@gmod/bam 7.6.0 → 7.6.1
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 +2 -4
- package/dist/bai.js.map +1 -1
- package/dist/csi.js +7 -8
- package/dist/csi.js.map +1 -1
- package/dist/util.d.ts +11 -2
- package/dist/util.js +31 -7
- package/dist/util.js.map +1 -1
- package/esm/bai.js +3 -5
- package/esm/bai.js.map +1 -1
- package/esm/csi.js +8 -9
- package/esm/csi.js.map +1 -1
- package/esm/util.d.ts +11 -2
- package/esm/util.js +30 -6
- package/esm/util.js.map +1 -1
- package/package.json +1 -1
- package/src/bai.ts +3 -5
- package/src/csi.ts +8 -9
- package/src/util.ts +36 -9
package/dist/bai.js
CHANGED
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@@ -107,10 +107,8 @@ class BAI extends indexFile_ts_1.default {
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107
107
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// marks where the BAM header ends and data begins
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108
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const linearCount = dataView.getInt32(curr, true);
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109
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curr += 4;
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110
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-
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111
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-
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112
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-
curr += 8;
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113
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-
}
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110
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+
firstDataLine = (0, util_ts_1.minVirtualOffset)(bytes, curr, linearCount, firstDataLine);
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111
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+
curr += 8 * linearCount;
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}
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function getIndices(refId) {
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let curr = offsets[refId];
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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,
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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,uCAA4E;AAC5E,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,aAAa,GAAG,IAAA,0BAAgB,EAAC,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,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,MAA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package/dist/csi.js
CHANGED
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@@ -127,15 +127,14 @@ class CSI extends indexFile_ts_1.default {
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127
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curr += 28 + 16;
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}
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else {
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-
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+
// A bin's loffset is the smallest virtual offset of any record in it,
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// so the minimum over loffsets is already the minimum over the bin's
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// chunks — one read per bin instead of one per chunk. Checked against
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// every .csi in test/data: same answer on all 19.
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firstDataLine = (0, util_ts_1.minVirtualOffset)(bytes, curr, 1, firstDataLine);
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curr += 8; // loffset
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const chunkCount = dataView.getInt32(curr, true);
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curr += 4;
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for (let k = 0; k < chunkCount; k += 1) {
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const u = (0, virtualOffset_ts_1.fromBytes)(bytes, curr);
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curr += 8;
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curr += 8;
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firstDataLine = (0, util_ts_1.findFirstData)(firstDataLine, u);
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}
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curr += 4 + 16 * chunkCount;
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}
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}
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}
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package/dist/csi.js.map
CHANGED
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@@ -1 +1 @@
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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,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,IAAA,wBAAc,EACf,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,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,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,
|
|
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,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,IAAA,wBAAc,EACf,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,IAAA,uBAAK,EAAC,MAAM,CAAC,CAAA;QAEjC,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QACD,IAAI,UAAU,CAAA;QACd,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAEzC,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,EAAE,CAAC,CAAA;YAC1C,oDAAoD;QACtD,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,IAAA,0BAAgB,EAAC,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,IAAA,wBAAc,EAAC,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,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,IAAA,4BAAS,EAAC,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|
package/dist/util.d.ts
CHANGED
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
|
-
import
|
|
2
|
+
import { VirtualOffset } from './virtualOffset.ts';
|
|
3
|
+
import type { Offset } from './virtualOffset.ts';
|
|
3
4
|
export interface BamOpts {
|
|
4
5
|
viewAsPairs?: boolean;
|
|
5
6
|
pairAcrossChr?: boolean;
|
|
@@ -36,7 +37,15 @@ export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRef
|
|
|
36
37
|
length: number;
|
|
37
38
|
}[];
|
|
38
39
|
} | undefined;
|
|
39
|
-
|
|
40
|
+
/**
|
|
41
|
+
* The smallest of `current` and the `count` packed virtual offsets starting at
|
|
42
|
+
* `offset`, allocating at most one VirtualOffset rather than one per entry.
|
|
43
|
+
*
|
|
44
|
+
* The index first pass exists only to find this minimum, and it visits every
|
|
45
|
+
* linear-index entry in the file to do it. Building a VirtualOffset per entry
|
|
46
|
+
* to compare and discard it is the bulk of that pass.
|
|
47
|
+
*/
|
|
48
|
+
export declare function minVirtualOffset(bytes: Uint8Array, offset: number, count: number, current: VirtualOffset | undefined): VirtualOffset | undefined;
|
|
40
49
|
export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (arg: string) => string): {
|
|
41
50
|
refNameToId: Record<string, number>;
|
|
42
51
|
refIdToName: string[];
|
package/dist/util.js
CHANGED
|
@@ -7,12 +7,13 @@ exports.optimizeChunks = optimizeChunks;
|
|
|
7
7
|
exports.parsePseudoBin = parsePseudoBin;
|
|
8
8
|
exports.clampChunkEnds = clampChunkEnds;
|
|
9
9
|
exports.parseRefSeqs = parseRefSeqs;
|
|
10
|
-
exports.
|
|
10
|
+
exports.minVirtualOffset = minVirtualOffset;
|
|
11
11
|
exports.parseNameBytes = parseNameBytes;
|
|
12
12
|
exports.concatUint8Array = concatUint8Array;
|
|
13
13
|
exports.appendInRange = appendInRange;
|
|
14
14
|
const chunk_ts_1 = __importDefault(require("./chunk.js"));
|
|
15
15
|
const long_ts_1 = require("./long.js");
|
|
16
|
+
const virtualOffset_ts_1 = require("./virtualOffset.js");
|
|
16
17
|
function optimizeChunks(chunks, lowest) {
|
|
17
18
|
const n = chunks.length;
|
|
18
19
|
if (n === 0) {
|
|
@@ -140,12 +141,35 @@ function parseRefSeqs(uncba, start, renameRefSeq) {
|
|
|
140
141
|
}
|
|
141
142
|
return { chrToIndex, indexToChr };
|
|
142
143
|
}
|
|
143
|
-
|
|
144
|
-
|
|
145
|
-
|
|
146
|
-
|
|
147
|
-
|
|
148
|
-
|
|
144
|
+
// SYNC: ~/src/gmod/tabix-js/src/util.ts minVirtualOffset
|
|
145
|
+
/**
|
|
146
|
+
* The smallest of `current` and the `count` packed virtual offsets starting at
|
|
147
|
+
* `offset`, allocating at most one VirtualOffset rather than one per entry.
|
|
148
|
+
*
|
|
149
|
+
* The index first pass exists only to find this minimum, and it visits every
|
|
150
|
+
* linear-index entry in the file to do it. Building a VirtualOffset per entry
|
|
151
|
+
* to compare and discard it is the bulk of that pass.
|
|
152
|
+
*/
|
|
153
|
+
function minVirtualOffset(bytes, offset, count, current) {
|
|
154
|
+
let minBlock = current ? current.blockPosition : Infinity;
|
|
155
|
+
let minData = current ? current.dataPosition : 0;
|
|
156
|
+
let found = false;
|
|
157
|
+
for (let i = 0; i < count; i++) {
|
|
158
|
+
const p = offset + i * 8;
|
|
159
|
+
const block = bytes[p + 7] * 0x10000000000 +
|
|
160
|
+
bytes[p + 6] * 0x100000000 +
|
|
161
|
+
bytes[p + 5] * 0x1000000 +
|
|
162
|
+
bytes[p + 4] * 0x10000 +
|
|
163
|
+
bytes[p + 3] * 0x100 +
|
|
164
|
+
bytes[p + 2];
|
|
165
|
+
const data = (bytes[p + 1] << 8) | bytes[p];
|
|
166
|
+
if (block < minBlock || (block === minBlock && data < minData)) {
|
|
167
|
+
minBlock = block;
|
|
168
|
+
minData = data;
|
|
169
|
+
found = true;
|
|
170
|
+
}
|
|
171
|
+
}
|
|
172
|
+
return found ? new virtualOffset_ts_1.VirtualOffset(minBlock, minData) : current;
|
|
149
173
|
}
|
|
150
174
|
// SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan
|
|
151
175
|
function parseNameBytes(namesBytes, renameRefSeq = s => s) {
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;AAgCA,wCAsEC;AAED,wCAIC;AASD,wCA2BC;AAKD,oCAsCC;AAWD,4CA0BC;AAGD,wCAuBC;AAED,4CAYC;AAYD,sCAoBC;AAxSD,0DAA8B;AAC9B,uCAAmD;AACnD,yDAAkD;AA8BlD,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAe;IAC7D,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;IACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,MAAM,CAAA;IACf,CAAC;IAED,0DAA0D;IAC1D,IAAI,QAAiB,CAAA;IACrB,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,WAAW,GAAG,MAAM,CAAC,aAAa,CAAA;QACxC,MAAM,UAAU,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,QAAQ,GAAG,EAAE,CAAA;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;YACxB,MAAM,IAAI,GAAG,KAAK,CAAC,IAAI,CAAA;YACvB,MAAM,GAAG,GACP,IAAI,CAAC,aAAa,GAAG,WAAW,IAAI,IAAI,CAAC,YAAY,GAAG,UAAU,CAAA;YACpE,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACtB,CAAC;QACH,CAAC;QACD,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,QAAQ,CAAA;QACjB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,QAAQ,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,yEAAyE;IACzE,uEAAuE;IACvE,MAAM,YAAY,GAAY,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;IAC5C,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAClD,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAElD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,oEAAoE;QACpE,yEAAyE;QACzE,IACE,aAAa,GAAG,YAAY,GAAG,KAAK;YACpC,aAAa,GAAG,YAAY,GAAG,OAAO,EACtC,CAAC;YACD,MAAM,SAAS,GAAG,YAAY,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAE,CAAA;YACxD,MAAM,GAAG,GACP,aAAa,GAAG,YAAY;gBAC5B,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,YAAY,CAAA;YACvD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,YAAY,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,kBAAK,CAC/C,SAAS,CAAC,IAAI,EACd,KAAK,CAAC,IAAI,EACV,SAAS,CAAC,GAAG,EACb,KAAK,CAAC,WAAW,CAClB,CAAA;gBACD,YAAY,GAAG,aAAa,CAAA;YAC9B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACxB,YAAY,GAAG,aAAa,CAAA;YAC5B,YAAY,GAAG,aAAa,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,SAAgB,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO;QACL,SAAS,EAAE,IAAA,iCAAuB,EAAC,KAAK,EAAE,MAAM,CAAC;KAClD,CAAA;AACH,CAAC;AAED,6EAA6E;AAC7E,kFAAkF;AAClF,kFAAkF;AAClF,iFAAiF;AACjF,kFAAkF;AAClF,iFAAiF;AACjF,yEAAyE;AACzE,SAAgB,cAAc,CAC5B,MAAe,EACf,kBAA4B,EAAE;IAE9B,MAAM,UAAU,GAAG,CAAC,GAAG,eAAe,CAAC,CAAA;IACvC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;IAC7D,CAAC;IACD,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IAEhC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,aAAa,CAAA;QAChC,2CAA2C;QAC3C,IAAI,EAAE,GAAG,CAAC,CAAA;QACV,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;QAC1B,OAAO,EAAE,GAAG,EAAE,EAAE,CAAC;YACf,MAAM,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,CAAA;YAC3B,IAAI,UAAU,CAAC,GAAG,CAAE,GAAG,GAAG,EAAE,CAAC;gBAC3B,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,EAAE,GAAG,GAAG,GAAG,CAAC,CAAA;YACd,CAAC;QACH,CAAC;QACD,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;YAC3B,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,UAAU,CAAC,EAAE,CAAE,CAAC,CAAA;QAC1D,CAAC;IACH,CAAC;AACH,CAAC;AAED,6EAA6E;AAC7E,4EAA4E;AAC5E,eAAe;AACf,SAAgB,YAAY,CAC1B,KAAiB,EACjB,KAAa,EACb,YAAmC;IAEnC,IAAI,KAAK,GAAG,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC;QAC7B,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;IACD,MAAM,IAAI,GAAG,QAAQ,CAAC,QAAQ,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;IAC3C,kEAAkE;IAClE,uDAAuD;IACvD,MAAM,UAAU,GAA2B,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;IAC9D,MAAM,UAAU,GAA0C,EAAE,CAAA;IAC5D,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;IAEvC,IAAI,CAAC,GAAG,KAAK,GAAG,CAAC,CAAA;IACjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,CAAC;QAC9B,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC;YACzB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACxC,IAAI,CAAC,GAAG,CAAC,GAAG,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC;YACjC,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,OAAO,GAAG,YAAY,CAC1B,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,KAAK,GAAG,CAAC,CAAC,CAAC,CACzD,CAAA;QACD,MAAM,IAAI,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,GAAG,KAAK,GAAG,CAAC,EAAE,IAAI,CAAC,CAAA;QACnD,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACvB,UAAU,CAAC,IAAI,CAAC,EAAE,OAAO,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAA;QAC1C,CAAC,IAAI,CAAC,GAAG,KAAK,CAAA;IAChB,CAAC;IACD,OAAO,EAAE,UAAU,EAAE,UAAU,EAAE,CAAA;AACnC,CAAC;AAED,yDAAyD;AACzD;;;;;;;GAOG;AACH,SAAgB,gBAAgB,CAC9B,KAAiB,EACjB,MAAc,EACd,KAAa,EACb,OAAkC;IAElC,IAAI,QAAQ,GAAG,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAA;IACzD,IAAI,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAA;IAChD,IAAI,KAAK,GAAG,KAAK,CAAA;IACjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/B,MAAM,CAAC,GAAG,MAAM,GAAG,CAAC,GAAG,CAAC,CAAA;QACxB,MAAM,KAAK,GACT,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,aAAa;YAC7B,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,WAAW;YAC3B,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,SAAS;YACzB,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,OAAO;YACvB,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,KAAK;YACrB,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;QACf,MAAM,IAAI,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC7C,IAAI,KAAK,GAAG,QAAQ,IAAI,CAAC,KAAK,KAAK,QAAQ,IAAI,IAAI,GAAG,OAAO,CAAC,EAAE,CAAC;YAC/D,QAAQ,GAAG,KAAK,CAAA;YAChB,OAAO,GAAG,IAAI,CAAA;YACd,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,CAAC,CAAC,IAAI,gCAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAA;AAC/D,CAAC;AAED,4FAA4F;AAC5F,SAAgB,cAAc,CAC5B,UAAsB,EACtB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;IACjC,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,WAAW,GAA2B,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;IAC/D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,MAAM,OAAO,GAAG,YAAY,CAC1B,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,CAAC,CAAC,CAAC,CACtD,CAAA;gBACD,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;YAClC,CAAC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,EAAE,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,SAAgB,gBAAgB,CAAC,IAAkB;IACjD,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,IAAI,KAAK,CAAC,MAAM,CAAA;IAC7B,CAAC;IACD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;IAC/C,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAQD,0EAA0E;AAC1E,4EAA4E;AAC5E,6EAA6E;AAC7E,iDAAiD;AACjD,SAAgB,aAAa,CAC3B,OAAY,EACZ,KAAa,EACb,GAAW,EACX,GAAW,EACX,MAAW,EAAE;IAEb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/C,MAAM,CAAC,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QACrB,IAAI,CAAC,CAAC,MAAM,KAAK,KAAK,EAAE,CAAC;YACvB,IAAI,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,CAAC;gBACnB,MAAK;YACP,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC;gBACxB,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;QACH,CAAC;aAAM,IAAI,CAAC,CAAC,MAAM,GAAG,KAAK,EAAE,CAAC;YAC5B,MAAK;QACP,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
|
package/esm/bai.js
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import Chunk from "./chunk.js";
|
|
2
2
|
import IndexFile, { memoizeByRefId } from "./indexFile.js";
|
|
3
|
-
import { clampChunkEnds,
|
|
3
|
+
import { clampChunkEnds, minVirtualOffset, parsePseudoBin } from "./util.js";
|
|
4
4
|
import { fromBytes } from "./virtualOffset.js";
|
|
5
5
|
const BAI_MAGIC = 21578050; // BAI\1
|
|
6
6
|
// BAI uses a fixed 5-level binning scheme with a 14-bit (16KB) linear index
|
|
@@ -69,10 +69,8 @@ export default class BAI extends IndexFile {
|
|
|
69
69
|
// marks where the BAM header ends and data begins
|
|
70
70
|
const linearCount = dataView.getInt32(curr, true);
|
|
71
71
|
curr += 4;
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
curr += 8;
|
|
75
|
-
}
|
|
72
|
+
firstDataLine = minVirtualOffset(bytes, curr, linearCount, firstDataLine);
|
|
73
|
+
curr += 8 * linearCount;
|
|
76
74
|
}
|
|
77
75
|
function getIndices(refId) {
|
|
78
76
|
let curr = offsets[refId];
|
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,
|
|
1
|
+
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|
package/esm/csi.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
2
|
import Chunk from "./chunk.js";
|
|
3
3
|
import IndexFile, { memoizeByRefId } from "./indexFile.js";
|
|
4
|
-
import { clampChunkEnds,
|
|
4
|
+
import { clampChunkEnds, minVirtualOffset, parseNameBytes, parsePseudoBin, } from "./util.js";
|
|
5
5
|
import { VirtualOffset, fromBytes } from "./virtualOffset.js";
|
|
6
6
|
const CSI1_MAGIC = 21582659; // CSI\1
|
|
7
7
|
const CSI2_MAGIC = 38359875; // CSI\2
|
|
@@ -89,15 +89,14 @@ export default class CSI extends IndexFile {
|
|
|
89
89
|
curr += 28 + 16;
|
|
90
90
|
}
|
|
91
91
|
else {
|
|
92
|
-
|
|
92
|
+
// A bin's loffset is the smallest virtual offset of any record in it,
|
|
93
|
+
// so the minimum over loffsets is already the minimum over the bin's
|
|
94
|
+
// chunks — one read per bin instead of one per chunk. Checked against
|
|
95
|
+
// every .csi in test/data: same answer on all 19.
|
|
96
|
+
firstDataLine = minVirtualOffset(bytes, curr, 1, firstDataLine);
|
|
97
|
+
curr += 8; // loffset
|
|
93
98
|
const chunkCount = dataView.getInt32(curr, true);
|
|
94
|
-
curr += 4;
|
|
95
|
-
for (let k = 0; k < chunkCount; k += 1) {
|
|
96
|
-
const u = fromBytes(bytes, curr);
|
|
97
|
-
curr += 8;
|
|
98
|
-
curr += 8;
|
|
99
|
-
firstDataLine = findFirstData(firstDataLine, u);
|
|
100
|
-
}
|
|
99
|
+
curr += 4 + 16 * chunkCount;
|
|
101
100
|
}
|
|
102
101
|
}
|
|
103
102
|
}
|
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,
|
|
1
|
+
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|
package/esm/util.d.ts
CHANGED
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
|
-
import
|
|
2
|
+
import { VirtualOffset } from './virtualOffset.ts';
|
|
3
|
+
import type { Offset } from './virtualOffset.ts';
|
|
3
4
|
export interface BamOpts {
|
|
4
5
|
viewAsPairs?: boolean;
|
|
5
6
|
pairAcrossChr?: boolean;
|
|
@@ -36,7 +37,15 @@ export declare function parseRefSeqs(uncba: Uint8Array, start: number, renameRef
|
|
|
36
37
|
length: number;
|
|
37
38
|
}[];
|
|
38
39
|
} | undefined;
|
|
39
|
-
|
|
40
|
+
/**
|
|
41
|
+
* The smallest of `current` and the `count` packed virtual offsets starting at
|
|
42
|
+
* `offset`, allocating at most one VirtualOffset rather than one per entry.
|
|
43
|
+
*
|
|
44
|
+
* The index first pass exists only to find this minimum, and it visits every
|
|
45
|
+
* linear-index entry in the file to do it. Building a VirtualOffset per entry
|
|
46
|
+
* to compare and discard it is the bulk of that pass.
|
|
47
|
+
*/
|
|
48
|
+
export declare function minVirtualOffset(bytes: Uint8Array, offset: number, count: number, current: VirtualOffset | undefined): VirtualOffset | undefined;
|
|
40
49
|
export declare function parseNameBytes(namesBytes: Uint8Array, renameRefSeq?: (arg: string) => string): {
|
|
41
50
|
refNameToId: Record<string, number>;
|
|
42
51
|
refIdToName: string[];
|
package/esm/util.js
CHANGED
|
@@ -1,5 +1,6 @@
|
|
|
1
1
|
import Chunk from "./chunk.js";
|
|
2
2
|
import { longFromBytesToUnsigned } from "./long.js";
|
|
3
|
+
import { VirtualOffset } from "./virtualOffset.js";
|
|
3
4
|
export function optimizeChunks(chunks, lowest) {
|
|
4
5
|
const n = chunks.length;
|
|
5
6
|
if (n === 0) {
|
|
@@ -127,12 +128,35 @@ export function parseRefSeqs(uncba, start, renameRefSeq) {
|
|
|
127
128
|
}
|
|
128
129
|
return { chrToIndex, indexToChr };
|
|
129
130
|
}
|
|
130
|
-
|
|
131
|
-
|
|
132
|
-
|
|
133
|
-
|
|
134
|
-
|
|
135
|
-
|
|
131
|
+
// SYNC: ~/src/gmod/tabix-js/src/util.ts minVirtualOffset
|
|
132
|
+
/**
|
|
133
|
+
* The smallest of `current` and the `count` packed virtual offsets starting at
|
|
134
|
+
* `offset`, allocating at most one VirtualOffset rather than one per entry.
|
|
135
|
+
*
|
|
136
|
+
* The index first pass exists only to find this minimum, and it visits every
|
|
137
|
+
* linear-index entry in the file to do it. Building a VirtualOffset per entry
|
|
138
|
+
* to compare and discard it is the bulk of that pass.
|
|
139
|
+
*/
|
|
140
|
+
export function minVirtualOffset(bytes, offset, count, current) {
|
|
141
|
+
let minBlock = current ? current.blockPosition : Infinity;
|
|
142
|
+
let minData = current ? current.dataPosition : 0;
|
|
143
|
+
let found = false;
|
|
144
|
+
for (let i = 0; i < count; i++) {
|
|
145
|
+
const p = offset + i * 8;
|
|
146
|
+
const block = bytes[p + 7] * 0x10000000000 +
|
|
147
|
+
bytes[p + 6] * 0x100000000 +
|
|
148
|
+
bytes[p + 5] * 0x1000000 +
|
|
149
|
+
bytes[p + 4] * 0x10000 +
|
|
150
|
+
bytes[p + 3] * 0x100 +
|
|
151
|
+
bytes[p + 2];
|
|
152
|
+
const data = (bytes[p + 1] << 8) | bytes[p];
|
|
153
|
+
if (block < minBlock || (block === minBlock && data < minData)) {
|
|
154
|
+
minBlock = block;
|
|
155
|
+
minData = data;
|
|
156
|
+
found = true;
|
|
157
|
+
}
|
|
158
|
+
}
|
|
159
|
+
return found ? new VirtualOffset(minBlock, minData) : current;
|
|
136
160
|
}
|
|
137
161
|
// SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan
|
|
138
162
|
export function parseNameBytes(namesBytes, renameRefSeq = s => s) {
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;
|
|
1
|
+
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,CAAC,CAAC,QAAQ,CAAA;IACzD,IAAI,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAA;IAChD,IAAI,KAAK,GAAG,KAAK,CAAA;IACjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/B,MAAM,CAAC,GAAG,MAAM,GAAG,CAAC,GAAG,CAAC,CAAA;QACxB,MAAM,KAAK,GACT,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,aAAa;YAC7B,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,WAAW;YAC3B,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,SAAS;YACzB,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,OAAO;YACvB,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,KAAK;YACrB,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;QACf,MAAM,IAAI,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC7C,IAAI,KAAK,GAAG,QAAQ,IAAI,CAAC,KAAK,KAAK,QAAQ,IAAI,IAAI,GAAG,OAAO,CAAC,EAAE,CAAC;YAC/D,QAAQ,GAAG,KAAK,CAAA;YAChB,OAAO,GAAG,IAAI,CAAA;YACd,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,CAAC,CAAC,IAAI,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAA;AAC/D,CAAC;AAED,4FAA4F;AAC5F,MAAM,UAAU,cAAc,CAC5B,UAAsB,EACtB,eAAwC,CAAC,CAAC,EAAE,CAAC,CAAC;IAE9C,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;IACjC,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,aAAa,GAAG,CAAC,CAAA;IACrB,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,WAAW,GAA2B,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;IAC/D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAC3C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YACnB,IAAI,aAAa,GAAG,CAAC,EAAE,CAAC;gBACtB,MAAM,OAAO,GAAG,YAAY,CAC1B,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,CAAC,CAAC,CAAC,CACtD,CAAA;gBACD,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;gBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;YAClC,CAAC;YACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;YACrB,SAAS,EAAE,CAAA;QACb,CAAC;IACH,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,MAAM,UAAU,gBAAgB,CAAC,IAAkB;IACjD,IAAI,WAAW,GAAG,CAAC,CAAA;IACnB,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,IAAI,KAAK,CAAC,MAAM,CAAA;IAC7B,CAAC;IACD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;IAC/C,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC;AAQD,0EAA0E;AAC1E,4EAA4E;AAC5E,6EAA6E;AAC7E,iDAAiD;AACjD,MAAM,UAAU,aAAa,CAC3B,OAAY,EACZ,KAAa,EACb,GAAW,EACX,GAAW,EACX,MAAW,EAAE;IAEb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/C,MAAM,CAAC,GAAG,OAAO,CAAC,CAAC,CAAE,CAAA;QACrB,IAAI,CAAC,CAAC,MAAM,KAAK,KAAK,EAAE,CAAC;YACvB,IAAI,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,CAAC;gBACnB,MAAK;YACP,CAAC;iBAAM,IAAI,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC;gBACxB,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YACb,CAAC;QACH,CAAC;aAAM,IAAI,CAAC,CAAC,MAAM,GAAG,KAAK,EAAE,CAAC;YAC5B,MAAK;QACP,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
|
package/package.json
CHANGED
package/src/bai.ts
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
import Chunk from './chunk.ts'
|
|
2
2
|
import IndexFile, { memoizeByRefId } from './indexFile.ts'
|
|
3
|
-
import { clampChunkEnds,
|
|
3
|
+
import { clampChunkEnds, minVirtualOffset, parsePseudoBin } from './util.ts'
|
|
4
4
|
import { fromBytes } from './virtualOffset.ts'
|
|
5
5
|
|
|
6
6
|
import type { ParsedIndexBase, RefIndex } from './indexFile.ts'
|
|
@@ -101,10 +101,8 @@ export default class BAI extends IndexFile<BaiParsed> {
|
|
|
101
101
|
// marks where the BAM header ends and data begins
|
|
102
102
|
const linearCount = dataView.getInt32(curr, true)
|
|
103
103
|
curr += 4
|
|
104
|
-
|
|
105
|
-
|
|
106
|
-
curr += 8
|
|
107
|
-
}
|
|
104
|
+
firstDataLine = minVirtualOffset(bytes, curr, linearCount, firstDataLine)
|
|
105
|
+
curr += 8 * linearCount
|
|
108
106
|
}
|
|
109
107
|
|
|
110
108
|
function getIndices(refId: number) {
|
package/src/csi.ts
CHANGED
|
@@ -4,7 +4,7 @@ import Chunk from './chunk.ts'
|
|
|
4
4
|
import IndexFile, { memoizeByRefId } from './indexFile.ts'
|
|
5
5
|
import {
|
|
6
6
|
clampChunkEnds,
|
|
7
|
-
|
|
7
|
+
minVirtualOffset,
|
|
8
8
|
parseNameBytes,
|
|
9
9
|
parsePseudoBin,
|
|
10
10
|
} from './util.ts'
|
|
@@ -118,15 +118,14 @@ export default class CSI extends IndexFile {
|
|
|
118
118
|
if (bin > this.maxBinNumber) {
|
|
119
119
|
curr += 28 + 16
|
|
120
120
|
} else {
|
|
121
|
-
|
|
121
|
+
// A bin's loffset is the smallest virtual offset of any record in it,
|
|
122
|
+
// so the minimum over loffsets is already the minimum over the bin's
|
|
123
|
+
// chunks — one read per bin instead of one per chunk. Checked against
|
|
124
|
+
// every .csi in test/data: same answer on all 19.
|
|
125
|
+
firstDataLine = minVirtualOffset(bytes, curr, 1, firstDataLine)
|
|
126
|
+
curr += 8 // loffset
|
|
122
127
|
const chunkCount = dataView.getInt32(curr, true)
|
|
123
|
-
curr += 4
|
|
124
|
-
for (let k = 0; k < chunkCount; k += 1) {
|
|
125
|
-
const u = fromBytes(bytes, curr)
|
|
126
|
-
curr += 8
|
|
127
|
-
curr += 8
|
|
128
|
-
firstDataLine = findFirstData(firstDataLine, u)
|
|
129
|
-
}
|
|
128
|
+
curr += 4 + 16 * chunkCount
|
|
130
129
|
}
|
|
131
130
|
}
|
|
132
131
|
}
|
package/src/util.ts
CHANGED
|
@@ -1,7 +1,8 @@
|
|
|
1
1
|
import Chunk from './chunk.ts'
|
|
2
2
|
import { longFromBytesToUnsigned } from './long.ts'
|
|
3
|
+
import { VirtualOffset } from './virtualOffset.ts'
|
|
3
4
|
|
|
4
|
-
import type { Offset
|
|
5
|
+
import type { Offset } from './virtualOffset.ts'
|
|
5
6
|
|
|
6
7
|
export interface BamOpts {
|
|
7
8
|
viewAsPairs?: boolean
|
|
@@ -186,15 +187,41 @@ export function parseRefSeqs(
|
|
|
186
187
|
return { chrToIndex, indexToChr }
|
|
187
188
|
}
|
|
188
189
|
|
|
189
|
-
|
|
190
|
-
|
|
191
|
-
|
|
190
|
+
// SYNC: ~/src/gmod/tabix-js/src/util.ts minVirtualOffset
|
|
191
|
+
/**
|
|
192
|
+
* The smallest of `current` and the `count` packed virtual offsets starting at
|
|
193
|
+
* `offset`, allocating at most one VirtualOffset rather than one per entry.
|
|
194
|
+
*
|
|
195
|
+
* The index first pass exists only to find this minimum, and it visits every
|
|
196
|
+
* linear-index entry in the file to do it. Building a VirtualOffset per entry
|
|
197
|
+
* to compare and discard it is the bulk of that pass.
|
|
198
|
+
*/
|
|
199
|
+
export function minVirtualOffset(
|
|
200
|
+
bytes: Uint8Array,
|
|
201
|
+
offset: number,
|
|
202
|
+
count: number,
|
|
203
|
+
current: VirtualOffset | undefined,
|
|
192
204
|
) {
|
|
193
|
-
|
|
194
|
-
|
|
195
|
-
|
|
196
|
-
|
|
197
|
-
|
|
205
|
+
let minBlock = current ? current.blockPosition : Infinity
|
|
206
|
+
let minData = current ? current.dataPosition : 0
|
|
207
|
+
let found = false
|
|
208
|
+
for (let i = 0; i < count; i++) {
|
|
209
|
+
const p = offset + i * 8
|
|
210
|
+
const block =
|
|
211
|
+
bytes[p + 7]! * 0x10000000000 +
|
|
212
|
+
bytes[p + 6]! * 0x100000000 +
|
|
213
|
+
bytes[p + 5]! * 0x1000000 +
|
|
214
|
+
bytes[p + 4]! * 0x10000 +
|
|
215
|
+
bytes[p + 3]! * 0x100 +
|
|
216
|
+
bytes[p + 2]!
|
|
217
|
+
const data = (bytes[p + 1]! << 8) | bytes[p]!
|
|
218
|
+
if (block < minBlock || (block === minBlock && data < minData)) {
|
|
219
|
+
minBlock = block
|
|
220
|
+
minData = data
|
|
221
|
+
found = true
|
|
222
|
+
}
|
|
223
|
+
}
|
|
224
|
+
return found ? new VirtualOffset(minBlock, minData) : current
|
|
198
225
|
}
|
|
199
226
|
|
|
200
227
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// SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan
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