@jbrowse/plugin-comparative-adapters 2.15.4 → 2.16.0

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Files changed (11) hide show
  1. package/dist/DeltaAdapter/util.js +4 -4
  2. package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts +2 -1
  3. package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js +21 -5
  4. package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts +2 -1
  5. package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js +25 -2
  6. package/esm/DeltaAdapter/util.js +4 -4
  7. package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts +2 -1
  8. package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js +21 -5
  9. package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts +2 -1
  10. package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js +25 -2
  11. package/package.json +2 -2
package/dist/DeltaAdapter/util.js CHANGED
@@ -74,10 +74,10 @@ function paf_delta2paf(buffer) {
74
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  const t3 = +t[3];
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  const t4 = +t[4];
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  strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
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- rs = +(t0 < t1 ? t0 : t1) - 1;
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- re = +(t1 > t0 ? t1 : t0);
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- qs = +(t2 < t3 ? t2 : t3) - 1;
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- qe = +(t3 > t2 ? t3 : t2);
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+ rs = +Math.min(t0, t1) - 1;
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+ re = +Math.max(t1, t0);
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+ qs = +Math.min(t2, t3) - 1;
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+ qe = +Math.max(t3, t2);
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  x = y = 0;
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  NM = t4;
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  cigar = [];
package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts CHANGED
@@ -21,7 +21,8 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
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  feats: Row[];
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  }>;
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  hasDataForRefName(): Promise<boolean>;
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- getRefNames(): Promise<never[]>;
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+ getAssemblyNames(): string[];
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+ getRefNames(opts?: BaseOptions): Promise<string[]>;
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  getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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  /**
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  * called to provide a hint that data tied to a certain region
package/dist/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js CHANGED
@@ -42,13 +42,29 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  };
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  }
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  async hasDataForRefName() {
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- // determining this properly is basically a call to getFeatures
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- // so is not really that important, and has to be true or else
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- // getFeatures is never called (BaseFeatureDataAdapter filters it out)
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+ // determining this properly is basically a call to getFeatures so is not
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+ // really that important, and has to be true or else getFeatures is never
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+ // called (BaseFeatureDataAdapter filters it out)
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  return true;
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  }
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- async getRefNames() {
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- // we cannot determine this accurately
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+ getAssemblyNames() {
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+ const assemblyNames = this.getConf('assemblyNames');
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+ return assemblyNames;
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+ }
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+ async getRefNames(opts = {}) {
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+ var _a;
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+ // @ts-expect-error
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+ const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
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+ const { feats } = await this.setup(opts);
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+ const idx = this.getAssemblyNames().indexOf(r1);
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+ if (idx !== -1) {
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+ const set = new Set();
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+ for (const feat of feats) {
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+ set.add(idx === 0 ? feat[0].refName : feat[1].refName);
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+ }
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+ return [...set];
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+ }
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+ console.warn('Unable to do ref renaming on adapter');
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  return [];
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  }
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  getFeatures(region, opts = {}) {
package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts CHANGED
@@ -29,7 +29,8 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
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  feats: Row[];
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  }>;
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  hasDataForRefName(): Promise<boolean>;
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- getRefNames(): Promise<never[]>;
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+ getAssemblyNames(): string[];
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+ getRefNames(opts?: BaseOptions): Promise<string[]>;
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  getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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  /**
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  * called to provide a hint that data tied to a certain region
package/dist/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js CHANGED
@@ -61,8 +61,31 @@ class MCScanAnchorsAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
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  // getFeatures is never called (BaseFeatureDataAdapter filters it out)
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  return true;
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  }
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- async getRefNames() {
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- // we cannot determine this accurately
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+ getAssemblyNames() {
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+ const assemblyNames = this.getConf('assemblyNames');
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+ return assemblyNames;
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+ }
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+ async getRefNames(opts = {}) {
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+ var _a;
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+ // @ts-expect-error
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+ const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
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+ const { feats } = await this.setup(opts);
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+ const idx = this.getAssemblyNames().indexOf(r1);
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+ if (idx !== -1) {
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+ const set = new Set();
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+ for (const feat of feats) {
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+ if (idx === 0) {
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+ set.add(feat[0].refName);
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+ set.add(feat[1].refName);
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+ }
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+ else {
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+ set.add(feat[2].refName);
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+ set.add(feat[3].refName);
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+ }
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+ }
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+ return [...set];
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+ }
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+ console.warn('Unable to do ref renaming on adapter');
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  return [];
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  }
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  getFeatures(region, opts = {}) {
package/esm/DeltaAdapter/util.js CHANGED
@@ -71,10 +71,10 @@ export function paf_delta2paf(buffer) {
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  const t3 = +t[3];
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  const t4 = +t[4];
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  strand = (t0 < t1 && t2 < t3) || (t0 > t1 && t2 > t3) ? 1 : -1;
74
- rs = +(t0 < t1 ? t0 : t1) - 1;
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- re = +(t1 > t0 ? t1 : t0);
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- qs = +(t2 < t3 ? t2 : t3) - 1;
77
- qe = +(t3 > t2 ? t3 : t2);
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+ rs = +Math.min(t0, t1) - 1;
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+ re = +Math.max(t1, t0);
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+ qs = +Math.min(t2, t3) - 1;
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+ qe = +Math.max(t3, t2);
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  x = y = 0;
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  NM = t4;
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  cigar = [];
package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.d.ts CHANGED
@@ -21,7 +21,8 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
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  feats: Row[];
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  }>;
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  hasDataForRefName(): Promise<boolean>;
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- getRefNames(): Promise<never[]>;
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+ getAssemblyNames(): string[];
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+ getRefNames(opts?: BaseOptions): Promise<string[]>;
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  getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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  /**
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  * called to provide a hint that data tied to a certain region
package/esm/MCScanAnchorsAdapter/MCScanAnchorsAdapter.js CHANGED
@@ -40,13 +40,29 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
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  };
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  }
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  async hasDataForRefName() {
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- // determining this properly is basically a call to getFeatures
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- // so is not really that important, and has to be true or else
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- // getFeatures is never called (BaseFeatureDataAdapter filters it out)
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+ // determining this properly is basically a call to getFeatures so is not
44
+ // really that important, and has to be true or else getFeatures is never
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+ // called (BaseFeatureDataAdapter filters it out)
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  return true;
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  }
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- async getRefNames() {
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- // we cannot determine this accurately
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+ getAssemblyNames() {
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+ const assemblyNames = this.getConf('assemblyNames');
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+ return assemblyNames;
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+ }
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+ async getRefNames(opts = {}) {
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+ var _a;
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+ // @ts-expect-error
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+ const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
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+ const { feats } = await this.setup(opts);
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+ const idx = this.getAssemblyNames().indexOf(r1);
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+ if (idx !== -1) {
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+ const set = new Set();
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+ for (const feat of feats) {
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+ set.add(idx === 0 ? feat[0].refName : feat[1].refName);
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+ }
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+ return [...set];
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+ }
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+ console.warn('Unable to do ref renaming on adapter');
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  return [];
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  }
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  getFeatures(region, opts = {}) {
package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.d.ts CHANGED
@@ -29,7 +29,8 @@ export default class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
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  feats: Row[];
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  }>;
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  hasDataForRefName(): Promise<boolean>;
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- getRefNames(): Promise<never[]>;
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+ getAssemblyNames(): string[];
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+ getRefNames(opts?: BaseOptions): Promise<string[]>;
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  getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
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  /**
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  * called to provide a hint that data tied to a certain region
package/esm/MCScanSimpleAnchorsAdapter/MCScanSimpleAnchorsAdapter.js CHANGED
@@ -56,8 +56,31 @@ class MCScanAnchorsAdapter extends BaseFeatureDataAdapter {
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  // getFeatures is never called (BaseFeatureDataAdapter filters it out)
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  return true;
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  }
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- async getRefNames() {
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- // we cannot determine this accurately
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+ getAssemblyNames() {
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+ const assemblyNames = this.getConf('assemblyNames');
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+ return assemblyNames;
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+ }
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+ async getRefNames(opts = {}) {
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+ var _a;
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+ // @ts-expect-error
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+ const r1 = (_a = opts.regions) === null || _a === void 0 ? void 0 : _a[0].assemblyName;
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+ const { feats } = await this.setup(opts);
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+ const idx = this.getAssemblyNames().indexOf(r1);
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+ if (idx !== -1) {
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+ const set = new Set();
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+ for (const feat of feats) {
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+ if (idx === 0) {
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+ set.add(feat[0].refName);
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+ set.add(feat[1].refName);
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+ }
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+ else {
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+ set.add(feat[2].refName);
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+ set.add(feat[3].refName);
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+ }
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+ }
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+ return [...set];
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+ }
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+ console.warn('Unable to do ref renaming on adapter');
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  return [];
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  }
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  getFeatures(region, opts = {}) {
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/plugin-comparative-adapters",
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- "version": "2.15.4",
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+ "version": "2.16.0",
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  "description": "JBrowse 2 comparative adapters",
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  "keywords": [
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  "jbrowse",
@@ -58,5 +58,5 @@
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  "publishConfig": {
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  "access": "public"
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  },
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- "gitHead": "686b4ad9016b3586e8230180f7adb44c238ba4fb"
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+ "gitHead": "1e6d4fbc27ce684eed19e3c217f34bd2da24ab75"
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  }