
|
|
84
61
|
}
|
|
85
62
|
else if (htsget) {
|
|
86
63
|
this.htsget = true;
|
|
@@ -91,7 +68,7 @@ class BamFile {
|
|
|
91
68
|
this.yieldThreadTime = yieldThreadTime;
|
|
92
69
|
}
|
|
93
70
|
async getHeaderPre(origOpts) {
|
|
94
|
-
const opts = (0,
|
|
71
|
+
const opts = (0, util_ts_1.makeOpts)(origOpts);
|
|
95
72
|
if (!this.index) {
|
|
96
73
|
return;
|
|
97
74
|
}
|
|
@@ -118,7 +95,7 @@ class BamFile {
|
|
|
118
95
|
const { chrToIndex, indexToChr } = await this._readRefSeqs(headLen + 8, 65535, opts);
|
|
119
96
|
this.chrToIndex = chrToIndex;
|
|
120
97
|
this.indexToChr = indexToChr;
|
|
121
|
-
return (0,
|
|
98
|
+
return (0, sam_ts_1.parseHeaderText)(this.header);
|
|
122
99
|
}
|
|
123
100
|
getHeader(opts) {
|
|
124
101
|
if (!this.headerP) {
|
|
@@ -163,7 +140,7 @@ class BamFile {
|
|
|
163
140
|
return { chrToIndex, indexToChr };
|
|
164
141
|
}
|
|
165
142
|
async getRecordsForRange(chr, min, max, opts) {
|
|
166
|
-
return (0,
|
|
143
|
+
return (0, util_ts_1.gen2array)(this.streamRecordsForRange(chr, min, max, opts));
|
|
167
144
|
}
|
|
168
145
|
async *streamRecordsForRange(chr, min, max, opts) {
|
|
169
146
|
await this.getHeader(opts);
|
|
@@ -181,7 +158,11 @@ class BamFile {
|
|
|
181
158
|
const feats = [];
|
|
182
159
|
let done = false;
|
|
183
160
|
for (const chunk of chunks) {
|
|
184
|
-
const
|
|
161
|
+
const { data, cpositions, dpositions } = await this._readChunk({
|
|
162
|
+
chunk,
|
|
163
|
+
opts,
|
|
164
|
+
});
|
|
165
|
+
const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
|
|
185
166
|
const recs = [];
|
|
186
167
|
for (const feature of records) {
|
|
187
168
|
if (feature.ref_id === chrId) {
|
|
@@ -202,7 +183,7 @@ class BamFile {
|
|
|
202
183
|
break;
|
|
203
184
|
}
|
|
204
185
|
}
|
|
205
|
-
(0,
|
|
186
|
+
(0, util_ts_1.checkAbortSignal)(opts.signal);
|
|
206
187
|
if (viewAsPairs) {
|
|
207
188
|
yield this.fetchPairs(chrId, feats, opts);
|
|
208
189
|
}
|
|
@@ -289,7 +270,7 @@ class BamFile {
|
|
|
289
270
|
}
|
|
290
271
|
// only try to read the feature if we have all the bytes for it
|
|
291
272
|
if (blockEnd < ba.length) {
|
|
292
|
-
const feature = new
|
|
273
|
+
const feature = new record_ts_1.default({
|
|
293
274
|
bytes: {
|
|
294
275
|
byteArray: ba,
|
|
295
276
|
start: blockStart,
|
|
@@ -327,7 +308,7 @@ class BamFile {
|
|
|
327
308
|
});
|
|
328
309
|
sink.push(feature);
|
|
329
310
|
if (this.yieldThreadTime && +Date.now() - last > this.yieldThreadTime) {
|
|
330
|
-
await (0,
|
|
311
|
+
await (0, util_ts_1.timeout)(1);
|
|
331
312
|
last = +Date.now();
|
|
332
313
|
}
|
|
333
314
|
}
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
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+
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QACX,IAAI,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;QAEtB,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,EAAE,CAAC,MAAM,CAAC,CAAA;QACxC,OAAO,UAAU,GAAG,CAAC,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;YAClC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,UAAU,EAAE,IAAI,CAAC,CAAA;YACrD,MAAM,QAAQ,GAAG,UAAU,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,CAAA;YAE/C,wDAAwD;YACxD,uEAAuE;YACvE,IAAI,UAAU,EAAE,CAAC;gBACf,OAAO,UAAU,GAAG,KAAK,CAAC,IAAI,CAAC,YAAY,IAAI,UAAU,CAAC,GAAG,EAAE,CAAE,EAAE,CAAC,CAAA,CAAC;gBACrE,GAAG,EAAE,CAAA;YACP,CAAC;YAED,+DAA+D;YAC/D,IAAI,QAAQ,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;gBACzB,MAAM,OAAO,GAAG,IAAI,mBAAU,CAAC;oBAC7B,KAAK,EAAE;wBACL,SAAS,EAAE,EAAE;wBACb,KAAK,EAAE,UAAU;wBACjB,GAAG,EAAE,QAAQ;qBACd;oBACD,qEAAqE;oBACrE,+DAA+D;oBAC/D,WAAW;oBACX,EAAE;oBACF,gEAAgE;oBAChE,aAAa;oBACb,EAAE;oBACF,gEAAgE;oBAChE,gEAAgE;oBAChE,UAAU;oBACV,EAAE;oBACF,qEAAqE;oBACrE,qEAAqE;oBACrE,4DAA4D;oBAC5D,EAAE;oBACF,gEAAgE;oBAChE,4DAA4D;oBAC5D,EAAE;oBACF,oEAAoE;oBACpE,uBAAuB;oBACvB,UAAU,EACR,UAAU,CAAC,MAAM,GAAG,CAAC;wBACnB,CAAC,CAAC,UAAU,CAAC,GAAG,CAAE,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;4BAC3B,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAE,CAAC;4BAC/B,KAAK,CAAC,IAAI,CAAC,YAAY;4BACvB,CAAC;wBACH,CAAC,CAAC,mEAAmE;4BACnE,sEAAsE;4BACtE,2GAA2G;4BAC3G,IAAA,eAAK,EAAC,EAAE,CAAC,QAAQ,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC,KAAK,CAAC;iBACrD,CAAC,CAAA;gBAEF,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;gBAClB,IAAI,IAAI,CAAC,eAAe,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,GAAG,IAAI,GAAG,IAAI,CAAC,eAAe,EAAE,CAAC;oBACtE,MAAM,IAAA,iBAAO,EAAC,CAAC,CAAC,CAAA;oBAChB,IAAI,GAAG,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;gBACpB,CAAC;YACH,CAAC;YAED,UAAU,GAAG,QAAQ,GAAG,CAAC,CAAA;QAC3B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe;QAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,OAAO,CAAC,CAAA;QACxC,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,EAAE,SAAS,CAAC,KAAK,CAAC,CAAA;IACnE,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe;QAC7B,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,OAAO,CAAC,CAAA;QACxC,OAAO,KAAK,KAAK,SAAS,IAAI,CAAC,IAAI,CAAC,KAAK,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,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,IAAI,CAAC,KAAK,CAAC,KAAK,EAAE,CAAA;QACxB,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,OAAO,CAAC,CAAA;QACxC,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;IAC1E,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,KAAa,EACb,GAAW,EACX,IAAe;QAEf,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,IAAI,CAAC,KAAK,CAAC,KAAK,EAAE,CAAA;QACxB,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,OAAO,CAAC,CAAA;QACxC,OAAO,KAAK,KAAK,SAAS;YACxB,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;CACF;AA7bD,0BA6bC"}
|
package/dist/chunk.d.ts
CHANGED
package/dist/chunk.js
CHANGED
|
@@ -2,11 +2,6 @@
|
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
// little class representing a chunk in the index
|
|
4
4
|
class Chunk {
|
|
5
|
-
minv;
|
|
6
|
-
maxv;
|
|
7
|
-
bin;
|
|
8
|
-
_fetchedSize;
|
|
9
|
-
buffer;
|
|
10
5
|
constructor(minv, maxv, bin, _fetchedSize) {
|
|
11
6
|
this.minv = minv;
|
|
12
7
|
this.maxv = maxv;
|
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;
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAGxB,YACS,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,YAAqB;QAHrB,SAAI,GAAJ,IAAI,CAAQ;QACZ,SAAI,GAAJ,IAAI,CAAQ;QACZ,QAAG,GAAH,GAAG,CAAQ;QACX,iBAAY,GAAZ,YAAY,CAAS;IAC3B,CAAC;IAEJ,cAAc;QACZ,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,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AAlCD,wBAkCC"}
|
package/dist/csi.d.ts
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
|
-
import Chunk from './chunk';
|
|
2
|
-
import IndexFile from './indexFile';
|
|
3
|
-
import {
|
|
4
|
-
import {
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import IndexFile from './indexFile.ts';
|
|
3
|
+
import { VirtualOffset } from './virtualOffset.ts';
|
|
4
|
+
import type { BaseOpts } from './util.ts';
|
|
5
5
|
export default class CSI extends IndexFile {
|
|
6
6
|
private maxBinNumber;
|
|
7
7
|
private depth;
|
package/dist/csi.js
CHANGED
|
@@ -5,10 +5,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
7
7
|
const quick_lru_1 = __importDefault(require("quick-lru"));
|
|
8
|
-
const
|
|
9
|
-
const
|
|
10
|
-
const
|
|
11
|
-
const
|
|
8
|
+
const chunk_ts_1 = __importDefault(require("./chunk.js"));
|
|
9
|
+
const indexFile_ts_1 = __importDefault(require("./indexFile.js"));
|
|
10
|
+
const util_ts_1 = require("./util.js");
|
|
11
|
+
const virtualOffset_ts_1 = require("./virtualOffset.js");
|
|
12
12
|
const CSI1_MAGIC = 21582659; // CSI\1
|
|
13
13
|
const CSI2_MAGIC = 38359875; // CSI\2
|
|
14
14
|
function lshift(num, bits) {
|
|
@@ -17,11 +17,13 @@ function lshift(num, bits) {
|
|
|
17
17
|
function rshift(num, bits) {
|
|
18
18
|
return Math.floor(num / 2 ** bits);
|
|
19
19
|
}
|
|
20
|
-
class CSI extends
|
|
21
|
-
|
|
22
|
-
|
|
23
|
-
|
|
24
|
-
|
|
20
|
+
class CSI extends indexFile_ts_1.default {
|
|
21
|
+
constructor() {
|
|
22
|
+
super(...arguments);
|
|
23
|
+
this.maxBinNumber = 0;
|
|
24
|
+
this.depth = 0;
|
|
25
|
+
this.minShift = 0;
|
|
26
|
+
}
|
|
25
27
|
async lineCount(refId, opts) {
|
|
26
28
|
const indexData = await this.parse(opts);
|
|
27
29
|
return indexData.indices(refId)?.stats?.lineCount || 0;
|
|
@@ -54,7 +56,7 @@ class CSI extends indexFile_1.default {
|
|
|
54
56
|
skipLines,
|
|
55
57
|
format,
|
|
56
58
|
formatFlags,
|
|
57
|
-
...(0,
|
|
59
|
+
...(0, util_ts_1.parseNameBytes)(bytes.subarray(offset + 28, offset + 28 + nameSectionLength), this.renameRefSeq),
|
|
58
60
|
};
|
|
59
61
|
}
|
|
60
62
|
// fetch and parse the index
|
|
@@ -100,10 +102,10 @@ class CSI extends indexFile_1.default {
|
|
|
100
102
|
const chunkCount = dataView.getInt32(curr, true);
|
|
101
103
|
curr += 4;
|
|
102
104
|
for (let k = 0; k < chunkCount; k += 1) {
|
|
103
|
-
const u = (0,
|
|
105
|
+
const u = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
|
|
104
106
|
curr += 8;
|
|
105
107
|
curr += 8;
|
|
106
|
-
firstDataLine = (0,
|
|
108
|
+
firstDataLine = (0, util_ts_1.findFirstData)(firstDataLine, u);
|
|
107
109
|
}
|
|
108
110
|
}
|
|
109
111
|
}
|
|
@@ -125,21 +127,21 @@ class CSI extends indexFile_1.default {
|
|
|
125
127
|
const bin = dataView.getUint32(curr, true);
|
|
126
128
|
curr += 4;
|
|
127
129
|
if (bin > maxBinNumber) {
|
|
128
|
-
pseudoBinStats = (0,
|
|
130
|
+
pseudoBinStats = (0, util_ts_1.parsePseudoBin)(bytes, curr + 28);
|
|
129
131
|
curr += 28 + 16;
|
|
130
132
|
}
|
|
131
133
|
else {
|
|
132
|
-
firstDataLine = (0,
|
|
134
|
+
firstDataLine = (0, util_ts_1.findFirstData)(firstDataLine, (0, virtualOffset_ts_1.fromBytes)(bytes, curr));
|
|
133
135
|
curr += 8;
|
|
134
136
|
const chunkCount = dataView.getInt32(curr, true);
|
|
135
137
|
curr += 4;
|
|
136
138
|
const chunks = new Array(chunkCount);
|
|
137
139
|
for (let k = 0; k < chunkCount; k += 1) {
|
|
138
|
-
const u = (0,
|
|
140
|
+
const u = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
|
|
139
141
|
curr += 8;
|
|
140
|
-
const v = (0,
|
|
142
|
+
const v = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
|
|
141
143
|
curr += 8;
|
|
142
|
-
chunks[k] = new
|
|
144
|
+
chunks[k] = new chunk_ts_1.default(u, v, bin);
|
|
143
145
|
}
|
|
144
146
|
binIndex[bin] = chunks;
|
|
145
147
|
}
|
|
@@ -193,7 +195,7 @@ class CSI extends indexFile_1.default {
|
|
|
193
195
|
}
|
|
194
196
|
}
|
|
195
197
|
}
|
|
196
|
-
return (0,
|
|
198
|
+
return (0, util_ts_1.optimizeChunks)(chunks, new virtualOffset_ts_1.VirtualOffset(0, 0));
|
|
197
199
|
}
|
|
198
200
|
/**
|
|
199
201
|
* calculate the list of bins that may overlap with region [beg,end)
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,0DAAgC;AAEhC,
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAC7C,0DAAgC;AAEhC,0DAA8B;AAC9B,kEAAsC;AACtC,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAA1C;;QACU,iBAAY,GAAG,CAAC,CAAA;QAChB,UAAK,GAAG,CAAC,CAAA;QACT,aAAQ,GAAG,CAAC,CAAA;IAuPtB,CAAC;IAnPC,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GACV,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EACnC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACpB,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,IAAA,wBAAc,EACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAA8B;QACzC,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;QAC3C,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;wBACT,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,CAAC,CAAC,CAAA;oBACjD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,MAAM,YAAY,GAAG,IAAI,mBAAQ,CAAwC;YACvE,OAAO,EAAE,CAAC;SACX,CAAC,CAAA;QAEF,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,cAAc,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,cAAc,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;oBACpE,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,OAAO;gBACL,QAAQ;gBACR,KAAK,EAAE,cAAc;aACtB,CAAA;QACH,CAAC;QAED,OAAO;YACL,UAAU;YACV,aAAa;YACb,OAAO,EAAE,CAAC,KAAa,EAAE,EAAE;gBACzB,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;oBAC7B,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBAChC,IAAI,MAAM,EAAE,CAAC;wBACX,YAAY,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;oBACjC,CAAC;oBACD,OAAO,MAAM,CAAA;gBACf,CAAC;gBACD,OAAO,YAAY,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAChC,CAAC;YACD,QAAQ;YACR,GAAG,EAAE,IAAI;YACT,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,GAAG,GAAG;SACP,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,KAAa,EACb,GAAW,EACX,GAAW,EACX,OAAiB,EAAE;QAEnB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAEnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAE/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,MAAM,GAAG,EAAE,CAAA;QACjB,sEAAsE;QACtE,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,IAAI,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,EAAE,CAAC;oBACrB,MAAM,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAE,CAAA;oBACnC,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;wBAC1B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBAChB,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxD,CAAC;IAED;;;OAGG;IACH,QAAQ,CAAC,GAAW,EAAE,GAAW;QAC/B,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;QACvC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QACD,IAAI,GAAG,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC;YAClB,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;QACf,CAAC,CAAC,wCAAwC;QAC1C,GAAG,IAAI,CAAC,CAAA;QACR,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,OAAO,CAAC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC5C,MAAM,IAAI,KAAK,CACb,SAAS,GAAG,IAAI,GAAG,mDAAmD,IAAI,CAAC,QAAQ,WAAW,IAAI,CAAC,KAAK,0DAA0D,CACnK,CAAA;YACH,CAAC;YACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAU,CAAC,CAAA;QAC5B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,OAAiB,EAAE;QAC7B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;gBACnD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;gBACvB,MAAM,CAAC,CAAA;YACT,CAAC,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,OAAiB,EAAE;QAChD,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACrC,OAAO,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,QAAQ,CAAA;IAC1C,CAAC;CACF;AA1PD,sBA0PC"}
|
package/dist/htsget.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
import BamFile from './bamFile';
|
|
2
|
-
import Chunk from './chunk';
|
|
3
|
-
import { BamOpts, BaseOpts } from './util';
|
|
1
|
+
import BamFile from './bamFile.ts';
|
|
2
|
+
import Chunk from './chunk.ts';
|
|
3
|
+
import type { BamOpts, BaseOpts } from './util.ts';
|
|
4
4
|
export default class HtsgetFile extends BamFile {
|
|
5
5
|
private baseUrl;
|
|
6
6
|
private trackId;
|
|
@@ -8,7 +8,7 @@ export default class HtsgetFile extends BamFile {
|
|
|
8
8
|
trackId: string;
|
|
9
9
|
baseUrl: string;
|
|
10
10
|
});
|
|
11
|
-
streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<import("./record").default[], void, unknown>;
|
|
11
|
+
streamRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): AsyncGenerator<import("./record.ts").default[], void, unknown>;
|
|
12
12
|
_readChunk({ chunk }: {
|
|
13
13
|
chunk: Chunk;
|
|
14
14
|
opts: BaseOpts;
|