@gmod/cram 4.0.1 → 4.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/cram-bundle.js +1 -1
- package/dist/cramFile/slice/index.d.ts +1 -1
- package/dist/cramFile/slice/index.js +3 -1
- package/dist/cramFile/slice/index.js.map +1 -1
- package/dist/indexedCramFile.d.ts +14 -8
- package/dist/indexedCramFile.js +16 -13
- package/dist/indexedCramFile.js.map +1 -1
- package/esm/cramFile/slice/index.d.ts +1 -1
- package/esm/cramFile/slice/index.js +3 -1
- package/esm/cramFile/slice/index.js.map +1 -1
- package/esm/indexedCramFile.d.ts +14 -8
- package/esm/indexedCramFile.js +16 -13
- package/esm/indexedCramFile.js.map +1 -1
- package/package.json +7 -7
- package/src/cramFile/slice/index.ts +3 -1
- package/src/indexedCramFile.ts +24 -17
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@@ -39,7 +39,7 @@ export default class CramSlice {
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_getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;
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getBlockByContentId(id: number): Promise<CramFileBlock | undefined>;
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getReferenceRegion(): Promise<{
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-
seq:
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+
seq: string;
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start: number;
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end: number;
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span: number;
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@@ -196,6 +196,7 @@ class CramSlice {
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}
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async getReferenceRegion() {
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// read the slice header
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+
const decoder = new TextDecoder('utf8');
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const sliceHeader = (await this.getHeader()).parsedContent;
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if (!(0, sectionParsers_1.isMappedSliceHeader)(sliceHeader)) {
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throw new Error('slice header not mapped');
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@@ -218,7 +219,8 @@ class CramSlice {
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// }
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// TODO verify
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return {
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-
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+
// @ts-expect-error
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+
seq: decoder.decode(refBlock.data),
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start: sliceHeader.refSeqStart,
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end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
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span: sliceHeader.refSeqSpan,
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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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|
@@ -19,10 +19,17 @@ export default class IndexedCramFile {
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|
|
19
19
|
*
|
|
20
20
|
* @param {object} args
|
|
21
21
|
* @param {CramFile} args.cram
|
|
22
|
-
*
|
|
23
|
-
* @param {
|
|
24
|
-
*
|
|
25
|
-
*
|
|
22
|
+
*
|
|
23
|
+
* @param {Index-like} args.index object that supports
|
|
24
|
+
* getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
|
|
25
|
+
*
|
|
26
|
+
* @param {number} [args.cacheSize] optional maximum number of CRAM records
|
|
27
|
+
* to cache. default 20,000
|
|
28
|
+
*
|
|
29
|
+
* @param {boolean} [args.checkSequenceMD5] - default true. if false,
|
|
30
|
+
* disables verifying the MD5 checksum of the reference sequence underlying a
|
|
31
|
+
* slice. In some applications, this check can cause an inconvenient amount
|
|
32
|
+
* (many megabases) of sequences to be fetched.
|
|
26
33
|
*/
|
|
27
34
|
constructor(args: {
|
|
28
35
|
index: CramIndexLike;
|
|
@@ -36,10 +43,9 @@ export default class IndexedCramFile {
|
|
|
36
43
|
} & CramFileSource)));
|
|
37
44
|
/**
|
|
38
45
|
*
|
|
39
|
-
* @param
|
|
40
|
-
* @param
|
|
41
|
-
* @param
|
|
42
|
-
* @returns {Promise[Array[CramRecord]]}
|
|
46
|
+
* @param seq numeric ID of the reference sequence
|
|
47
|
+
* @param start start of the range of interest. 1-based closed coordinates.
|
|
48
|
+
* @param end end of the range of interest. 1-based closed coordinates.
|
|
43
49
|
*/
|
|
44
50
|
getRecordsForRange(seq: number, start: number, end: number, opts?: {
|
|
45
51
|
viewAsPairs?: boolean;
|
package/dist/indexedCramFile.js
CHANGED
|
@@ -10,13 +10,19 @@ class IndexedCramFile {
|
|
|
10
10
|
*
|
|
11
11
|
* @param {object} args
|
|
12
12
|
* @param {CramFile} args.cram
|
|
13
|
-
*
|
|
14
|
-
* @param {
|
|
15
|
-
*
|
|
16
|
-
*
|
|
13
|
+
*
|
|
14
|
+
* @param {Index-like} args.index object that supports
|
|
15
|
+
* getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
|
|
16
|
+
*
|
|
17
|
+
* @param {number} [args.cacheSize] optional maximum number of CRAM records
|
|
18
|
+
* to cache. default 20,000
|
|
19
|
+
*
|
|
20
|
+
* @param {boolean} [args.checkSequenceMD5] - default true. if false,
|
|
21
|
+
* disables verifying the MD5 checksum of the reference sequence underlying a
|
|
22
|
+
* slice. In some applications, this check can cause an inconvenient amount
|
|
23
|
+
* (many megabases) of sequences to be fetched.
|
|
17
24
|
*/
|
|
18
25
|
constructor(args) {
|
|
19
|
-
// { cram, index, seqFetch /* fasta, fastaIndex */ }) {
|
|
20
26
|
this.cram =
|
|
21
27
|
args.cram ??
|
|
22
28
|
new cramFile_1.default({
|
|
@@ -34,10 +40,9 @@ class IndexedCramFile {
|
|
|
34
40
|
}
|
|
35
41
|
/**
|
|
36
42
|
*
|
|
37
|
-
* @param
|
|
38
|
-
* @param
|
|
39
|
-
* @param
|
|
40
|
-
* @returns {Promise[Array[CramRecord]]}
|
|
43
|
+
* @param seq numeric ID of the reference sequence
|
|
44
|
+
* @param start start of the range of interest. 1-based closed coordinates.
|
|
45
|
+
* @param end end of the range of interest. 1-based closed coordinates.
|
|
41
46
|
*/
|
|
42
47
|
async getRecordsForRange(seq, start, end, opts = {}) {
|
|
43
48
|
opts.viewAsPairs = opts.viewAsPairs || false;
|
|
@@ -49,13 +54,11 @@ class IndexedCramFile {
|
|
|
49
54
|
}
|
|
50
55
|
const seqId = seq;
|
|
51
56
|
const slices = await this.index.getEntriesForRange(seqId, start, end);
|
|
52
|
-
// TODO: do we need to merge or de-duplicate the blocks?
|
|
53
57
|
// fetch all the slices and parse the feature data
|
|
54
|
-
const
|
|
58
|
+
const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, feature => feature.sequenceId === seq &&
|
|
55
59
|
feature.alignmentStart <= end &&
|
|
56
60
|
feature.lengthOnRef !== undefined &&
|
|
57
|
-
feature.alignmentStart + feature.lengthOnRef - 1 >= start;
|
|
58
|
-
const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, filter)));
|
|
61
|
+
feature.alignmentStart + feature.lengthOnRef - 1 >= start)));
|
|
59
62
|
let ret = Array.prototype.concat(...sliceResults);
|
|
60
63
|
if (opts.viewAsPairs) {
|
|
61
64
|
const readNames = {};
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":";;;;;AACA,0DAAiC;AAGjC,qCAAiD;AAmBjD,MAAqB,eAAe;IAIlC
|
|
1
|
+
{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":";;;;;AACA,0DAAiC;AAGjC,qCAAiD;AAmBjD,MAAqB,eAAe;IAIlC;;;;;;;;;;;;;;;OAeG;IACH,YACE,IAUC;QAED,IAAI,CAAC,IAAI;YACP,IAAI,CAAC,IAAI;gBACT,IAAI,kBAAQ,CAAC;oBACX,GAAG,EAAE,IAAI,CAAC,OAAO;oBACjB,IAAI,EAAE,IAAI,CAAC,QAAQ;oBACnB,UAAU,EAAE,IAAI,CAAC,cAAc;oBAC/B,QAAQ,EAAE,IAAI,CAAC,QAAQ;oBACvB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;oBACvC,SAAS,EAAE,IAAI,CAAC,SAAS;iBAC1B,CAAC,CAAA;QAEJ,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,YAAY,kBAAQ,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAA;QACnD,CAAC;QAED,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IACzB,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,KAAa,EACb,GAAW,EACX,OAII,EAAE;QAEN,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,IAAI,KAAK,CAAA;QAC5C,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,KAAK,CAAA;QAChD,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,MAAM,CAAA;QAEjD,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;YAC5B,wDAAwD;YACxD,MAAM,IAAI,+BAAsB,CAC9B,yCAAyC,CAC1C,CAAA;QACH,CAAC;QACD,MAAM,KAAK,GAAG,GAAG,CAAA;QACjB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;QAErE,kDAAkD;QAClD,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CACjB,IAAI,CAAC,iBAAiB,CACpB,KAAK,EACL,OAAO,CAAC,EAAE,CACR,OAAO,CAAC,UAAU,KAAK,GAAG;YAC1B,OAAO,CAAC,cAAc,IAAI,GAAG;YAC7B,OAAO,CAAC,WAAW,KAAK,SAAS;YACjC,OAAO,CAAC,cAAc,GAAG,OAAO,CAAC,WAAW,GAAG,CAAC,IAAI,KAAK,CAC5D,CACF,CACF,CAAA;QAED,IAAI,GAAG,GAAiB,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/D,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,MAAM,SAAS,GAA2B,EAAE,CAAA;YAC5C,MAAM,OAAO,GAA2B,EAAE,CAAA;YAC1C,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;gBACvB,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAA;gBAC1B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,MAAM,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAA;gBACxB,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;oBACrB,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACrB,CAAC;gBACD,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,OAAO,CAAC,EAAE,CAAC,GAAG,CAAC,CAAA;YACjB,CAAC;YACD,MAAM,YAAY,GAA4B,EAAE,CAAA;YAChD,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE;gBAC3C,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;oBACZ,YAAY,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;gBACxB,CAAC;YACH,CAAC,CAAC,CAAA;YACF,MAAM,YAAY,GAAG,EAAE,CAAA;YACvB,KAAK,MAAM,UAAU,IAAI,GAAG,EAAE,CAAC;gBAC7B,MAAM,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;gBAChC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,IACE,YAAY,CAAC,IAAI,CAAC;oBAClB,UAAU,CAAC,IAAI;oBACf,CAAC,UAAU,CAAC,IAAI,CAAC,UAAU,KAAK,KAAK,IAAI,IAAI,CAAC,aAAa,CAAC;oBAC5D,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,cAAc,GAAG,UAAU,CAAC,IAAI,CAAC,cAAc,CAAC;wBAClE,IAAI,CAAC,aAAa,EACpB,CAAC;oBACD,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAC9C,UAAU,CAAC,IAAI,CAAC,UAAU,EAC1B,UAAU,CAAC,IAAI,CAAC,cAAc,EAC9B,UAAU,CAAC,IAAI,CAAC,cAAc,GAAG,CAAC,CACnC,CAAA;oBACD,YAAY,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;gBAC/B,CAAC;YACH,CAAC;YACD,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;YAClD,IAAI,UAAU,GAAG,EAAa,CAAA;YAC9B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;gBAC/B,UAAU,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAA;YAC3B,CAAC;YACD,wBAAwB;YACxB,UAAU,GAAG,UAAU;iBACpB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;iBACxD,MAAM,CACL,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CACjB,CAAC,GAAG,IAAI,IAAI,CAAC,QAAQ,EAAE,KAAK,GAAG,CAAC,GAAG,GAAG,CAAC,CAAE,CAAC,QAAQ,EAAE,CACvD,CAAA;YAEH,MAAM,kBAAkB,GAAG,EAAE,CAAA;YAC7B,MAAM,gBAAgB,GAA4B,EAAE,CAAA;YACpD,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;gBAC3B,IAAI,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAA;gBAC5D,IAAI,CAAC,aAAa,EAAE,CAAC;oBACnB,aAAa,GAAG,IAAI,CAAC,iBAAiB,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,CAAA;oBACrD,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,aAAa,CAAC,CAAA;gBACzD,CAAC;gBACD,kBAAkB,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;gBACtC,MAAM,WAAW,GAAG,aAAa,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE;oBAC7C,MAAM,QAAQ,GAAG,EAAE,CAAA;oBACnB,KAAK,MAAM,OAAO,IAAI,KAAK,EAAE,CAAC;wBAC5B,IAAI,OAAO,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;4BACnC,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;wBACvC,CAAC;wBACD,IAAI,YAAY,CAAC,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;4BACjE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;wBACxB,CAAC;oBACH,CAAC;oBACD,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBACF,gBAAgB,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;YACD,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAA;YACxD,IAAI,YAAY,CAAC,MAAM,EAAE,CAAC;gBACxB,MAAM,QAAQ,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CACvD,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CACvB,CAAA;gBACD,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,iBAAiB,CACf,EACE,cAAc,EACd,UAAU,EACV,UAAU,GACyD,EACrE,cAA0C;QAE1C,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,sBAAsB,CAAC,cAAc,CAAC,CAAA;QAClE,MAAM,KAAK,GAAG,SAAS,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,CAAC,CAAA;QACxD,OAAO,KAAK,CAAC,UAAU,CAAC,cAAc,CAAC,CAAA;IACzC,CAAC;IAED;;;;;OAKG;IACH,2BAA2B,CAAC,KAAa;QACvC,OAAO,IAAI,CAAC,KAAK,CAAC,2BAA2B,CAAC,KAAK,CAAC,CAAA;IACtD,CAAC;CACF;AA9MD,kCA8MC"}
|
|
@@ -39,7 +39,7 @@ export default class CramSlice {
|
|
|
39
39
|
_getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;
|
|
40
40
|
getBlockByContentId(id: number): Promise<CramFileBlock | undefined>;
|
|
41
41
|
getReferenceRegion(): Promise<{
|
|
42
|
-
seq:
|
|
42
|
+
seq: string;
|
|
43
43
|
start: number;
|
|
44
44
|
end: number;
|
|
45
45
|
span: number;
|
|
@@ -191,6 +191,7 @@ export default class CramSlice {
|
|
|
191
191
|
}
|
|
192
192
|
async getReferenceRegion() {
|
|
193
193
|
// read the slice header
|
|
194
|
+
const decoder = new TextDecoder('utf8');
|
|
194
195
|
const sliceHeader = (await this.getHeader()).parsedContent;
|
|
195
196
|
if (!isMappedSliceHeader(sliceHeader)) {
|
|
196
197
|
throw new Error('slice header not mapped');
|
|
@@ -213,7 +214,8 @@ export default class CramSlice {
|
|
|
213
214
|
// }
|
|
214
215
|
// TODO verify
|
|
215
216
|
return {
|
|
216
|
-
|
|
217
|
+
// @ts-expect-error
|
|
218
|
+
seq: decoder.decode(refBlock.data),
|
|
217
219
|
start: sliceHeader.refSeqStart,
|
|
218
220
|
end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
|
|
219
221
|
span: sliceHeader.refSeqSpan,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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,cAAc,cAAc,CACrD,CAAA;YACH,CAAC;YACD,4DAA4D;YAC5D,MAAM,OAAO,GAAG,KAAK,CAAC,MAAM,CAC1B,IAAI,EACJ,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;YACD,OAAO,OAAO,CAAA;QAChB,CAAC,CAAA;QACD,MAAM,OAAO,GAAiB,IAAI,KAAK,CACrC,WAAW,CAAC,aAAa,CAAC,UAAU,CACrC,CAAA;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC3C,IAAI,CAAC;gBACH,MAAM,IAAI,GAAG,YAAY,CACvB,IAAI,EACJ,gBAAgB,EAChB,iBAAiB,EACjB,WAAW,EACX,aAAa,EACb,iBAAiB,EACjB,OAAO,EACP,YAAY,EACZ,CAAC,CACF,CAAA;gBACD,OAAO,CAAC,CAAC,CAAC,GAAG,IAAI,UAAU,CAAC;oBAC1B,GAAG,IAAI;oBACP,QAAQ,EACN,WAAW,CAAC,eAAe;wBAC3B,WAAW,CAAC,aAAa,CAAC,aAAa;wBACvC,CAAC;wBACD,CAAC;iBACJ,CAAC,CAAA;YACJ,CAAC;YAAC,OAAO,CAAC,EAAE,CAAC;gBACX,IAAI,CAAC,YAAY,sBAAsB,EAAE,CAAC;oBACxC,OAAO,CAAC,IAAI,CACV,4DAA4D,CAC7D,CAAA;oBACD,MAAK;gBACP,CAAC;qBAAM,CAAC;oBACN,MAAM,CAAC,CAAA;gBACT,CAAC;YACH,CAAC;QACH,CAAC;QAED,uEAAuE;QACvE,2EAA2E;QAC3E,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC3C,MAAM,EAAE,gBAAgB,EAAE,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;YACxC,IAAI,gBAAgB,KAAK,SAAS,IAAI,gBAAgB,IAAI,CAAC,EAAE,CAAC;gBAC5D,uBAAuB,CACrB,OAAO,EACP,CAAC,EACD,OAAO,CAAC,CAAC,CAAE,EACX,OAAO,CAAC,gBAAgB,CAAE,CAC3B,CAAA;YACH,CAAC;QACH,CAAC;QAED,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,cAA0C;QACzD,sEAAsE;QACtE,MAAM,QAAQ,GAAG,IAAI,CAAC,SAAS,CAAC,YAAY,GAAG,IAAI,CAAC,iBAAiB,CAAA;QACrE,IAAI,cAAc,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,QAAQ,CAAC,QAAQ,EAAE,CAAC,CAAA;QACpE,IAAI,CAAC,cAAc,EAAE,CAAC;YACpB,cAAc,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;YACrC,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,QAAQ,CAAC,QAAQ,EAAE,EAAE,cAAc,CAAC,CAAA;QACjE,CAAC;QAED,MAAM,UAAU,GAAG,MAAM,cAAc,CAAA;QACvC,MAAM,OAAO,GAAG,UAAU,CAAC,MAAM,CAAC,cAAc,CAAC,CAAA;QAEjD,gFAAgF;QAChF,IAAI,OAAO,CAAC,MAAM,IAAI,IAAI,CAAC,IAAI,CAAC,8BAA8B,EAAE,CAAC;YAC/D,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC1C,IACE,mBAAmB,CAAC,WAAW,CAAC,aAAa,CAAC;gBAC9C,CAAC,WAAW,CAAC,aAAa,CAAC,QAAQ,IAAI,CAAC,IAAI,mBAAmB;oBAC7D,WAAW,CAAC,aAAa,CAAC,QAAQ,KAAK,CAAC,CAAC,CAAC,CAAC,kBAAkB;cAC/D,CAAC;gBACD,MAAM,WAAW,GACf,WAAW,CAAC,aAAa,CAAC,QAAQ,IAAI,CAAC;oBACrC,CAAC,CAAC,WAAW,CAAC,aAAa,CAAC,QAAQ;oBACpC,CAAC,CAAC,SAAS,CAAA;gBACf,MAAM,iBAAiB,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,oBAAoB,EAAE,CAAA;gBACrE,IAAI,iBAAiB,KAAK,SAAS,EAAE,CAAC;oBACpC,MAAM,IAAI,KAAK,CAAC,8BAA8B,CAAC,CAAA;gBACjD,CAAC;gBACD,MAAM,UAAU,GAGZ,EAAE,CAAA;gBAEN,8DAA8D;gBAC9D,6BAA6B;gBAC7B,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;oBAC7B,MAAM,KAAK,GACT,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC,UAAU,CAAA;oBAC7D,IAAI,SAAS,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACjC,IAAI,CAAC,SAAS,EAAE,CAAC;wBACf,SAAS,GAAG;4BACV,EAAE,EAAE,KAAK;4BACT,KAAK,EAAE,MAAM,CAAC,cAAc;4BAC5B,GAAG,EAAE,MAAM,CAAC,iBAAiB;4BAC7B,GAAG,EAAE,IAAI;yBACV,CAAA;wBACD,UAAU,CAAC,KAAK,CAAC,GAAG,SAAS,CAAA;oBAC/B,CAAC;oBAED,MAAM,GAAG,GACP,MAAM,CAAC,cAAc;wBACrB,CAAC,MAAM,CAAC,WAAW,IAAI,MAAM,CAAC,UAAU,CAAC;wBACzC,CAAC,CAAA;oBACH,IAAI,GAAG,GAAG,SAAS,CAAC,GAAG,EAAE,CAAC;wBACxB,SAAS,CAAC,GAAG,GAAG,GAAG,CAAA;oBACrB,CAAC;oBACD,IAAI,MAAM,CAAC,cAAc,GAAG,SAAS,CAAC,KAAK,EAAE,CAAC;wBAC5C,SAAS,CAAC,KAAK,GAAG,MAAM,CAAC,cAAc,CAAA;oBACzC,CAAC;gBACH,CAAC;gBAED,6CAA6C;gBAC7C,MAAM,OAAO,CAAC,GAAG,CACf,MAAM,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,KAAK,EAAC,SAAS,EAAC,EAAE;oBAC9C,IACE,SAAS,CAAC,EAAE,KAAK,CAAC,CAAC;wBACnB,SAAS,CAAC,KAAK,IAAI,SAAS,CAAC,GAAG;wBAChC,IAAI,CAAC,IAAI,CAAC,8BAA8B,EACxC,CAAC;wBACD,SAAS,CAAC,GAAG,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,8BAA8B,CAC5D,SAAS,CAAC,EAAE,EACZ,SAAS,CAAC,KAAK,EACf,SAAS,CAAC,GAAG,CACd,CAAA;oBACH,CAAC;gBACH,CAAC,CAAC,CACH,CAAA;gBAED,yCAAyC;gBACzC,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;oBAC7B,MAAM,KAAK,GACT,WAAW,KAAK,SAAS,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,MAAM,CAAC,UAAU,CAAA;oBAC7D,MAAM,SAAS,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;oBACnC,IAAI,SAAS,EAAE,GAAG,EAAE,CAAC;wBACnB,MAAM,GAAG,GAAG,SAAS,CAAC,GAAG,CAAA;wBACzB,MAAM,CAAC,oBAAoB,CACzB,EAAE,GAAG,SAAS,EAAE,GAAG,EAAE,EACrB,iBAAiB,CAClB,CAAA;oBACH,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,OAAO,OAAO,CAAA;IAChB,CAAC;CACF;AAED,uDAAuD;AACvD,8CAA8C,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IACzE,WAAW,CAAC,SAAS,EAAE,MAAM,CAAC,CAAA;AAChC,CAAC,CAAC,CAAA"}
|
package/esm/indexedCramFile.d.ts
CHANGED
|
@@ -19,10 +19,17 @@ export default class IndexedCramFile {
|
|
|
19
19
|
*
|
|
20
20
|
* @param {object} args
|
|
21
21
|
* @param {CramFile} args.cram
|
|
22
|
-
*
|
|
23
|
-
* @param {
|
|
24
|
-
*
|
|
25
|
-
*
|
|
22
|
+
*
|
|
23
|
+
* @param {Index-like} args.index object that supports
|
|
24
|
+
* getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
|
|
25
|
+
*
|
|
26
|
+
* @param {number} [args.cacheSize] optional maximum number of CRAM records
|
|
27
|
+
* to cache. default 20,000
|
|
28
|
+
*
|
|
29
|
+
* @param {boolean} [args.checkSequenceMD5] - default true. if false,
|
|
30
|
+
* disables verifying the MD5 checksum of the reference sequence underlying a
|
|
31
|
+
* slice. In some applications, this check can cause an inconvenient amount
|
|
32
|
+
* (many megabases) of sequences to be fetched.
|
|
26
33
|
*/
|
|
27
34
|
constructor(args: {
|
|
28
35
|
index: CramIndexLike;
|
|
@@ -36,10 +43,9 @@ export default class IndexedCramFile {
|
|
|
36
43
|
} & CramFileSource)));
|
|
37
44
|
/**
|
|
38
45
|
*
|
|
39
|
-
* @param
|
|
40
|
-
* @param
|
|
41
|
-
* @param
|
|
42
|
-
* @returns {Promise[Array[CramRecord]]}
|
|
46
|
+
* @param seq numeric ID of the reference sequence
|
|
47
|
+
* @param start start of the range of interest. 1-based closed coordinates.
|
|
48
|
+
* @param end end of the range of interest. 1-based closed coordinates.
|
|
43
49
|
*/
|
|
44
50
|
getRecordsForRange(seq: number, start: number, end: number, opts?: {
|
|
45
51
|
viewAsPairs?: boolean;
|
package/esm/indexedCramFile.js
CHANGED
|
@@ -5,13 +5,19 @@ export default class IndexedCramFile {
|
|
|
5
5
|
*
|
|
6
6
|
* @param {object} args
|
|
7
7
|
* @param {CramFile} args.cram
|
|
8
|
-
*
|
|
9
|
-
* @param {
|
|
10
|
-
*
|
|
11
|
-
*
|
|
8
|
+
*
|
|
9
|
+
* @param {Index-like} args.index object that supports
|
|
10
|
+
* getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
|
|
11
|
+
*
|
|
12
|
+
* @param {number} [args.cacheSize] optional maximum number of CRAM records
|
|
13
|
+
* to cache. default 20,000
|
|
14
|
+
*
|
|
15
|
+
* @param {boolean} [args.checkSequenceMD5] - default true. if false,
|
|
16
|
+
* disables verifying the MD5 checksum of the reference sequence underlying a
|
|
17
|
+
* slice. In some applications, this check can cause an inconvenient amount
|
|
18
|
+
* (many megabases) of sequences to be fetched.
|
|
12
19
|
*/
|
|
13
20
|
constructor(args) {
|
|
14
|
-
// { cram, index, seqFetch /* fasta, fastaIndex */ }) {
|
|
15
21
|
this.cram =
|
|
16
22
|
args.cram ??
|
|
17
23
|
new CramFile({
|
|
@@ -29,10 +35,9 @@ export default class IndexedCramFile {
|
|
|
29
35
|
}
|
|
30
36
|
/**
|
|
31
37
|
*
|
|
32
|
-
* @param
|
|
33
|
-
* @param
|
|
34
|
-
* @param
|
|
35
|
-
* @returns {Promise[Array[CramRecord]]}
|
|
38
|
+
* @param seq numeric ID of the reference sequence
|
|
39
|
+
* @param start start of the range of interest. 1-based closed coordinates.
|
|
40
|
+
* @param end end of the range of interest. 1-based closed coordinates.
|
|
36
41
|
*/
|
|
37
42
|
async getRecordsForRange(seq, start, end, opts = {}) {
|
|
38
43
|
opts.viewAsPairs = opts.viewAsPairs || false;
|
|
@@ -44,13 +49,11 @@ export default class IndexedCramFile {
|
|
|
44
49
|
}
|
|
45
50
|
const seqId = seq;
|
|
46
51
|
const slices = await this.index.getEntriesForRange(seqId, start, end);
|
|
47
|
-
// TODO: do we need to merge or de-duplicate the blocks?
|
|
48
52
|
// fetch all the slices and parse the feature data
|
|
49
|
-
const
|
|
53
|
+
const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, feature => feature.sequenceId === seq &&
|
|
50
54
|
feature.alignmentStart <= end &&
|
|
51
55
|
feature.lengthOnRef !== undefined &&
|
|
52
|
-
feature.alignmentStart + feature.lengthOnRef - 1 >= start;
|
|
53
|
-
const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, filter)));
|
|
56
|
+
feature.alignmentStart + feature.lengthOnRef - 1 >= start)));
|
|
54
57
|
let ret = Array.prototype.concat(...sliceResults);
|
|
55
58
|
if (opts.viewAsPairs) {
|
|
56
59
|
const readNames = {};
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":"AACA,OAAO,QAAQ,MAAM,YAAY,CAAA;AAGjC,OAAO,EAAE,sBAAsB,EAAE,MAAM,UAAU,CAAA;AAmBjD,MAAM,CAAC,OAAO,OAAO,eAAe;IAIlC
|
|
1
|
+
{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":"AACA,OAAO,QAAQ,MAAM,YAAY,CAAA;AAGjC,OAAO,EAAE,sBAAsB,EAAE,MAAM,UAAU,CAAA;AAmBjD,MAAM,CAAC,OAAO,OAAO,eAAe;IAIlC;;;;;;;;;;;;;;;OAeG;IACH,YACE,IAUC;QAED,IAAI,CAAC,IAAI;YACP,IAAI,CAAC,IAAI;gBACT,IAAI,QAAQ,CAAC;oBACX,GAAG,EAAE,IAAI,CAAC,OAAO;oBACjB,IAAI,EAAE,IAAI,CAAC,QAAQ;oBACnB,UAAU,EAAE,IAAI,CAAC,cAAc;oBAC/B,QAAQ,EAAE,IAAI,CAAC,QAAQ;oBACvB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;oBACvC,SAAS,EAAE,IAAI,CAAC,SAAS;iBAC1B,CAAC,CAAA;QAEJ,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,YAAY,QAAQ,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAA;QACnD,CAAC;QAED,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;IACzB,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,KAAa,EACb,GAAW,EACX,OAII,EAAE;QAEN,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,IAAI,KAAK,CAAA;QAC5C,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,KAAK,CAAA;QAChD,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,MAAM,CAAA;QAEjD,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;YAC5B,wDAAwD;YACxD,MAAM,IAAI,sBAAsB,CAC9B,yCAAyC,CAC1C,CAAA;QACH,CAAC;QACD,MAAM,KAAK,GAAG,GAAG,CAAA;QACjB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;QAErE,kDAAkD;QAClD,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CACjB,IAAI,CAAC,iBAAiB,CACpB,KAAK,EACL,OAAO,CAAC,EAAE,CACR,OAAO,CAAC,UAAU,KAAK,GAAG;YAC1B,OAAO,CAAC,cAAc,IAAI,GAAG;YAC7B,OAAO,CAAC,WAAW,KAAK,SAAS;YACjC,OAAO,CAAC,cAAc,GAAG,OAAO,CAAC,WAAW,GAAG,CAAC,IAAI,KAAK,CAC5D,CACF,CACF,CAAA;QAED,IAAI,GAAG,GAAiB,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/D,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,MAAM,SAAS,GAA2B,EAAE,CAAA;YAC5C,MAAM,OAAO,GAA2B,EAAE,CAAA;YAC1C,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;gBACvB,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAA;gBAC1B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,MAAM,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAA;gBACxB,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;oBACrB,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACrB,CAAC;gBACD,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,OAAO,CAAC,EAAE,CAAC,GAAG,CAAC,CAAA;YACjB,CAAC;YACD,MAAM,YAAY,GAA4B,EAAE,CAAA;YAChD,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE;gBAC3C,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;oBACZ,YAAY,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;gBACxB,CAAC;YACH,CAAC,CAAC,CAAA;YACF,MAAM,YAAY,GAAG,EAAE,CAAA;YACvB,KAAK,MAAM,UAAU,IAAI,GAAG,EAAE,CAAC;gBAC7B,MAAM,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;gBAChC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,IACE,YAAY,CAAC,IAAI,CAAC;oBAClB,UAAU,CAAC,IAAI;oBACf,CAAC,UAAU,CAAC,IAAI,CAAC,UAAU,KAAK,KAAK,IAAI,IAAI,CAAC,aAAa,CAAC;oBAC5D,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,cAAc,GAAG,UAAU,CAAC,IAAI,CAAC,cAAc,CAAC;wBAClE,IAAI,CAAC,aAAa,EACpB,CAAC;oBACD,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAC9C,UAAU,CAAC,IAAI,CAAC,UAAU,EAC1B,UAAU,CAAC,IAAI,CAAC,cAAc,EAC9B,UAAU,CAAC,IAAI,CAAC,cAAc,GAAG,CAAC,CACnC,CAAA;oBACD,YAAY,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;gBAC/B,CAAC;YACH,CAAC;YACD,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;YAClD,IAAI,UAAU,GAAG,EAAa,CAAA;YAC9B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;gBAC/B,UAAU,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAA;YAC3B,CAAC;YACD,wBAAwB;YACxB,UAAU,GAAG,UAAU;iBACpB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;iBACxD,MAAM,CACL,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CACjB,CAAC,GAAG,IAAI,IAAI,CAAC,QAAQ,EAAE,KAAK,GAAG,CAAC,GAAG,GAAG,CAAC,CAAE,CAAC,QAAQ,EAAE,CACvD,CAAA;YAEH,MAAM,kBAAkB,GAAG,EAAE,CAAA;YAC7B,MAAM,gBAAgB,GAA4B,EAAE,CAAA;YACpD,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;gBAC3B,IAAI,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAA;gBAC5D,IAAI,CAAC,aAAa,EAAE,CAAC;oBACnB,aAAa,GAAG,IAAI,CAAC,iBAAiB,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,CAAA;oBACrD,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,aAAa,CAAC,CAAA;gBACzD,CAAC;gBACD,kBAAkB,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;gBACtC,MAAM,WAAW,GAAG,aAAa,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE;oBAC7C,MAAM,QAAQ,GAAG,EAAE,CAAA;oBACnB,KAAK,MAAM,OAAO,IAAI,KAAK,EAAE,CAAC;wBAC5B,IAAI,OAAO,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;4BACnC,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;wBACvC,CAAC;wBACD,IAAI,YAAY,CAAC,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;4BACjE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;wBACxB,CAAC;oBACH,CAAC;oBACD,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBACF,gBAAgB,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;YACD,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAA;YACxD,IAAI,YAAY,CAAC,MAAM,EAAE,CAAC;gBACxB,MAAM,QAAQ,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CACvD,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CACvB,CAAA;gBACD,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,iBAAiB,CACf,EACE,cAAc,EACd,UAAU,EACV,UAAU,GACyD,EACrE,cAA0C;QAE1C,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,sBAAsB,CAAC,cAAc,CAAC,CAAA;QAClE,MAAM,KAAK,GAAG,SAAS,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,CAAC,CAAA;QACxD,OAAO,KAAK,CAAC,UAAU,CAAC,cAAc,CAAC,CAAA;IACzC,CAAC;IAED;;;;;OAKG;IACH,2BAA2B,CAAC,KAAa;QACvC,OAAO,IAAI,CAAC,KAAK,CAAC,2BAA2B,CAAC,KAAK,CAAC,CAAA;IACtD,CAAC;CACF"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/cram",
|
|
3
|
-
"version": "4.0.
|
|
3
|
+
"version": "4.0.3",
|
|
4
4
|
"description": "read CRAM files with pure Javascript",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/cram-js",
|
|
@@ -25,13 +25,13 @@
|
|
|
25
25
|
"lint": "eslint --report-unused-disable-directives --max-warnings 0",
|
|
26
26
|
"format": "prettier --write .",
|
|
27
27
|
"docs": "documentation readme --shallow src/indexedCramFile.ts --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/craiIndex.ts --section=CraiIndex; documentation readme --shallow errors.ts '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
|
|
28
|
-
"prebuild": "
|
|
28
|
+
"prebuild": "yarn clean",
|
|
29
29
|
"clean": "rimraf dist esm",
|
|
30
30
|
"build:esm": "tsc --outDir esm",
|
|
31
31
|
"build:es5": "tsc --module commonjs --outDir dist",
|
|
32
|
-
"build": "
|
|
32
|
+
"build": "yarn build:esm && yarn build:es5",
|
|
33
33
|
"postbuild": "webpack",
|
|
34
|
-
"
|
|
34
|
+
"preversion": "yarn test --run && yarn build && cp dist/errors.js errors.js",
|
|
35
35
|
"postpublish": "rm errors.js",
|
|
36
36
|
"postversion": "git push --follow-tags"
|
|
37
37
|
},
|
|
@@ -44,7 +44,7 @@
|
|
|
44
44
|
"dependencies": {
|
|
45
45
|
"bzip2": "^0.1.1",
|
|
46
46
|
"crc": "^4.3.2",
|
|
47
|
-
"generic-filehandle2": "^0.0
|
|
47
|
+
"generic-filehandle2": "^1.0.0",
|
|
48
48
|
"long": "^4.0.0",
|
|
49
49
|
"md5": "^2.2.1",
|
|
50
50
|
"pako": "^1.0.4",
|
|
@@ -52,7 +52,7 @@
|
|
|
52
52
|
"xz-decompress": "^0.2.1"
|
|
53
53
|
},
|
|
54
54
|
"devDependencies": {
|
|
55
|
-
"@gmod/indexedfasta": "^
|
|
55
|
+
"@gmod/indexedfasta": "^3.0.0",
|
|
56
56
|
"@types/long": "^4.0.0",
|
|
57
57
|
"@types/md5": "^2.3.2",
|
|
58
58
|
"@types/pako": "^1.0.3",
|
|
@@ -63,7 +63,7 @@
|
|
|
63
63
|
"documentation": "^14.0.3",
|
|
64
64
|
"eslint": "^9.9.0",
|
|
65
65
|
"eslint-plugin-import": "^2.31.0",
|
|
66
|
-
"eslint-plugin-unicorn": "^
|
|
66
|
+
"eslint-plugin-unicorn": "^56.0.1",
|
|
67
67
|
"mock-fs": "^5.2.0",
|
|
68
68
|
"prettier": "^3.2.5",
|
|
69
69
|
"rimraf": "^6.0.1",
|
|
@@ -267,6 +267,7 @@ export default class CramSlice {
|
|
|
267
267
|
|
|
268
268
|
async getReferenceRegion() {
|
|
269
269
|
// read the slice header
|
|
270
|
+
const decoder = new TextDecoder('utf8')
|
|
270
271
|
const sliceHeader = (await this.getHeader()).parsedContent
|
|
271
272
|
if (!isMappedSliceHeader(sliceHeader)) {
|
|
272
273
|
throw new Error('slice header not mapped')
|
|
@@ -298,7 +299,8 @@ export default class CramSlice {
|
|
|
298
299
|
|
|
299
300
|
// TODO verify
|
|
300
301
|
return {
|
|
301
|
-
|
|
302
|
+
// @ts-expect-error
|
|
303
|
+
seq: decoder.decode(refBlock.data),
|
|
302
304
|
start: sliceHeader.refSeqStart,
|
|
303
305
|
end: sliceHeader.refSeqStart + sliceHeader.refSeqSpan - 1,
|
|
304
306
|
span: sliceHeader.refSeqSpan,
|
package/src/indexedCramFile.ts
CHANGED
|
@@ -29,10 +29,17 @@ export default class IndexedCramFile {
|
|
|
29
29
|
*
|
|
30
30
|
* @param {object} args
|
|
31
31
|
* @param {CramFile} args.cram
|
|
32
|
-
*
|
|
33
|
-
* @param {
|
|
34
|
-
*
|
|
35
|
-
*
|
|
32
|
+
*
|
|
33
|
+
* @param {Index-like} args.index object that supports
|
|
34
|
+
* getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
|
|
35
|
+
*
|
|
36
|
+
* @param {number} [args.cacheSize] optional maximum number of CRAM records
|
|
37
|
+
* to cache. default 20,000
|
|
38
|
+
*
|
|
39
|
+
* @param {boolean} [args.checkSequenceMD5] - default true. if false,
|
|
40
|
+
* disables verifying the MD5 checksum of the reference sequence underlying a
|
|
41
|
+
* slice. In some applications, this check can cause an inconvenient amount
|
|
42
|
+
* (many megabases) of sequences to be fetched.
|
|
36
43
|
*/
|
|
37
44
|
constructor(
|
|
38
45
|
args: {
|
|
@@ -47,7 +54,6 @@ export default class IndexedCramFile {
|
|
|
47
54
|
} & CramFileSource)
|
|
48
55
|
),
|
|
49
56
|
) {
|
|
50
|
-
// { cram, index, seqFetch /* fasta, fastaIndex */ }) {
|
|
51
57
|
this.cram =
|
|
52
58
|
args.cram ??
|
|
53
59
|
new CramFile({
|
|
@@ -68,10 +74,9 @@ export default class IndexedCramFile {
|
|
|
68
74
|
|
|
69
75
|
/**
|
|
70
76
|
*
|
|
71
|
-
* @param
|
|
72
|
-
* @param
|
|
73
|
-
* @param
|
|
74
|
-
* @returns {Promise[Array[CramRecord]]}
|
|
77
|
+
* @param seq numeric ID of the reference sequence
|
|
78
|
+
* @param start start of the range of interest. 1-based closed coordinates.
|
|
79
|
+
* @param end end of the range of interest. 1-based closed coordinates.
|
|
75
80
|
*/
|
|
76
81
|
async getRecordsForRange(
|
|
77
82
|
seq: number,
|
|
@@ -96,16 +101,18 @@ export default class IndexedCramFile {
|
|
|
96
101
|
const seqId = seq
|
|
97
102
|
const slices = await this.index.getEntriesForRange(seqId, start, end)
|
|
98
103
|
|
|
99
|
-
// TODO: do we need to merge or de-duplicate the blocks?
|
|
100
|
-
|
|
101
104
|
// fetch all the slices and parse the feature data
|
|
102
|
-
const filter = (feature: CramRecord) =>
|
|
103
|
-
feature.sequenceId === seq &&
|
|
104
|
-
feature.alignmentStart <= end &&
|
|
105
|
-
feature.lengthOnRef !== undefined &&
|
|
106
|
-
feature.alignmentStart + feature.lengthOnRef - 1 >= start
|
|
107
105
|
const sliceResults = await Promise.all(
|
|
108
|
-
slices.map(slice =>
|
|
106
|
+
slices.map(slice =>
|
|
107
|
+
this.getRecordsInSlice(
|
|
108
|
+
slice,
|
|
109
|
+
feature =>
|
|
110
|
+
feature.sequenceId === seq &&
|
|
111
|
+
feature.alignmentStart <= end &&
|
|
112
|
+
feature.lengthOnRef !== undefined &&
|
|
113
|
+
feature.alignmentStart + feature.lengthOnRef - 1 >= start,
|
|
114
|
+
),
|
|
115
|
+
),
|
|
109
116
|
)
|
|
110
117
|
|
|
111
118
|
let ret: CramRecord[] = Array.prototype.concat(...sliceResults)
|