@gmod/bam 7.6.2 → 7.7.0
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/dist/bai.d.ts +6 -3
- package/dist/bai.js +32 -16
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +3 -3
- package/dist/bamFile.js +39 -12
- package/dist/bamFile.js.map +1 -1
- package/dist/chunk.d.ts +0 -1
- package/dist/chunk.js +0 -5
- package/dist/chunk.js.map +1 -1
- package/dist/csi.d.ts +0 -2
- package/dist/csi.js +4 -11
- package/dist/csi.js.map +1 -1
- package/dist/indexFile.d.ts +2 -3
- package/dist/indexFile.js.map +1 -1
- package/dist/sam.js +8 -3
- package/dist/sam.js.map +1 -1
- package/dist/util.d.ts +3 -3
- package/dist/util.js +21 -5
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.d.ts +8 -3
- package/dist/virtualOffset.js +0 -3
- package/dist/virtualOffset.js.map +1 -1
- package/esm/bai.d.ts +6 -3
- package/esm/bai.js +32 -16
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +3 -3
- package/esm/bamFile.js +39 -12
- package/esm/bamFile.js.map +1 -1
- package/esm/chunk.d.ts +0 -1
- package/esm/chunk.js +0 -5
- package/esm/chunk.js.map +1 -1
- package/esm/csi.d.ts +0 -2
- package/esm/csi.js +4 -11
- package/esm/csi.js.map +1 -1
- package/esm/indexFile.d.ts +2 -3
- package/esm/indexFile.js.map +1 -1
- package/esm/sam.js +8 -3
- package/esm/sam.js.map +1 -1
- package/esm/util.d.ts +3 -3
- package/esm/util.js +21 -5
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.d.ts +8 -3
- package/esm/virtualOffset.js +0 -3
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +1 -1
- package/src/bai.ts +42 -20
- package/src/bamFile.ts +38 -11
- package/src/chunk.ts +0 -8
- package/src/csi.ts +4 -10
- package/src/indexFile.ts +2 -3
- package/src/sam.ts +8 -3
- package/src/util.ts +28 -8
- package/src/virtualOffset.ts +9 -8
- package/dist/long.d.ts +0 -1
- package/dist/long.js +0 -17
- package/dist/long.js.map +0 -1
- package/esm/long.d.ts +0 -1
- package/esm/long.js +0 -14
- package/esm/long.js.map +0 -1
- package/src/long.ts +0 -16
package/dist/util.js.map
CHANGED
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@@ -1 +1 @@
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-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;
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package/dist/virtualOffset.d.ts
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/**
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* The two coordinates a virtual offset packs, without the `blockPos:dataPos`
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* string form. What every consumer that only compares positions needs — the
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* BAI linear index stores these as raw numbers and materializes no object.
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*/
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export interface OffsetCoords {
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blockPosition: number;
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dataPosition: number;
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}
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export interface Offset extends OffsetCoords {
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toString(): string;
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compareTo(arg: Offset): number;
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}
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export declare class VirtualOffset {
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blockPosition: number;
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dataPosition: number;
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constructor(blockPosition: number, dataPosition: number);
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toString(): string;
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compareTo(b: VirtualOffset): number;
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}
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export declare function fromBytes(bytes: Uint8Array, offset?: number): VirtualOffset;
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package/dist/virtualOffset.js
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toString() {
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return `${this.blockPosition}:${this.dataPosition}`;
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}
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compareTo(b) {
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return (this.blockPosition - b.blockPosition || this.dataPosition - b.dataPosition);
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}
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}
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exports.VirtualOffset = VirtualOffset;
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function fromBytes(bytes, offset = 0) {
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{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;
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+
{"version":3,"file":"virtualOffset.js","sourceRoot":"","sources":["../src/virtualOffset.ts"],"names":[],"mappings":";;;AA0BA,8BAUC;AAtBD,MAAa,aAAa;IACjB,aAAa,CAAQ;IACrB,YAAY,CAAQ;IAC3B,YAAY,aAAqB,EAAE,YAAoB;QACrD,IAAI,CAAC,aAAa,GAAG,aAAa,CAAA,CAAC,wCAAwC;QAC3E,IAAI,CAAC,YAAY,GAAG,YAAY,CAAA,CAAC,sCAAsC;IACzE,CAAC;IAED,QAAQ;QACN,OAAO,GAAG,IAAI,CAAC,aAAa,IAAI,IAAI,CAAC,YAAY,EAAE,CAAA;IACrD,CAAC;CACF;AAXD,sCAWC;AACD,SAAgB,SAAS,CAAC,KAAiB,EAAE,MAAM,GAAG,CAAC;IACrD,OAAO,IAAI,aAAa,CACtB,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,aAAa;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,WAAW;QAChC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,SAAS;QAC9B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,OAAO;QAC5B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,KAAK;QAC1B,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,EACpB,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,MAAM,CAAE,CAC3C,CAAA;AACH,CAAC"}
|
package/esm/bai.d.ts
CHANGED
|
@@ -1,9 +1,9 @@
|
|
|
1
1
|
import IndexFile from './indexFile.ts';
|
|
2
2
|
import type { ParsedIndexBase, RefIndex } from './indexFile.ts';
|
|
3
3
|
import type { BaseOpts } from './util.ts';
|
|
4
|
-
import type { VirtualOffset } from './virtualOffset.ts';
|
|
5
4
|
interface BaiRefIndex extends RefIndex {
|
|
6
|
-
|
|
5
|
+
linearBlockPositions: Float64Array;
|
|
6
|
+
linearDataPositions: Float64Array;
|
|
7
7
|
}
|
|
8
8
|
interface BaiParsed extends ParsedIndexBase<BaiRefIndex> {
|
|
9
9
|
bai: true;
|
|
@@ -17,6 +17,9 @@ export default class BAI extends IndexFile<BaiParsed> {
|
|
|
17
17
|
_parse(opts: BaseOpts): Promise<BaiParsed>;
|
|
18
18
|
indexCov(seqId: number, start?: number, end?: number, opts?: BaseOpts): Promise<IndexCovEntry[]>;
|
|
19
19
|
protected reg2bins(min: number, max: number): readonly [readonly [0, 0], readonly [number, number], readonly [number, number], readonly [number, number], readonly [number, number], readonly [number, number]];
|
|
20
|
-
protected getLowestChunk(refIndex: BaiRefIndex, min: number):
|
|
20
|
+
protected getLowestChunk(refIndex: BaiRefIndex, min: number): {
|
|
21
|
+
blockPosition: number;
|
|
22
|
+
dataPosition: number;
|
|
23
|
+
} | undefined;
|
|
21
24
|
}
|
|
22
25
|
export {};
|
package/esm/bai.js
CHANGED
|
@@ -108,22 +108,32 @@ export default class BAI extends IndexFile {
|
|
|
108
108
|
}
|
|
109
109
|
const linearCount = dataView.getInt32(curr, true);
|
|
110
110
|
curr += 4;
|
|
111
|
-
const
|
|
111
|
+
const linearBlockPositions = new Float64Array(linearCount);
|
|
112
|
+
const linearDataPositions = new Float64Array(linearCount);
|
|
112
113
|
for (let j = 0; j < linearCount; j++) {
|
|
113
|
-
|
|
114
|
+
// a virtual offset is a 48-bit block position in the high bytes and a
|
|
115
|
+
// 16-bit data position in the low two
|
|
116
|
+
linearBlockPositions[j] =
|
|
117
|
+
bytes[curr + 7] * 0x10000000000 +
|
|
118
|
+
bytes[curr + 6] * 0x100000000 +
|
|
119
|
+
bytes[curr + 5] * 0x1000000 +
|
|
120
|
+
bytes[curr + 4] * 0x10000 +
|
|
121
|
+
bytes[curr + 3] * 0x100 +
|
|
122
|
+
bytes[curr + 2];
|
|
123
|
+
linearDataPositions[j] = (bytes[curr + 1] << 8) | bytes[curr];
|
|
114
124
|
curr += 8;
|
|
115
125
|
}
|
|
116
|
-
clampChunkEnds(Object.values(binIndex).flat(),
|
|
126
|
+
clampChunkEnds(Object.values(binIndex).flat(), linearBlockPositions);
|
|
117
127
|
return {
|
|
118
128
|
binIndex,
|
|
119
|
-
|
|
129
|
+
linearBlockPositions,
|
|
130
|
+
linearDataPositions,
|
|
120
131
|
stats,
|
|
121
132
|
};
|
|
122
133
|
}
|
|
123
134
|
return {
|
|
124
135
|
bai: true,
|
|
125
136
|
firstDataLine,
|
|
126
|
-
maxBlockSize: 1 << 16,
|
|
127
137
|
indices: memoizeByRefId(getIndices),
|
|
128
138
|
refCount,
|
|
129
139
|
};
|
|
@@ -136,17 +146,18 @@ export default class BAI extends IndexFile {
|
|
|
136
146
|
if (!seqIdx) {
|
|
137
147
|
return [];
|
|
138
148
|
}
|
|
139
|
-
const {
|
|
140
|
-
|
|
149
|
+
const { linearBlockPositions, stats } = seqIdx;
|
|
150
|
+
const nintv = linearBlockPositions.length;
|
|
151
|
+
if (nintv === 0) {
|
|
141
152
|
return [];
|
|
142
153
|
}
|
|
143
|
-
const e = end === undefined ? (
|
|
154
|
+
const e = end === undefined ? (nintv - 1) * v : roundUp(end, v);
|
|
144
155
|
const s = start === undefined ? 0 : roundDown(start, v);
|
|
145
156
|
const depths = range
|
|
146
157
|
? new Array((e - s) / v)
|
|
147
|
-
: new Array(
|
|
148
|
-
const totalSize =
|
|
149
|
-
if (e > (
|
|
158
|
+
: new Array(nintv - 1);
|
|
159
|
+
const totalSize = linearBlockPositions[nintv - 1];
|
|
160
|
+
if (e > (nintv - 1) * v) {
|
|
150
161
|
throw new Error('query outside of range of linear index');
|
|
151
162
|
}
|
|
152
163
|
// Scale the block-delta into a read count as we go, rather than building the
|
|
@@ -154,9 +165,9 @@ export default class BAI extends IndexFile {
|
|
|
154
165
|
// multiply-then-divide order: hoisting lineCount/totalSize into a factor
|
|
155
166
|
// reassociates the arithmetic and shifts scores by an ulp.
|
|
156
167
|
const lineCount = stats?.lineCount ?? 0;
|
|
157
|
-
let currentPos =
|
|
168
|
+
let currentPos = linearBlockPositions[s / v];
|
|
158
169
|
for (let i = s / v, j = 0; i < e / v; i++, j++) {
|
|
159
|
-
const nextPos =
|
|
170
|
+
const nextPos = linearBlockPositions[i + 1];
|
|
160
171
|
depths[j] = {
|
|
161
172
|
score: ((nextPos - currentPos) * lineCount) / totalSize,
|
|
162
173
|
start: i * v,
|
|
@@ -173,9 +184,14 @@ export default class BAI extends IndexFile {
|
|
|
173
184
|
// contain alignments in the region. Linear index entries are monotonically
|
|
174
185
|
// non-decreasing, so the first entry at minLin is the minimum.
|
|
175
186
|
getLowestChunk(refIndex, min) {
|
|
176
|
-
const {
|
|
177
|
-
const
|
|
178
|
-
return
|
|
187
|
+
const { linearBlockPositions, linearDataPositions } = refIndex;
|
|
188
|
+
const i = Math.min(min >> BAI_LINEAR_SHIFT, linearBlockPositions.length - 1);
|
|
189
|
+
return i < 0
|
|
190
|
+
? undefined
|
|
191
|
+
: {
|
|
192
|
+
blockPosition: linearBlockPositions[i],
|
|
193
|
+
dataPosition: linearDataPositions[i],
|
|
194
|
+
};
|
|
179
195
|
}
|
|
180
196
|
}
|
|
181
197
|
//# sourceMappingURL=bai.js.map
|
package/esm/bai.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC5E,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC5E,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAuB9C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEnC,4EAA4E;AAC5E,gDAAgD;AAChD,8DAA8D;AAC9D,MAAM,gBAAgB,GAAG,EAAE,CAAA;AAC3B,MAAM,mBAAmB,GAAG,CAAC,IAAI,gBAAgB,CAAA,CAAC,QAAQ;AAE1D,SAAS,SAAS,CAAC,CAAS,EAAE,QAAgB;IAC5C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,CAAA;AAC3B,CAAC;AACD,SAAS,OAAO,CAAC,CAAS,EAAE,QAAgB;IAC1C,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,QAAQ,CAAC,GAAG,QAAQ,CAAA;AACtC,CAAC;AAQD,4EAA4E;AAC5E,qEAAqE;AACrE,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,gBAAgB,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,gBAAgB,CAAC,CAAC;KAC5D,CAAA;AACZ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAoB;IACnD,KAAK,CAAC,MAAM,CAAC,IAAc;QACzB,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,0BAA0B;QAC1B,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC3C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,aAAwC,CAAA;QAE5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAE9C,IAAI,IAAI,CAAC,CAAA;YAET,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;oBACX,CAAC;gBACH,CAAC;YACH,CAAC;YAED,mEAAmE;YACnE,kDAAkD;YAClD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,aAAa,GAAG,gBAAgB,CAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,CAAC,CAAA;YACzE,IAAI,IAAI,CAAC,GAAG,WAAW,CAAA;QACzB,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,KAAK,CAAA;YAET,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,GAAG,cAAc,CAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,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,EAAE,EAAE,CAAC;wBACpC,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,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,oBAAoB,GAAG,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YAC1D,MAAM,mBAAmB,GAAG,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,sEAAsE;gBACtE,sCAAsC;gBACtC,oBAAoB,CAAC,CAAC,CAAC;oBACrB,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,aAAa;wBAChC,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,WAAW;wBAC9B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,SAAS;wBAC5B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,OAAO;wBAC1B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,KAAK;wBACxB,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,CAAA;gBAClB,mBAAmB,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,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|
package/esm/bamFile.d.ts
CHANGED
|
@@ -72,7 +72,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
72
72
|
tag: string;
|
|
73
73
|
value: string;
|
|
74
74
|
}[];
|
|
75
|
-
}[]
|
|
75
|
+
}[]>;
|
|
76
76
|
/**
|
|
77
77
|
* Installs the header text and ref name/id maps from the start of a
|
|
78
78
|
* decompressed BAM stream, returning the parsed SAM header lines. Returns
|
|
@@ -92,7 +92,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
92
92
|
tag: string;
|
|
93
93
|
value: string;
|
|
94
94
|
}[];
|
|
95
|
-
}[]
|
|
95
|
+
}[]>;
|
|
96
96
|
getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
|
|
97
97
|
private getSeqId;
|
|
98
98
|
/**
|
|
@@ -113,7 +113,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
113
113
|
features: T[];
|
|
114
114
|
bytes: number;
|
|
115
115
|
}>;
|
|
116
|
-
readBamFeatures(ba: Uint8Array, cpositions: number
|
|
116
|
+
readBamFeatures(ba: Uint8Array, cpositions: ArrayLike<number>, dpositions: ArrayLike<number>, chunk: Chunk): T[];
|
|
117
117
|
hasRefSeq(seqName: string, opts?: BaseOpts): Promise<boolean>;
|
|
118
118
|
lineCount(seqName: string, opts?: BaseOpts): Promise<number>;
|
|
119
119
|
indexCov(seqName: string, start?: number, end?: number): Promise<never[] | import("./bai.ts").IndexCovEntry[]>;
|
package/esm/bamFile.js
CHANGED
|
@@ -130,7 +130,12 @@ export default class BamFile {
|
|
|
130
130
|
}
|
|
131
131
|
async getHeaderPre(opts = {}) {
|
|
132
132
|
if (!this.index) {
|
|
133
|
-
|
|
133
|
+
// Only reachable via `new BamFile({htsget: true})` used directly rather
|
|
134
|
+
// than through HtsgetFile, which overrides this. Throwing rather than
|
|
135
|
+
// returning undefined keeps `| undefined` off getHeader()'s public type,
|
|
136
|
+
// and makes that misuse loud instead of silently answering every query
|
|
137
|
+
// with zero records (getSeqId would find no chrToIndex).
|
|
138
|
+
throw new Error('no index to read a header from: use HtsgetFile for htsget sources');
|
|
134
139
|
}
|
|
135
140
|
const indexData = await this.index.parse(opts);
|
|
136
141
|
// The records start at firstDataLine, so reading up to it plus the bgzf
|
|
@@ -361,21 +366,38 @@ export default class BamFile {
|
|
|
361
366
|
const chunks = res[i];
|
|
362
367
|
for (let j = 0, jl = chunks.length; j < jl; j++) {
|
|
363
368
|
const m = chunks[j];
|
|
364
|
-
|
|
369
|
+
// Key on the virtual-offset span — the same key _cachedChunkFeatures
|
|
370
|
+
// uses. Chunk.toString() also folds in `bin` and fetchedSize(), which
|
|
371
|
+
// keeps two chunks covering an identical span apart here even though
|
|
372
|
+
// the cache below collapses them, so their records came back twice.
|
|
373
|
+
map.set(chunkCacheKey(m), m);
|
|
365
374
|
}
|
|
366
375
|
}
|
|
367
|
-
const
|
|
368
|
-
|
|
369
|
-
|
|
370
|
-
|
|
371
|
-
|
|
372
|
-
|
|
373
|
-
|
|
374
|
-
|
|
376
|
+
const mateChunks = [...map.values()];
|
|
377
|
+
// Bounded for the reason ADR 0008 bounds the main query path: a viewAsPairs
|
|
378
|
+
// query over a busy region resolves to many distinct mate chunks, and an
|
|
379
|
+
// unbounded fan-out inflates every one of them at once. Same inline pool
|
|
380
|
+
// shape as _fetchChunkFeatures — ADR 0009 measured extracting a shared
|
|
381
|
+
// mapConcurrent helper at ~11% on the hot path, so it stays inline.
|
|
382
|
+
const mateFeatLists = new Array(mateChunks.length);
|
|
383
|
+
let next = 0;
|
|
384
|
+
const readNext = async () => {
|
|
385
|
+
while (next < mateChunks.length) {
|
|
386
|
+
const ci = next++;
|
|
387
|
+
const features = await this._cachedChunkFeatures(mateChunks[ci], opts);
|
|
388
|
+
const mateRecs = [];
|
|
389
|
+
for (let i = 0, l = features.length; i < l; i++) {
|
|
390
|
+
const feature = features[i];
|
|
391
|
+
if (readNameCounts.get(feature.name) === 1 &&
|
|
392
|
+
!readIds.has(feature.fileOffset)) {
|
|
393
|
+
mateRecs.push(feature);
|
|
394
|
+
}
|
|
375
395
|
}
|
|
396
|
+
mateFeatLists[ci] = mateRecs;
|
|
376
397
|
}
|
|
377
|
-
|
|
378
|
-
|
|
398
|
+
};
|
|
399
|
+
const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, mateChunks.length);
|
|
400
|
+
await Promise.all(Array.from({ length: workers }, () => readNext()));
|
|
379
401
|
return mateFeatLists.flat();
|
|
380
402
|
}
|
|
381
403
|
async _readChunkFeatures(chunk, opts) {
|
|
@@ -393,6 +415,11 @@ export default class BamFile {
|
|
|
393
415
|
bytes: data.byteLength,
|
|
394
416
|
};
|
|
395
417
|
}
|
|
418
|
+
// cpositions/dpositions are `ArrayLike`, not `number[]`, because the wasm
|
|
419
|
+
// decompressor produces them as Float64Arrays — @gmod/bgzf-filehandle spreads
|
|
420
|
+
// them into plain arrays on the way out, and this signature is what lets that
|
|
421
|
+
// copy be dropped there without a change here. Only indexed reads and
|
|
422
|
+
// `.length` are used below either way.
|
|
396
423
|
readBamFeatures(ba, cpositions, dpositions, chunk) {
|
|
397
424
|
let blockStart = 0;
|
|
398
425
|
const sink = [];
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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G,EAAE,CAAA;gBACP,CAAC;YACH,CAAC;YAED,IAAI,QAAQ,GAAG,EAAE,CAAC,MAAM,EAAE,CAAC;gBACzB,MAAM,OAAO,GAAG,IAAI,IAAI,CAAC,WAAW,CAClC,EAAE,EACF,UAAU,EACV,QAAQ,EACR,aAAa;oBACX,CAAC,CAAC,UAAU,CAAC,GAAG,CAAE,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;wBAC3B,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAE,CAAC;wBAC/B,KAAK,CAAC,IAAI,CAAC,YAAY;wBACvB,CAAC;oBACH,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC,QAAQ,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAC,KAAK,CAAC,EAClD,QAAQ,CACT,CAAA;gBAED,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;YACpB,CAAC;YAED,UAAU,GAAG,QAAQ,GAAG,CAAC,CAAA;QAC3B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,IAAe;QAC9C,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,KAAK;YACP,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,KAAK,CAAC,CAAA;IACjC,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,IAAe;QAC9C,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS,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,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAA;QAC1C,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,QAAQ,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;IAC5C,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,KAAa,EACb,GAAW,EACX,IAAe;QAEf,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;QAChD,OAAO,CAAC,IAAI,CAAC,KAAK,IAAI,KAAK,KAAK,SAAS;YACvC,CAAC,CAAC,EAAE;YACJ,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,iBAAiB;QACf,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,CAAA;IAChC,CAAC;IAED,KAAK,CAAC,wBAAwB,CAC5B,OAA0D,EAC1D,IAAe;QAEf,IAAI,CAAC,IAAI,CAAC,KAAK,EAAE,CAAC;YAChB,OAAO,CAAC,CAAA;QACV,CAAC;QACD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACjC,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;YAC1C,OAAO,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QAC3E,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,KAAK,CAAC,wBAAwB,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAC1D,CAAC;CACF"}
|
package/esm/chunk.d.ts
CHANGED
package/esm/chunk.js
CHANGED
|
@@ -17,11 +17,6 @@ export default class Chunk {
|
|
|
17
17
|
toString() {
|
|
18
18
|
return `${this.minv.toString()}..${this.maxv.toString()} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
|
|
19
19
|
}
|
|
20
|
-
compareTo(b) {
|
|
21
|
-
return (this.minv.compareTo(b.minv) ||
|
|
22
|
-
this.maxv.compareTo(b.maxv) ||
|
|
23
|
-
this.bin - b.bin);
|
|
24
|
-
}
|
|
25
20
|
fetchedSize() {
|
|
26
21
|
return this.endPosition - this.minv.blockPosition;
|
|
27
22
|
}
|
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;IACjB,IAAI,CAAQ;IACZ,IAAI,CAAQ;IACZ,GAAG,CAAQ;IAClB,2EAA2E;IAC3E,0EAA0E;IAC1E,8EAA8E;IAC9E,oEAAoE;IAC7D,WAAW,CAAQ;IAE1B,YACE,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,WAAW,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;QAE5C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IAED,QAAQ;QACN,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,
|
|
1
|
+
{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":"AAEA,iDAAiD;AACjD,MAAM,CAAC,OAAO,OAAO,KAAK;IACjB,IAAI,CAAQ;IACZ,IAAI,CAAQ;IACZ,GAAG,CAAQ;IAClB,2EAA2E;IAC3E,0EAA0E;IAC1E,8EAA8E;IAC9E,oEAAoE;IAC7D,WAAW,CAAQ;IAE1B,YACE,IAAY,EACZ,IAAY,EACZ,GAAW,EACX,WAAW,GAAG,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC;QAE5C,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,WAAW,GAAG,WAAW,CAAA;IAChC,CAAC;IAED,QAAQ;QACN,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,WAAW;QACT,OAAO,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACnD,CAAC;CACF"}
|
package/esm/csi.d.ts
CHANGED
|
@@ -36,7 +36,6 @@ export default class CSI extends IndexFile {
|
|
|
36
36
|
skipLines?: number | undefined;
|
|
37
37
|
format?: string | undefined;
|
|
38
38
|
formatFlags?: number | undefined;
|
|
39
|
-
csiVersion: number;
|
|
40
39
|
firstDataLine: VirtualOffset | undefined;
|
|
41
40
|
indices: (refId: number) => {
|
|
42
41
|
binIndex: Record<number, Chunk[]>;
|
|
@@ -46,7 +45,6 @@ export default class CSI extends IndexFile {
|
|
|
46
45
|
} | undefined;
|
|
47
46
|
refCount: number;
|
|
48
47
|
csi: boolean;
|
|
49
|
-
maxBlockSize: number;
|
|
50
48
|
}>;
|
|
51
49
|
protected getLowestChunk(): VirtualOffset;
|
|
52
50
|
/**
|
package/esm/csi.js
CHANGED
|
@@ -54,17 +54,12 @@ export default class CSI extends IndexFile {
|
|
|
54
54
|
const buffer = await this.filehandle.readFile(opts);
|
|
55
55
|
const bytes = await unzip(buffer);
|
|
56
56
|
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
57
|
-
|
|
57
|
+
// CSI\1 and CSI\2 are parsed identically here — v2 only adds fields this
|
|
58
|
+
// reader doesn't consume — so the version is validated, not retained.
|
|
58
59
|
const magic = dataView.getUint32(0, true);
|
|
59
|
-
if (magic
|
|
60
|
-
csiVersion = 1;
|
|
61
|
-
}
|
|
62
|
-
else if (magic === CSI2_MAGIC) {
|
|
63
|
-
csiVersion = 2;
|
|
64
|
-
}
|
|
65
|
-
else {
|
|
66
|
-
throw new Error(`Not a CSI file ${magic}`);
|
|
60
|
+
if (magic !== CSI1_MAGIC && magic !== CSI2_MAGIC) {
|
|
67
61
|
// TODO: do we need to support big-endian CSI files?
|
|
62
|
+
throw new Error(`Not a CSI file ${magic}`);
|
|
68
63
|
}
|
|
69
64
|
this.minShift = dataView.getInt32(4, true);
|
|
70
65
|
this.depth = dataView.getInt32(8, true);
|
|
@@ -139,12 +134,10 @@ export default class CSI extends IndexFile {
|
|
|
139
134
|
};
|
|
140
135
|
}
|
|
141
136
|
return {
|
|
142
|
-
csiVersion,
|
|
143
137
|
firstDataLine,
|
|
144
138
|
indices: memoizeByRefId(getIndices),
|
|
145
139
|
refCount,
|
|
146
140
|
csi: true,
|
|
147
|
-
maxBlockSize: 1 << 16,
|
|
148
141
|
...aux,
|
|
149
142
|
};
|
|
150
143
|
}
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EACL,cAAc,EACd,gBAAgB,EAChB,cAAc,EACd,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,aAAa,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,WAAW,GAAG,IAAI,aAAa,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,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;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,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,MAAM,WAAW,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;QACpD,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,CAAC,SAAS,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC3D,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;QACrE,CAAC;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;YAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;SAC1C,CAAA;QACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAA;QAChE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;QAE9D,OAAO;YACL,aAAa;YACb,cAAc;YACd,SAAS;YACT,QAAQ;YACR,SAAS;YACT,MAAM;YACN,WAAW;YACX,GAAG,cAAc,CACf,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,EAC5D,IAAI,CAAC,YAAY,CAClB;SACF,CAAA;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,IAAc;QACzB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QACnD,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,yEAAyE;QACzE,sEAAsE;QACtE,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,KAAK,KAAK,UAAU,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACjD,oDAAoD;YACpD,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;QAC5C,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GAAG,SAAS,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACtE,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,mEAAmE;QACnE,+CAA+C;QAC/C,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;oBAC5B,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,sEAAsE;oBACtE,qEAAqE;oBACrE,sEAAsE;oBACtE,kDAAkD;oBAClD,aAAa,GAAG,gBAAgB,CAAC,KAAK,EAAE,IAAI,EAAE,CAAC,EAAE,aAAa,CAAC,CAAA;oBAC/D,IAAI,IAAI,CAAC,CAAA,CAAC,UAAU;oBACpB,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAA;gBAC7B,CAAC;YACH,CAAC;QACH,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,cAAc,CAAA;YAClB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,cAAc,GAAG,cAAc,CAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACjD,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA;gBACjB,CAAC;qBAAM,CAAC;oBACN,IAAI,IAAI,CAAC,CAAA,CAAC,6DAA6D;oBACvE,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,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|
package/esm/indexFile.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import type Chunk from './chunk.ts';
|
|
2
2
|
import type { BaseOpts } from './util.ts';
|
|
3
|
-
import type {
|
|
3
|
+
import type { OffsetCoords, VirtualOffset } from './virtualOffset.ts';
|
|
4
4
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
5
5
|
export interface Region {
|
|
6
6
|
refId: number;
|
|
@@ -16,7 +16,6 @@ export interface RefIndex {
|
|
|
16
16
|
export interface ParsedIndexBase<R extends RefIndex = RefIndex> {
|
|
17
17
|
firstDataLine: VirtualOffset | undefined;
|
|
18
18
|
refCount: number;
|
|
19
|
-
maxBlockSize: number;
|
|
20
19
|
indices: (refId: number) => R | undefined;
|
|
21
20
|
}
|
|
22
21
|
export declare function memoizeByRefId<T>(getIndices: (refId: number) => T | undefined, maxSize?: number): (refId: number) => T | undefined;
|
|
@@ -35,7 +34,7 @@ export default abstract class IndexFile<TParsed extends ParsedIndexBase = Parsed
|
|
|
35
34
|
score: number;
|
|
36
35
|
}[]>;
|
|
37
36
|
protected abstract reg2bins(min: number, max: number): readonly (readonly [number, number])[];
|
|
38
|
-
protected abstract getLowestChunk(refIndex: RefIndex, min: number):
|
|
37
|
+
protected abstract getLowestChunk(refIndex: RefIndex, min: number): OffsetCoords | undefined;
|
|
39
38
|
blocksForRange(refId: number, min: number, max: number, opts?: BaseOpts): Promise<Chunk[]>;
|
|
40
39
|
parse(opts?: BaseOpts): Promise<TParsed>;
|
|
41
40
|
lineCount(refId: number, opts?: BaseOpts): Promise<number>;
|
package/esm/indexFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,oBAAoB,CAAA;AAEzC,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;
|
|
1
|
+
{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAM,oBAAoB,CAAA;AAEzC,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAwB1C,uDAAuD;AACvD,6EAA6E;AAC7E,2CAA2C;AAC3C,MAAM,UAAU,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,KAAK,GAAG,IAAI,QAAQ,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAClD,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,IAAI,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;YACrB,OAAO,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QACzB,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,EAAE,CAAC;YACX,KAAK,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC1B,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAgB,SAAS;IAG9B,UAAU,CAAmB;IAC7B,YAAY,CAAuB;IAElC,MAAM,CAAmB;IAEjC,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;IAwBD,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;QACD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,eAAe,GAAG,IAAI,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;QAC/C,IAAI,eAAe,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACjC,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAY,EAAE,CAAA;QAC1B,MAAM,EAAE,QAAQ,EAAE,GAAG,EAAE,CAAA;QACvB,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,MAAM,SAAS,GAAG,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAC/B,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;wBACjD,MAAM,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAE,CAAC,CAAA;oBAC5B,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,cAAc,CAAC,MAAM,EAAE,IAAI,CAAC,cAAc,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,CAAA;IAC7D,CAAC;IAED,KAAK,CAAC,OAAiB,EAAE;QACvB,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,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;IACxD,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,KAAa,EAAE,IAAe;QAC5C,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,OAAO,CAAC,CAAC,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;IACnC,CAAC;IAED,KAAK,CAAC,wBAAwB,CAAC,OAAiB,EAAE,IAAe;QAC/D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC,CACrE,CAAA;QAED,8DAA8D;QAC9D,MAAM,YAAY,GAAG,cAAc,CAAC,YAAY,CAAC,IAAI,EAAE,CAAC,CAAA;QAExD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,YAAY,EAAE,CAAC;YACjC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;CACF"}
|
package/esm/sam.js
CHANGED
|
@@ -8,9 +8,14 @@ export function parseHeaderText(text) {
|
|
|
8
8
|
tag: tag.slice(1),
|
|
9
9
|
data: fields.map(f => {
|
|
10
10
|
const r = f.indexOf(':');
|
|
11
|
-
|
|
12
|
-
|
|
13
|
-
|
|
11
|
+
// A field with no colon is not a TAG:VALUE pair — @CO lines are free
|
|
12
|
+
// text, one comment per line (`samtools view -H c2#pad.3.0.cram`).
|
|
13
|
+
// Without this branch `slice(0, -1)` silently drops the comment's last
|
|
14
|
+
// character into the tag. Same shape @gmod/cram's parseHeaderText
|
|
15
|
+
// returns, so both feed a consumer's header parser identically.
|
|
16
|
+
return r === -1
|
|
17
|
+
? { tag: f, value: '' }
|
|
18
|
+
: { tag: f.slice(0, r), value: f.slice(r + 1) };
|
|
14
19
|
}),
|
|
15
20
|
});
|
|
16
21
|
}
|
package/esm/sam.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,
|
|
1
|
+
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAA8D,EAAE,CAAA;IAC1E,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,qEAAqE;oBACrE,mEAAmE;oBACnE,uEAAuE;oBACvE,kEAAkE;oBAClE,gEAAgE;oBAChE,OAAO,CAAC,KAAK,CAAC,CAAC;wBACb,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,EAAE,EAAE;wBACvB,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE,CAAA;gBACnD,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
|