@gmod/bam 7.3.3 → 7.4.0
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.js +10 -7
- package/dist/bai.js.map +1 -1
- package/dist/bamFile.d.ts +25 -6
- package/dist/bamFile.js +91 -33
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +2 -2
- package/dist/csi.js.map +1 -1
- package/dist/htsget.js +2 -2
- package/dist/htsget.js.map +1 -1
- package/dist/index.d.ts +1 -1
- package/dist/index.js +2 -1
- package/dist/index.js.map +1 -1
- package/dist/long.d.ts +0 -2
- package/dist/long.js +2 -4
- package/dist/long.js.map +1 -1
- package/dist/record.d.ts +3 -2
- package/dist/record.js +198 -178
- package/dist/record.js.map +1 -1
- package/dist/util.d.ts +1 -1
- package/dist/util.js +11 -12
- package/dist/util.js.map +1 -1
- package/dist/virtualOffset.d.ts +1 -1
- package/dist/virtualOffset.js +1 -4
- package/dist/virtualOffset.js.map +1 -1
- package/esm/bai.js +10 -7
- package/esm/bai.js.map +1 -1
- package/esm/bamFile.d.ts +25 -6
- package/esm/bamFile.js +91 -33
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +2 -2
- package/esm/csi.js.map +1 -1
- package/esm/htsget.js +2 -2
- package/esm/htsget.js.map +1 -1
- package/esm/index.d.ts +1 -1
- package/esm/index.js +1 -1
- package/esm/index.js.map +1 -1
- package/esm/long.d.ts +0 -2
- package/esm/long.js +1 -2
- package/esm/long.js.map +1 -1
- package/esm/record.d.ts +3 -2
- package/esm/record.js +198 -178
- package/esm/record.js.map +1 -1
- package/esm/util.d.ts +1 -1
- package/esm/util.js +11 -11
- package/esm/util.js.map +1 -1
- package/esm/virtualOffset.d.ts +1 -1
- package/esm/virtualOffset.js +1 -4
- package/esm/virtualOffset.js.map +1 -1
- package/package.json +2 -1
- package/src/bai.ts +15 -8
- package/src/bamFile.ts +117 -40
- package/src/csi.ts +10 -2
- package/src/htsget.ts +6 -2
- package/src/index.ts +1 -1
- package/src/long.ts +1 -2
- package/src/record.ts +231 -192
- package/src/util.ts +24 -14
- package/src/virtualOffset.ts +1 -5
package/dist/bai.js
CHANGED
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@@ -68,7 +68,7 @@ function reg2bins(beg, end) {
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class BAI extends indexFile_ts_1.default {
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async _parse(opts) {
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const bytes = await this.filehandle.readFile(opts);
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-
const dataView = new DataView(bytes.buffer);
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+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
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// check BAI magic numbers
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if (dataView.getUint32(0, true) !== BAI_MAGIC) {
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throw new Error('Not a BAI file');
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@@ -189,19 +189,22 @@ class BAI extends indexFile_ts_1.default {
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if (e > (linearIndex.length - 1) * v) {
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throw new Error('query outside of range of linear index');
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}
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+
// Scale the block-delta into a read count as we go, rather than building the
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// entries and then rebuilding every one of them to apply the scale. Keep the
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// multiply-then-divide order: hoisting lineCount/totalSize into a factor
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// reassociates the arithmetic and shifts scores by an ulp.
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const lineCount = stats?.lineCount ?? 0;
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let currentPos = linearIndex[s / v].blockPosition;
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for (let i = s / v, j = 0; i < e / v; i++, j++) {
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const nextPos = linearIndex[i + 1].blockPosition;
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depths[j] = {
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score:
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score: ((nextPos - currentPos) * lineCount) / totalSize,
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start: i * v,
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end: i * v + v,
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};
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-
currentPos =
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+
currentPos = nextPos;
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}
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-
return depths
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-
...d,
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-
score: (d.score * (stats?.lineCount ?? 0)) / totalSize,
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-
}));
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+
return depths;
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}
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reg2bins(min, max) {
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return reg2bins(min, max);
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package/dist/bai.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAAyE;AACzE,yDAA8C;AAc9C,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,MAAqB,GAAI,SAAQ,sBAAoB;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,
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1
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+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAAyE;AACzE,yDAA8C;AAc9C,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,MAAqB,GAAI,SAAQ,sBAAoB;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,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,aAAa,GAAG,IAAA,uBAAa,EAAC,aAAa,EAAE,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;gBACpE,IAAI,IAAI,CAAC,CAAA;YACX,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,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,IAAA,wBAAc,EAAC,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,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,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,WAAW,GAAG,IAAI,KAAK,CAAgB,WAAW,CAAC,CAAA;YACzD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACvC,IAAI,IAAI,CAAC,CAAA;YACX,CAAC;YAED,IAAA,wBAAc,EACZ,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,EAC9B,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CACtC,CAAA;YACD,OAAO;gBACL,QAAQ;gBACR,WAAW;gBACX,KAAK;aACN,CAAA;QACH,CAAC;QAED,OAAO;YACL,GAAG,EAAE,IAAI;YACT,aAAa;YACb,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,OAAO,EAAE,IAAA,6BAAc,EAAC,UAAU,CAAC;YACnC,QAAQ;SACT,CAAA;IACH,CAAC;IAED,KAAK,CAAC,QAAQ,CACZ,KAAa,EACb,KAAc,EACd,GAAY,EACZ,IAAe;QAEf,MAAM,CAAC,GAAG,mBAAmB,CAAA;QAC7B,MAAM,KAAK,GAAG,KAAK,KAAK,SAAS,CAAA;QACjC,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,MAAM,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAEvC,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,WAAW,EAAE,KAAK,EAAE,GAAG,MAAM,CAAA;QACrC,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,CAAC,GAAG,GAAG,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;QAC5E,MAAM,CAAC,GAAG,KAAK,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QACvD,MAAM,MAAM,GAAoB,KAAK;YACnC,CAAC,CAAC,IAAI,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC;YACxB,CAAC,CAAC,IAAI,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAA;QACrC,MAAM,SAAS,GAAG,WAAW,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAE,CAAC,aAAa,CAAA;QACpE,IAAI,CAAC,GAAG,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,wCAAwC,CAAC,CAAA;QAC3D,CAAC;QACD,6EAA6E;QAC7E,6EAA6E;QAC7E,yEAAyE;QACzE,2DAA2D;QAC3D,MAAM,SAAS,GAAG,KAAK,EAAE,SAAS,IAAI,CAAC,CAAA;QACvC,IAAI,UAAU,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,aAAa,CAAA;QAClD,KAAK,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,EAAE,EAAE,CAAC;YAC/C,MAAM,OAAO,GAAG,WAAW,CAAC,CAAC,GAAG,CAAC,CAAE,CAAC,aAAa,CAAA;YACjD,MAAM,CAAC,CAAC,CAAC,GAAG;gBACV,KAAK,EAAE,CAAC,CAAC,OAAO,GAAG,UAAU,CAAC,GAAG,SAAS,CAAC,GAAG,SAAS;gBACvD,KAAK,EAAE,CAAC,GAAG,CAAC;gBACZ,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,CAAC;aACf,CAAA;YACD,UAAU,GAAG,OAAO,CAAA;QACtB,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAES,QAAQ,CAAC,GAAW,EAAE,GAAW;QACzC,OAAO,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA;IAC3B,CAAC;IAED,0EAA0E;IAC1E,2EAA2E;IAC3E,+DAA+D;IACrD,cAAc,CAAC,QAAqB,EAAE,GAAW;QACzD,MAAM,EAAE,WAAW,EAAE,GAAG,QAAQ,CAAA;QAChC,MAAM,KAAK,GAAG,WAAW,CAAC,MAAM,CAAA;QAChC,OAAO,WAAW,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,gBAAgB,EAAE,KAAK,GAAG,CAAC,CAAC,CAAC,CAAA;IAClE,CAAC;CACF;AAjLD,sBAiLC"}
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package/dist/bamFile.d.ts
CHANGED
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@@ -1,4 +1,3 @@
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-
import QuickLRU from '@jbrowse/quick-lru';
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import BAI from './bai.ts';
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import CSI from './csi.ts';
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import BAMFeature from './record.ts';
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@@ -26,8 +25,23 @@ export declare const BAM_MAGIC = 21840194;
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interface ChunkEntry<T> {
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minBlock: number;
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maxBlock: number;
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bytes: number;
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features: T[];
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|
30
30
|
}
|
|
31
|
+
export declare const DEFAULT_MAX_CACHE_BYTES: number;
|
|
32
|
+
declare class ChunkFeatureCache<T> {
|
|
33
|
+
maxBytes: number;
|
|
34
|
+
private entries;
|
|
35
|
+
private bytes;
|
|
36
|
+
constructor(maxBytes: number);
|
|
37
|
+
get size(): number;
|
|
38
|
+
get byteSize(): number;
|
|
39
|
+
get(key: string): ChunkEntry<T> | undefined;
|
|
40
|
+
set(key: string, entry: ChunkEntry<T>): void;
|
|
41
|
+
delete(key: string): void;
|
|
42
|
+
clear(): void;
|
|
43
|
+
[Symbol.iterator](): MapIterator<[string, ChunkEntry<T>]>;
|
|
44
|
+
}
|
|
31
45
|
export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
32
46
|
renameRefSeq: (a: string) => string;
|
|
33
47
|
bam: GenericFilehandle;
|
|
@@ -40,9 +54,9 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
40
54
|
index?: BAI | CSI;
|
|
41
55
|
htsget: boolean;
|
|
42
56
|
headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
|
|
43
|
-
chunkFeatureCache:
|
|
57
|
+
chunkFeatureCache: ChunkFeatureCache<T>;
|
|
44
58
|
private RecordClass;
|
|
45
|
-
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, }: {
|
|
59
|
+
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
|
|
46
60
|
bamFilehandle?: GenericFilehandle;
|
|
47
61
|
bamPath?: string;
|
|
48
62
|
bamUrl?: string;
|
|
@@ -55,6 +69,8 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
55
69
|
renameRefSeqs?: (a: string) => string;
|
|
56
70
|
htsget?: boolean;
|
|
57
71
|
recordClass?: BamRecordClass<T>;
|
|
72
|
+
/** budget for the parsed-chunk cache, in decompressed bytes */
|
|
73
|
+
maxCacheBytes?: number;
|
|
58
74
|
});
|
|
59
75
|
getHeaderPre(opts?: BaseOpts): Promise<{
|
|
60
76
|
tag: string;
|
|
@@ -74,10 +90,13 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
74
90
|
private getSeqId;
|
|
75
91
|
getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
|
|
76
92
|
private evictOverlappingChunks;
|
|
77
|
-
private
|
|
93
|
+
private _fetchChunkFeatures;
|
|
78
94
|
fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
|
|
79
|
-
_readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<
|
|
80
|
-
|
|
95
|
+
_readChunkFeatures(chunk: Chunk, opts: BaseOpts): Promise<{
|
|
96
|
+
features: T[];
|
|
97
|
+
bytes: number;
|
|
98
|
+
}>;
|
|
99
|
+
readBamFeatures(ba: Uint8Array, cpositions: number[], dpositions: number[], chunk: Chunk): T[];
|
|
81
100
|
hasRefSeq(seqName: string, opts?: BaseOpts): Promise<boolean>;
|
|
82
101
|
lineCount(seqName: string, opts?: BaseOpts): Promise<number>;
|
|
83
102
|
indexCov(seqName: string, start?: number, end?: number): Promise<never[] | import("./bai.ts").IndexCovEntry[]>;
|
package/dist/bamFile.js
CHANGED
|
@@ -3,9 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.BAM_MAGIC = void 0;
|
|
6
|
+
exports.DEFAULT_MAX_CACHE_BYTES = exports.BAM_MAGIC = void 0;
|
|
7
7
|
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
|
|
8
|
-
const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
|
|
9
8
|
const crc32_1 = __importDefault(require("crc/calculators/crc32"));
|
|
10
9
|
const generic_filehandle2_1 = require("generic-filehandle2");
|
|
11
10
|
const bai_ts_1 = __importDefault(require("./bai.js"));
|
|
@@ -20,9 +19,68 @@ function resolveFilehandle(filehandle, path, url) {
|
|
|
20
19
|
return (filehandle ??
|
|
21
20
|
(path ? new generic_filehandle2_1.LocalFile(path) : url ? new generic_filehandle2_1.RemoteFile(url) : undefined));
|
|
22
21
|
}
|
|
23
|
-
|
|
22
|
+
// Keyed on the chunk's byte span only, not on filterBy: the cached value is the
|
|
23
|
+
// unfiltered parsed records (decompression + parse is the expensive part).
|
|
24
|
+
// Filters are applied cheaply on retrieval so toggling a filter over the same
|
|
25
|
+
// region is a cache hit rather than a re-decompress.
|
|
26
|
+
function chunkCacheKey(chunk) {
|
|
24
27
|
const { minv, maxv } = chunk;
|
|
25
|
-
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}
|
|
28
|
+
return `${minv.blockPosition}:${minv.dataPosition}-${maxv.blockPosition}:${maxv.dataPosition}`;
|
|
29
|
+
}
|
|
30
|
+
// Every record in an entry is a view into its chunk's decompressed buffer, so
|
|
31
|
+
// caching one entry pins that whole buffer — 8MB apiece on the nanopore and
|
|
32
|
+
// 2kb-read test files, and optimizeChunks merges spans up to 5MB *compressed*,
|
|
33
|
+
// so tens of MB is possible. A count-based LRU therefore gives no bound on
|
|
34
|
+
// memory at all, which is why this budgets by decompressed bytes instead.
|
|
35
|
+
exports.DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
|
|
36
|
+
class ChunkFeatureCache {
|
|
37
|
+
maxBytes;
|
|
38
|
+
entries = new Map();
|
|
39
|
+
bytes = 0;
|
|
40
|
+
constructor(maxBytes) {
|
|
41
|
+
this.maxBytes = maxBytes;
|
|
42
|
+
}
|
|
43
|
+
get size() {
|
|
44
|
+
return this.entries.size;
|
|
45
|
+
}
|
|
46
|
+
get byteSize() {
|
|
47
|
+
return this.bytes;
|
|
48
|
+
}
|
|
49
|
+
get(key) {
|
|
50
|
+
const entry = this.entries.get(key);
|
|
51
|
+
if (entry) {
|
|
52
|
+
// re-insert so Map iteration order stays least-recently-used first
|
|
53
|
+
this.entries.delete(key);
|
|
54
|
+
this.entries.set(key, entry);
|
|
55
|
+
}
|
|
56
|
+
return entry;
|
|
57
|
+
}
|
|
58
|
+
set(key, entry) {
|
|
59
|
+
this.delete(key);
|
|
60
|
+
this.entries.set(key, entry);
|
|
61
|
+
this.bytes += entry.bytes;
|
|
62
|
+
// Evict from the least-recently-used end. The size > 1 guard means a single
|
|
63
|
+
// chunk larger than the whole budget is still kept: the caller needs it for
|
|
64
|
+
// the query in flight, and dropping it would only force a re-decompress.
|
|
65
|
+
const lru = this.entries.keys();
|
|
66
|
+
while (this.bytes > this.maxBytes && this.entries.size > 1) {
|
|
67
|
+
this.delete(lru.next().value);
|
|
68
|
+
}
|
|
69
|
+
}
|
|
70
|
+
delete(key) {
|
|
71
|
+
const entry = this.entries.get(key);
|
|
72
|
+
if (entry) {
|
|
73
|
+
this.entries.delete(key);
|
|
74
|
+
this.bytes -= entry.bytes;
|
|
75
|
+
}
|
|
76
|
+
}
|
|
77
|
+
clear() {
|
|
78
|
+
this.entries.clear();
|
|
79
|
+
this.bytes = 0;
|
|
80
|
+
}
|
|
81
|
+
[Symbol.iterator]() {
|
|
82
|
+
return this.entries[Symbol.iterator]();
|
|
83
|
+
}
|
|
26
84
|
}
|
|
27
85
|
class BamFile {
|
|
28
86
|
renameRefSeq;
|
|
@@ -35,13 +93,12 @@ class BamFile {
|
|
|
35
93
|
headerP;
|
|
36
94
|
// Cache for parsed features by chunk
|
|
37
95
|
// When a new chunk overlaps a cached chunk, we evict the cached one
|
|
38
|
-
chunkFeatureCache
|
|
39
|
-
maxSize: 100,
|
|
40
|
-
});
|
|
96
|
+
chunkFeatureCache;
|
|
41
97
|
RecordClass;
|
|
42
|
-
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, }) {
|
|
98
|
+
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = exports.DEFAULT_MAX_CACHE_BYTES, }) {
|
|
43
99
|
this.renameRefSeq = renameRefSeqs;
|
|
44
100
|
this.RecordClass = (recordClass ?? record_ts_1.default);
|
|
101
|
+
this.chunkFeatureCache = new ChunkFeatureCache(maxCacheBytes);
|
|
45
102
|
const bamFh = resolveFilehandle(bamFilehandle, bamPath, bamUrl);
|
|
46
103
|
if (bamFh) {
|
|
47
104
|
this.bam = bamFh;
|
|
@@ -81,7 +138,7 @@ class BamFile {
|
|
|
81
138
|
? await this.bam.readFile()
|
|
82
139
|
: await this.bam.read(readLen, 0);
|
|
83
140
|
let uncba = await (0, bgzf_filehandle_1.unzip)(buffer);
|
|
84
|
-
const dataView = new DataView(uncba.buffer);
|
|
141
|
+
const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
|
|
85
142
|
if (dataView.getInt32(0, true) !== exports.BAM_MAGIC) {
|
|
86
143
|
throw new Error('Not a BAM file');
|
|
87
144
|
}
|
|
@@ -129,7 +186,7 @@ class BamFile {
|
|
|
129
186
|
return [];
|
|
130
187
|
}
|
|
131
188
|
const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
|
|
132
|
-
return this.
|
|
189
|
+
return this._fetchChunkFeatures(chunks, chrId, min, max, opts);
|
|
133
190
|
}
|
|
134
191
|
// Evict any cached chunks whose block range overlaps [minBlock, maxBlock]
|
|
135
192
|
evictOverlappingChunks(minBlock, maxBlock) {
|
|
@@ -139,7 +196,7 @@ class BamFile {
|
|
|
139
196
|
}
|
|
140
197
|
}
|
|
141
198
|
}
|
|
142
|
-
async
|
|
199
|
+
async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
|
|
143
200
|
const { viewAsPairs, filterBy, onProgress } = opts;
|
|
144
201
|
const result = [];
|
|
145
202
|
let totalBytes = 0;
|
|
@@ -150,24 +207,19 @@ class BamFile {
|
|
|
150
207
|
onProgress?.(0, totalBytes);
|
|
151
208
|
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
152
209
|
const chunk = chunks[ci];
|
|
153
|
-
const cacheKey = chunkCacheKey(chunk
|
|
210
|
+
const cacheKey = chunkCacheKey(chunk);
|
|
154
211
|
const minBlock = chunk.minv.blockPosition;
|
|
155
212
|
const maxBlock = chunk.maxv.blockPosition;
|
|
156
|
-
let
|
|
157
|
-
|
|
158
|
-
if (cached) {
|
|
159
|
-
records = cached.features;
|
|
160
|
-
}
|
|
161
|
-
else {
|
|
213
|
+
let cached = this.chunkFeatureCache.get(cacheKey);
|
|
214
|
+
if (!cached) {
|
|
162
215
|
this.evictOverlappingChunks(minBlock, maxBlock);
|
|
163
|
-
const
|
|
164
|
-
|
|
165
|
-
this.chunkFeatureCache.set(cacheKey,
|
|
166
|
-
minBlock,
|
|
167
|
-
maxBlock,
|
|
168
|
-
features: records,
|
|
169
|
-
});
|
|
216
|
+
const { features, bytes } = await this._readChunkFeatures(chunk, opts);
|
|
217
|
+
cached = { minBlock, maxBlock, bytes, features };
|
|
218
|
+
this.chunkFeatureCache.set(cacheKey, cached);
|
|
170
219
|
}
|
|
220
|
+
const records = filterBy
|
|
221
|
+
? (0, util_ts_1.applyFilters)(cached.features, filterBy)
|
|
222
|
+
: cached.features;
|
|
171
223
|
downloadedBytes += chunk.fetchedSize();
|
|
172
224
|
onProgress?.(downloadedBytes, totalBytes);
|
|
173
225
|
(0, util_ts_1.appendInRange)(records, chrId, min, max, result);
|
|
@@ -182,12 +234,15 @@ class BamFile {
|
|
|
182
234
|
}
|
|
183
235
|
async fetchPairs(chrId, records, opts) {
|
|
184
236
|
const { pairAcrossChr, maxInsertSize = 200000 } = opts;
|
|
185
|
-
|
|
237
|
+
// Map, not a plain object: read names come from the file, and on a plain
|
|
238
|
+
// object a read named "constructor" would read back Object.prototype's and
|
|
239
|
+
// make the count NaN.
|
|
240
|
+
const readNameCounts = new Map();
|
|
186
241
|
const readIds = new Set();
|
|
187
242
|
for (let i = 0, l = records.length; i < l; i++) {
|
|
188
243
|
const r = records[i];
|
|
189
244
|
const name = r.name;
|
|
190
|
-
readNameCounts
|
|
245
|
+
readNameCounts.set(name, (readNameCounts.get(name) ?? 0) + 1);
|
|
191
246
|
readIds.add(r.fileOffset);
|
|
192
247
|
}
|
|
193
248
|
const matePromises = [];
|
|
@@ -195,7 +250,7 @@ class BamFile {
|
|
|
195
250
|
const f = records[i];
|
|
196
251
|
const name = f.name;
|
|
197
252
|
if (this.index &&
|
|
198
|
-
readNameCounts
|
|
253
|
+
readNameCounts.get(name) === 1 &&
|
|
199
254
|
(pairAcrossChr ||
|
|
200
255
|
(f.next_refid === chrId &&
|
|
201
256
|
Math.abs(f.start - f.next_pos) < maxInsertSize))) {
|
|
@@ -212,11 +267,11 @@ class BamFile {
|
|
|
212
267
|
}
|
|
213
268
|
}
|
|
214
269
|
const mateFeatLists = await Promise.all([...map.values()].map(async (c) => {
|
|
215
|
-
const features = await this._readChunkFeatures(c, opts);
|
|
270
|
+
const { features } = await this._readChunkFeatures(c, opts);
|
|
216
271
|
const mateRecs = [];
|
|
217
272
|
for (let i = 0, l = features.length; i < l; i++) {
|
|
218
273
|
const feature = features[i];
|
|
219
|
-
if (readNameCounts
|
|
274
|
+
if (readNameCounts.get(feature.name) === 1 &&
|
|
220
275
|
!readIds.has(feature.fileOffset)) {
|
|
221
276
|
mateRecs.push(feature);
|
|
222
277
|
}
|
|
@@ -235,13 +290,16 @@ class BamFile {
|
|
|
235
290
|
signal: opts.signal,
|
|
236
291
|
});
|
|
237
292
|
const { buffer: data, cpositions, dpositions, } = await (0, bgzf_filehandle_1.unzipChunkSlice)(buf, chunk);
|
|
238
|
-
return
|
|
293
|
+
return {
|
|
294
|
+
features: this.readBamFeatures(data, cpositions, dpositions, chunk),
|
|
295
|
+
bytes: data.byteLength,
|
|
296
|
+
};
|
|
239
297
|
}
|
|
240
|
-
|
|
298
|
+
readBamFeatures(ba, cpositions, dpositions, chunk) {
|
|
241
299
|
let blockStart = 0;
|
|
242
300
|
const sink = [];
|
|
243
301
|
let pos = 0;
|
|
244
|
-
const dataView = new DataView(ba.buffer);
|
|
302
|
+
const dataView = new DataView(ba.buffer, ba.byteOffset, ba.byteLength);
|
|
245
303
|
const hasDpositions = dpositions.length > 0;
|
|
246
304
|
const hasCpositions = cpositions.length > 0;
|
|
247
305
|
while (blockStart + 4 < ba.length) {
|
package/dist/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
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+
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|
package/dist/csi.js
CHANGED
|
@@ -60,7 +60,7 @@ class CSI extends indexFile_ts_1.default {
|
|
|
60
60
|
return [];
|
|
61
61
|
}
|
|
62
62
|
parseAuxData(bytes, offset) {
|
|
63
|
-
const dataView = new DataView(bytes.buffer);
|
|
63
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
64
64
|
const formatFlags = dataView.getUint32(offset, true);
|
|
65
65
|
const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
|
|
66
66
|
const format = ['generic', 'SAM', 'VCF'][formatFlags & 0xf];
|
|
@@ -91,7 +91,7 @@ class CSI extends indexFile_ts_1.default {
|
|
|
91
91
|
async _parse(opts) {
|
|
92
92
|
const buffer = await this.filehandle.readFile(opts);
|
|
93
93
|
const bytes = await (0, bgzf_filehandle_1.unzip)(buffer);
|
|
94
|
-
const dataView = new DataView(bytes.buffer);
|
|
94
|
+
const dataView = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength);
|
|
95
95
|
let csiVersion;
|
|
96
96
|
const magic = dataView.getUint32(0, true);
|
|
97
97
|
if (magic === CSI1_MAGIC) {
|
package/dist/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,+DAA0D;AAC1D,uCAKkB;AAClB,yDAA6D;AAI7D,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,MAAM,WAAW,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;AAE3C,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,sBAAS;IAChC,YAAY,GAAG,CAAC,CAAA;IAChB,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEpB,uEAAuE;IACvE,iEAAiE;IACjE,KAAK,CAAC,QAAQ;QACZ,OAAO,EAAE,CAAA;IACX,CAAC;IAED,YAAY,CAAC,KAAiB,EAAE,MAAc;QAC5C,MAAM,QAAQ,GAAG,IAAI,QAAQ,
|
|
1
|
+
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|
package/dist/htsget.js
CHANGED
|
@@ -85,7 +85,7 @@ class HtsgetFile extends bamFile_ts_1.default {
|
|
|
85
85
|
signal: opts?.signal,
|
|
86
86
|
});
|
|
87
87
|
const zero = new virtualOffset_ts_1.VirtualOffset(0, 0);
|
|
88
|
-
const allRecords =
|
|
88
|
+
const allRecords = this.readBamFeatures(uncba, [], [], new chunk_ts_1.default(zero, zero, 0));
|
|
89
89
|
return (0, util_ts_1.appendInRange)(allRecords, chrId, min, max);
|
|
90
90
|
}
|
|
91
91
|
async getHeaderPre(opts = {}) {
|
|
@@ -95,7 +95,7 @@ class HtsgetFile extends bamFile_ts_1.default {
|
|
|
95
95
|
const uncba = await fetchAndConcat(data.htsget.urls, {
|
|
96
96
|
signal: opts.signal,
|
|
97
97
|
});
|
|
98
|
-
const dataView = new DataView(uncba.buffer);
|
|
98
|
+
const dataView = new DataView(uncba.buffer, uncba.byteOffset, uncba.byteLength);
|
|
99
99
|
if (dataView.getInt32(0, true) !== bamFile_ts_1.BAM_MAGIC) {
|
|
100
100
|
throw new Error('Not a BAM file');
|
|
101
101
|
}
|
package/dist/htsget.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"htsget.js","sourceRoot":"","sources":["../src/htsget.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,2DAA6C;AAE7C,2DAAiD;AACjD,0DAA8B;AAC9B,qCAA0C;AAC1C,uCAA2D;AAC3D,yDAAkD;AAWlD,KAAK,UAAU,OAAO,CAAC,GAAW,EAAE,IAAkB;IACpD,MAAM,GAAG,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;IAClC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,QAAQ,GAAG,CAAC,MAAM,aAAa,GAAG,KAAK,MAAM,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,CAAA;IAC5E,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,KAAK,UAAU,UAAU,CAAC,EAAE,GAAG,EAAE,OAAO,EAAe,EAAE,IAAkB;IACzE,0EAA0E;IAC1E,uDAAuD;IACvD,+CAA+C;IAC/C,MAAM,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,EAAE,GAAG,OAAO,IAAI,EAAE,CAAA;IACpD,MAAM,GAAG,GAAG,GAAG,CAAC,UAAU,CAAC,OAAO,CAAC;QACjC,CAAC,CAAC,MAAM,OAAO,CAAC,GAAG,CAAC;QACpB,CAAC,CAAC,MAAM,OAAO,CAAC,GAAG,EAAE,EAAE,GAAG,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAA;IAClD,OAAO,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;AAChD,CAAC;AAED,KAAK,UAAU,cAAc,CAAC,GAAkB,EAAE,IAAkB;IAClE,2EAA2E;IAC3E,OAAO,IAAA,0BAAgB,EACrB,MAAM,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,EAAC,CAAC,EAAC,EAAE,CAAC,IAAA,uBAAK,EAAC,MAAM,UAAU,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,CAAC,CACxE,CAAA;AACH,CAAC;AAED,MAAqB,UAEnB,SAAQ,oBAAU;IACV,OAAO,CAAQ;IAEf,OAAO,CAAQ;IAEvB,YAAY,IAIX;QACC,KAAK,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,WAAW,EAAE,IAAI,CAAC,WAAW,EAAE,CAAC,CAAA;QACtD,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;QAC3B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAA;IAC7B,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,GAAW,EACX,GAAW,EACX,IAAc;QAEd,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC1B,MAAM,IAAI,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,EAAE,CAAA;QAC9C,MAAM,GAAG,GAAG,GAAG,IAAI,kBAAkB,GAAG,UAAU,GAAG,QAAQ,GAAG,aAAa,CAAA;QAC7E,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;YAC5D,MAAM,EAAE,IAAI,EAAE,MAAM;SACrB,CAAC,CAAA;QAEF,MAAM,IAAI,GAAG,IAAI,gCAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;QACpC,MAAM,UAAU,GAAG,IAAI,CAAC,eAAe,CACrC,KAAK,EACL,EAAE,EACF,EAAE,EACF,IAAI,kBAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,CACzB,CAAA;QAED,OAAO,IAAA,uBAAa,EAAC,UAAU,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,CAAC,CAAA;IACnD,CAAC;IAED,KAAK,CAAC,YAAY,CAAC,OAAiB,EAAE;QACpC,MAAM,GAAG,GAAG,GAAG,IAAI,CAAC,OAAO,IAAI,IAAI,CAAC,OAAO,gCAAgC,CAAA;QAC3E,MAAM,MAAM,GAAG,MAAM,OAAO,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;QACvC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,IAAI,EAAE,CAAA;QAChC,MAAM,KAAK,GAAG,MAAM,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,EAAE;YACnD,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CAAC,CAAA;QACF,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,IAAI,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,sBAAS,EAAE,CAAC;YAC7C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QACD,MAAM,OAAO,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAE1C,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;QACjC,MAAM,UAAU,GAAG,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,CAAC,CAAA;QACjE,MAAM,SAAS,GAAG,IAAA,wBAAe,EAAC,UAAU,CAAC,CAAA;QAE7C,oDAAoD;QACpD,+CAA+C;QAC/C,MAAM,QAAQ,GAA0C,EAAE,CAAA;QAC1D,MAAM,QAAQ,GAA2B,EAAE,CAAA;QAC3C,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,IAAI,CAAC,CAAA;QACrD,KAAK,MAAM,CAAC,KAAK,EAAE,MAAM,CAAC,IAAI,OAAO,CAAC,OAAO,EAAE,EAAE,CAAC;YAChD,IAAI,OAAO,GAAG,EAAE,CAAA;YAChB,IAAI,MAAM,GAAG,CAAC,CAAA;YACd,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,IAAI,EAAE,CAAC;gBAC/B,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBACtB,OAAO,GAAG,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;qBAAM,IAAI,IAAI,CAAC,GAAG,KAAK,IAAI,EAAE,CAAC;oBAC7B,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,CAAA;gBACtB,CAAC;YACH,CAAC;YACD,QAAQ,CAAC,OAAO,CAAC,GAAG,KAAK,CAAA;YACzB,QAAQ,CAAC,KAAK,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,CAAA;QACvC,CAAC;QACD,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,IAAI,CAAC,UAAU,GAAG,QAAQ,CAAA;QAC1B,OAAO,SAAS,CAAA;IAClB,CAAC;CACF;AA3FD,6BA2FC"}
|
package/dist/index.d.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
1
|
export { default as BAI } from './bai.ts';
|
|
2
|
-
export { default as BamFile } from './bamFile.ts';
|
|
2
|
+
export { DEFAULT_MAX_CACHE_BYTES, default as BamFile } from './bamFile.ts';
|
|
3
3
|
export { default as CSI } from './csi.ts';
|
|
4
4
|
export { default as BamRecord } from './record.ts';
|
|
5
5
|
export { default as HtsgetFile } from './htsget.ts';
|
package/dist/index.js
CHANGED
|
@@ -3,10 +3,11 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.BAI = void 0;
|
|
6
|
+
exports.HtsgetFile = exports.BamRecord = exports.CSI = exports.BamFile = exports.DEFAULT_MAX_CACHE_BYTES = exports.BAI = void 0;
|
|
7
7
|
var bai_ts_1 = require("./bai.js");
|
|
8
8
|
Object.defineProperty(exports, "BAI", { enumerable: true, get: function () { return __importDefault(bai_ts_1).default; } });
|
|
9
9
|
var bamFile_ts_1 = require("./bamFile.js");
|
|
10
|
+
Object.defineProperty(exports, "DEFAULT_MAX_CACHE_BYTES", { enumerable: true, get: function () { return bamFile_ts_1.DEFAULT_MAX_CACHE_BYTES; } });
|
|
10
11
|
Object.defineProperty(exports, "BamFile", { enumerable: true, get: function () { return __importDefault(bamFile_ts_1).default; } });
|
|
11
12
|
var csi_ts_1 = require("./csi.js");
|
|
12
13
|
Object.defineProperty(exports, "CSI", { enumerable: true, get: function () { return __importDefault(csi_ts_1).default; } });
|
package/dist/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,2CAA0E;AAAjE,qHAAA,uBAAuB,OAAA;AAAE,sHAAA,OAAO,OAAW;AACpD,mCAAyC;AAAhC,8GAAA,OAAO,OAAO;AACvB,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,yCAAmD;AAA1C,wHAAA,OAAO,OAAc"}
|
package/dist/long.d.ts
CHANGED
package/dist/long.js
CHANGED
|
@@ -1,9 +1,7 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL = void 0;
|
|
4
3
|
exports.longFromBytesToUnsigned = longFromBytesToUnsigned;
|
|
5
|
-
|
|
6
|
-
exports.TWO_PWR_32_DBL = exports.TWO_PWR_16_DBL * exports.TWO_PWR_16_DBL;
|
|
4
|
+
const TWO_PWR_32_DBL = 2 ** 32;
|
|
7
5
|
// avoids dependency on long.js
|
|
8
6
|
function longFromBytesToUnsigned(source, i = 0) {
|
|
9
7
|
const low = source[i] |
|
|
@@ -14,6 +12,6 @@ function longFromBytesToUnsigned(source, i = 0) {
|
|
|
14
12
|
(source[i + 5] << 8) |
|
|
15
13
|
(source[i + 6] << 16) |
|
|
16
14
|
(source[i + 7] << 24);
|
|
17
|
-
return (high >>> 0) *
|
|
15
|
+
return (high >>> 0) * TWO_PWR_32_DBL + (low >>> 0);
|
|
18
16
|
}
|
|
19
17
|
//# sourceMappingURL=long.js.map
|
package/dist/long.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"long.js","sourceRoot":"","sources":["../src/long.ts"],"names":[],"mappings":";;AAGA,0DAYC;AAfD,MAAM,cAAc,GAAG,CAAC,IAAI,EAAE,CAAA;AAE9B,+BAA+B;AAC/B,SAAgB,uBAAuB,CAAC,MAAkB,EAAE,CAAC,GAAG,CAAC;IAC/D,MAAM,GAAG,GACP,MAAM,CAAC,CAAC,CAAE;QACV,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,MAAM,IAAI,GACR,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE;QACd,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC;QACrB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC;QACtB,CAAC,MAAM,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,EAAE,CAAC,CAAA;IACxB,OAAO,CAAC,IAAI,KAAK,CAAC,CAAC,GAAG,cAAc,GAAG,CAAC,GAAG,KAAK,CAAC,CAAC,CAAA;AACpD,CAAC"}
|
package/dist/record.d.ts
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
export type NumericCigar = Uint32Array | Int32Array | number[];
|
|
1
2
|
export interface Bytes {
|
|
2
3
|
start: number;
|
|
3
4
|
end: number;
|
|
@@ -36,7 +37,7 @@ export default class BamRecord {
|
|
|
36
37
|
get NUMERIC_MD(): Uint8Array<ArrayBufferLike> | undefined;
|
|
37
38
|
get tags(): Record<string, unknown>;
|
|
38
39
|
getTag(tagName: string): unknown;
|
|
39
|
-
getTagRaw(tagName: string):
|
|
40
|
+
getTagRaw(tagName: string): unknown;
|
|
40
41
|
private _findTag;
|
|
41
42
|
private _computeTags;
|
|
42
43
|
isPaired(): boolean;
|
|
@@ -55,7 +56,7 @@ export default class BamRecord {
|
|
|
55
56
|
private _computeLengthOnRef;
|
|
56
57
|
private _computeNumericCigar;
|
|
57
58
|
get length_on_ref(): number;
|
|
58
|
-
get NUMERIC_CIGAR():
|
|
59
|
+
get NUMERIC_CIGAR(): NumericCigar;
|
|
59
60
|
get CIGAR(): string;
|
|
60
61
|
get num_cigar_ops(): number;
|
|
61
62
|
get num_cigar_bytes(): number;
|