@gmod/bam 7.5.0 → 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/bamFile.d.ts +12 -6
- package/dist/bamFile.js +110 -24
- package/dist/bamFile.js.map +1 -1
- package/dist/csi.js +7 -8
- package/dist/csi.js.map +1 -1
- package/dist/record.d.ts +1 -5
- package/dist/record.js +12 -6
- package/dist/record.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/bamFile.d.ts +12 -6
- package/esm/bamFile.js +110 -24
- package/esm/bamFile.js.map +1 -1
- package/esm/csi.js +8 -9
- package/esm/csi.js.map +1 -1
- package/esm/record.d.ts +1 -5
- package/esm/record.js +12 -6
- package/esm/record.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/bamFile.ts +132 -26
- package/src/csi.ts +8 -9
- package/src/record.ts +18 -6
- package/src/util.ts +36 -9
package/dist/util.js
CHANGED
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@@ -7,12 +7,13 @@ exports.optimizeChunks = optimizeChunks;
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7
7
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exports.parsePseudoBin = parsePseudoBin;
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8
8
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exports.clampChunkEnds = clampChunkEnds;
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9
9
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exports.parseRefSeqs = parseRefSeqs;
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10
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-
exports.
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10
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+
exports.minVirtualOffset = minVirtualOffset;
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11
11
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exports.parseNameBytes = parseNameBytes;
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12
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exports.concatUint8Array = concatUint8Array;
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exports.appendInRange = appendInRange;
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const chunk_ts_1 = __importDefault(require("./chunk.js"));
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15
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const long_ts_1 = require("./long.js");
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16
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+
const virtualOffset_ts_1 = require("./virtualOffset.js");
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function optimizeChunks(chunks, lowest) {
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const n = chunks.length;
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if (n === 0) {
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@@ -140,12 +141,35 @@ function parseRefSeqs(uncba, start, renameRefSeq) {
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}
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return { chrToIndex, indexToChr };
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}
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-
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-
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-
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-
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-
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-
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+
// SYNC: ~/src/gmod/tabix-js/src/util.ts minVirtualOffset
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145
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/**
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146
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* The smallest of `current` and the `count` packed virtual offsets starting at
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147
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* `offset`, allocating at most one VirtualOffset rather than one per entry.
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148
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*
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* The index first pass exists only to find this minimum, and it visits every
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150
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* linear-index entry in the file to do it. Building a VirtualOffset per entry
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151
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* to compare and discard it is the bulk of that pass.
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*/
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+
function minVirtualOffset(bytes, offset, count, current) {
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let minBlock = current ? current.blockPosition : Infinity;
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let minData = current ? current.dataPosition : 0;
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let found = false;
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for (let i = 0; i < count; i++) {
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const p = offset + i * 8;
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const block = bytes[p + 7] * 0x10000000000 +
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bytes[p + 6] * 0x100000000 +
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bytes[p + 5] * 0x1000000 +
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bytes[p + 4] * 0x10000 +
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bytes[p + 3] * 0x100 +
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bytes[p + 2];
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const data = (bytes[p + 1] << 8) | bytes[p];
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if (block < minBlock || (block === minBlock && data < minData)) {
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minBlock = block;
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minData = data;
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found = true;
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}
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}
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return found ? new virtualOffset_ts_1.VirtualOffset(minBlock, minData) : current;
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}
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// SYNC: ~/src/gmod/tabix-js/src/util.ts parseNameBytes uses indexOf(0) instead of byte scan
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function parseNameBytes(namesBytes, renameRefSeq = s => s) {
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package/dist/util.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;
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1
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+
{"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"}
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package/esm/bai.js
CHANGED
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@@ -1,6 +1,6 @@
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import Chunk from "./chunk.js";
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import IndexFile, { memoizeByRefId } from "./indexFile.js";
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import { clampChunkEnds,
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import { clampChunkEnds, minVirtualOffset, parsePseudoBin } from "./util.js";
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import { fromBytes } from "./virtualOffset.js";
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const BAI_MAGIC = 21578050; // BAI\1
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// BAI uses a fixed 5-level binning scheme with a 14-bit (16KB) linear index
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@@ -69,10 +69,8 @@ export default class BAI extends IndexFile {
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// marks where the BAM header ends and data begins
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const linearCount = dataView.getInt32(curr, true);
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curr += 4;
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curr += 8;
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}
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firstDataLine = minVirtualOffset(bytes, curr, linearCount, firstDataLine);
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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];
|
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
|
+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC5E,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;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,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAoB;IACnD,KAAK,CAAC,MAAM,CAAC,IAAc;QACzB,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,0BAA0B;QAC1B,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC3C,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,QAAQ,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnD,+CAA+C;QAC/C,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,aAAwC,CAAA;QAE5C,MAAM,OAAO,GAAG,EAAc,CAAA;QAC9B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAE9C,IAAI,IAAI,CAAC,CAAA;YAET,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,IAAI,IAAI,CAAC,CAAA;wBACT,IAAI,IAAI,CAAC,CAAA;oBACX,CAAC;gBACH,CAAC;YACH,CAAC;YAED,mEAAmE;YACnE,kDAAkD;YAClD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,aAAa,GAAG,gBAAgB,CAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,CAAC,CAAA;YACzE,IAAI,IAAI,CAAC,GAAG,WAAW,CAAA;QACzB,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,IAAI,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YACzB,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;gBACvB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,KAAK,CAAA;YAET,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAE5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,KAAK,QAAQ,GAAG,CAAC,EAAE,CAAC;oBACzB,IAAI,IAAI,CAAC,CAAA;oBACT,KAAK,GAAG,cAAc,CAAC,KAAK,EAAE,IAAI,GAAG,EAAE,CAAC,CAAA;oBACxC,IAAI,IAAI,EAAE,CAAA;gBACZ,CAAC;qBAAM,IAAI,GAAG,GAAG,QAAQ,GAAG,CAAC,EAAE,CAAC;oBAC9B,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;gBACrE,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,CAAA;oBACT,MAAM,MAAM,GAAG,IAAI,KAAK,CAAQ,UAAU,CAAC,CAAA;oBAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,MAAM,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,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;gBACvC,IAAI,IAAI,CAAC,CAAA;YACX,CAAC;YAED,cAAc,CACZ,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,cAAc,CAAC,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"}
|
package/esm/bamFile.d.ts
CHANGED
|
@@ -2,7 +2,6 @@ import BAI from './bai.ts';
|
|
|
2
2
|
import CSI from './csi.ts';
|
|
3
3
|
import BAMFeature from './record.ts';
|
|
4
4
|
import type Chunk from './chunk.ts';
|
|
5
|
-
import type { Bytes } from './record.ts';
|
|
6
5
|
import type { BamOpts, BaseOpts } from './util.ts';
|
|
7
6
|
import type { GenericFilehandle } from 'generic-filehandle2';
|
|
8
7
|
export interface BamRecordLike {
|
|
@@ -16,11 +15,7 @@ export interface BamRecordLike {
|
|
|
16
15
|
flags: number;
|
|
17
16
|
tags: Record<string, unknown>;
|
|
18
17
|
}
|
|
19
|
-
export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (
|
|
20
|
-
bytes: Bytes;
|
|
21
|
-
fileOffset: number;
|
|
22
|
-
dataView: DataView;
|
|
23
|
-
}) => T;
|
|
18
|
+
export type BamRecordClass<T extends BamRecordLike = BAMFeature> = new (byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView) => T;
|
|
24
19
|
export declare const BAM_MAGIC = 21840194;
|
|
25
20
|
interface ChunkEntry<T> {
|
|
26
21
|
bytes: number;
|
|
@@ -53,6 +48,7 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
53
48
|
htsget: boolean;
|
|
54
49
|
headerP?: ReturnType<BamFile<T>['getHeaderPre']>;
|
|
55
50
|
chunkFeatureCache: ChunkFeatureCache<T>;
|
|
51
|
+
private inFlightChunks;
|
|
56
52
|
private RecordClass;
|
|
57
53
|
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs, recordClass, maxCacheBytes, }: {
|
|
58
54
|
bamFilehandle?: GenericFilehandle;
|
|
@@ -86,7 +82,17 @@ export default class BamFile<T extends BamRecordLike = BAMFeature> {
|
|
|
86
82
|
}[] | undefined>;
|
|
87
83
|
getHeaderText(opts?: BaseOpts): Promise<string | undefined>;
|
|
88
84
|
private getSeqId;
|
|
85
|
+
/**
|
|
86
|
+
* Records overlapping `chr:min-max`.
|
|
87
|
+
*
|
|
88
|
+
* The returned records are CACHED AND SHARED — two queries resolving to the
|
|
89
|
+
* same chunk span get the same objects back, so treat them as read-only.
|
|
90
|
+
* Anything you want to attach for the duration of one query belongs on a
|
|
91
|
+
* wrapper you own, never on the record; writing a field here silently rebinds
|
|
92
|
+
* it for every other query still holding that read. See ADR 0006.
|
|
93
|
+
*/
|
|
89
94
|
getRecordsForRange(chr: string, min: number, max: number, opts?: BamOpts): Promise<T[]>;
|
|
95
|
+
private _startChunkRead;
|
|
90
96
|
private _cachedChunkFeatures;
|
|
91
97
|
private _fetchChunkFeatures;
|
|
92
98
|
fetchPairs(chrId: number, records: T[], opts: BamOpts): Promise<T[]>;
|
package/esm/bamFile.js
CHANGED
|
@@ -25,6 +25,10 @@ function chunkCacheKey(chunk) {
|
|
|
25
25
|
// the *only* bound: a query keeps every chunk it parsed, since a chunk dropped
|
|
26
26
|
// here costs a re-download and re-decompress the next time the view moves.
|
|
27
27
|
export const DEFAULT_MAX_CACHE_BYTES = 100 * 1024 * 1024;
|
|
28
|
+
// How many of a query's chunks to read at once. Six is the HTTP/1.1
|
|
29
|
+
// per-host connection cap browsers enforce, so going much above it buys
|
|
30
|
+
// nothing on the transport that matters and only widens peak memory.
|
|
31
|
+
const MAX_CONCURRENT_CHUNK_READS = 6;
|
|
28
32
|
class ChunkFeatureCache {
|
|
29
33
|
maxBytes;
|
|
30
34
|
entries = new Map();
|
|
@@ -85,6 +89,10 @@ export default class BamFile {
|
|
|
85
89
|
headerP;
|
|
86
90
|
// Cache for parsed features by chunk, bounded by decompressed bytes
|
|
87
91
|
chunkFeatureCache;
|
|
92
|
+
// Chunks currently being read, so concurrent queries share one decompress
|
|
93
|
+
// instead of racing. Entries live only until the read settles; the resolved
|
|
94
|
+
// features land in chunkFeatureCache.
|
|
95
|
+
inFlightChunks = new Map();
|
|
88
96
|
RecordClass;
|
|
89
97
|
constructor({ bamFilehandle, bamPath, bamUrl, baiPath, baiFilehandle, baiUrl, csiPath, csiFilehandle, csiUrl, htsget, renameRefSeqs = n => n, recordClass, maxCacheBytes = DEFAULT_MAX_CACHE_BYTES, }) {
|
|
90
98
|
this.renameRefSeq = renameRefSeqs;
|
|
@@ -171,6 +179,15 @@ export default class BamFile {
|
|
|
171
179
|
await this.getHeader(opts);
|
|
172
180
|
return this.chrToIndex?.[seqName];
|
|
173
181
|
}
|
|
182
|
+
/**
|
|
183
|
+
* Records overlapping `chr:min-max`.
|
|
184
|
+
*
|
|
185
|
+
* The returned records are CACHED AND SHARED — two queries resolving to the
|
|
186
|
+
* same chunk span get the same objects back, so treat them as read-only.
|
|
187
|
+
* Anything you want to attach for the duration of one query belongs on a
|
|
188
|
+
* wrapper you own, never on the record; writing a field here silently rebinds
|
|
189
|
+
* it for every other query still holding that read. See ADR 0006.
|
|
190
|
+
*/
|
|
174
191
|
async getRecordsForRange(chr, min, max, opts) {
|
|
175
192
|
const chrId = await this.getSeqId(chr, opts);
|
|
176
193
|
if (chrId === undefined || !this.index) {
|
|
@@ -179,18 +196,65 @@ export default class BamFile {
|
|
|
179
196
|
const chunks = await this.index.blocksForRange(chrId, min - 1, max, opts);
|
|
180
197
|
return this._fetchChunkFeatures(chunks, chrId, min, max, opts);
|
|
181
198
|
}
|
|
199
|
+
// Read a chunk, publish it to the cache, and keep the in-flight promise
|
|
200
|
+
// discoverable while it runs.
|
|
201
|
+
_startChunkRead(cacheKey, chunk, opts) {
|
|
202
|
+
const promise = this._readChunkFeatures(chunk, opts).then(entry => {
|
|
203
|
+
this.chunkFeatureCache.set(cacheKey, entry);
|
|
204
|
+
return entry;
|
|
205
|
+
});
|
|
206
|
+
const inFlight = { promise, signal: opts.signal };
|
|
207
|
+
this.inFlightChunks.set(cacheKey, inFlight);
|
|
208
|
+
// Only clear our own entry: a retry may already have replaced it. `.then(f,
|
|
209
|
+
// f)` rather than `.finally(f)` so the handler's own promise never carries
|
|
210
|
+
// an unhandled rejection.
|
|
211
|
+
const clear = () => {
|
|
212
|
+
if (this.inFlightChunks.get(cacheKey) === inFlight) {
|
|
213
|
+
this.inFlightChunks.delete(cacheKey);
|
|
214
|
+
}
|
|
215
|
+
};
|
|
216
|
+
promise.then(clear, clear);
|
|
217
|
+
return promise;
|
|
218
|
+
}
|
|
182
219
|
// Parsed records for a chunk, reading and decompressing it only on a miss.
|
|
183
220
|
// Every path that wants a chunk's features goes through here — mate lookups
|
|
184
221
|
// included, since a viewAsPairs query revisits the same mate chunks each time
|
|
185
222
|
// the view moves.
|
|
223
|
+
//
|
|
224
|
+
// This hands the SAME record objects to every query that hits the key, which
|
|
225
|
+
// is what makes callers' per-query writes onto a record leak across queries
|
|
226
|
+
// (ADR 0006). Caching the inflated buffer and re-scanning per query would give
|
|
227
|
+
// each caller its own objects, but roughly doubles a warm query on dense data
|
|
228
|
+
// — measured, and rejected, in that ADR.
|
|
186
229
|
async _cachedChunkFeatures(chunk, opts) {
|
|
187
230
|
const cacheKey = chunkCacheKey(chunk);
|
|
188
|
-
|
|
189
|
-
if (
|
|
190
|
-
|
|
191
|
-
|
|
231
|
+
const cached = this.chunkFeatureCache.get(cacheKey);
|
|
232
|
+
if (cached) {
|
|
233
|
+
return cached.features;
|
|
234
|
+
}
|
|
235
|
+
// Join a read already running for this chunk rather than decompressing it a
|
|
236
|
+
// second time. jbrowse fetches a row of adjacent blocks concurrently and
|
|
237
|
+
// they collapse onto very few chunk keys, so without this a query pays for
|
|
238
|
+
// the same inflate several times over — the dominant cost of a cold query
|
|
239
|
+
// (ADR 0003).
|
|
240
|
+
const pending = this.inFlightChunks.get(cacheKey);
|
|
241
|
+
if (!pending) {
|
|
242
|
+
return (await this._startChunkRead(cacheKey, chunk, opts)).features;
|
|
243
|
+
}
|
|
244
|
+
try {
|
|
245
|
+
return (await pending.promise).features;
|
|
246
|
+
}
|
|
247
|
+
catch (e) {
|
|
248
|
+
// The read we joined was started by another caller. If that caller
|
|
249
|
+
// aborted and we did not, the failure is theirs and says nothing about
|
|
250
|
+
// our query, so start over — which picks up the cache, joins a sibling's
|
|
251
|
+
// retry, or reads under our own signal. Any other failure (and our own
|
|
252
|
+
// abort) propagates as it would have without sharing.
|
|
253
|
+
if (!pending.signal?.aborted || opts.signal?.aborted) {
|
|
254
|
+
throw e;
|
|
255
|
+
}
|
|
256
|
+
return this._cachedChunkFeatures(chunk, opts);
|
|
192
257
|
}
|
|
193
|
-
return entry.features;
|
|
194
258
|
}
|
|
195
259
|
async _fetchChunkFeatures(chunks, chrId, min, max, opts = {}) {
|
|
196
260
|
const { viewAsPairs, onProgress } = opts;
|
|
@@ -201,12 +265,42 @@ export default class BamFile {
|
|
|
201
265
|
}
|
|
202
266
|
let downloadedBytes = 0;
|
|
203
267
|
onProgress?.(0, totalBytes);
|
|
268
|
+
const featureLists = new Array(chunks.length);
|
|
269
|
+
if (chunks.length === 1) {
|
|
270
|
+
// Very common — most small files, and any query landing inside one bin.
|
|
271
|
+
// Worth its own path: the pool below allocates a closure, a worker array
|
|
272
|
+
// and a Promise.all, all of which is pure overhead for one chunk and
|
|
273
|
+
// measurable on queries that take ~0.2ms.
|
|
274
|
+
featureLists[0] = await this._cachedChunkFeatures(chunks[0], opts);
|
|
275
|
+
onProgress?.(totalBytes, totalBytes);
|
|
276
|
+
}
|
|
277
|
+
else {
|
|
278
|
+
// Fetch the chunks concurrently. A query routinely spans a dozen or more
|
|
279
|
+
// chunks (14.8 on average for a 20kb window on the test 18MB file) and
|
|
280
|
+
// each is its own range request, so reading them one after another costs
|
|
281
|
+
// a network round trip apiece — the dominant cost of a remote query, well
|
|
282
|
+
// ahead of decompression. Bounded because browsers cap concurrent
|
|
283
|
+
// connections per host anyway, and an unbounded fan-out would inflate
|
|
284
|
+
// every chunk of a whole-chromosome query at once.
|
|
285
|
+
let next = 0;
|
|
286
|
+
const readNext = async () => {
|
|
287
|
+
while (next < chunks.length) {
|
|
288
|
+
const ci = next++;
|
|
289
|
+
const chunk = chunks[ci];
|
|
290
|
+
featureLists[ci] = await this._cachedChunkFeatures(chunk, opts);
|
|
291
|
+
downloadedBytes += chunk.fetchedSize();
|
|
292
|
+
onProgress?.(downloadedBytes, totalBytes);
|
|
293
|
+
}
|
|
294
|
+
};
|
|
295
|
+
const workers = Math.min(MAX_CONCURRENT_CHUNK_READS, chunks.length);
|
|
296
|
+
await Promise.all(Array.from({ length: workers }, () => readNext()));
|
|
297
|
+
}
|
|
298
|
+
// Append in chunk order, not completion order, so the result is the same
|
|
299
|
+
// sequence a sequential walk produced. (That is not coordinate order — bins
|
|
300
|
+
// at different levels cover overlapping spans — but it is what every caller
|
|
301
|
+
// has always been handed.)
|
|
204
302
|
for (let ci = 0, cl = chunks.length; ci < cl; ci++) {
|
|
205
|
-
|
|
206
|
-
const features = await this._cachedChunkFeatures(chunk, opts);
|
|
207
|
-
downloadedBytes += chunk.fetchedSize();
|
|
208
|
-
onProgress?.(downloadedBytes, totalBytes);
|
|
209
|
-
appendInRange(features, chrId, min, max, result);
|
|
303
|
+
appendInRange(featureLists[ci], chrId, min, max, result);
|
|
210
304
|
}
|
|
211
305
|
if (viewAsPairs) {
|
|
212
306
|
const pairs = await this.fetchPairs(chrId, result, opts);
|
|
@@ -296,20 +390,12 @@ export default class BamFile {
|
|
|
296
390
|
}
|
|
297
391
|
}
|
|
298
392
|
if (blockEnd < ba.length) {
|
|
299
|
-
const feature = new this.RecordClass(
|
|
300
|
-
|
|
301
|
-
|
|
302
|
-
|
|
303
|
-
|
|
304
|
-
|
|
305
|
-
fileOffset: hasCpositions
|
|
306
|
-
? cpositions[pos] * (1 << 8) +
|
|
307
|
-
(blockStart - dpositions[pos]) +
|
|
308
|
-
chunk.minv.dataPosition +
|
|
309
|
-
1
|
|
310
|
-
: crc32(ba.subarray(blockStart, blockEnd)) >>> 0,
|
|
311
|
-
dataView,
|
|
312
|
-
});
|
|
393
|
+
const feature = new this.RecordClass(ba, blockStart, blockEnd, hasCpositions
|
|
394
|
+
? cpositions[pos] * (1 << 8) +
|
|
395
|
+
(blockStart - dpositions[pos]) +
|
|
396
|
+
chunk.minv.dataPosition +
|
|
397
|
+
1
|
|
398
|
+
: crc32(ba.subarray(blockStart, blockEnd)) >>> 0, dataView);
|
|
313
399
|
sink.push(feature);
|
|
314
400
|
}
|
|
315
401
|
blockStart = blockEnd + 1;
|
package/esm/bamFile.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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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
|
+
{"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,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,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,EAAE,CAAC;wBACvC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAA;wBAChC,IAAI,IAAI,CAAC,CAAA;wBACT,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;oBAClC,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YAED,cAAc,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAC9C,OAAO;gBACL,QAAQ;gBACR,KAAK,EAAE,cAAc;aACtB,CAAA;QACH,CAAC;QAED,OAAO;YACL,UAAU;YACV,aAAa;YACb,OAAO,EAAE,cAAc,CAAC,UAAU,CAAC;YACnC,QAAQ;YACR,GAAG,EAAE,IAAI;YACT,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,GAAG,GAAG;SACP,CAAA;IACH,CAAC;IAED,2EAA2E;IACjE,cAAc;QACtB,OAAO,WAAW,CAAA;IACpB,CAAC;IAED;;;;OAIG;IACH,gDAAgD;IACtC,QAAQ,CAAC,GAAW,EAAE,GAAW;QACzC,2EAA2E;QAC3E,wEAAwE;QACxE,MAAM,MAAM,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QACpD,IAAI,GAAG,GAAG,MAAM,EAAE,CAAC;YACjB,GAAG,GAAG,MAAM,CAAA;QACd,CAAC;QACD,GAAG,IAAI,CAAC,CAAA;QACR,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACtC,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,OAAO,CAAC,IAAI,IAAI,CAAC,KAAK,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YAC9D,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YAC5B,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE,CAAC;gBAC5C,MAAM,IAAI,KAAK,CACb,SAAS,GAAG,IAAI,GAAG,mDAAmD,IAAI,CAAC,QAAQ,WAAW,IAAI,CAAC,KAAK,0DAA0D,CACnK,CAAA;YACH,CAAC;YACD,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAU,CAAC,CAAA;QAC5B,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
|
package/esm/record.d.ts
CHANGED
|
@@ -16,11 +16,7 @@ export default class BamRecord {
|
|
|
16
16
|
private _cachedNumericCigar?;
|
|
17
17
|
private _cachedNUMERIC_MD?;
|
|
18
18
|
private _cachedSeqStart?;
|
|
19
|
-
constructor(
|
|
20
|
-
bytes: Bytes;
|
|
21
|
-
fileOffset: number;
|
|
22
|
-
dataView: DataView;
|
|
23
|
-
});
|
|
19
|
+
constructor(byteArray: Uint8Array, start: number, end: number, fileOffset: number, dataView: DataView);
|
|
24
20
|
get byteArray(): Uint8Array<ArrayBufferLike>;
|
|
25
21
|
get flags(): number;
|
|
26
22
|
get ref_id(): number;
|
package/esm/record.js
CHANGED
|
@@ -258,12 +258,18 @@ export default class BamRecord {
|
|
|
258
258
|
_cachedNumericCigar;
|
|
259
259
|
_cachedNUMERIC_MD;
|
|
260
260
|
_cachedSeqStart;
|
|
261
|
-
|
|
262
|
-
|
|
263
|
-
|
|
264
|
-
|
|
265
|
-
|
|
266
|
-
|
|
261
|
+
// Positional rather than an options object, because every argument is
|
|
262
|
+
// unpacked into a field immediately and nothing keeps the wrapper. The
|
|
263
|
+
// options form allocated two throwaway objects for each of the ~200k records
|
|
264
|
+
// a deep pileup decodes — the `{byteArray, start, end}` literal and the
|
|
265
|
+
// `{bytes, fileOffset, dataView}` around it — purely to be taken apart again
|
|
266
|
+
// one line later.
|
|
267
|
+
constructor(byteArray, start, end, fileOffset, dataView) {
|
|
268
|
+
this._byteArray = byteArray;
|
|
269
|
+
this._start = start;
|
|
270
|
+
this._end = end;
|
|
271
|
+
this.fileOffset = fileOffset;
|
|
272
|
+
this._dataView = dataView;
|
|
267
273
|
}
|
|
268
274
|
get byteArray() {
|
|
269
275
|
return this._byteArray;
|