jbrowse-plugin-mafviewer 1.6.0 → 1.6.1

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Files changed (23) hide show
  1. package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js +14 -11
  2. package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js.map +1 -1
  3. package/dist/BigMafAdapter/BigMafAdapter.js +16 -13
  4. package/dist/BigMafAdapter/BigMafAdapter.js.map +1 -1
  5. package/dist/LinearMafRenderer/LinearMafRenderer.d.ts +1 -1
  6. package/dist/MafTabixAdapter/MafTabixAdapter.js +9 -7
  7. package/dist/MafTabixAdapter/MafTabixAdapter.js.map +1 -1
  8. package/dist/jbrowse-plugin-mafviewer.umd.production.min.js +6 -6
  9. package/dist/jbrowse-plugin-mafviewer.umd.production.min.js.map +3 -3
  10. package/dist/util/parseAssemblyName.d.ts +10 -0
  11. package/dist/util/parseAssemblyName.js +21 -0
  12. package/dist/util/parseAssemblyName.js.map +1 -1
  13. package/dist/util/parseAssemblyName.test.js +32 -1
  14. package/dist/util/parseAssemblyName.test.js.map +1 -1
  15. package/dist/version.d.ts +1 -1
  16. package/dist/version.js +1 -1
  17. package/package.json +1 -1
  18. package/src/BgzipTaffyAdapter/BgzipTaffyAdapter.ts +17 -11
  19. package/src/BigMafAdapter/BigMafAdapter.ts +20 -16
  20. package/src/MafTabixAdapter/MafTabixAdapter.ts +9 -7
  21. package/src/util/parseAssemblyName.test.ts +38 -0
  22. package/src/util/parseAssemblyName.ts +29 -0
  23. package/src/version.ts +1 -1
package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js CHANGED
@@ -6,7 +6,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
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  import VirtualOffset from './virtualOffset';
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  import { filterFirstLineInstructions, parseRowInstructions, } from './rowInstructions';
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  import MafFeature from '../MafFeature';
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- import { parseAssemblyAndChrSimple } from '../util/parseAssemblyName';
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+ import { matchSampleId, parseAssemblyAndChrSimple, } from '../util/parseAssemblyName';
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  import { getSamplesFromConfig } from '../util/getSamples';
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  /**
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  * Binary search to find the index of the first element >= target
@@ -218,17 +218,20 @@ export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
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  const row0 = block.rows[0];
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  const alignments = {};
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  for (const row of block.rows) {
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- const { assemblyName, chr } = parseAssemblyAndChrSimple(row.sequenceName);
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- if (sampleFilter && !sampleFilter.has(assemblyName)) {
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- continue;
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+ // Known set → resolve the token against it so haplotype-suffixed names
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+ // (`Species1.1`) match exactly. No set → dot-position split.
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+ const parsed = sampleFilter
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+ ? matchSampleId(row.sequenceName, sampleFilter)
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+ : parseAssemblyAndChrSimple(row.sequenceName);
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+ if (parsed?.assemblyName) {
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+ alignments[parsed.assemblyName] = {
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+ chr: parsed.chr,
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+ start: row.start,
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+ srcSize: row.sequenceLength,
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+ strand: row.strand,
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+ seq: row.bases,
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+ };
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  }
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- alignments[assemblyName] = {
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- chr,
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- start: row.start,
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- srcSize: row.sequenceLength,
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- strand: row.strand,
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- seq: row.bases,
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- };
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  }
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  return {
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  uniqueId: `${row0.start}-${row0.length}`,
package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js.map CHANGED
@@ -1 +1 @@
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1
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package/dist/BigMafAdapter/BigMafAdapter.js CHANGED
@@ -3,7 +3,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
3
3
  import { getSnapshot } from '@jbrowse/mobx-state-tree';
4
4
  import MafFeature from '../MafFeature';
5
5
  import { subscribeToObservable } from '../util/observableUtils';
6
- import { parseAssemblyAndChrSimple } from '../util/parseAssemblyName';
6
+ import { matchSampleId, parseAssemblyAndChrSimple, } from '../util/parseAssemblyName';
7
7
  import { getSamplesFromConfig } from '../util/getSamples';
8
8
  export default class BigMafAdapter extends BaseFeatureDataAdapter {
9
9
  setupP;
@@ -37,7 +37,7 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
37
37
  const WHITESPACE_REGEX = / +/;
38
38
  return ObservableCreate(async (observer) => {
39
39
  const { adapter } = await this.setupPre();
40
- const sampleFilter = opts?.samples
40
+ const sampleIds = opts?.samples
41
41
  ? new Set(opts.samples.map(s => s.id))
42
42
  : undefined;
43
43
  await subscribeToObservable(adapter.getFeatures(query, opts), feature => {
@@ -50,21 +50,24 @@ export default class BigMafAdapter extends BaseFeatureDataAdapter {
50
50
  const parts = block.split(WHITESPACE_REGEX);
51
51
  const sequence = parts[6];
52
52
  const organismChr = parts[1];
53
- const { assemblyName: org, chr } = parseAssemblyAndChrSimple(organismChr);
54
53
  if (referenceSeq === undefined) {
55
54
  referenceSeq = sequence;
56
55
  }
57
- if (sampleFilter && !sampleFilter.has(org)) {
58
- continue;
56
+ // Known set → resolve the token against it so haplotype-suffixed
57
+ // names (`Species1.1`) match exactly. No set → dot-position split.
58
+ const parsed = sampleIds
59
+ ? matchSampleId(organismChr, sampleIds)
60
+ : parseAssemblyAndChrSimple(organismChr);
61
+ if (parsed?.assemblyName) {
62
+ alignments[parsed.assemblyName] = {
63
+ chr: parsed.chr,
64
+ start: +parts[2],
65
+ srcSize: +parts[3],
66
+ strand: parts[4] === '+' ? 1 : -1,
67
+ unknown: +parts[5],
68
+ seq: sequence,
69
+ };
59
70
  }
60
- alignments[org] = {
61
- chr,
62
- start: +parts[2],
63
- srcSize: +parts[3],
64
- strand: parts[4] === '+' ? 1 : -1,
65
- unknown: +parts[5],
66
- seq: sequence,
67
- };
68
71
  }
69
72
  }
70
73
  observer.next(new MafFeature(feature.id(), feature.get('start'), feature.get('end'), feature.get('refName'), 0, // strand not in BigMaf format
package/dist/BigMafAdapter/BigMafAdapter.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"BigMafAdapter.js","sourceRoot":"","sources":["../../src/BigMafAdapter/BigMafAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AAEtD,OAAO,UAAU,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EAAE,yBAAyB,EAAE,MAAM,2BAA2B,CAAA;AACrE,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AAKzD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IACxD,MAAM,CAA+C;IAE5D,KAAK,CAAC,KAAK;QACT,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,OAAO;YACL,OAAO,EAAE,CACP,MAAM,IAAI,CAAC,aAAa,CAAC;gBACvB,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC3B,IAAI,EAAE,eAAe;aACtB,CAAC,CACH,CAAC,WAAqC;SACxC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YAChD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACzC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACzC,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,IAAwB;QACjD,MAAM,gBAAgB,GAAG,IAAI,CAAA;QAE7B,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;YAEzC,MAAM,YAAY,GAAG,IAAI,EAAE,OAAO;gBAChC,CAAC,CAAC,IAAI,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;gBACtC,CAAC,CAAC,SAAS,CAAA;YAEb,MAAM,qBAAqB,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,OAAO,CAAC,EAAE;gBACtE,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,UAAU,CAAW,CAAA;gBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBAC7B,MAAM,UAAU,GAAG,EAAqC,CAAA;gBACxD,IAAI,YAAgC,CAAA;gBAEpC,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;oBAC3B,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC1B,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAA;wBAC3C,MAAM,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;wBAC1B,MAAM,WAAW,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;wBAE7B,MAAM,EAAE,YAAY,EAAE,GAAG,EAAE,GAAG,EAAE,GAC9B,yBAAyB,CAAC,WAAW,CAAC,CAAA;wBAExC,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;4BAC/B,YAAY,GAAG,QAAQ,CAAA;wBACzB,CAAC;wBAED,IAAI,YAAY,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;4BAC3C,SAAQ;wBACV,CAAC;wBAED,UAAU,CAAC,GAAG,CAAC,GAAG;4BAChB,GAAG;4BACH,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;4BACjB,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;4BACnB,MAAM,EAAE,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;4BACjC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;4BACnB,GAAG,EAAE,QAAQ;yBACd,CAAA;oBACH,CAAC;gBACH,CAAC;gBAED,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CACZ,OAAO,CAAC,EAAE,EAAE,EACZ,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,EACpB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAClB,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,EACtB,CAAC,EAAE,8BAA8B;gBACjC,UAAU,EACV,YAAY,IAAI,EAAE,CACnB,CACF,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,EAAE,SAAS,CAAC,CAAA;IACrB,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,MAAc;QAC7B,OAAO,oBAAoB,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;IACtD,CAAC;IAED,aAAa,KAAU,CAAC;CACzB"}
1
+ {"version":3,"file":"BigMafAdapter.js","sourceRoot":"","sources":["../../src/BigMafAdapter/BigMafAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAA;AAChF,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AAEtD,OAAO,UAAU,MAAM,eAAe,CAAA;AACtC,OAAO,EAAE,qBAAqB,EAAE,MAAM,yBAAyB,CAAA;AAC/D,OAAO,EACL,aAAa,EACb,yBAAyB,GAC1B,MAAM,2BAA2B,CAAA;AAClC,OAAO,EAAE,oBAAoB,EAAE,MAAM,oBAAoB,CAAA;AAKzD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,sBAAsB;IACxD,MAAM,CAA+C;IAE5D,KAAK,CAAC,KAAK;QACT,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;QAC/C,CAAC;QACD,OAAO;YACL,OAAO,EAAE,CACP,MAAM,IAAI,CAAC,aAAa,CAAC;gBACvB,GAAG,WAAW,CAAC,IAAI,CAAC,MAAM,CAAC;gBAC3B,IAAI,EAAE,eAAe;aACtB,CAAC,CACH,CAAC,WAAqC;SACxC,CAAA;IACH,CAAC;IACD,KAAK,CAAC,QAAQ;QACZ,IAAI,CAAC,MAAM,KAAK,IAAI,CAAC,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAU,EAAE,EAAE;YAChD,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;YACvB,MAAM,CAAC,CAAA;QACT,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,KAAK,CAAC,WAAW;QACf,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACzC,OAAO,OAAO,CAAC,WAAW,EAAE,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,SAAS;QACb,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;QACzC,OAAO,OAAO,CAAC,SAAS,EAAE,CAAA;IAC5B,CAAC;IAED,WAAW,CAAC,KAAa,EAAE,IAAwB;QACjD,MAAM,gBAAgB,GAAG,IAAI,CAAA;QAE7B,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,OAAO,EAAE,GAAG,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAA;YAEzC,MAAM,SAAS,GAAG,IAAI,EAAE,OAAO;gBAC7B,CAAC,CAAC,IAAI,GAAG,CAAC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;gBACtC,CAAC,CAAC,SAAS,CAAA;YAEb,MAAM,qBAAqB,CAAC,OAAO,CAAC,WAAW,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,OAAO,CAAC,EAAE;gBACtE,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,UAAU,CAAW,CAAA;gBAC7C,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;gBAC7B,MAAM,UAAU,GAAG,EAAqC,CAAA;gBACxD,IAAI,YAAgC,CAAA;gBAEpC,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;oBAC3B,IAAI,KAAK,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;wBAC1B,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAA;wBAC3C,MAAM,QAAQ,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;wBAC1B,MAAM,WAAW,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;wBAE7B,IAAI,YAAY,KAAK,SAAS,EAAE,CAAC;4BAC/B,YAAY,GAAG,QAAQ,CAAA;wBACzB,CAAC;wBAED,iEAAiE;wBACjE,mEAAmE;wBACnE,MAAM,MAAM,GAAG,SAAS;4BACtB,CAAC,CAAC,aAAa,CAAC,WAAW,EAAE,SAAS,CAAC;4BACvC,CAAC,CAAC,yBAAyB,CAAC,WAAW,CAAC,CAAA;wBAE1C,IAAI,MAAM,EAAE,YAAY,EAAE,CAAC;4BACzB,UAAU,CAAC,MAAM,CAAC,YAAY,CAAC,GAAG;gCAChC,GAAG,EAAE,MAAM,CAAC,GAAG;gCACf,KAAK,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;gCACjB,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;gCACnB,MAAM,EAAE,KAAK,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;gCACjC,OAAO,EAAE,CAAC,KAAK,CAAC,CAAC,CAAE;gCACnB,GAAG,EAAE,QAAQ;6BACd,CAAA;wBACH,CAAC;oBACH,CAAC;gBACH,CAAC;gBAED,QAAQ,CAAC,IAAI,CACX,IAAI,UAAU,CACZ,OAAO,CAAC,EAAE,EAAE,EACZ,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,EACpB,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAClB,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,EACtB,CAAC,EAAE,8BAA8B;gBACjC,UAAU,EACV,YAAY,IAAI,EAAE,CACnB,CACF,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,EAAE,SAAS,CAAC,CAAA;IACrB,CAAC;IAED,KAAK,CAAC,UAAU,CAAC,MAAc;QAC7B,OAAO,oBAAoB,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAA;IACtD,CAAC;IAED,aAAa,KAAU,CAAC;CACzB"}
package/dist/LinearMafRenderer/LinearMafRenderer.d.ts CHANGED
@@ -17,8 +17,8 @@ export default class LinearMafRenderer extends FeatureRendererType {
17
17
  start: number;
18
18
  end: number;
19
19
  refName: string;
20
- reversed?: boolean | undefined;
21
20
  assemblyName: string;
21
+ reversed?: boolean | undefined;
22
22
  };
23
23
  render(renderProps: RenderArgs): Promise<{
24
24
  imageData: unknown;
package/dist/MafTabixAdapter/MafTabixAdapter.js CHANGED
@@ -4,7 +4,7 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
4
4
  import { getSnapshot } from '@jbrowse/mobx-state-tree';
5
5
  import MafFeature from '../MafFeature';
6
6
  import { subscribeToObservable } from '../util/observableUtils';
7
- import { parseAssemblyAndChr, selectReferenceSequenceString, } from '../util/parseAssemblyName';
7
+ import { matchSampleId, parseAssemblyAndChr, selectReferenceSequenceString, } from '../util/parseAssemblyName';
8
8
  import { getSamplesFromConfig } from '../util/getSamples';
9
9
  export default class MafTabixAdapter extends BaseFeatureDataAdapter {
10
10
  setupP;
@@ -42,7 +42,7 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
42
42
  const { adapter } = await this.setupPre(opts);
43
43
  let firstAssemblyNameFound = '';
44
44
  const refAssemblyName = this.getConf('refAssemblyName');
45
- const sampleFilter = opts?.samples
45
+ const sampleIds = opts?.samples
46
46
  ? new Set(opts.samples.map(s => s.id))
47
47
  : undefined;
48
48
  await subscribeToObservable(adapter.getFeatures(query, opts), feature => {
@@ -55,14 +55,16 @@ export default class MafTabixAdapter extends BaseFeatureDataAdapter {
55
55
  if (!assemblyAndChr || !seq) {
56
56
  continue;
57
57
  }
58
- const { assemblyName, chr } = parseAssemblyAndChr(assemblyAndChr);
59
- if (assemblyName) {
58
+ // Known set → resolve the token against it so haplotype-suffixed
59
+ // names (`Species1.1`) match exactly. No set → dot-position split.
60
+ const parsed = sampleIds
61
+ ? matchSampleId(assemblyAndChr, sampleIds)
62
+ : parseAssemblyAndChr(assemblyAndChr);
63
+ if (parsed?.assemblyName) {
64
+ const { assemblyName, chr } = parsed;
60
65
  if (!firstAssemblyNameFound) {
61
66
  firstAssemblyNameFound = assemblyName;
62
67
  }
63
- if (sampleFilter && !sampleFilter.has(assemblyName)) {
64
- continue;
65
- }
66
68
  alignments[assemblyName] = {
67
69
  chr,
68
70
  start: +startStr,
package/dist/MafTabixAdapter/MafTabixAdapter.js.map CHANGED
@@ -1 +1 @@
1
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