@gmod/bam 5.0.7 → 6.0.0
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/CHANGELOG.md +3 -3
- 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 +17 -11
- 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/esm/bai.js
CHANGED
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@@ -1,8 +1,8 @@
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import QuickLRU from 'quick-lru';
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-
import Chunk from
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import IndexFile from
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import { findFirstData, optimizeChunks, parsePseudoBin } from
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import { fromBytes } from
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import Chunk from "./chunk.js";
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import IndexFile from "./indexFile.js";
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import { findFirstData, optimizeChunks, parsePseudoBin, } from "./util.js";
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import { fromBytes } from "./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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];
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}
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export default class BAI extends IndexFile {
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setupP;
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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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package/esm/bai.js.map
CHANGED
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@@ -1 +1 @@
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1
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+
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|
package/esm/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/esm/bamFile.js
CHANGED
|
@@ -1,40 +1,17 @@
|
|
|
1
|
-
import AbortablePromiseCache from '@gmod/abortable-promise-cache';
|
|
2
1
|
import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
|
|
3
2
|
import crc32 from 'crc/calculators/crc32';
|
|
4
3
|
import { LocalFile, RemoteFile } from 'generic-filehandle2';
|
|
5
|
-
import
|
|
6
|
-
import
|
|
7
|
-
import
|
|
8
|
-
import
|
|
9
|
-
import
|
|
10
|
-
import {
|
|
11
|
-
import { checkAbortSignal, gen2array, makeOpts, timeout, } from './util';
|
|
4
|
+
import BAI from "./bai.js";
|
|
5
|
+
import CSI from "./csi.js";
|
|
6
|
+
import NullFilehandle from "./nullFilehandle.js";
|
|
7
|
+
import BAMFeature from "./record.js";
|
|
8
|
+
import { parseHeaderText } from "./sam.js";
|
|
9
|
+
import { checkAbortSignal, gen2array, makeOpts, timeout } from "./util.js";
|
|
12
10
|
export const BAM_MAGIC = 21840194;
|
|
13
11
|
const blockLen = 1 << 16;
|
|
14
12
|
export default class BamFile {
|
|
15
|
-
renameRefSeq;
|
|
16
|
-
bam;
|
|
17
|
-
header;
|
|
18
|
-
chrToIndex;
|
|
19
|
-
indexToChr;
|
|
20
|
-
yieldThreadTime;
|
|
21
|
-
index;
|
|
22
|
-
htsget = false;
|
|
23
|
-
headerP;
|
|
24
|
-
featureCache = new AbortablePromiseCache({
|
|
25
|
-
cache: new QuickLRU({
|
|
26
|
-
maxSize: 50,
|
|
27
|
-
}),
|
|
28
|
-
fill: async (args, signal) => {
|
|
29
|
-
const { chunk, opts } = args;
|
|
30
|
-
const { data, cpositions, dpositions } = await this._readChunk({
|
|
31
|
-
chunk,
|
|
32
|
-
opts: { ...opts, signal },
|
|
33
|
-
});
|
|
34
|
-
return this.readBamFeatures(data, cpositions, dpositions, chunk);
|
|
35
|
-
},
|
|
36
|
-
});
|
|
37
13
|
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, yieldThreadTime = 100, renameRefSeqs = n => n, }) {
|
|
14
|
+
this.htsget = false;
|
|
38
15
|
this.renameRefSeq = renameRefSeqs;
|
|
39
16
|
if (bamFilehandle) {
|
|
40
17
|
this.bam = bamFilehandle;
|
|
@@ -175,7 +152,11 @@ export default class BamFile {
|
|
|
175
152
|
const feats = [];
|
|
176
153
|
let done = false;
|
|
177
154
|
for (const chunk of chunks) {
|
|
178
|
-
const
|
|
155
|
+
const { data, cpositions, dpositions } = await this._readChunk({
|
|
156
|
+
chunk,
|
|
157
|
+
opts,
|
|
158
|
+
});
|
|
159
|
+
const records = await this.readBamFeatures(data, cpositions, dpositions, chunk);
|
|
179
160
|
const recs = [];
|
|
180
161
|
for (const feature of records) {
|
|
181
162
|
if (feature.ref_id === chrId) {
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
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+
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O,EAAE,IAAI,EAAE,UAAU,EAAE,UAAU,EAAE,KAAK,EAAE,CAAA;IAChD,CAAC;IAED,KAAK,CAAC,eAAe,CACnB,EAAc,EACd,UAAoB,EACpB,UAAoB,EACpB,KAAY;QAEZ,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,MAAM,IAAI,GAAG,EAAkB,CAAA;QAC/B,IAAI,GAAG,GAAG,CAAC,CAAA;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,UAAU,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,KAAK,CAAC,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,OAAO,CAAC,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"}
|
package/esm/chunk.d.ts
CHANGED
package/esm/chunk.js
CHANGED
package/esm/chunk.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,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"}
|
package/esm/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/esm/csi.js
CHANGED
|
@@ -1,9 +1,9 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
2
|
import QuickLRU from 'quick-lru';
|
|
3
|
-
import Chunk from
|
|
4
|
-
import IndexFile from
|
|
5
|
-
import { findFirstData, optimizeChunks, parseNameBytes, parsePseudoBin, } from
|
|
6
|
-
import { VirtualOffset, fromBytes } from
|
|
3
|
+
import Chunk from "./chunk.js";
|
|
4
|
+
import IndexFile from "./indexFile.js";
|
|
5
|
+
import { findFirstData, optimizeChunks, parseNameBytes, parsePseudoBin, } from "./util.js";
|
|
6
|
+
import { VirtualOffset, fromBytes } from "./virtualOffset.js";
|
|
7
7
|
const CSI1_MAGIC = 21582659; // CSI\1
|
|
8
8
|
const CSI2_MAGIC = 38359875; // CSI\2
|
|
9
9
|
function lshift(num, bits) {
|
|
@@ -13,10 +13,12 @@ function rshift(num, bits) {
|
|
|
13
13
|
return Math.floor(num / 2 ** bits);
|
|
14
14
|
}
|
|
15
15
|
export default class CSI extends IndexFile {
|
|
16
|
-
|
|
17
|
-
|
|
18
|
-
|
|
19
|
-
|
|
16
|
+
constructor() {
|
|
17
|
+
super(...arguments);
|
|
18
|
+
this.maxBinNumber = 0;
|
|
19
|
+
this.depth = 0;
|
|
20
|
+
this.minShift = 0;
|
|
21
|
+
}
|
|
20
22
|
async lineCount(refId, opts) {
|
|
21
23
|
const indexData = await this.parse(opts);
|
|
22
24
|
return indexData.indices(refId)?.stats?.lineCount || 0;
|
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;AAC7C,OAAO,QAAQ,MAAM,WAAW,CAAA;AAEhC,OAAO,KAAK,MAAM,
|
|
1
|
+
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AAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,SAAS,CAAC,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,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,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,cAAc,CAAC,MAAM,EAAE,IAAI,aAAa,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"}
|
package/esm/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;
|
package/esm/htsget.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
|
-
import BamFile, { BAM_MAGIC } from
|
|
3
|
-
import { parseHeaderText } from
|
|
4
|
-
import { concatUint8Array } from
|
|
2
|
+
import BamFile, { BAM_MAGIC } from "./bamFile.js";
|
|
3
|
+
import { parseHeaderText } from "./sam.js";
|
|
4
|
+
import { concatUint8Array } from "./util.js";
|
|
5
5
|
async function concat(arr, opts) {
|
|
6
6
|
const res = await Promise.all(arr.map(async (chunk) => {
|
|
7
7
|
const { url, headers } = chunk;
|
|
@@ -32,8 +32,6 @@ async function concat(arr, opts) {
|
|
|
32
32
|
return concatUint8Array(await Promise.all(res.map(elt => unzip(elt))));
|
|
33
33
|
}
|
|
34
34
|
export default class HtsgetFile extends BamFile {
|
|
35
|
-
baseUrl;
|
|
36
|
-
trackId;
|
|
37
35
|
constructor(args) {
|
|
38
36
|
super({ htsget: true });
|
|
39
37
|
this.baseUrl = args.baseUrl;
|
package/esm/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,
|
|
1
|
+
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|
package/esm/index.d.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
export { default as BAI } from './bai';
|
|
2
|
-
export { default as BamFile } from './bamFile';
|
|
3
|
-
export { default as CSI } from './csi';
|
|
4
|
-
export { default as BamRecord } from './record';
|
|
5
|
-
export { default as HtsgetFile } from './htsget';
|
|
1
|
+
export { default as BAI } from './bai.ts';
|
|
2
|
+
export { default as BamFile } from './bamFile.ts';
|
|
3
|
+
export { default as CSI } from './csi.ts';
|
|
4
|
+
export { default as BamRecord } from './record.ts';
|
|
5
|
+
export { default as HtsgetFile } from './htsget.ts';
|
package/esm/index.js
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
|
-
export { default as BAI } from
|
|
2
|
-
export { default as BamFile } from
|
|
3
|
-
export { default as CSI } from
|
|
4
|
-
export { default as BamRecord } from
|
|
5
|
-
export { default as HtsgetFile } from
|
|
1
|
+
export { default as BAI } from "./bai.js";
|
|
2
|
+
export { default as BamFile } from "./bamFile.js";
|
|
3
|
+
export { default as CSI } from "./csi.js";
|
|
4
|
+
export { default as BamRecord } from "./record.js";
|
|
5
|
+
export { default as HtsgetFile } from "./htsget.js";
|
|
6
6
|
//# sourceMappingURL=index.js.map
|
package/esm/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,OAAO,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,EAAE,OAAO,IAAI,GAAG,EAAE,MAAM,UAAU,CAAA;AACzC,OAAO,EAAE,OAAO,IAAI,SAAS,EAAE,MAAM,aAAa,CAAA;AAClD,OAAO,EAAE,OAAO,IAAI,UAAU,EAAE,MAAM,aAAa,CAAA"}
|
package/esm/indexFile.d.ts
CHANGED
|
@@ -1,13 +1,9 @@
|
|
|
1
|
-
import Chunk from './chunk';
|
|
2
|
-
import { BaseOpts } from './util';
|
|
1
|
+
import Chunk from './chunk.ts';
|
|
2
|
+
import { BaseOpts } from './util.ts';
|
|
3
3
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
4
4
|
export default abstract class IndexFile {
|
|
5
5
|
filehandle: GenericFilehandle;
|
|
6
6
|
renameRefSeq: (s: string) => string;
|
|
7
|
-
/**
|
|
8
|
-
* @param {filehandle} filehandle
|
|
9
|
-
* @param {function} renameRefSeqs
|
|
10
|
-
*/
|
|
11
7
|
constructor({ filehandle, renameRefSeq, }: {
|
|
12
8
|
filehandle: GenericFilehandle;
|
|
13
9
|
renameRefSeq?: (a: string) => string;
|
package/esm/indexFile.js
CHANGED
|
@@ -1,10 +1,4 @@
|
|
|
1
1
|
export default class IndexFile {
|
|
2
|
-
filehandle;
|
|
3
|
-
renameRefSeq;
|
|
4
|
-
/**
|
|
5
|
-
* @param {filehandle} filehandle
|
|
6
|
-
* @param {function} renameRefSeqs
|
|
7
|
-
*/
|
|
8
2
|
constructor({ filehandle, renameRefSeq = (n) => n, }) {
|
|
9
3
|
this.filehandle = filehandle;
|
|
10
4
|
this.renameRefSeq = renameRefSeq;
|
package/esm/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAKA,MAAM,CAAC,OAAO,OAAgB,SAAS;
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAKA,MAAM,CAAC,OAAO,OAAgB,SAAS;IAIrC,YAAY,EACV,UAAU,EACV,YAAY,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIhC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;IAClC,CAAC;CAcF"}
|
package/esm/nullIndex.d.ts
CHANGED
package/esm/nullIndex.js
CHANGED
package/esm/nullIndex.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"nullIndex.js","sourceRoot":"","sources":["../src/nullIndex.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,
|
|
1
|
+
{"version":3,"file":"nullIndex.js","sourceRoot":"","sources":["../src/nullIndex.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,gBAAgB,CAAA;AAEtC,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,SAAS;IACvC,SAAS;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IACS,MAAM;QACd,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,KAAK,CAAC,QAAQ;QACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;IAEM,cAAc;QACnB,MAAM,IAAI,KAAK,CAAC,cAAc,CAAC,CAAA;IACjC,CAAC;CACF"}
|