@gmod/bam 7.6.1 → 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/README.md +109 -98
- 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 +16 -3
- package/dist/bamFile.js +83 -36
- 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/htsget.d.ts +16 -0
- package/dist/htsget.js +72 -52
- package/dist/htsget.js.map +1 -1
- package/dist/index.d.ts +1 -0
- 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 +11 -3
- package/dist/util.js +35 -8
- 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 +16 -3
- package/esm/bamFile.js +83 -36
- 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/htsget.d.ts +16 -0
- package/esm/htsget.js +73 -53
- package/esm/htsget.js.map +1 -1
- package/esm/index.d.ts +1 -0
- 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 +11 -3
- package/esm/util.js +35 -8
- 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 +3 -3
- package/src/bai.ts +42 -20
- package/src/bamFile.ts +86 -38
- package/src/chunk.ts +0 -8
- package/src/csi.ts +4 -10
- package/src/htsget.ts +117 -62
- package/src/index.ts +2 -0
- package/src/indexFile.ts +2 -3
- package/src/sam.ts +8 -3
- package/src/util.ts +44 -11
- 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/esm/bamFile.js.map
CHANGED
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1
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-
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1
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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
|
-
{"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,
|
|
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/htsget.d.ts
CHANGED
|
@@ -2,14 +2,30 @@ import BamFile from './bamFile.ts';
|
|
|
2
2
|
import type { BamRecordClass, BamRecordLike } from './bamFile.ts';
|
|
3
3
|
import type BamRecord from './record.ts';
|
|
4
4
|
import type { BamOpts, BaseOpts } from './util.ts';
|
|
5
|
+
import type { Fetcher } from 'generic-filehandle2';
|
|
5
6
|
export default class HtsgetFile<T extends BamRecordLike = BamRecord> extends BamFile<T> {
|
|
6
7
|
private baseUrl;
|
|
7
8
|
private trackId;
|
|
9
|
+
private fetchFn;
|
|
8
10
|
constructor(args: {
|
|
9
11
|
trackId: string;
|
|
10
12
|
baseUrl: string;
|
|
11
13
|
recordClass?: BamRecordClass<T>;
|
|
14
|
+
/**
|
|
15
|
+
* fetch implementation used for every request, so an `Authorization: Bearer
|
|
16
|
+
* <token>` header can be added for servers that require one. It is also
|
|
17
|
+
* called with the data-block urls from the ticket, which may point at
|
|
18
|
+
* third-party hosts, so only attach credentials to hosts you trust — the
|
|
19
|
+
* spec has servers put whatever a data block needs in that url's own
|
|
20
|
+
* `headers` field, which is applied either way.
|
|
21
|
+
*/
|
|
22
|
+
fetch?: Fetcher;
|
|
12
23
|
});
|
|
24
|
+
/**
|
|
25
|
+
* Requests a ticket and returns its data blocks decompressed and
|
|
26
|
+
* concatenated, which per the spec is a complete BAM stream.
|
|
27
|
+
*/
|
|
28
|
+
private fetchTicket;
|
|
13
29
|
getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
|
|
14
30
|
getHeaderPre(opts?: BaseOpts): Promise<{
|
|
15
31
|
tag: string;
|
package/esm/htsget.js
CHANGED
|
@@ -1,91 +1,111 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
2
|
import BamFile, { BAM_MAGIC } from "./bamFile.js";
|
|
3
3
|
import Chunk from "./chunk.js";
|
|
4
|
-
import {
|
|
5
|
-
import { appendInRange, concatUint8Array } from "./util.js";
|
|
4
|
+
import { appendInRange, concatUint8Array, parseRefSeqs } from "./util.js";
|
|
6
5
|
import { VirtualOffset } from "./virtualOffset.js";
|
|
7
|
-
|
|
8
|
-
|
|
6
|
+
// Errors carry a JSON body naming the error type, e.g. {"htsget":
|
|
7
|
+
// {"error":"InvalidAuthentication","message":"..."}}. Surface that rather than
|
|
8
|
+
// the raw payload, since 401/403 are the first thing a misconfigured token hits.
|
|
9
|
+
function htsgetErrorMessage(text) {
|
|
10
|
+
let parsed;
|
|
11
|
+
try {
|
|
12
|
+
parsed = JSON.parse(text);
|
|
13
|
+
}
|
|
14
|
+
catch {
|
|
15
|
+
// not JSON, fall through to the raw body
|
|
16
|
+
}
|
|
17
|
+
const err = parsed?.htsget;
|
|
18
|
+
return err?.error === undefined
|
|
19
|
+
? text
|
|
20
|
+
: err.message === undefined
|
|
21
|
+
? err.error
|
|
22
|
+
: `${err.error}: ${err.message}`;
|
|
23
|
+
}
|
|
24
|
+
/**
|
|
25
|
+
* Offset of the first alignment record in the concatenated ticket blocks.
|
|
26
|
+
*
|
|
27
|
+
* The spec has the client concatenate the blocks in ticket order to get a
|
|
28
|
+
* complete data stream, so whether the header is its own block is up to the
|
|
29
|
+
* server: htsnexus splits it into a leading `data:` url, while htsget-rs
|
|
30
|
+
* returns header and records together in a single url. Either way the
|
|
31
|
+
* concatenation starts with the BAM header, so seek past it rather than
|
|
32
|
+
* dropping blocks — a url count or class attribute can't tell the two layouts
|
|
33
|
+
* apart. Returns 0 when the stream has no header, which is what a server
|
|
34
|
+
* sending body-only blocks produces.
|
|
35
|
+
*/
|
|
36
|
+
function recordsOffset(uncba) {
|
|
37
|
+
const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
|
|
38
|
+
if (uncba.byteLength < 8 || dataView.getInt32(0, true) !== BAM_MAGIC) {
|
|
39
|
+
return 0;
|
|
40
|
+
}
|
|
41
|
+
const refs = parseRefSeqs(uncba, 8 + dataView.getInt32(4, true), n => n);
|
|
42
|
+
if (!refs) {
|
|
43
|
+
throw new Error('truncated BAM header in htsget response');
|
|
44
|
+
}
|
|
45
|
+
return refs.end;
|
|
46
|
+
}
|
|
47
|
+
async function fetchOk(fetchFn, url, opts) {
|
|
48
|
+
const res = await fetchFn(url, opts);
|
|
9
49
|
if (!res.ok) {
|
|
10
|
-
throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
|
|
50
|
+
throw new Error(`HTTP ${res.status} fetching ${url}: ${htsgetErrorMessage(await res.text())}`);
|
|
11
51
|
}
|
|
12
52
|
return res;
|
|
13
53
|
}
|
|
14
|
-
async function fetchChunk({ url, headers }, opts) {
|
|
54
|
+
async function fetchChunk(fetchFn, { url, headers }, opts) {
|
|
15
55
|
// pass base64 data URLs straight to fetch; otherwise apply headers (minus
|
|
16
56
|
// referer, which isn't a permitted client-set header).
|
|
17
57
|
// https://stackoverflow.com/a/54123275/2129219
|
|
18
58
|
const { referer: _referer, ...rest } = headers ?? {};
|
|
19
59
|
const res = url.startsWith('data:')
|
|
20
|
-
? await fetchOk(url)
|
|
21
|
-
: await fetchOk(url, { ...opts, headers: rest });
|
|
60
|
+
? await fetchOk(fetchFn, url)
|
|
61
|
+
: await fetchOk(fetchFn, url, { ...opts, headers: rest });
|
|
22
62
|
return new Uint8Array(await res.arrayBuffer());
|
|
23
63
|
}
|
|
24
|
-
async function fetchAndConcat(arr, opts) {
|
|
64
|
+
async function fetchAndConcat(fetchFn, arr, opts) {
|
|
25
65
|
// Pipeline unzip after each fetch so decompression overlaps later fetches.
|
|
26
|
-
return concatUint8Array(await Promise.all(arr.map(async (c) => unzip(await fetchChunk(c, opts)))));
|
|
66
|
+
return concatUint8Array(await Promise.all(arr.map(async (c) => unzip(await fetchChunk(fetchFn, c, opts)))));
|
|
27
67
|
}
|
|
28
68
|
export default class HtsgetFile extends BamFile {
|
|
29
69
|
baseUrl;
|
|
30
70
|
trackId;
|
|
71
|
+
fetchFn;
|
|
31
72
|
constructor(args) {
|
|
32
73
|
super({ htsget: true, recordClass: args.recordClass });
|
|
33
74
|
this.baseUrl = args.baseUrl;
|
|
34
75
|
this.trackId = args.trackId;
|
|
76
|
+
this.fetchFn = args.fetch ?? ((input, init) => fetch(input, init));
|
|
77
|
+
}
|
|
78
|
+
/**
|
|
79
|
+
* Requests a ticket and returns its data blocks decompressed and
|
|
80
|
+
* concatenated, which per the spec is a complete BAM stream.
|
|
81
|
+
*/
|
|
82
|
+
async fetchTicket(query, opts) {
|
|
83
|
+
const url = `${this.baseUrl}/${this.trackId}?${query}`;
|
|
84
|
+
const res = await fetchOk(this.fetchFn, url, { signal: opts?.signal });
|
|
85
|
+
const ticket = await res.json();
|
|
86
|
+
return fetchAndConcat(this.fetchFn, ticket.htsget.urls, {
|
|
87
|
+
signal: opts?.signal,
|
|
88
|
+
});
|
|
35
89
|
}
|
|
36
90
|
async getRecordsForRange(chr, min, max, opts) {
|
|
37
91
|
await this.getHeader(opts);
|
|
38
|
-
const base = `${this.baseUrl}/${this.trackId}`;
|
|
39
|
-
const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
|
|
40
92
|
const chrId = this.chrToIndex?.[chr];
|
|
41
93
|
if (chrId === undefined) {
|
|
42
94
|
return [];
|
|
43
95
|
}
|
|
44
|
-
const
|
|
45
|
-
const data = await result.json();
|
|
46
|
-
const uncba = await fetchAndConcat(data.htsget.urls.slice(1), {
|
|
47
|
-
signal: opts?.signal,
|
|
48
|
-
});
|
|
96
|
+
const uncba = await this.fetchTicket(`referenceName=${chr}&start=${min}&end=${max}&format=BAM`, opts);
|
|
49
97
|
const zero = new VirtualOffset(0, 0);
|
|
50
|
-
const
|
|
51
|
-
return appendInRange(
|
|
98
|
+
const records = this.readBamFeatures(uncba.subarray(recordsOffset(uncba)), [], [], new Chunk(zero, zero, 0));
|
|
99
|
+
return appendInRange(records, chrId, min, max);
|
|
52
100
|
}
|
|
53
101
|
async getHeaderPre(opts = {}) {
|
|
54
|
-
|
|
55
|
-
|
|
56
|
-
const
|
|
57
|
-
const
|
|
58
|
-
|
|
59
|
-
|
|
60
|
-
const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
|
|
61
|
-
if (dataView.getInt32(0, true) !== BAM_MAGIC) {
|
|
62
|
-
throw new Error('Not a BAM file');
|
|
63
|
-
}
|
|
64
|
-
const headLen = dataView.getInt32(4, true);
|
|
65
|
-
const decoder = new TextDecoder();
|
|
66
|
-
const headerText = decoder.decode(uncba.subarray(8, 8 + headLen));
|
|
67
|
-
const samHeader = parseHeaderText(headerText);
|
|
68
|
-
// use the @SQ lines in the header to figure out the
|
|
69
|
-
// mapping between ref ref ID numbers and names
|
|
70
|
-
const idToName = [];
|
|
71
|
-
const nameToId = {};
|
|
72
|
-
const sqLines = samHeader.filter(l => l.tag === 'SQ');
|
|
73
|
-
for (const [refId, sqLine] of sqLines.entries()) {
|
|
74
|
-
let refName = '';
|
|
75
|
-
let length = 0;
|
|
76
|
-
for (const item of sqLine.data) {
|
|
77
|
-
if (item.tag === 'SN') {
|
|
78
|
-
refName = item.value;
|
|
79
|
-
}
|
|
80
|
-
else if (item.tag === 'LN') {
|
|
81
|
-
length = +item.value;
|
|
82
|
-
}
|
|
83
|
-
}
|
|
84
|
-
nameToId[refName] = refId;
|
|
85
|
-
idToName[refId] = { refName, length };
|
|
102
|
+
// format is the only parameter the spec permits alongside class=header;
|
|
103
|
+
// servers SHOULD reject anything else with InvalidInput
|
|
104
|
+
const uncba = await this.fetchTicket('class=header&format=BAM', opts);
|
|
105
|
+
const samHeader = this.applyHeader(uncba);
|
|
106
|
+
if (!samHeader) {
|
|
107
|
+
throw new Error('Insufficient data for reference sequences');
|
|
86
108
|
}
|
|
87
|
-
this.chrToIndex = nameToId;
|
|
88
|
-
this.indexToChr = idToName;
|
|
89
109
|
return samHeader;
|
|
90
110
|
}
|
|
91
111
|
}
|
package/esm/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,OAAO,EAAE,EAAE,SAAS,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,YAAY,EAAE,MAAM,WAAW,CAAA;AACzE,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAuBlD,kEAAkE;AAClE,+EAA+E;AAC/E,iFAAiF;AACjF,SAAS,kBAAkB,CAAC,IAAY;IACtC,IAAI,MAAmC,CAAA;IACvC,IAAI,CAAC;QACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IAC3B,CAAC;IAAC,MAAM,CAAC;QACP,yCAAyC;IAC3C,CAAC;IACD,MAAM,GAAG,GAAG,MAAM,EAAE,MAAM,CAAA;IAC1B,OAAO,GAAG,EAAE,KAAK,KAAK,SAAS;QAC7B,CAAC,CAAC,IAAI;QACN,CAAC,CAAC,GAAG,CAAC,OAAO,KAAK,SAAS;YACzB,CAAC,CAAC,GAAG,CAAC,KAAK;YACX,CAAC,CAAC,GAAG,GAAG,CAAC,KAAK,KAAK,GAAG,CAAC,OAAO,EAAE,CAAA;AACtC,CAAC;AAED;;;;;;;;;;;GAWG;AACH,SAAS,aAAa,CAAC,KAAiB;IACtC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;IACD,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;QACrE,OAAO,CAAC,CAAA;IACV,CAAC;IACD,MAAM,IAAI,GAAG,YAAY,CAAC,KAAK,EAAE,CAAC,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;IACxE,IAAI,CAAC,IAAI,EAAE,CAAC;QACV,MAAM,IAAI,KAAK,CAAC,yCAAyC,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,IAAI,CAAC,GAAG,CAAA;AACjB,CAAC;AAED,KAAK,UAAU,OAAO,CAAC,OAAgB,EAAE,GAAW,EAAE,IAAkB;IACtE,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IACpC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CACb,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,kBAAkB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,CAAC,EAAE,CAC9E,CAAA;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,KAAK,UAAU,UAAU,CACvB,OAAgB,EAChB,EAAE,GAAG,EAAE,OAAO,EAAe,EAC7B,IAAkB;IAElB,0EAA0E;IAC1E,uDAAuD;IACvD,+CAA+C;IAC/C,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;IACpD,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC;QACjC,CAAC,CAAC,MAAM,OAAO,CAAC,OAAO,EAAE,GAAG,CAAC;QAC7B,CAAC,CAAC,MAAM,OAAO,CAAC,OAAO,EAAE,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAC3D,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;AAChD,CAAC;AAED,KAAK,UAAU,cAAc,CAC3B,OAAgB,EAChB,GAAkB,EAClB,IAAkB;IAElB,2EAA2E;IAC3E,OAAO,gBAAgB,CACrB,MAAM,OAAO,CAAC,GAAG,CACf,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE,CAAC,KAAK,CAAC,MAAM,UAAU,CAAC,OAAO,EAAE,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAC9D,CACF,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAEnB,SAAQ,OAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEf,OAAO,CAAS;IAExB,YAAY,IAaX;QACC,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;QACtD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC,KAAK,EAAE,IAAI,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;IACpE,CAAC;IAED;;;OAGG;IACK,KAAK,CAAC,WAAW,CAAC,KAAa,EAAE,IAAe;QACtD,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,IAAI,KAAK,EAAE,CAAA;QACtD,MAAM,GAAG,GAAG,MAAM,OAAO,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAA;QACtE,MAAM,MAAM,GAAiB,MAAM,GAAG,CAAC,IAAI,EAAE,CAAA;QAC7C,OAAO,cAAc,CAAC,IAAI,CAAC,OAAO,EAAE,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE;YACtD,MAAM,EAAE,IAAI,EAAE,MAAM;SACrB,CAAC,CAAA;IACJ,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAClC,iBAAiB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,EACzD,IAAI,CACL,CAAA;QACD,MAAM,IAAI,GAAG,IAAI,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,OAAO,GAAG,IAAI,CAAC,eAAe,CAClC,KAAK,CAAC,QAAQ,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,EACpC,EAAE,EACF,EAAE,EACF,IAAI,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QACD,OAAO,aAAa,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IAChD,CAAC;IAED,KAAK,CAAC,YAAY,CAAC,OAAiB,EAAE;QACpC,wEAAwE;QACxE,wDAAwD;QACxD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,yBAAyB,EAAE,IAAI,CAAC,CAAA;QACrE,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,CAAC,KAAK,CAAC,CAAA;QACzC,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CAAC,2CAA2C,CAAC,CAAA;QAC9D,CAAC;QACD,OAAO,SAAS,CAAA;IAClB,CAAC;CACF"}
|
package/esm/index.d.ts
CHANGED
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"}
|
package/esm/util.d.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
2
|
import { VirtualOffset } from './virtualOffset.ts';
|
|
3
|
-
import type {
|
|
3
|
+
import type { OffsetCoords } from './virtualOffset.ts';
|
|
4
4
|
export interface BamOpts {
|
|
5
5
|
viewAsPairs?: boolean;
|
|
6
6
|
pairAcrossChr?: boolean;
|
|
@@ -25,22 +25,30 @@ export interface BaseOpts {
|
|
|
25
25
|
*/
|
|
26
26
|
onProgress?: (bytesDownloaded: number, totalBytes?: number) => void;
|
|
27
27
|
}
|
|
28
|
-
export declare function optimizeChunks(chunks: Chunk[], lowest?:
|
|
28
|
+
export declare function optimizeChunks(chunks: Chunk[], lowest?: OffsetCoords): Chunk[];
|
|
29
29
|
export declare function parsePseudoBin(bytes: Uint8Array, offset: number): {
|
|
30
30
|
lineCount: number;
|
|
31
31
|
};
|
|
32
|
-
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number
|
|
32
|
+
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: ArrayLike<number>): void;
|
|
33
33
|
export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRefSeq: (s: string) => string): {
|
|
34
34
|
chrToIndex: Record<string, number>;
|
|
35
35
|
indexToChr: {
|
|
36
36
|
refName: string;
|
|
37
37
|
length: number;
|
|
38
38
|
}[];
|
|
39
|
+
end: number;
|
|
39
40
|
} | undefined;
|
|
40
41
|
/**
|
|
41
42
|
* The smallest of `current` and the `count` packed virtual offsets starting at
|
|
42
43
|
* `offset`, allocating at most one VirtualOffset rather than one per entry.
|
|
43
44
|
*
|
|
45
|
+
* 0:0 is skipped rather than treated as the minimum. No BAM record can live
|
|
46
|
+
* there — the magic and header occupy the start of the file — so it is the
|
|
47
|
+
* "unset" placeholder htslib leaves in linear-index windows ahead of a
|
|
48
|
+
* reference's first read (see test/data/HG00096_illumina_lowcov.bam.bai, whose
|
|
49
|
+
* first three windows are 0). Counting it collapses firstDataLine to 0:0 and
|
|
50
|
+
* makes callers size a header read from nothing.
|
|
51
|
+
*
|
|
44
52
|
* The index first pass exists only to find this minimum, and it visits every
|
|
45
53
|
* linear-index entry in the file to do it. Building a VirtualOffset per entry
|
|
46
54
|
* to compare and discard it is the bulk of that pass.
|
package/esm/util.js
CHANGED
|
@@ -1,5 +1,4 @@
|
|
|
1
1
|
import Chunk from "./chunk.js";
|
|
2
|
-
import { longFromBytesToUnsigned } from "./long.js";
|
|
3
2
|
import { VirtualOffset } from "./virtualOffset.js";
|
|
4
3
|
export function optimizeChunks(chunks, lowest) {
|
|
5
4
|
const n = chunks.length;
|
|
@@ -60,9 +59,20 @@ export function optimizeChunks(chunks, lowest) {
|
|
|
60
59
|
}
|
|
61
60
|
return mergedChunks;
|
|
62
61
|
}
|
|
62
|
+
// The pseudo-bin's mapped-record count, a little-endian uint64. Read as two
|
|
63
|
+
// 32-bit halves rather than via BigInt: exact up to Number.MAX_SAFE_INTEGER,
|
|
64
|
+
// which is far past any real record count, and allocates nothing.
|
|
63
65
|
export function parsePseudoBin(bytes, offset) {
|
|
66
|
+
const low = bytes[offset] |
|
|
67
|
+
(bytes[offset + 1] << 8) |
|
|
68
|
+
(bytes[offset + 2] << 16) |
|
|
69
|
+
(bytes[offset + 3] << 24);
|
|
70
|
+
const high = bytes[offset + 4] |
|
|
71
|
+
(bytes[offset + 5] << 8) |
|
|
72
|
+
(bytes[offset + 6] << 16) |
|
|
73
|
+
(bytes[offset + 7] << 24);
|
|
64
74
|
return {
|
|
65
|
-
lineCount:
|
|
75
|
+
lineCount: (high >>> 0) * 2 ** 32 + (low >>> 0),
|
|
66
76
|
};
|
|
67
77
|
}
|
|
68
78
|
// Tighten each chunk's endPosition (default: a full max-size BGZF block past
|
|
@@ -73,11 +83,17 @@ export function parsePseudoBin(bytes, offset) {
|
|
|
73
83
|
// least the true block end, so the clamped fetch still contains the whole block.
|
|
74
84
|
// Shrinks both the byte estimate and the actual fetch with no extra I/O.
|
|
75
85
|
export function clampChunkEnds(chunks, extraBoundaries = []) {
|
|
76
|
-
|
|
86
|
+
// Float64Array rather than number[]: `extraBoundaries` is the linear index,
|
|
87
|
+
// which runs to tens of thousands of entries on a human-sized reference, and
|
|
88
|
+
// this is the only place they get copied.
|
|
89
|
+
const boundaries = new Float64Array(extraBoundaries.length + chunks.length * 2);
|
|
90
|
+
boundaries.set(extraBoundaries);
|
|
91
|
+
let n = extraBoundaries.length;
|
|
77
92
|
for (const c of chunks) {
|
|
78
|
-
boundaries
|
|
93
|
+
boundaries[n++] = c.minv.blockPosition;
|
|
94
|
+
boundaries[n++] = c.maxv.blockPosition;
|
|
79
95
|
}
|
|
80
|
-
boundaries.sort(
|
|
96
|
+
boundaries.sort();
|
|
81
97
|
for (const c of chunks) {
|
|
82
98
|
const max = c.maxv.blockPosition;
|
|
83
99
|
// first boundary strictly greater than max
|
|
@@ -126,13 +142,23 @@ export function parseRefSeqs(uncba, start, renameRefSeq) {
|
|
|
126
142
|
indexToChr.push({ refName, length: lRef });
|
|
127
143
|
p += 8 + lName;
|
|
128
144
|
}
|
|
129
|
-
|
|
145
|
+
// end is the offset just past the header, i.e. where alignment records start
|
|
146
|
+
return { chrToIndex, indexToChr, end: p };
|
|
130
147
|
}
|
|
131
|
-
// SYNC: ~/src/gmod/tabix-js/src/util.ts minVirtualOffset
|
|
148
|
+
// SYNC: ~/src/gmod/tabix-js/src/util.ts minVirtualOffset — but NOT the 0:0
|
|
149
|
+
// skip below, which is only sound for BAM. A tabix'd file with no header lines
|
|
150
|
+
// really does have its first record at 0:0.
|
|
132
151
|
/**
|
|
133
152
|
* The smallest of `current` and the `count` packed virtual offsets starting at
|
|
134
153
|
* `offset`, allocating at most one VirtualOffset rather than one per entry.
|
|
135
154
|
*
|
|
155
|
+
* 0:0 is skipped rather than treated as the minimum. No BAM record can live
|
|
156
|
+
* there — the magic and header occupy the start of the file — so it is the
|
|
157
|
+
* "unset" placeholder htslib leaves in linear-index windows ahead of a
|
|
158
|
+
* reference's first read (see test/data/HG00096_illumina_lowcov.bam.bai, whose
|
|
159
|
+
* first three windows are 0). Counting it collapses firstDataLine to 0:0 and
|
|
160
|
+
* makes callers size a header read from nothing.
|
|
161
|
+
*
|
|
136
162
|
* The index first pass exists only to find this minimum, and it visits every
|
|
137
163
|
* linear-index entry in the file to do it. Building a VirtualOffset per entry
|
|
138
164
|
* to compare and discard it is the bulk of that pass.
|
|
@@ -150,7 +176,8 @@ export function minVirtualOffset(bytes, offset, count, current) {
|
|
|
150
176
|
bytes[p + 3] * 0x100 +
|
|
151
177
|
bytes[p + 2];
|
|
152
178
|
const data = (bytes[p + 1] << 8) | bytes[p];
|
|
153
|
-
if (block
|
|
179
|
+
if ((block !== 0 || data !== 0) &&
|
|
180
|
+
(block < minBlock || (block === minBlock && data < minData))) {
|
|
154
181
|
minBlock = block;
|
|
155
182
|
minData = data;
|
|
156
183
|
found = true;
|