@gmod/bam 7.7.0 → 7.7.1
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 +7 -2
- package/dist/bai.js.map +1 -1
- package/dist/util.js +22 -7
- package/dist/util.js.map +1 -1
- package/esm/bai.js +7 -2
- package/esm/bai.js.map +1 -1
- package/esm/util.js +22 -7
- package/esm/util.js.map +1 -1
- package/package.json +1 -1
- package/src/bai.ts +10 -2
- package/src/util.ts +22 -7
package/dist/bai.js
CHANGED
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@@ -40,6 +40,7 @@ const chunk_ts_1 = __importDefault(require("./chunk.js"));
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const indexFile_ts_1 = __importStar(require("./indexFile.js"));
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const util_ts_1 = require("./util.js");
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const virtualOffset_ts_1 = require("./virtualOffset.js");
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+
const EMPTY_POSITIONS = new Float64Array(0);
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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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// resolution. See SAMv1.pdf §5.1.3 (hts-specs).
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@@ -146,8 +147,12 @@ class BAI extends indexFile_ts_1.default {
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}
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const linearCount = dataView.getInt32(curr, true);
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curr += 4;
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-
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-
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+
// Share one empty array rather than allocating a pair per reference. An
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// assembly with tens of thousands of unplaced scaffolds (cho.bam.bai:
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// 28751 references, 205 linear entries between them) reaches here once
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+
// per reference, and almost every one of those has an empty linear index.
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const linearBlockPositions = linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount);
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+
const linearDataPositions = linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount);
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for (let j = 0; j < linearCount; j++) {
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// a virtual offset is a 48-bit block position in the high bytes and a
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// 16-bit data position in the low two
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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,uCAA4E;AAC5E,yDAA8C;
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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;AAmB9C,MAAM,eAAe,GAAG,IAAI,YAAY,CAAC,CAAC,CAAC,CAAA;AAM3C,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,wEAAwE;YACxE,sEAAsE;YACtE,uEAAuE;YACvE,0EAA0E;YAC1E,MAAM,oBAAoB,GACxB,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YACrE,MAAM,mBAAmB,GACvB,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YACrE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,sEAAsE;gBACtE,sCAAsC;gBACtC,oBAAoB,CAAC,CAAC,CAAC;oBACrB,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,aAAa;wBAChC,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,WAAW;wBAC9B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,SAAS;wBAC5B,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,OAAO;wBAC1B,KAAK,CAAC,IAAI,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package/dist/util.js
CHANGED
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@@ -96,17 +96,32 @@ function parsePseudoBin(bytes, offset) {
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// least the true block end, so the clamped fetch still contains the whole block.
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}
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// runs once per reference, and an assembly with tens of thousands of unplaced
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// scaffolds (cho.bam.bai has 28751 references) pays the allocation that many
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// times over, where each individual boundary list is a handful of entries.
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// The small-allocation cost dominates the faster typed sort by a wide margin
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// at that shape. Filling by index still avoids the intermediate array that
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// mapping the linear index to block positions used to build.
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// Pre-sized and filled by index. Measured against both alternatives on five
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// real .bai shapes (min of 21, interleaved, sign-stable over 3 runs):
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// building with push instead is 5-8% slower here, and a Float64Array is
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// faster to sort but allocates per reference, which costs 1.7x on an
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// assembly with 28751 scaffolds. Filling by index also avoids the
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// intermediate array that mapping the linear index used to build.
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const boundaries = new Array(extraBoundaries.length + chunks.length * 2);
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}
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boundaries.sort();
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boundaries.sort((a, b) => a - b);
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for (const c of chunks) {
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const max = c.maxv.blockPosition;
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// first boundary strictly greater than max
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package/dist/util.js.map
CHANGED
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{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;AA+BA,wCAsEC;AAKD,wCAcC;AASD,
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|
+
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|
package/esm/bai.js
CHANGED
|
@@ -2,6 +2,7 @@ import Chunk from "./chunk.js";
|
|
|
2
2
|
import IndexFile, { memoizeByRefId } from "./indexFile.js";
|
|
3
3
|
import { clampChunkEnds, minVirtualOffset, parsePseudoBin } from "./util.js";
|
|
4
4
|
import { fromBytes } from "./virtualOffset.js";
|
|
5
|
+
const EMPTY_POSITIONS = new Float64Array(0);
|
|
5
6
|
const BAI_MAGIC = 21578050; // BAI\1
|
|
6
7
|
// BAI uses a fixed 5-level binning scheme with a 14-bit (16KB) linear index
|
|
7
8
|
// resolution. See SAMv1.pdf §5.1.3 (hts-specs).
|
|
@@ -108,8 +109,12 @@ export default class BAI extends IndexFile {
|
|
|
108
109
|
}
|
|
109
110
|
const linearCount = dataView.getInt32(curr, true);
|
|
110
111
|
curr += 4;
|
|
111
|
-
|
|
112
|
-
|
|
112
|
+
// Share one empty array rather than allocating a pair per reference. An
|
|
113
|
+
// assembly with tens of thousands of unplaced scaffolds (cho.bam.bai:
|
|
114
|
+
// 28751 references, 205 linear entries between them) reaches here once
|
|
115
|
+
// per reference, and almost every one of those has an empty linear index.
|
|
116
|
+
const linearBlockPositions = linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount);
|
|
117
|
+
const linearDataPositions = linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount);
|
|
113
118
|
for (let j = 0; j < linearCount; j++) {
|
|
114
119
|
// a virtual offset is a 48-bit block position in the high bytes and a
|
|
115
120
|
// 16-bit data position in the low two
|
package/esm/bai.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC5E,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;
|
|
1
|
+
{"version":3,"file":"bai.js","sourceRoot":"","sources":["../src/bai.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,EAAE,EAAE,cAAc,EAAE,MAAM,gBAAgB,CAAA;AAC1D,OAAO,EAAE,cAAc,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAC5E,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAmB9C,MAAM,eAAe,GAAG,IAAI,YAAY,CAAC,CAAC,CAAC,CAAA;AAM3C,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,wEAAwE;YACxE,sEAAsE;YACtE,uEAAuE;YACvE,0EAA0E;YAC1E,MAAM,oBAAoB,GACxB,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YACrE,MAAM,mBAAmB,GACvB,WAAW,KAAK,CAAC,CAAC,CAAC,CAAC,eAAe,CAAC,CAAC,CAAC,IAAI,YAAY,CAAC,WAAW,CAAC,CAAA;YACrE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,sEAAsE;gBACtE,sCAAsC;gBACtC,oBAAoB,CAAC,CAAC,CAAC;oBACrB,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,aAAa;wBAChC,KAAK,CAAC,IAAI,GAAG,CAAC,CAAE,GAAG,WAAW;wBAC9B,KAAK,CAAC,IAAI,GAAG,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|
package/esm/util.js
CHANGED
|
@@ -83,17 +83,32 @@ export function parsePseudoBin(bytes, offset) {
|
|
|
83
83
|
// least the true block end, so the clamped fetch still contains the whole block.
|
|
84
84
|
// Shrinks both the byte estimate and the actual fetch with no extra I/O.
|
|
85
85
|
export function clampChunkEnds(chunks, extraBoundaries = []) {
|
|
86
|
-
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
|
|
86
|
+
if (chunks.length === 0) {
|
|
87
|
+
return;
|
|
88
|
+
}
|
|
89
|
+
// A plain array, sized once and filled by index. Not a Float64Array: this
|
|
90
|
+
// runs once per reference, and an assembly with tens of thousands of unplaced
|
|
91
|
+
// scaffolds (cho.bam.bai has 28751 references) pays the allocation that many
|
|
92
|
+
// times over, where each individual boundary list is a handful of entries.
|
|
93
|
+
// The small-allocation cost dominates the faster typed sort by a wide margin
|
|
94
|
+
// at that shape. Filling by index still avoids the intermediate array that
|
|
95
|
+
// mapping the linear index to block positions used to build.
|
|
96
|
+
// Pre-sized and filled by index. Measured against both alternatives on five
|
|
97
|
+
// real .bai shapes (min of 21, interleaved, sign-stable over 3 runs):
|
|
98
|
+
// building with push instead is 5-8% slower here, and a Float64Array is
|
|
99
|
+
// faster to sort but allocates per reference, which costs 1.7x on an
|
|
100
|
+
// assembly with 28751 scaffolds. Filling by index also avoids the
|
|
101
|
+
// intermediate array that mapping the linear index used to build.
|
|
102
|
+
const boundaries = new Array(extraBoundaries.length + chunks.length * 2);
|
|
103
|
+
let n = 0;
|
|
104
|
+
for (let i = 0, l = extraBoundaries.length; i < l; i++) {
|
|
105
|
+
boundaries[n++] = extraBoundaries[i];
|
|
106
|
+
}
|
|
92
107
|
for (const c of chunks) {
|
|
93
108
|
boundaries[n++] = c.minv.blockPosition;
|
|
94
109
|
boundaries[n++] = c.maxv.blockPosition;
|
|
95
110
|
}
|
|
96
|
-
boundaries.sort();
|
|
111
|
+
boundaries.sort((a, b) => a - b);
|
|
97
112
|
for (const c of chunks) {
|
|
98
113
|
const max = c.maxv.blockPosition;
|
|
99
114
|
// first boundary strictly greater than max
|
package/esm/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
package/package.json
CHANGED
package/src/bai.ts
CHANGED
|
@@ -20,6 +20,8 @@ interface BaiRefIndex extends RefIndex {
|
|
|
20
20
|
linearDataPositions: Float64Array
|
|
21
21
|
}
|
|
22
22
|
|
|
23
|
+
const EMPTY_POSITIONS = new Float64Array(0)
|
|
24
|
+
|
|
23
25
|
interface BaiParsed extends ParsedIndexBase<BaiRefIndex> {
|
|
24
26
|
bai: true
|
|
25
27
|
}
|
|
@@ -151,8 +153,14 @@ export default class BAI extends IndexFile<BaiParsed> {
|
|
|
151
153
|
|
|
152
154
|
const linearCount = dataView.getInt32(curr, true)
|
|
153
155
|
curr += 4
|
|
154
|
-
|
|
155
|
-
|
|
156
|
+
// Share one empty array rather than allocating a pair per reference. An
|
|
157
|
+
// assembly with tens of thousands of unplaced scaffolds (cho.bam.bai:
|
|
158
|
+
// 28751 references, 205 linear entries between them) reaches here once
|
|
159
|
+
// per reference, and almost every one of those has an empty linear index.
|
|
160
|
+
const linearBlockPositions =
|
|
161
|
+
linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount)
|
|
162
|
+
const linearDataPositions =
|
|
163
|
+
linearCount === 0 ? EMPTY_POSITIONS : new Float64Array(linearCount)
|
|
156
164
|
for (let j = 0; j < linearCount; j++) {
|
|
157
165
|
// a virtual offset is a 48-bit block position in the high bytes and a
|
|
158
166
|
// 16-bit data position in the low two
|
package/src/util.ts
CHANGED
|
@@ -131,19 +131,34 @@ export function clampChunkEnds(
|
|
|
131
131
|
chunks: Chunk[],
|
|
132
132
|
extraBoundaries: ArrayLike<number> = [],
|
|
133
133
|
) {
|
|
134
|
-
|
|
135
|
-
|
|
136
|
-
|
|
137
|
-
|
|
134
|
+
if (chunks.length === 0) {
|
|
135
|
+
return
|
|
136
|
+
}
|
|
137
|
+
// A plain array, sized once and filled by index. Not a Float64Array: this
|
|
138
|
+
// runs once per reference, and an assembly with tens of thousands of unplaced
|
|
139
|
+
// scaffolds (cho.bam.bai has 28751 references) pays the allocation that many
|
|
140
|
+
// times over, where each individual boundary list is a handful of entries.
|
|
141
|
+
// The small-allocation cost dominates the faster typed sort by a wide margin
|
|
142
|
+
// at that shape. Filling by index still avoids the intermediate array that
|
|
143
|
+
// mapping the linear index to block positions used to build.
|
|
144
|
+
// Pre-sized and filled by index. Measured against both alternatives on five
|
|
145
|
+
// real .bai shapes (min of 21, interleaved, sign-stable over 3 runs):
|
|
146
|
+
// building with push instead is 5-8% slower here, and a Float64Array is
|
|
147
|
+
// faster to sort but allocates per reference, which costs 1.7x on an
|
|
148
|
+
// assembly with 28751 scaffolds. Filling by index also avoids the
|
|
149
|
+
// intermediate array that mapping the linear index used to build.
|
|
150
|
+
const boundaries = new Array<number>(
|
|
138
151
|
extraBoundaries.length + chunks.length * 2,
|
|
139
152
|
)
|
|
140
|
-
|
|
141
|
-
let
|
|
153
|
+
let n = 0
|
|
154
|
+
for (let i = 0, l = extraBoundaries.length; i < l; i++) {
|
|
155
|
+
boundaries[n++] = extraBoundaries[i]!
|
|
156
|
+
}
|
|
142
157
|
for (const c of chunks) {
|
|
143
158
|
boundaries[n++] = c.minv.blockPosition
|
|
144
159
|
boundaries[n++] = c.maxv.blockPosition
|
|
145
160
|
}
|
|
146
|
-
boundaries.sort()
|
|
161
|
+
boundaries.sort((a, b) => a - b)
|
|
147
162
|
|
|
148
163
|
for (const c of chunks) {
|
|
149
164
|
const max = c.maxv.blockPosition
|