@gmod/hic 1.2.0 → 1.3.0
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 +19 -14
- package/dist/bufferedFile.d.ts +2 -2
- package/dist/bufferedFile.js +5 -5
- package/dist/bufferedFile.js.map +1 -1
- package/dist/hicFile.d.ts +9 -10
- package/dist/hicFile.js +167 -174
- package/dist/hicFile.js.map +1 -1
- package/dist/index.d.ts +1 -1
- package/dist/lru.js +0 -2
- package/dist/lru.js.map +1 -1
- package/dist/normalizationVector.d.ts +2 -2
- package/dist/normalizationVector.js +18 -3
- package/dist/normalizationVector.js.map +1 -1
- package/dist/reader.js +4 -2
- package/dist/reader.js.map +1 -1
- package/dist/types.d.ts +8 -2
- package/esm/bufferedFile.d.ts +2 -2
- package/esm/bufferedFile.js +5 -5
- package/esm/bufferedFile.js.map +1 -1
- package/esm/hicFile.d.ts +9 -10
- package/esm/hicFile.js +167 -174
- package/esm/hicFile.js.map +1 -1
- package/esm/index.d.ts +1 -1
- package/esm/lru.js +0 -2
- package/esm/lru.js.map +1 -1
- package/esm/normalizationVector.d.ts +2 -2
- package/esm/normalizationVector.js +18 -3
- package/esm/normalizationVector.js.map +1 -1
- package/esm/reader.js +4 -2
- package/esm/reader.js.map +1 -1
- package/esm/types.d.ts +8 -2
- package/package.json +11 -8
- package/src/bufferedFile.ts +10 -6
- package/src/hicFile.ts +227 -188
- package/src/index.ts +1 -0
- package/src/lru.ts +0 -2
- package/src/normalizationVector.ts +20 -4
- package/src/reader.ts +5 -3
- package/src/types.ts +13 -2
package/dist/hicFile.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
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1
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+
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|
package/dist/index.d.ts
CHANGED
|
@@ -2,4 +2,4 @@ export { HicFile, NO_DATA_FOR_RESOLUTION } from './hicFile.ts';
|
|
|
2
2
|
export { readerFromFilehandle } from './reader.ts';
|
|
3
3
|
export type { HicConfig } from './hicFile.ts';
|
|
4
4
|
export type { ContactRecords } from './contactRecords.ts';
|
|
5
|
-
export type { Chromosome, HicMetadata, HicRegion, ProgressCallback, ProgressOpts, Reader, Zoom, } from './types.ts';
|
|
5
|
+
export type { BaseOpts, Chromosome, HicMetadata, HicRegion, ProgressCallback, ProgressOpts, Reader, Zoom, } from './types.ts';
|
package/dist/lru.js
CHANGED
|
@@ -41,8 +41,6 @@ class LRU {
|
|
|
41
41
|
this.delete(oldest);
|
|
42
42
|
}
|
|
43
43
|
}
|
|
44
|
-
// Used to evict a rejected in-flight promise so the next caller retries
|
|
45
|
-
// rather than resolving against a cached failure forever.
|
|
46
44
|
delete(key) {
|
|
47
45
|
const existing = this.map.get(key);
|
|
48
46
|
if (existing !== undefined) {
|
package/dist/lru.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lru.js","sourceRoot":"","sources":["../src/lru.ts"],"names":[],"mappings":";;AAmBA,MAAqB,GAAG;IACd,GAAG,CAAQ;IACX,GAAG,GAAG,IAAI,GAAG,EAAQ,CAAA;IACrB,MAAM,GAAG,CAAC,CAAA;IACV,UAAU,CAA2B;IAE7C,YAAY,GAAG,GAAG,EAAE,EAAE,UAA0B;QAC9C,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;IAC9B,CAAC;IAED,GAAG,CAAC,GAAM;QACR,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAC9B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,cAAc;YACd,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;YACpB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACzB,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,GAAG,CAAC,GAAM,EAAE,GAAM;QAChB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACtB,kEAAkE;YAClE,gEAAgE;YAChE,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QAClB,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QACtB,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,UAAU,EAAE,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;QAE/C,yEAAyE;QACzE,2EAA2E;QAC3E,4EAA4E;QAC5E,sCAAsC;QACtC,OACE,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG;YACxB,CAAC,IAAI,CAAC,UAAU,KAAK,SAAS;gBAC5B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ;gBACtC,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC,EACpB,CAAC;YACD,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;YAC3C,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;gBACzB,MAAK;YACP,CAAC;YACD,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACrB,CAAC;IACH,CAAC;IAED,
|
|
1
|
+
{"version":3,"file":"lru.js","sourceRoot":"","sources":["../src/lru.ts"],"names":[],"mappings":";;AAmBA,MAAqB,GAAG;IACd,GAAG,CAAQ;IACX,GAAG,GAAG,IAAI,GAAG,EAAQ,CAAA;IACrB,MAAM,GAAG,CAAC,CAAA;IACV,UAAU,CAA2B;IAE7C,YAAY,GAAG,GAAG,EAAE,EAAE,UAA0B;QAC9C,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;IAC9B,CAAC;IAED,GAAG,CAAC,GAAM;QACR,MAAM,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAC9B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;YACvB,cAAc;YACd,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;YACpB,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACzB,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,GAAG,CAAC,GAAM,EAAE,GAAM;QAChB,IAAI,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACtB,kEAAkE;YAClE,gEAAgE;YAChE,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QAClB,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QACtB,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,UAAU,EAAE,KAAK,CAAC,GAAG,CAAC,IAAI,CAAC,CAAA;QAE/C,yEAAyE;QACzE,2EAA2E;QAC3E,4EAA4E;QAC5E,sCAAsC;QACtC,OACE,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG;YACxB,CAAC,IAAI,CAAC,UAAU,KAAK,SAAS;gBAC5B,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ;gBACtC,IAAI,CAAC,GAAG,CAAC,IAAI,GAAG,CAAC,CAAC,EACpB,CAAC;YACD,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,IAAI,EAAE,CAAC,KAAK,CAAA;YAC3C,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;gBACzB,MAAK;YACP,CAAC;YACD,IAAI,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;QACrB,CAAC;IACH,CAAC;IAED,MAAM,CAAC,GAAM;QACX,MAAM,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QAClC,IAAI,QAAQ,KAAK,SAAS,EAAE,CAAC;YAC3B,IAAI,CAAC,MAAM,IAAI,IAAI,CAAC,UAAU,EAAE,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACtD,CAAC;QACD,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;IACtB,CAAC;CACF;AAvDD,sBAuDC"}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import type { Reader } from './types.ts';
|
|
1
|
+
import type { BaseOpts, Reader } from './types.ts';
|
|
2
2
|
export default class NormalizationVector {
|
|
3
3
|
private cache;
|
|
4
4
|
private file;
|
|
@@ -6,5 +6,5 @@ export default class NormalizationVector {
|
|
|
6
6
|
private nValues;
|
|
7
7
|
private dataType;
|
|
8
8
|
constructor(file: Reader, filePosition: number, nValues: number, dataType: number);
|
|
9
|
-
getValues(start: number, end: number): Promise<Float64Array<ArrayBufferLike>>;
|
|
9
|
+
getValues(start: number, end: number, opts?: BaseOpts): Promise<Float64Array<ArrayBufferLike>>;
|
|
10
10
|
}
|
|
@@ -17,7 +17,7 @@ class NormalizationVector {
|
|
|
17
17
|
this.nValues = nValues;
|
|
18
18
|
this.dataType = dataType;
|
|
19
19
|
}
|
|
20
|
-
async getValues(start, end) {
|
|
20
|
+
async getValues(start, end, opts) {
|
|
21
21
|
// The read below clamps to `nValues`, so the cache can never cover past it.
|
|
22
22
|
// Compare against the clamped bound or a request that runs off the end of
|
|
23
23
|
// the vector — reachable when the assembly's refseq is longer than the size
|
|
@@ -25,11 +25,26 @@ class NormalizationVector {
|
|
|
25
25
|
// forever, and every call re-reads the same range from the file.
|
|
26
26
|
const wanted = Math.min(end, this.nValues);
|
|
27
27
|
if (!this.cache || start < this.cache.start || wanted > this.cache.end) {
|
|
28
|
-
const adjustedStart = Math.max(0, start - 1000);
|
|
29
28
|
const adjustedEnd = Math.min(this.nValues, end + 1000);
|
|
29
|
+
// Clamped against `adjustedEnd`, and not merely against zero, or a window
|
|
30
|
+
// starting past the vector produces a NEGATIVE `n` — and a negative read
|
|
31
|
+
// length reaches the reader as `new Uint8Array(-8)`, a RangeError that
|
|
32
|
+
// fails the whole fetch instead of the empty answer the caller below
|
|
33
|
+
// already handles. The padding is what sets how far past is far enough:
|
|
34
|
+
// more than 1000 bins, which at a fine binsize is not far at all.
|
|
35
|
+
//
|
|
36
|
+
// Reachable exactly where the comment above says: the assembly's refseq
|
|
37
|
+
// is longer than the size the `.hic` recorded for that chromosome, so a
|
|
38
|
+
// view of the tail of it asks for bins the vector never had.
|
|
39
|
+
const adjustedStart = Math.min(Math.max(0, start - 1000), adjustedEnd);
|
|
30
40
|
const startPosition = this.filePosition + adjustedStart * this.dataType;
|
|
31
41
|
const n = adjustedEnd - adjustedStart;
|
|
32
|
-
|
|
42
|
+
// Nothing to read when the window is entirely past the vector, and on a
|
|
43
|
+
// remote file a zero-length range request is still a round trip — one per
|
|
44
|
+
// region pair, on every fetch, for as long as the view stays there.
|
|
45
|
+
const data = n > 0
|
|
46
|
+
? await this.file.read(startPosition, n * this.dataType, opts)
|
|
47
|
+
: new ArrayBuffer(0);
|
|
33
48
|
const parser = new binary_ts_1.default(new DataView(data));
|
|
34
49
|
const values = new Float64Array(n);
|
|
35
50
|
for (let i = 0; i < n; i++) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"normalizationVector.js","sourceRoot":"","sources":["../src/normalizationVector.ts"],"names":[],"mappings":";;;;;AAAA,4DAAsC;AAItC,MAAM,MAAM,GAAG,CAAC,CAAA;AAEhB,MAAqB,mBAAmB;IAC9B,KAAK,CACqD;IAE1D,IAAI,CAAQ;IACZ,YAAY,CAAQ;IACpB,OAAO,CAAQ;IACf,QAAQ,CAAQ;IAExB,YACE,IAAY,EACZ,YAAoB,EACpB,OAAe,EACf,QAAgB;QAEhB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAChC,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;QACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,GAAW;
|
|
1
|
+
{"version":3,"file":"normalizationVector.js","sourceRoot":"","sources":["../src/normalizationVector.ts"],"names":[],"mappings":";;;;;AAAA,4DAAsC;AAItC,MAAM,MAAM,GAAG,CAAC,CAAA;AAEhB,MAAqB,mBAAmB;IAC9B,KAAK,CACqD;IAE1D,IAAI,CAAQ;IACZ,YAAY,CAAQ;IACpB,OAAO,CAAQ;IACf,QAAQ,CAAQ;IAExB,YACE,IAAY,EACZ,YAAoB,EACpB,OAAe,EACf,QAAgB;QAEhB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA;QAChC,IAAI,CAAC,OAAO,GAAG,OAAO,CAAA;QACtB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,GAAW,EAAE,IAAe;QACzD,4EAA4E;QAC5E,0EAA0E;QAC1E,4EAA4E;QAC5E,0EAA0E;QAC1E,iEAAiE;QACjE,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,IAAI,CAAC,OAAO,CAAC,CAAA;QAC1C,IAAI,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,IAAI,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC;YACvE,MAAM,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,GAAG,IAAI,CAAC,CAAA;YACtD,0EAA0E;YAC1E,yEAAyE;YACzE,uEAAuE;YACvE,qEAAqE;YACrE,wEAAwE;YACxE,kEAAkE;YAClE,EAAE;YACF,wEAAwE;YACxE,wEAAwE;YACxE,6DAA6D;YAC7D,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,KAAK,GAAG,IAAI,CAAC,EAAE,WAAW,CAAC,CAAA;YACtE,MAAM,aAAa,GAAG,IAAI,CAAC,YAAY,GAAG,aAAa,GAAG,IAAI,CAAC,QAAQ,CAAA;YACvE,MAAM,CAAC,GAAG,WAAW,GAAG,aAAa,CAAA;YACrC,wEAAwE;YACxE,0EAA0E;YAC1E,oEAAoE;YACpE,MAAM,IAAI,GACR,CAAC,GAAG,CAAC;gBACH,CAAC,CAAC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,GAAG,IAAI,CAAC,QAAQ,EAAE,IAAI,CAAC;gBAC9D,CAAC,CAAC,IAAI,WAAW,CAAC,CAAC,CAAC,CAAA;YACxB,MAAM,MAAM,GAAG,IAAI,mBAAY,CAAC,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAA;YACnD,MAAM,MAAM,GAAG,IAAI,YAAY,CAAC,CAAC,CAAC,CAAA;YAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3B,MAAM,CAAC,CAAC,CAAC;oBACP,IAAI,CAAC,QAAQ,KAAK,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,SAAS,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;YACrE,CAAC;YACD,IAAI,CAAC,KAAK,GAAG,EAAE,KAAK,EAAE,aAAa,EAAE,GAAG,EAAE,WAAW,EAAE,MAAM,EAAE,CAAA;QACjE,CAAC;QAED,4EAA4E;QAC5E,sEAAsE;QACtE,wEAAwE;QACxE,2EAA2E;QAC3E,iCAAiC;QACjC,MAAM,UAAU,GAAG,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,KAAK,CAAA;QAC3C,OAAO,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,GAAG,CAAC,GAAG,GAAG,KAAK,CAAC,CAAC,CAAA;IAC3E,CAAC;CACF;AAnED,sCAmEC"}
|
package/dist/reader.js
CHANGED
|
@@ -3,8 +3,10 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
3
3
|
exports.readerFromFilehandle = readerFromFilehandle;
|
|
4
4
|
function readerFromFilehandle(filehandle) {
|
|
5
5
|
return {
|
|
6
|
-
async read(position, length) {
|
|
7
|
-
const buf = await filehandle.read(length, position
|
|
6
|
+
async read(position, length, opts) {
|
|
7
|
+
const buf = await filehandle.read(length, position, {
|
|
8
|
+
signal: opts?.signal,
|
|
9
|
+
});
|
|
8
10
|
return buf.buffer.slice(buf.byteOffset, buf.byteOffset + buf.byteLength);
|
|
9
11
|
},
|
|
10
12
|
};
|
package/dist/reader.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"reader.js","sourceRoot":"","sources":["../src/reader.ts"],"names":[],"mappings":";;AAGA,
|
|
1
|
+
{"version":3,"file":"reader.js","sourceRoot":"","sources":["../src/reader.ts"],"names":[],"mappings":";;AAGA,oDASC;AATD,SAAgB,oBAAoB,CAAC,UAA6B;IAChE,OAAO;QACL,KAAK,CAAC,IAAI,CAAC,QAAgB,EAAE,MAAc,EAAE,IAAe;YAC1D,MAAM,GAAG,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,MAAM,EAAE,QAAQ,EAAE;gBAClD,MAAM,EAAE,IAAI,EAAE,MAAM;aACrB,CAAC,CAAA;YACF,OAAO,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,UAAU,EAAE,GAAG,CAAC,UAAU,GAAG,GAAG,CAAC,UAAU,CAAC,CAAA;QAC1E,CAAC;KACF,CAAA;AACH,CAAC"}
|
package/dist/types.d.ts
CHANGED
|
@@ -4,9 +4,15 @@
|
|
|
4
4
|
* reads past the end to discover whether a file carries normalization data at
|
|
5
5
|
* all. `generic-filehandle2` handles behave this way (a remote 416 included),
|
|
6
6
|
* and `readerFromFilehandle` adapts one to this shape.
|
|
7
|
+
*
|
|
8
|
+
* A reader that ignores `opts.signal` still cancels, only later: the parser
|
|
9
|
+
* checks the signal when a fetch of blocks lands.
|
|
7
10
|
*/
|
|
8
11
|
export interface Reader {
|
|
9
|
-
read: (position: number, length: number) => Promise<ArrayBuffer>;
|
|
12
|
+
read: (position: number, length: number, opts?: BaseOpts) => Promise<ArrayBuffer>;
|
|
13
|
+
}
|
|
14
|
+
export interface BaseOpts {
|
|
15
|
+
signal?: AbortSignal;
|
|
10
16
|
}
|
|
11
17
|
/**
|
|
12
18
|
* Progress within one phase: `current` of `total` units done, called as the
|
|
@@ -28,7 +34,7 @@ export type ProgressCallback = (current: number, total: number) => void;
|
|
|
28
34
|
* belongs to the operation a caller is waiting on, and a file-wide callback
|
|
29
35
|
* could not say which of several concurrent fetches it was describing.
|
|
30
36
|
*/
|
|
31
|
-
export interface ProgressOpts {
|
|
37
|
+
export interface ProgressOpts extends BaseOpts {
|
|
32
38
|
onProgress?: ProgressCallback;
|
|
33
39
|
}
|
|
34
40
|
export interface Chromosome {
|
package/esm/bufferedFile.d.ts
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import type { Reader } from './types.ts';
|
|
1
|
+
import type { BaseOpts, Reader } from './types.ts';
|
|
2
2
|
export default class BufferedFile {
|
|
3
3
|
private file;
|
|
4
4
|
private size;
|
|
@@ -9,5 +9,5 @@ export default class BufferedFile {
|
|
|
9
9
|
file: Reader;
|
|
10
10
|
size?: number;
|
|
11
11
|
});
|
|
12
|
-
read(position: number, length: number): Promise<ArrayBuffer>;
|
|
12
|
+
read(position: number, length: number, opts?: BaseOpts): Promise<ArrayBuffer>;
|
|
13
13
|
}
|
package/esm/bufferedFile.js
CHANGED
|
@@ -14,7 +14,7 @@ export default class BufferedFile {
|
|
|
14
14
|
this.file = args.file;
|
|
15
15
|
this.size = args.size ?? 64000;
|
|
16
16
|
}
|
|
17
|
-
async read(position, length) {
|
|
17
|
+
async read(position, length, opts) {
|
|
18
18
|
const start = position;
|
|
19
19
|
const end = position + length;
|
|
20
20
|
const bufferStart = this.bufferStart;
|
|
@@ -26,7 +26,7 @@ export default class BufferedFile {
|
|
|
26
26
|
this.buffer = undefined;
|
|
27
27
|
this.bufferStart = 0;
|
|
28
28
|
this.bufferLength = 0;
|
|
29
|
-
result = await this.file.read(position, length);
|
|
29
|
+
result = await this.file.read(position, length, opts);
|
|
30
30
|
}
|
|
31
31
|
else if (buf && start >= bufferStart && end <= bufferEnd) {
|
|
32
32
|
// Request within buffer bounds
|
|
@@ -36,7 +36,7 @@ export default class BufferedFile {
|
|
|
36
36
|
else if (buf && start < bufferStart && end > bufferStart) {
|
|
37
37
|
// Overlap left (unexpected in straw); we don't adjust the buffer
|
|
38
38
|
const l1 = bufferStart - start;
|
|
39
|
-
const a1 = await this.file.read(position, l1);
|
|
39
|
+
const a1 = await this.file.read(position, l1, opts);
|
|
40
40
|
const l2 = length - l1;
|
|
41
41
|
if (l2 > 0) {
|
|
42
42
|
result = concatBuffers(a1, buf.slice(0, l2));
|
|
@@ -51,7 +51,7 @@ export default class BufferedFile {
|
|
|
51
51
|
const a1 = buf.slice(this.bufferLength - l1, this.bufferLength);
|
|
52
52
|
const l2 = length - l1;
|
|
53
53
|
if (l2 > 0) {
|
|
54
|
-
const next = await this.file.read(bufferEnd, this.size);
|
|
54
|
+
const next = await this.file.read(bufferEnd, this.size, opts);
|
|
55
55
|
this.buffer = next;
|
|
56
56
|
this.bufferStart = bufferEnd;
|
|
57
57
|
this.bufferLength = next.byteLength;
|
|
@@ -63,7 +63,7 @@ export default class BufferedFile {
|
|
|
63
63
|
}
|
|
64
64
|
else {
|
|
65
65
|
// No overlap with buffer
|
|
66
|
-
const next = await this.file.read(position, this.size);
|
|
66
|
+
const next = await this.file.read(position, this.size, opts);
|
|
67
67
|
this.buffer = next;
|
|
68
68
|
this.bufferStart = position;
|
|
69
69
|
this.bufferLength = next.byteLength;
|
package/esm/bufferedFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bufferedFile.js","sourceRoot":"","sources":["../src/bufferedFile.ts"],"names":[],"mappings":"AAEA,SAAS,aAAa,CAAC,OAAoB,EAAE,OAAoB;IAC/D,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC,OAAO,CAAC,UAAU,GAAG,OAAO,CAAC,UAAU,CAAC,CAAA;IACnE,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAA;IACnC,GAAG,CAAC,GAAG,CAAC,IAAI,UAAU,CAAC,OAAO,CAAC,EAAE,OAAO,CAAC,UAAU,CAAC,CAAA;IACpD,OAAO,GAAG,CAAC,MAAM,CAAA;AACnB,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,YAAY;IACvB,IAAI,CAAQ;IACZ,IAAI,CAAQ;IACZ,WAAW,GAAG,CAAC,CAAA;IACf,YAAY,GAAG,CAAC,CAAA;IAChB,MAAM,CAAyB;IAEvC,YAAY,IAAqC;QAC/C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAA;QACrB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,IAAI,KAAK,CAAA;IAChC,CAAC;IAED,KAAK,CAAC,IAAI,
|
|
1
|
+
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|
package/esm/hicFile.d.ts
CHANGED
|
@@ -2,7 +2,7 @@ import Matrix from './matrix.ts';
|
|
|
2
2
|
import NormalizationVector from './normalizationVector.ts';
|
|
3
3
|
import type { ContactRecords } from './contactRecords.ts';
|
|
4
4
|
import type MatrixZoomData from './matrixZoomData.ts';
|
|
5
|
-
import type { BlockIndexEntry, HicMetadata, HicRegion, ProgressOpts, Reader } from './types.ts';
|
|
5
|
+
import type { BaseOpts, BlockIndexEntry, HicMetadata, HicRegion, ProgressOpts, Reader } from './types.ts';
|
|
6
6
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
7
7
|
/**
|
|
8
8
|
* Prefix of the error thrown when a region pair has no matrix at the requested
|
|
@@ -39,19 +39,17 @@ interface Block {
|
|
|
39
39
|
export declare class HicFile {
|
|
40
40
|
private config;
|
|
41
41
|
private file;
|
|
42
|
+
private headerCache;
|
|
43
|
+
private normVectorIndexCache;
|
|
42
44
|
private normVectorCache;
|
|
43
|
-
private normalizationTypes;
|
|
44
45
|
private matrixCache;
|
|
45
46
|
private blockCache;
|
|
46
47
|
private normVectorIndexPosition;
|
|
47
48
|
private normVectorIndexSize;
|
|
48
|
-
private initPromise;
|
|
49
|
-
private normVectorIndexP;
|
|
50
49
|
private version;
|
|
51
50
|
private genomeId;
|
|
52
51
|
private footerPosition;
|
|
53
52
|
normExpectedValueVectorsPosition: number | undefined;
|
|
54
|
-
private normVectorIndex;
|
|
55
53
|
private chromosomes;
|
|
56
54
|
private chromosomeIndexMap;
|
|
57
55
|
private chrAliasTable;
|
|
@@ -59,11 +57,11 @@ export declare class HicFile {
|
|
|
59
57
|
private masterIndex;
|
|
60
58
|
private meta;
|
|
61
59
|
constructor(config: HicConfig);
|
|
62
|
-
init(): Promise<void>;
|
|
63
|
-
getMetaData(): Promise<HicMetadata>;
|
|
60
|
+
init(opts?: BaseOpts): Promise<void>;
|
|
61
|
+
getMetaData(opts?: BaseOpts): Promise<HicMetadata>;
|
|
64
62
|
private readHeaderAndFooter;
|
|
65
63
|
private readFooter;
|
|
66
|
-
getMatrix(chrIdx1: number, chrIdx2: number): Promise<Matrix | undefined>;
|
|
64
|
+
getMatrix(chrIdx1: number, chrIdx2: number, opts?: BaseOpts): Promise<Matrix | undefined>;
|
|
67
65
|
private readMatrix;
|
|
68
66
|
getContactRecords(normalization: string, region1: HicRegion, region2: HicRegion, units: string, binsize: number, opts?: ProgressOpts): Promise<{
|
|
69
67
|
records: ContactRecords;
|
|
@@ -72,7 +70,7 @@ export declare class HicFile {
|
|
|
72
70
|
}>;
|
|
73
71
|
private getNormVectors;
|
|
74
72
|
getBlocks(region1: HicRegion, region2: HicRegion, binSize: number, opts?: ProgressOpts): Promise<(Block | undefined)[]>;
|
|
75
|
-
readBlock(blockNumber: number, zd: MatrixZoomData): Promise<Block | undefined>;
|
|
73
|
+
readBlock(blockNumber: number, zd: MatrixZoomData, opts?: BaseOpts): Promise<Block | undefined>;
|
|
76
74
|
/**
|
|
77
75
|
* Decode one block's records straight into typed arrays.
|
|
78
76
|
*
|
|
@@ -83,9 +81,10 @@ export declare class HicFile {
|
|
|
83
81
|
* of the session, so it is worth one memcpy not to pin an oversized buffer.
|
|
84
82
|
*/
|
|
85
83
|
private parseBlockRecords;
|
|
86
|
-
getNormalizationVector(type: string, chr: string, unit: string, binSize: number): Promise<NormalizationVector | undefined>;
|
|
84
|
+
getNormalizationVector(type: string, chr: string, unit: string, binSize: number, opts?: BaseOpts): Promise<NormalizationVector | undefined>;
|
|
87
85
|
private readNormalizationVector;
|
|
88
86
|
getNormVectorIndex(opts?: ProgressOpts): Promise<Record<string, BlockIndexEntry> | undefined>;
|
|
87
|
+
private getParsedNormVectorIndex;
|
|
89
88
|
private loadNormVectorIndex;
|
|
90
89
|
getNormalizationOptions(opts?: ProgressOpts): Promise<string[]>;
|
|
91
90
|
private readNormVectorIndex;
|