@gmod/bam 7.3.4 → 7.5.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +11 -29
- package/dist/bai.js +10 -7
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +26 -9
- package/dist/bamFile.js +95 -47
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +2 -2
- package/dist/csi.js.map +1 -1
- package/dist/htsget.js +2 -2
- package/dist/htsget.js.map +1 -1
- package/dist/index.d.ts +1 -2
- package/dist/index.js +2 -1
- package/dist/index.js.map +1 -1
- package/dist/record.d.ts +2 -1
- package/dist/record.js +150 -39
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +0 -18
- package/dist/util.js +5 -36
- package/dist/util.js.map +1 -1
- package/esm/bai.js +10 -7
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +26 -9
- package/esm/bamFile.js +95 -47
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +2 -2
- package/esm/csi.js.map +1 -1
- package/esm/htsget.js +2 -2
- package/esm/htsget.js.map +1 -1
- package/esm/index.d.ts +1 -2
- package/esm/index.js +1 -1
- package/esm/index.js.map +1 -1
- package/esm/record.d.ts +2 -1
- package/esm/record.js +150 -39
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +0 -18
- package/esm/util.js +5 -32
- package/esm/util.js.map +1 -1
- package/package.json +3 -1
- package/src/bai.ts +15 -8
- package/src/bamFile.ts +121 -57
- package/src/csi.ts +10 -2
- package/src/htsget.ts +6 -2
- package/src/index.ts +1 -2
- package/src/record.ts +163 -46
- package/src/util.ts +13 -63
package/README.md
CHANGED
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@@ -59,8 +59,7 @@ const records = await ti.getRecordsForRange('1', 2000000, 2000001)
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Let us know if it doesn't work for your use case.
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Caveat: htsget `getRecordsForRange` does not honor `viewAsPairs`,
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-
`pairAcrossChr`,
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server as-is.
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`pairAcrossChr`, or `maxInsertSize`. The range is fetched from the server as-is.
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## Documentation
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@@ -93,8 +92,16 @@ Note: requires calling `getHeader` first.
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chromosomes. default: false
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- `opts.maxInsertSize` - control the viewAsPairs option behavior to limit
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distance within a chromosome to fetch. default: 200kb
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-
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-
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Records come back unfiltered. Filter the returned array yourself — the flag
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helpers (`record.isSecondary()` and friends) and `record.getTag(name)` cover it,
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and `getTag` decodes just the one tag rather than every tag on the read:
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```typescript
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const records = (await bam.getRecordsForRange('chr1', 0, 100000)).filter(
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r => r.isProperlyPaired() && !r.isSecondary() && r.getTag('RG') === 'rg1',
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)
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```
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### async getHeader(opts?)
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@@ -173,31 +180,6 @@ record.seqAt(idx) // get single base at position
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record.toJSON() // serialize record
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```
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### FilterBy
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```typescript
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interface FilterBy {
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flagInclude?: number // only include reads where all these flag bits are set
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flagExclude?: number // exclude reads where any of these flag bits are set
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tagFilter?: {
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tag: string // aux tag name, e.g. 'RG'
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value?: string // omit to filter by tag presence only
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}
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}
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```
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Example — fetch only properly-paired primary alignments from read-group `rg1`:
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```typescript
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const records = await bam.getRecordsForRange('chr1', 0, 100000, {
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filterBy: {
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flagInclude: 0x2, // properly paired
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flagExclude: 0x900, // not secondary or supplementary
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tagFilter: { tag: 'RG', value: 'rg1' },
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},
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})
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```
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-
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### Custom BamRecord class
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You can provide your own BamRecord class to add custom properties or methods:
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package/dist/bai.js
CHANGED
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@@ -68,7 +68,7 @@ function reg2bins(beg, end) {
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class BAI extends indexFile_ts_1.default {
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async _parse(opts) {
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const bytes = await this.filehandle.readFile(opts);
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const dataView = new DataView(bytes.buffer);
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const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
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// check BAI magic numbers
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if (dataView.getUint32(0, true) !== BAI_MAGIC) {
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throw new Error('Not a BAI file');
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@@ -189,19 +189,22 @@ class BAI extends indexFile_ts_1.default {
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if (e > (linearIndex.length - 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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// entries and then rebuilding every one of them to apply the scale. Keep the
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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 = linearIndex[s / v].blockPosition;
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for (let i = s / v, j = 0; i < e / v; i++, j++) {
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const nextPos = linearIndex[i + 1].blockPosition;
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depths[j] = {
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score:
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score: ((nextPos - currentPos) * lineCount) / totalSize,
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start: i * v,
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end: i * v + v,
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};
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currentPos =
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currentPos = nextPos;
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}
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return depths
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...d,
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score: (d.score * (stats?.lineCount ?? 0)) / totalSize,
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}));
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return depths;
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}
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reg2bins(min, max) {
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return reg2bins(min, max);
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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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-
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+
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|
package/dist/bamFile.d.ts
CHANGED
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
import QuickLRU from '@jbrowse/quick-lru';
|
|
2
1
|
import BAI from './bai.ts';
|
|
3
2
|
import CSI from './csi.ts';
|
|
4
3
|
import BAMFeature from './record.ts';
|
|
@@ -24,10 +23,23 @@ export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (args: {
|
|
|
24
23
|
}) => T;
|
|
25
24
|
export declare const BAM_MAGIC = 21840194;
|
|
26
25
|
interface ChunkEntry<T> {
|
|
27
|
-
|
|
28
|
-
maxBlock: number;
|
|
26
|
+
bytes: number;
|
|
29
27
|
features: T[];
|
|
30
28
|
}
|
|
29
|
+
export declare const DEFAULT_MAX_CACHE_BYTES: number;
|
|
30
|
+
declare class ChunkFeatureCache<T> {
|
|
31
|
+
maxBytes: number;
|
|
32
|
+
private entries;
|
|
33
|
+
private bytes;
|
|
34
|
+
constructor(maxBytes: number);
|
|
35
|
+
get size(): number;
|
|
36
|
+
get byteSize(): number;
|
|
37
|
+
get(key: string): ChunkEntry<T> | undefined;
|
|
38
|
+
set(key: string, entry: ChunkEntry<T>): void;
|
|
39
|
+
delete(key: string): void;
|
|
40
|
+
clear(): void;
|
|
41
|
+
[Symbol.iterator](): MapIterator<[string, ChunkEntry<T>]>;
|
|
42
|
+
}
|
|
31
43
|
export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
32
44
|
renameRefSeq: (a: string) => string;
|
|
33
45
|
bam: GenericFilehandle;
|
|
@@ -40,9 +52,9 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
40
52
|
index?: BAI | CSI;
|
|
41
53
|
htsget: boolean;
|
|
42
54
|
headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
|
|
43
|
-
chunkFeatureCache:
|
|
55
|
+
chunkFeatureCache: ChunkFeatureCache<T>;
|
|
44
56
|
private RecordClass;
|
|
45
|
-
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, }: {
|
|
57
|
+
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
|
|
46
58
|
bamFilehandle?: GenericFilehandle;
|
|
47
59
|
bamPath?: string;
|
|
48
60
|
bamUrl?: string;
|
|
@@ -55,6 +67,8 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
55
67
|
renameRefSeqs?: (a: string) => string;
|
|
56
68
|
htsget?: boolean;
|
|
57
69
|
recordClass?: BamRecordClass<T>;
|
|
70
|
+
/** budget for the parsed-chunk cache, in decompressed bytes */
|
|
71
|
+
maxCacheBytes?: number;
|
|
58
72
|
});
|
|
59
73
|
getHeaderPre(opts?: BaseOpts): Promise<{
|
|
60
74
|
tag: string;
|
|
@@ -73,11 +87,14 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
73
87
|
getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
|
|
74
88
|
private getSeqId;
|
|
75
89
|
getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
|
|
76
|
-
private
|
|
77
|
-
private
|
|
90
|
+
private _cachedChunkFeatures;
|
|
91
|
+
private _fetchChunkFeatures;
|
|
78
92
|
fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
|
|
79
|
-
_readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<
|
|
80
|
-
|
|
93
|
+
_readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<{
|
|
94
|
+
features: T[];
|
|
95
|
+
bytes: number;
|
|
96
|
+
}>;
|
|
97
|
+
readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): T[];
|
|
81
98
|
hasRefSeq(seqName: string, opts?: BaseOpts): Promise<boolean>;
|
|
82
99
|
lineCount(seqName: string, opts?: BaseOpts): Promise<number>;
|
|
83
100
|
indexCov(seqName: string, start?: number, end?: number): Promise<never[] | import("./bai.ts").IndexCovEntry[]>;
|
package/dist/bamFile.js
CHANGED
|
@@ -3,9 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.BAM_MAGIC = void 0;
|
|
6
|
+
exports.DEFAULT_MAX_CACHE_BYTES = exports.BAM_MAGIC = void 0;
|
|
7
7
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
8
|
-
const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
|
|
9
8
|
const crc32_1 = __importDefault(require("crc/calculators/crc32"));
|
|
10
9
|
const generic_filehandle2_1 = require("generic-filehandle2");
|
|
11
10
|
const bai_ts_1 = __importDefault(require("./bai.js"));
|
|
@@ -20,9 +19,66 @@ function resolveFilehandle(filehandle, path, url) {
|
|
|
20
19
|
return (filehandle ??
|
|
21
20
|
(path ? new generic_filehandle2_1.LocalFile(path) : url ? new generic_filehandle2_1.RemoteFile(url) : undefined));
|
|
22
21
|
}
|
|
23
|
-
function chunkCacheKey(chunk
|
|
22
|
+
function chunkCacheKey(chunk) {
|
|
24
23
|
const { minv, maxv } = chunk;
|
|
25
|
-
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}
|
|
24
|
+
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
|
|
25
|
+
}
|
|
26
|
+
// Every record in an entry is a view into its chunk's decompressed buffer, so
|
|
27
|
+
// caching one entry pins that whole buffer — 8MB apiece on the nanopore and
|
|
28
|
+
// 2kb-read test files, and optimizeChunks merges spans up to 5MB *compressed*,
|
|
29
|
+
// so tens of MB is possible. A count-based LRU therefore gives no bound on
|
|
30
|
+
// memory at all, which is why this budgets by decompressed bytes instead. It is
|
|
31
|
+
// the *only* bound: a query keeps every chunk it parsed, since a chunk dropped
|
|
32
|
+
// here costs a re-download and re-decompress the next time the view moves.
|
|
33
|
+
exports.DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
|
|
34
|
+
class ChunkFeatureCache {
|
|
35
|
+
maxBytes;
|
|
36
|
+
entries = new Map();
|
|
37
|
+
bytes = 0;
|
|
38
|
+
constructor(maxBytes) {
|
|
39
|
+
this.maxBytes = maxBytes;
|
|
40
|
+
}
|
|
41
|
+
get size() {
|
|
42
|
+
return this.entries.size;
|
|
43
|
+
}
|
|
44
|
+
get byteSize() {
|
|
45
|
+
return this.bytes;
|
|
46
|
+
}
|
|
47
|
+
get(key) {
|
|
48
|
+
const entry = this.entries.get(key);
|
|
49
|
+
if (entry) {
|
|
50
|
+
// re-insert so Map iteration order stays least-recently-used first
|
|
51
|
+
this.entries.delete(key);
|
|
52
|
+
this.entries.set(key, entry);
|
|
53
|
+
}
|
|
54
|
+
return entry;
|
|
55
|
+
}
|
|
56
|
+
set(key, entry) {
|
|
57
|
+
this.delete(key);
|
|
58
|
+
this.entries.set(key, entry);
|
|
59
|
+
this.bytes += entry.bytes;
|
|
60
|
+
// Evict from the least-recently-used end. The size > 1 guard means a single
|
|
61
|
+
// chunk larger than the whole budget is still kept: the caller needs it for
|
|
62
|
+
// the query in flight, and dropping it would only force a re-decompress.
|
|
63
|
+
const lru = this.entries.keys();
|
|
64
|
+
while (this.bytes > this.maxBytes && this.entries.size > 1) {
|
|
65
|
+
this.delete(lru.next().value);
|
|
66
|
+
}
|
|
67
|
+
}
|
|
68
|
+
delete(key) {
|
|
69
|
+
const entry = this.entries.get(key);
|
|
70
|
+
if (entry) {
|
|
71
|
+
this.entries.delete(key);
|
|
72
|
+
this.bytes -= entry.bytes;
|
|
73
|
+
}
|
|
74
|
+
}
|
|
75
|
+
clear() {
|
|
76
|
+
this.entries.clear();
|
|
77
|
+
this.bytes = 0;
|
|
78
|
+
}
|
|
79
|
+
[Symbol.iterator]() {
|
|
80
|
+
return this.entries[Symbol.iterator]();
|
|
81
|
+
}
|
|
26
82
|
}
|
|
27
83
|
class BamFile {
|
|
28
84
|
renameRefSeq;
|
|
@@ -33,15 +89,13 @@ class BamFile {
|
|
|
33
89
|
index;
|
|
34
90
|
htsget = false;
|
|
35
91
|
headerP;
|
|
36
|
-
// Cache for parsed features by chunk
|
|
37
|
-
|
|
38
|
-
chunkFeatureCache = new quick_lru_1.default({
|
|
39
|
-
maxSize: 100,
|
|
40
|
-
});
|
|
92
|
+
// Cache for parsed features by chunk, bounded by decompressed bytes
|
|
93
|
+
chunkFeatureCache;
|
|
41
94
|
RecordClass;
|
|
42
|
-
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
|
|
95
|
+
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = exports.DEFAULT_MAX_CACHE_BYTES, }) {
|
|
43
96
|
this.renameRefSeq = renameRefSeqs;
|
|
44
97
|
this.RecordClass = (recordClass ?? record_ts_1.default);
|
|
98
|
+
this.chunkFeatureCache = new ChunkFeatureCache(maxCacheBytes);
|
|
45
99
|
const bamFh = resolveFilehandle(bamFilehandle, bamPath, bamUrl);
|
|
46
100
|
if (bamFh) {
|
|
47
101
|
this.bam = bamFh;
|
|
@@ -81,7 +135,7 @@ class BamFile {
|
|
|
81
135
|
? await this.bam.readFile()
|
|
82
136
|
: await this.bam.read(readLen, 0);
|
|
83
137
|
let uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
|
|
84
|
-
const dataView = new DataView(uncba.buffer);
|
|
138
|
+
const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
|
|
85
139
|
if (dataView.getInt32(0, true) !== exports.BAM_MAGIC) {
|
|
86
140
|
throw new Error('Not a BAM file');
|
|
87
141
|
}
|
|
@@ -129,18 +183,23 @@ class BamFile {
|
|
|
129
183
|
return [];
|
|
130
184
|
}
|
|
131
185
|
const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
|
|
132
|
-
return this.
|
|
186
|
+
return this._fetchChunkFeatures(chunks, chrId, min, max, opts);
|
|
133
187
|
}
|
|
134
|
-
//
|
|
135
|
-
|
|
136
|
-
|
|
137
|
-
|
|
138
|
-
|
|
139
|
-
|
|
188
|
+
// Parsed records for a chunk, reading and decompressing it only on a miss.
|
|
189
|
+
// Every path that wants a chunk's features goes through here — mate lookups
|
|
190
|
+
// included, since a viewAsPairs query revisits the same mate chunks each time
|
|
191
|
+
// the view moves.
|
|
192
|
+
async _cachedChunkFeatures(chunk, opts) {
|
|
193
|
+
const cacheKey = chunkCacheKey(chunk);
|
|
194
|
+
let entry = this.chunkFeatureCache.get(cacheKey);
|
|
195
|
+
if (!entry) {
|
|
196
|
+
entry = await this._readChunkFeatures(chunk, opts);
|
|
197
|
+
this.chunkFeatureCache.set(cacheKey, entry);
|
|
140
198
|
}
|
|
199
|
+
return entry.features;
|
|
141
200
|
}
|
|
142
|
-
async
|
|
143
|
-
const { viewAsPairs,
|
|
201
|
+
async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
|
|
202
|
+
const { viewAsPairs, onProgress } = opts;
|
|
144
203
|
const result = [];
|
|
145
204
|
let totalBytes = 0;
|
|
146
205
|
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
@@ -150,27 +209,10 @@ class BamFile {
|
|
|
150
209
|
onProgress?.(0, totalBytes);
|
|
151
210
|
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
152
211
|
const chunk = chunks[ci];
|
|
153
|
-
const
|
|
154
|
-
const minBlock = chunk.minv.blockPosition;
|
|
155
|
-
const maxBlock = chunk.maxv.blockPosition;
|
|
156
|
-
let records;
|
|
157
|
-
const cached = this.chunkFeatureCache.get(cacheKey);
|
|
158
|
-
if (cached) {
|
|
159
|
-
records = cached.features;
|
|
160
|
-
}
|
|
161
|
-
else {
|
|
162
|
-
this.evictOverlappingChunks(minBlock, maxBlock);
|
|
163
|
-
const allRecords = await this._readChunkFeatures(chunk, opts);
|
|
164
|
-
records = filterBy ? (0, util_ts_1.applyFilters)(allRecords, filterBy) : allRecords;
|
|
165
|
-
this.chunkFeatureCache.set(cacheKey, {
|
|
166
|
-
minBlock,
|
|
167
|
-
maxBlock,
|
|
168
|
-
features: records,
|
|
169
|
-
});
|
|
170
|
-
}
|
|
212
|
+
const features = await this._cachedChunkFeatures(chunk, opts);
|
|
171
213
|
downloadedBytes += chunk.fetchedSize();
|
|
172
214
|
onProgress?.(downloadedBytes, totalBytes);
|
|
173
|
-
(0, util_ts_1.appendInRange)(
|
|
215
|
+
(0, util_ts_1.appendInRange)(features, chrId, min, max, result);
|
|
174
216
|
}
|
|
175
217
|
if (viewAsPairs) {
|
|
176
218
|
const pairs = await this.fetchPairs(chrId, result, opts);
|
|
@@ -182,12 +224,15 @@ class BamFile {
|
|
|
182
224
|
}
|
|
183
225
|
async fetchPairs(chrId, records, opts) {
|
|
184
226
|
const { pairAcrossChr, maxInsertSize = 200000 } = opts;
|
|
185
|
-
|
|
227
|
+
// Map, not a plain object: read names come from the file, and on a plain
|
|
228
|
+
// object a read named "constructor" would read back Object.prototype's and
|
|
229
|
+
// make the count NaN.
|
|
230
|
+
const readNameCounts = new Map();
|
|
186
231
|
const readIds = new Set();
|
|
187
232
|
for (let i = 0, l = records.length; i < l; i++) {
|
|
188
233
|
const r = records[i];
|
|
189
234
|
const name = r.name;
|
|
190
|
-
readNameCounts
|
|
235
|
+
readNameCounts.set(name, (readNameCounts.get(name) ?? 0) + 1);
|
|
191
236
|
readIds.add(r.fileOffset);
|
|
192
237
|
}
|
|
193
238
|
const matePromises = [];
|
|
@@ -195,7 +240,7 @@ class BamFile {
|
|
|
195
240
|
const f = records[i];
|
|
196
241
|
const name = f.name;
|
|
197
242
|
if (this.index &&
|
|
198
|
-
readNameCounts
|
|
243
|
+
readNameCounts.get(name) === 1 &&
|
|
199
244
|
(pairAcrossChr ||
|
|
200
245
|
(f.next_refid === chrId &&
|
|
201
246
|
Math.abs(f.start - f.next_pos) < maxInsertSize))) {
|
|
@@ -212,11 +257,11 @@ class BamFile {
|
|
|
212
257
|
}
|
|
213
258
|
}
|
|
214
259
|
const mateFeatLists = await Promise.all([...map.values()].map(async (c) => {
|
|
215
|
-
const features = await this.
|
|
260
|
+
const features = await this._cachedChunkFeatures(c, opts);
|
|
216
261
|
const mateRecs = [];
|
|
217
262
|
for (let i = 0, l = features.length; i < l; i++) {
|
|
218
263
|
const feature = features[i];
|
|
219
|
-
if (readNameCounts
|
|
264
|
+
if (readNameCounts.get(feature.name) === 1 &&
|
|
220
265
|
!readIds.has(feature.fileOffset)) {
|
|
221
266
|
mateRecs.push(feature);
|
|
222
267
|
}
|
|
@@ -235,13 +280,16 @@ class BamFile {
|
|
|
235
280
|
signal: opts.signal,
|
|
236
281
|
});
|
|
237
282
|
const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
|
|
238
|
-
return
|
|
283
|
+
return {
|
|
284
|
+
features: this.readBamFeatures(data, cpositions, dpositions, chunk),
|
|
285
|
+
bytes: data.byteLength,
|
|
286
|
+
};
|
|
239
287
|
}
|
|
240
|
-
|
|
288
|
+
readBamFeatures(ba, cpositions, dpositions, chunk) {
|
|
241
289
|
let blockStart = 0;
|
|
242
290
|
const sink = [];
|
|
243
291
|
let pos = 0;
|
|
244
|
-
const dataView = new DataView(ba.buffer);
|
|
292
|
+
const dataView = new DataView(ba.buffer, ba.byteOffset, ba.byteLength);
|
|
245
293
|
const hasDpositions = dpositions.length > 0;
|
|
246
294
|
const hasCpositions = cpositions.length > 0;
|
|
247
295
|
while (blockStart + 4 < ba.length) {
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
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+
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|
package/dist/csi.js
CHANGED
|
@@ -60,7 +60,7 @@ class CSI extends indexFile_ts_1.default {
|
|
|
60
60
|
return [];
|
|
61
61
|
}
|
|
62
62
|
parseAuxData(bytes, offset) {
|
|
63
|
-
const dataView = new DataView(bytes.buffer);
|
|
63
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
64
64
|
const formatFlags = dataView.getUint32(offset, true);
|
|
65
65
|
const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
|
|
66
66
|
const format = ['generic', 'SAM', 'VCF'][formatFlags & 0xf];
|
|
@@ -91,7 +91,7 @@ class CSI extends indexFile_ts_1.default {
|
|
|
91
91
|
async _parse(opts) {
|
|
92
92
|
const buffer = await this.filehandle.readFile(opts);
|
|
93
93
|
const bytes = await (0, bgzf_filehandle_1.unzip)(buffer);
|
|
94
|
-
const dataView = new DataView(bytes.buffer);
|
|
94
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
95
95
|
let csiVersion;
|
|
96
96
|
const magic = dataView.getUint32(0, true);
|
|
97
97
|
if (magic === CSI1_MAGIC) {
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
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,
|
|
1
|
+
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|
package/dist/htsget.js
CHANGED
|
@@ -85,7 +85,7 @@ class HtsgetFile extends bamFile_ts_1.default {
|
|
|
85
85
|
signal: opts?.signal,
|
|
86
86
|
});
|
|
87
87
|
const zero = new virtualOffset_ts_1.VirtualOffset(0, 0);
|
|
88
|
-
const allRecords =
|
|
88
|
+
const allRecords = this.readBamFeatures(uncba, [], [], new chunk_ts_1.default(zero, zero, 0));
|
|
89
89
|
return (0, util_ts_1.appendInRange)(allRecords, chrId, min, max);
|
|
90
90
|
}
|
|
91
91
|
async getHeaderPre(opts = {}) {
|
|
@@ -95,7 +95,7 @@ class HtsgetFile extends bamFile_ts_1.default {
|
|
|
95
95
|
const uncba = await fetchAndConcat(data.htsget.urls, {
|
|
96
96
|
signal: opts.signal,
|
|
97
97
|
});
|
|
98
|
-
const dataView = new DataView(uncba.buffer);
|
|
98
|
+
const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
|
|
99
99
|
if (dataView.getInt32(0, true) !== bamFile_ts_1.BAM_MAGIC) {
|
|
100
100
|
throw new Error('Not a BAM file');
|
|
101
101
|
}
|
package/dist/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,2DAAiD;AACjD,0DAA8B;AAC9B,qCAA0C;AAC1C,uCAA2D;AAC3D,yDAAkD;AAWlD,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAkB;IACpD,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAClC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,CAAA;IAC5E,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,KAAK,UAAU,UAAU,CAAC,EAAE,GAAG,EAAE,OAAO,EAAe,EAAE,IAAkB;IACzE,0EAA0E;IAC1E,uDAAuD;IACvD,+CAA+C;IAC/C,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;IACpD,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC;QACjC,CAAC,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC;QACpB,CAAC,CAAC,MAAM,OAAO,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAClD,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;AAChD,CAAC;AAED,KAAK,UAAU,cAAc,CAAC,GAAkB,EAAE,IAAkB;IAClE,2EAA2E;IAC3E,OAAO,IAAA,0BAAgB,EACrB,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,MAAM,UAAU,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CACxE,CAAA;AACH,CAAC;AAED,MAAqB,UAEnB,SAAQ,oBAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEvB,YAAY,IAIX;QACC,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;QACtD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;YAC5D,MAAM,EAAE,IAAI,EAAE,MAAM;SACrB,CAAC,CAAA;QAEF,MAAM,IAAI,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,IAAI,CAAC,eAAe,CACrC,KAAK,EACL,EAAE,EACF,EAAE,EACF,IAAI,kBAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QAED,OAAO,IAAA,uBAAa,EAAC,UAAU,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IACnD,CAAC;IAED,KAAK,CAAC,YAAY,CAAC,OAAiB,EAAE;QACpC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE;YACnD,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CAAC,CAAA;QACF,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,sBAAS,EAAE,CAAC;YAC7C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAE1C,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;QACjC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAC,CAAA;QACjE,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF;AA3FD,6BA2FC"}
|
package/dist/index.d.ts
CHANGED
|
@@ -1,8 +1,7 @@
|
|
|
1
1
|
export { default as BAI } from './bai.ts';
|
|
2
|
-
export { default as BamFile } from './bamFile.ts';
|
|
2
|
+
export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from './bamFile.ts';
|
|
3
3
|
export { default as CSI } from './csi.ts';
|
|
4
4
|
export { default as BamRecord } from './record.ts';
|
|
5
5
|
export { default as HtsgetFile } from './htsget.ts';
|
|
6
6
|
export type { Bytes } from './record.ts';
|
|
7
|
-
export type { FilterBy, TagFilter } from './util.ts';
|
|
8
7
|
export type { BamRecordClass, BamRecordLike } from './bamFile.ts';
|
package/dist/index.js
CHANGED
|
@@ -3,10 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.BAI = void 0;
|
|
6
|
+
exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.BAI = void 0;
|
|
7
7
|
var bai_ts_1 = require("./bai.js");
|
|
8
8
|
Object.defineProperty(exports, "BAI", { enumerable: true, get: function () { return __importDefault(bai_ts_1).default; } });
|
|
9
9
|
var bamFile_ts_1 = require("./bamFile.js");
|
|
10
|
+
Object.defineProperty(exports, "DEFAULT_MAX_CACHE_BYTES", { enumerable: true, get: function () { return bamFile_ts_1.DEFAULT_MAX_CACHE_BYTES; } });
|
|
10
11
|
Object.defineProperty(exports, "BamFile", { enumerable: true, get: function () { return __importDefault(bamFile_ts_1).default; } });
|
|
11
12
|
var csi_ts_1 = require("./csi.js");
|
|
12
13
|
Object.defineProperty(exports, "CSI", { enumerable: true, get: function () { return __importDefault(csi_ts_1).default; } });
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAA0E;AAAjE,qHAAA,uBAAuB,OAAA;AAAE,sHAAA,OAAO,OAAW;AACpD,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc"}
|
package/dist/record.d.ts
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
export type NumericCigar = Uint32Array | Int32Array | number[];
|
|
1
2
|
export interface Bytes {
|
|
2
3
|
start: number;
|
|
3
4
|
end: number;
|
|
@@ -55,7 +56,7 @@ export default class BamRecord {
|
|
|
55
56
|
private _computeLengthOnRef;
|
|
56
57
|
private _computeNumericCigar;
|
|
57
58
|
get length_on_ref(): number;
|
|
58
|
-
get NUMERIC_CIGAR():
|
|
59
|
+
get NUMERIC_CIGAR(): NumericCigar;
|
|
59
60
|
get CIGAR(): string;
|
|
60
61
|
get num_cigar_ops(): number;
|
|
61
62
|
get num_cigar_bytes(): number;
|