@gmod/cram 8.0.2 → 8.0.3

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Files changed (7) hide show
  1. package/dist/cram-bundle.js +1 -1
  2. package/dist/cramFile/record.js +12 -16
  3. package/dist/cramFile/record.js.map +1 -1
  4. package/esm/cramFile/record.js +12 -16
  5. package/esm/cramFile/record.js.map +1 -1
  6. package/package.json +1 -1
  7. package/src/cramFile/record.ts +15 -16
package/dist/cramFile/record.js CHANGED
@@ -5,6 +5,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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  Object.defineProperty(exports, "__esModule", { value: true });
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  exports.MateFlagsDecoder = exports.CramFlagsDecoder = exports.BamFlagsDecoder = exports.MateFlags = exports.CramFlags = exports.BamFlags = exports.defaultDecodeOptions = void 0;
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  const constants_ts_1 = __importDefault(require("./constants.js"));
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+ // precomputed pair orientation strings indexed by ((flags >> 4) & 0xF) | (isize > 0 ? 16 : 0)
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+ // bits 0-3 encode flag bits 0x10(reverse),0x20(mate reverse),0x40(read1),0x80(read2)
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+ // bit 4 encodes whether isize > 0
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+ // prettier-ignore
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+ const PAIR_ORIENTATION_TABLE = [
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+ 'F F ', 'F R ', 'R F ', 'R R ', 'F2F1', 'F2R1', 'R2F1', 'R2R1',
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+ 'F1F2', 'F1R2', 'R1F2', 'R1R2', 'F2F1', 'F2R1', 'R2F1', 'R2R1',
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+ 'F F ', 'R F ', 'F R ', 'R R ', 'F1F2', 'R1F2', 'F1R2', 'R1R2',
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+ 'F2F1', 'R2F1', 'F2R1', 'R2R1', 'F1F2', 'R1F2', 'F1R2', 'R1R2',
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+ ];
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  exports.defaultDecodeOptions = {
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  decodeTags: true,
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  };
@@ -296,29 +306,15 @@ class CramRecord {
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  return this.readBases;
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  }
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  // adapted from igv.js
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- // inlines flag checks and uses template literal instead of array+join
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+ // uses precomputed lookup table indexed by flag bits + isize sign
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  getPairOrientation() {
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  const f = this.flags;
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  // combined check: paired (0x1) set, unmapped (0x4) clear, mate unmapped (0x8) clear
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  if ((f & 0xd) !== 0x1 || this.sequenceId !== this.mate?.sequenceId) {
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  return undefined;
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  }
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- const s1 = f & 0x10 ? 'R' : 'F';
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- const s2 = f & 0x20 ? 'R' : 'F';
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- let o1 = ' ';
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- let o2 = ' ';
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- if (f & 0x40) {
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- o1 = '1';
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- o2 = '2';
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- }
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- else if (f & 0x80) {
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- o1 = '2';
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- o2 = '1';
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- }
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  const isize = this.templateLength || this.templateSize || 0;
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- return isize > 0
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- ? `${s1}${o1}${s2}${o2}`
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- : `${s2}${o2}${s1}${o1}`;
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+ return PAIR_ORIENTATION_TABLE[((f >> 4) & 0xf) | (isize > 0 ? 16 : 0)];
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  }
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  /**
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  * Annotates this feature with the given reference sequence basepair
package/dist/cramFile/record.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"record.js","sourceRoot":"","sources":["../../src/cramFile/record.ts"],"names":[],"mappings":";;;;;;AAAA,kEAAsC;AAKtC,8FAA8F;AAC9F,qFAAqF;AACrF,kCAAkC;AAClC,kBAAkB;AAClB,MAAM,sBAAsB,GAAG;IAC7B,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM;IACvD,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM;IACvD,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM;IACvD,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM,EAAC,MAAM;CACxD,CAAA;AAsBY,QAAA,oBAAoB,GAA4B;IAC3D,UAAU,EAAE,IAAI;CACjB,CAAA;AAED,SAAS,kBAAkB,CAAC,UAAsB,EAAE,SAAoB;IACtE,0CAA0C;IAC1C,IAAI,CAAC,UAAU,CAAC,WAAW,IAAI,CAAC,UAAU,CAAC,UAAU,EAAE,CAAC;QACtD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,IAAI,UAAU,CAAC,cAAc,EAAE,EAAE,CAAC;QAChC,OAAO,IAAI,CAAA;IACb,CAAC;IAED,+CAA+C;IAC/C,MAAM,eAAe,GAAG,UAAU,CAAC,cAAc,GAAG,SAAS,CAAC,KAAK,CAAA;IAEnE,IAAI,CAAC,UAAU,CAAC,YAAY,EAAE,CAAC;QAC7B,OAAO,SAAS,CAAC,GAAG;aACjB,KAAK,CAAC,eAAe,EAAE,eAAe,GAAG,CAAC,UAAU,CAAC,WAAW,IAAI,CAAC,CAAC,CAAC;aACvE,WAAW,EAAE,CAAA;IAClB,CAAC;IAED,IAAI,KAAK,GAAG,EAAE,CAAA;IACd,IAAI,SAAS,GAAG,eAAe,CAAA;IAC/B,IAAI,kBAAkB,GAAG,CAAC,CAAA;IAC1B,OAAO,KAAK,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,EAAE,CAAC;QAC5C,IAAI,kBAAkB,GAAG,UAAU,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC;YACxD,MAAM,OAAO,GAAG,UAAU,CAAC,YAAY,CAAC,kBAAkB,CAAE,CAAA;YAC5D,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;gBACjD,kBAAkB,IAAI,CAAC,CAAA;YACzB,CAAC;iBAAM,IAAI,OAAO,CAAC,GAAG,KAAK,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC5C,2BAA2B;gBAC3B,kBAAkB,IAAI,CAAC,CAAA;gBAEvB,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBACzB,sCAAsC;oBACtC,MAAM,KAAK,GAAG,OAAO,CAAC,IAAI,CAAA;oBAC1B,KAAK,IAAI,KAAK,CAAA;oBACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;gBAC3B,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,mCAAmC;oBACnC,0DAA0D;oBAC1D,KAAK,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBACxB,SAAS,IAAI,CAAC,CAAA;gBAChB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,oBAAoB;oBACpB,KAAK,IAAI,OAAO,CAAC,GAAG,CAAA;oBACpB,SAAS,IAAI,CAAC,CAAA;gBAChB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,YAAY;oBACZ,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;gBACvB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,WAAW;oBACX,SAAS,IAAI,OAAO,CAAC,IAAI,CAAA;gBAC3B,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,qBAAqB;oBACrB,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;gBACvB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,oCAAoC;oBACpC,aAAa;oBACb,iDAAiD;oBACjD,SAAS,IAAI,OAAO,CAAC,IAAI,CAAA;gBAC3B,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,4DAA4D;oBAC5D,iEAAiE;oBACjE,KAAK,IAAI,OAAO,CAAC,IAAI,CAAA;gBACvB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,sBAAsB;gBACxB,CAAC;qBAAM,IAAI,OAAO,CAAC,IAAI,KAAK,GAAG,EAAE,CAAC;oBAChC,wBAAwB;gBAC1B,CAAC;YACH,CAAC;iBAAM,IAAI,kBAAkB,GAAG,UAAU,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC;gBAC/D,2DAA2D;gBAC3D,MAAM,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,KAAK,CAC/B,SAAS,EACT,SAAS,GAAG,OAAO,CAAC,GAAG,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,CAC3C,CAAA;gBACD,KAAK,IAAI,KAAK,CAAA;gBACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;YAC3B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,2DAA2D;YAC3D,MAAM,KAAK,GAAG,SAAS,CAAC,GAAG,CAAC,KAAK,CAC/B,SAAS,EACT,SAAS,GAAG,UAAU,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,CACjD,CAAA;YACD,KAAK,IAAI,KAAK,CAAA;YACd,SAAS,IAAI,KAAK,CAAC,MAAM,CAAA;QAC3B,CAAC;IACH,CAAC;IAED,OAAO,KAAK,CAAC,WAAW,EAAE,CAAA;AAC5B,CAAC;AAED,MAAM,WAAW,GAAG;IAClB,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;IACJ,CAAC,EAAE,CAAC;CACL,CAAA;AAED,SAAS,sBAAsB,CAC7B,UAAsB,EACtB,SAAoB,EACpB,iBAAiD,EACjD,WAAwB;IAExB,8DAA8D;IAC9D,MAAM,QAAQ,GAAG,WAAW,CAAC,MAAM,GAAG,SAAS,CAAC,KAAK,CAAA;IACrD,MAAM,OAAO,GAAG,SAAS,CAAC,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;IAC9C,IAAI,OAAO,EAAE,CAAC;QACZ,WAAW,CAAC,GAAG,GAAG,OAAO,CAAA;IAC3B,CAAC;IACD,IAAI,UAAU,GAAI,WAAmB,CAAC,OAAO,CAAC,CAAA;IAC9C,IAAI,UAAU,KAAK,SAAS,EAAE,CAAC;QAC7B,UAAU,GAAG,CAAC,CAAA;IAChB,CAAC;IACD,MAAM,kBAAkB,GAAG,iBAAiB,CAAC,kBAAkB,CAAC,UAAU,CAAE,CAAA;IAC5E,MAAM,IAAI,GAAG,kBAAkB,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACjD,IAAI,IAAI,EAAE,CAAC;QACT,WAAW,CAAC,GAAG,GAAG,IAAI,CAAA;IACxB,CAAC;AACH,CAAC;AAWY,QAAA,QAAQ,GAAG;IACtB,CAAC,GAAG,EAAE,QAAQ,CAAC;IACf,CAAC,GAAG,EAAE,gBAAgB,CAAC;IACvB,CAAC,GAAG,EAAE,iBAAiB,CAAC;IACxB,CAAC,GAAG,EAAE,cAAc,CAAC;IACrB,CAAC,IAAI,EAAE,qBAAqB,CAAC;IAC7B,4CAA4C;IAC5C,CAAC,IAAI,EAAE,yBAAyB,CAAC;IACjC,iBAAiB;IACjB,CAAC,IAAI,EAAE,OAAO,CAAC;IACf,iBAAiB;IACjB,CAAC,IAAI,EAAE,OAAO,CAAC;IACf,yBAAyB;IACzB,CAAC,KAAK,EAAE,WAAW,CAAC;IACpB,cAAc;IACd,CAAC,KAAK,EAAE,UAAU,CAAC;IACnB,4BAA4B;IAC5B,CAAC,KAAK,EAAE,WAAW,CAAC;IACpB,2BAA2B;IAC3B,CAAC,KAAK,EAAE,eAAe,CAAC;CAChB,CAAA;AAEG,QAAA,SAAS,GAAG;IACvB,CAAC,GAAG,EAAE,yBAAyB,CAAC;IAChC,CAAC,GAAG,EAAE,UAAU,CAAC;IACjB,CAAC,GAAG,EAAE,oBAAoB,CAAC;IAC3B,CAAC,GAAG,EAAE,sBAAsB,CAAC;CACrB,CAAA;AAEG,QAAA,SAAS,GAAG;IACvB,CAAC,GAAG,EAAE,kBAAkB,CAAC;IACzB,CAAC,GAAG,EAAE,UAAU,CAAC;CACT,CAAA;AAcV,SAAS,eAAe,CACtB,CAAoC;IAEpC,MAAM,CAAC,GAAQ,EAAE,CAAA;IACjB,KAAK,MAAM,CAAC,IAAI,EAAE,IAAI,CAAC,IAA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package/esm/cramFile/record.js CHANGED
@@ -1,4 +1,14 @@
1
1
  import Constants from "./constants.js";
2
+ // precomputed pair orientation strings indexed by ((flags >> 4) & 0xF) | (isize > 0 ? 16 : 0)
3
+ // bits 0-3 encode flag bits 0x10(reverse),0x20(mate reverse),0x40(read1),0x80(read2)
4
+ // bit 4 encodes whether isize > 0
5
+ // prettier-ignore
6
+ const PAIR_ORIENTATION_TABLE = [
7
+ 'F F ', 'F R ', 'R F ', 'R R ', 'F2F1', 'F2R1', 'R2F1', 'R2R1',
8
+ 'F1F2', 'F1R2', 'R1F2', 'R1R2', 'F2F1', 'F2R1', 'R2F1', 'R2R1',
9
+ 'F F ', 'R F ', 'F R ', 'R R ', 'F1F2', 'R1F2', 'F1R2', 'R1R2',
10
+ 'F2F1', 'R2F1', 'F2R1', 'R2R1', 'F1F2', 'R1F2', 'F1R2', 'R1R2',
11
+ ];
2
12
  export const defaultDecodeOptions = {
3
13
  decodeTags: true,
4
14
  };
@@ -290,29 +300,15 @@ export default class CramRecord {
290
300
  return this.readBases;
291
301
  }
292
302
  // adapted from igv.js
293
- // inlines flag checks and uses template literal instead of array+join
303
+ // uses precomputed lookup table indexed by flag bits + isize sign
294
304
  getPairOrientation() {
295
305
  const f = this.flags;
296
306
  // combined check: paired (0x1) set, unmapped (0x4) clear, mate unmapped (0x8) clear
297
307
  if ((f & 0xd) !== 0x1 || this.sequenceId !== this.mate?.sequenceId) {
298
308
  return undefined;
299
309
  }
300
- const s1 = f & 0x10 ? 'R' : 'F';
301
- const s2 = f & 0x20 ? 'R' : 'F';
302
- let o1 = ' ';
303
- let o2 = ' ';
304
- if (f & 0x40) {
305
- o1 = '1';
306
- o2 = '2';
307
- }
308
- else if (f & 0x80) {
309
- o1 = '2';
310
- o2 = '1';
311
- }
312
310
  const isize = this.templateLength || this.templateSize || 0;
313
- return isize > 0
314
- ? `${s1}${o1}${s2}${o2}`
315
- : `${s2}${o2}${s1}${o1}`;
311
+ return PAIR_ORIENTATION_TABLE[((f >> 4) & 0xf) | (isize > 0 ? 16 : 0)];
316
312
  }
317
313
  /**
318
314
  * Annotates this feature with the given reference sequence basepair
package/esm/cramFile/record.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@gmod/cram",
3
- "version": "8.0.2",
3
+ "version": "8.0.3",
4
4
  "description": "read CRAM files with pure Javascript",
5
5
  "license": "MIT",
6
6
  "repository": "GMOD/cram-js",
package/src/cramFile/record.ts CHANGED
@@ -3,6 +3,17 @@ import CramContainerCompressionScheme from './container/compressionScheme.ts'
3
3
 
4
4
  import type decodeRecord from './slice/decodeRecord.ts'
5
5
 
6
+ // precomputed pair orientation strings indexed by ((flags >> 4) & 0xF) | (isize > 0 ? 16 : 0)
7
+ // bits 0-3 encode flag bits 0x10(reverse),0x20(mate reverse),0x40(read1),0x80(read2)
8
+ // bit 4 encodes whether isize > 0
9
+ // prettier-ignore
10
+ const PAIR_ORIENTATION_TABLE = [
11
+ 'F F ','F R ','R F ','R R ','F2F1','F2R1','R2F1','R2R1',
12
+ 'F1F2','F1R2','R1F2','R1R2','F2F1','F2R1','R2F1','R2R1',
13
+ 'F F ','R F ','F R ','R R ','F1F2','R1F2','F1R2','R1R2',
14
+ 'F2F1','R2F1','F2R1','R2R1','F1F2','R1F2','F1R2','R1R2',
15
+ ]
16
+
6
17
  export interface RefRegion {
7
18
  start: number
8
19
  end: number
@@ -411,29 +422,17 @@ export default class CramRecord {
411
422
  }
412
423
 
413
424
  // adapted from igv.js
414
- // inlines flag checks and uses template literal instead of array+join
425
+ // uses precomputed lookup table indexed by flag bits + isize sign
415
426
  getPairOrientation() {
416
427
  const f = this.flags
417
428
  // combined check: paired (0x1) set, unmapped (0x4) clear, mate unmapped (0x8) clear
418
429
  if ((f & 0xd) !== 0x1 || this.sequenceId !== this.mate?.sequenceId) {
419
430
  return undefined
420
431
  }
421
- const s1 = f & 0x10 ? 'R' : 'F'
422
- const s2 = f & 0x20 ? 'R' : 'F'
423
- let o1 = ' '
424
- let o2 = ' '
425
- if (f & 0x40) {
426
- o1 = '1'
427
- o2 = '2'
428
- } else if (f & 0x80) {
429
- o1 = '2'
430
- o2 = '1'
431
- }
432
-
433
432
  const isize = this.templateLength || this.templateSize || 0
434
- return isize > 0
435
- ? `${s1}${o1}${s2}${o2}`
436
- : `${s2}${o2}${s1}${o1}`
433
+ return PAIR_ORIENTATION_TABLE[
434
+ ((f >> 4) & 0xf) | (isize > 0 ? 16 : 0)
435
+ ]
437
436
  }
438
437
 
439
438
  /**