@jbrowse/plugin-alignments 2.3.1 → 2.3.3

package/esm/PileupRPC/methods/GetGlobalValueForTag.js.map

@@ -1 +1 @@
-{"version":3,"file":"GetGlobalValueForTag.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetGlobalValueForTag.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAIzE,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAEnC,MAAM,CAAC,OAAO,OAAO,0BAA2B,SAAQ,aAAa;IAArE;;QACE,SAAI,GAAG,4BAA4B,CAAA;IA+BrC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,EAAE,GAC9C,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAElD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAA;QAClE,MAAM,aAAa,GAAG,MAAM,QAAQ,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,SAAS,EAAE,CAAA;QAChE,OAAO;YACL,GAAG,IAAI,GAAG,CACR,aAAa;iBACV,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;iBACpC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;iBAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CACpB;SACF,CAAA;IACH,CAAC;CACF"}
+{"version":3,"file":"GetGlobalValueForTag.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetGlobalValueForTag.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAIzE,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAErC,SAAS;AACT,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAEnC,MAAM,CAAC,OAAO,OAAO,0BAA2B,SAAQ,aAAa;IAArE;;QACE,SAAI,GAAG,4BAA4B,CAAA;IA+BrC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,EAAE,GAC9C,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAElD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,QAAQ,GAAG,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAA;QAClE,MAAM,aAAa,GAAG,MAAM,cAAc,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAAC,CAAA;QACpE,OAAO;YACL,GAAG,IAAI,GAAG,CACR,aAAa;iBACV,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;iBACpC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,KAAK,SAAS,CAAC;iBAC5B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,CACpB;SACF,CAAA;IACH,CAAC;CACF"}

package/esm/PileupRPC/methods/GetReducedFeatures.js

@@ -1,6 +1,7 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { dedupe } from '@jbrowse/core/util';
 import { toArray } from 'rxjs/operators';
+import { firstValueFrom } from 'rxjs';
 // locals
 import { filterForPairs, getInsertSizeStats } from '../util';
 import PileupBaseRPC from '../base';
@@ -15,10 +16,7 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC {
         const des = await this.deserializeArguments(args, rpcDriver);
         const { adapterConfig, sessionId, regions } = des;
         const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await dataAdapter
-            .getFeaturesInMultipleRegions(regions, des)
-            .pipe(toArray())
-            .toPromise();
+        const featuresArray = await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions, des).pipe(toArray()));
         const reduced = dedupe(featuresArray.map(f => ({
             id: f.id(),
             refName: f.get('refName'),

package/esm/PileupRPC/methods/GetReducedFeatures.js.map

@@ -1 +1 @@
-{"version":3,"file":"GetReducedFeatures.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetReducedFeatures.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,EAAU,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAGnD,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAExC,SAAS;AACT,OAAO,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,SAAS,CAAA;AAE5D,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAEnC,mEAAmE;AACnE,MAAM,CAAC,OAAO,OAAO,wBAAyB,SAAQ,aAAa;IAAnE;;QACE,SAAI,GAAG,0BAA0B,CAAA;IA6DnC,CAAC;IA3DC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAC5D,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,GAAG,CAAA;QACjD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,WAAW;aACpC,4BAA4B,CAAC,OAAO,EAAE,GAAG,CAAC;aAC1C,IAAI,CAAC,OAAO,EAAE,CAAC;aACf,SAAS,EAAE,CAAA;QAEd,MAAM,OAAO,GAAG,MAAM,CACpB,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACtB,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE;YACV,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;YACnB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC;YACvB,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;YACjB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,iBAAiB,CAAC;YAC9B,gBAAgB,EAAE,CAAC,CAAC,GAAG,CAAC,kBAAkB,CAAC;YAC3C,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,EAAE,EAAE,MAAM,CAAC,CAAC,EAAE,IAAI,CAAC;SACpB,CAAC,CAAC,EACH,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CACV,CAAA;QAED,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,kBAAkB,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACxE,MAAM,MAAM,GAAG,EAAyC,CAAA;QAExD,gBAAgB;QAChB,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAClB,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE;gBACnB,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;aACpB;YACD,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACxB,CAAC,CAAC,CAAA;QACF,OAAO;YACL,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC;YAC7B,KAAK;YACL,SAAS,EAAE,CAAC,CAAC,KAAK;YAClB,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF"}
+{"version":3,"file":"GetReducedFeatures.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetReducedFeatures.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AACzE,OAAO,EAAU,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAGnD,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AACrC,SAAS;AACT,OAAO,EAAE,cAAc,EAAE,kBAAkB,EAAE,MAAM,SAAS,CAAA;AAE5D,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,MAAM,EAAE,MAAM,YAAY,CAAA;AAEnC,mEAAmE;AACnE,MAAM,CAAC,OAAO,OAAO,wBAAyB,SAAQ,aAAa;IAAnE;;QACE,SAAI,GAAG,0BAA0B,CAAA;IA4DnC,CAAC;IA1DC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAC5D,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GAAG,GAAG,CAAA;QACjD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,cAAc,CACxC,WAAW,CAAC,4BAA4B,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CACvE,CAAA;QAED,MAAM,OAAO,GAAG,MAAM,CACpB,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC;YACtB,EAAE,EAAE,CAAC,CAAC,EAAE,EAAE;YACV,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;YACnB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,MAAM,EAAE,CAAC,CAAC,GAAG,CAAC,QAAQ,CAAC;YACvB,GAAG,EAAE,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC;YACjB,KAAK,EAAE,CAAC,CAAC,GAAG,CAAC,OAAO,CAAC;YACrB,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,iBAAiB,CAAC;YAC9B,gBAAgB,EAAE,CAAC,CAAC,GAAG,CAAC,kBAAkB,CAAC;YAC3C,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,QAAQ,EAAE,CAAC,CAAC,GAAG,CAAC,UAAU,CAAC;YAC3B,OAAO,EAAE,CAAC,CAAC,GAAG,CAAC,SAAS,CAAC;YACzB,EAAE,EAAE,MAAM,CAAC,CAAC,EAAE,IAAI,CAAC;SACpB,CAAC,CAAC,EACH,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CACV,CAAA;QAED,MAAM,QAAQ,GAAG,cAAc,CAAC,OAAO,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,kBAAkB,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;QACxE,MAAM,MAAM,GAAG,EAAyC,CAAA;QAExD,gBAAgB;QAChB,OAAO,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAClB,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE;gBACnB,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,CAAA;aACpB;YACD,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACxB,CAAC,CAAC,CAAA;QACF,OAAO;YACL,MAAM,EAAE,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC;YAC7B,KAAK;YACL,SAAS,EAAE,CAAC,CAAC,KAAK;YAClB,uBAAuB,EAAE,IAAI;SAC9B,CAAA;IACH,CAAC;CACF"}

package/esm/PileupRPC/methods/GetVisibleModifications.js

@@ -1,5 +1,6 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { toArray } from 'rxjs/operators';
+import { firstValueFrom } from 'rxjs';
 // locals
 import { getModificationTypes } from '../../MismatchParser';
 import PileupBaseRPC from '../base';
@@ -12,10 +13,7 @@ export default class PileupGetVisibleModifications extends PileupBaseRPC {
     async execute(args, rpcDriver) {
         const { adapterConfig, sessionId, regions } = await this.deserializeArguments(args, rpcDriver);
         const dataAdapter = (await getAdapter(this.pluginManager, sessionId, adapterConfig)).dataAdapter;
-        const featuresArray = await dataAdapter
-            .getFeaturesInMultipleRegions(regions)
-            .pipe(toArray())
-            .toPromise();
+        const featuresArray = await firstValueFrom(dataAdapter.getFeaturesInMultipleRegions(regions).pipe(toArray()));
         const uniqueValues = new Set();
         featuresArray.forEach(f => {
             getModificationTypes(getTagAlt(f, 'MM', 'Mm') || '').forEach(t => uniqueValues.add(t));

package/esm/PileupRPC/methods/GetVisibleModifications.js.map

@@ -1 +1 @@
-{"version":3,"file":"GetVisibleModifications.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetVisibleModifications.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAIzE,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAExC,SAAS;AACT,OAAO,EAAE,oBAAoB,EAAE,MAAM,sBAAsB,CAAA;AAC3D,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAA;AAEtC,MAAM,CAAC,OAAO,OAAO,6BAA8B,SAAQ,aAAa;IAAxE;;QACE,SAAI,GAAG,+BAA+B,CAAA;IAgCxC,CAAC;IA9BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GACzC,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAClD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,WAAW;aACpC,4BAA4B,CAAC,OAAO,CAAC;aACrC,IAAI,CAAC,OAAO,EAAE,CAAC;aACf,SAAS,EAAE,CAAA;QAEd,MAAM,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACtC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACxB,oBAAoB,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAC/D,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CACpB,CAAA;QACH,CAAC,CAAC,CAAA;QACF,OAAO,CAAC,GAAG,YAAY,CAAC,CAAA;IAC1B,CAAC;CACF"}
+{"version":3,"file":"GetVisibleModifications.js","sourceRoot":"","sources":["../../../src/PileupRPC/methods/GetVisibleModifications.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,8CAA8C,CAAA;AAIzE,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAErC,SAAS;AACT,OAAO,EAAE,oBAAoB,EAAE,MAAM,sBAAsB,CAAA;AAC3D,OAAO,aAAa,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,SAAS,EAAE,MAAM,YAAY,CAAA;AAEtC,MAAM,CAAC,OAAO,OAAO,6BAA8B,SAAQ,aAAa;IAAxE;;QACE,SAAI,GAAG,+BAA+B,CAAA;IA+BxC,CAAC;IA7BC,KAAK,CAAC,OAAO,CACX,IAOC,EACD,SAAiB;QAEjB,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,OAAO,EAAE,GACzC,MAAM,IAAI,CAAC,oBAAoB,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;QAClD,MAAM,WAAW,GAAG,CAClB,MAAM,UAAU,CAAC,IAAI,CAAC,aAAa,EAAE,SAAS,EAAE,aAAa,CAAC,CAC/D,CAAC,WAAqC,CAAA;QAEvC,MAAM,aAAa,GAAG,MAAM,cAAc,CACxC,WAAW,CAAC,4BAA4B,CAAC,OAAO,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CAClE,CAAA;QAED,MAAM,YAAY,GAAG,IAAI,GAAG,EAAU,CAAA;QACtC,aAAa,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YACxB,oBAAoB,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE,CAC/D,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,CACpB,CAAA;QACH,CAAC,CAAC,CAAA;QACF,OAAO,CAAC,GAAG,YAAY,CAAC,CAAA;IAC1B,CAAC;CACF"}

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -2,6 +2,8 @@ import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { toArray } from 'rxjs/operators';
+import { firstValueFrom } from 'rxjs';
+// locals
 import generateCoverageBins from './generateCoverageBins';
 import { fetchSequence } from '../util';
 export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
@@ -31,10 +33,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { subadapter } = await this.configure();
-            const feats = await subadapter
-                .getFeatures(region, opts)
-                .pipe(toArray())
-                .toPromise();
+            const feats = await firstValueFrom(subadapter.getFeatures(region, opts).pipe(toArray()));
             const { bins, skipmap } = await generateCoverageBins(feats, region, opts, arg => this.fetchSequence(arg));
             bins.forEach((bin, index) => {
                 const start = region.start + index;

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map

@@ -1 +1 @@
-{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,EAAE,aAAa,EAAE,MAAM,SAAS,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,UAAU;iBAC3B,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC;iBACzB,IAAI,CAAC,OAAO,EAAE,CAAC;iBACf,SAAS,EAAE,CAAA;YAEd,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,oBAAoB,CAClD,KAAK,EACL,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAC/B,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAC3C,OAAO,EAAE,YAAY,EAAE,CAAA"}
+{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAErC,SAAS;AACT,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,EAAE,aAAa,EAAE,MAAM,SAAS,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,cAAc,CAChC,UAAU,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CACrD,CAAA;YAED,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,oBAAoB,CAClD,KAAK,EACL,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAC/B,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,OAAiB,EAAE,IAAkB;QAC9D,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,oBAAoB,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACvD,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC;AAED,MAAM,EAAE,YAAY,EAAE,GAAG,kBAAkB,CAAA;AAC3C,OAAO,EAAE,YAAY,EAAE,CAAA"}

package/esm/util.js

@@ -1,4 +1,5 @@
 import { toArray } from 'rxjs/operators';
+import { firstValueFrom } from 'rxjs';
 // get tag from BAM or CRAM feature, where CRAM uses feature.get('tags') and
 // BAM does not
 export function getTag(feature, tag) {
@@ -66,14 +67,13 @@ export function getColorWGBS(strand, base) {
 export async function fetchSequence(region, adapter) {
     var _a;
     const { end, originalRefName, refName } = region;
-    const feats = await adapter
+    const feats = await firstValueFrom(adapter
         .getFeatures({
         ...region,
         refName: originalRefName || refName,
         end: end + 1,
     })
-        .pipe(toArray())
-        .toPromise();
+        .pipe(toArray()));
     return (_a = feats[0]) === null || _a === void 0 ? void 0 : _a.get('seq');
 }
 // has to check underlying C-G (aka CpG) on the reference sequence

package/esm/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAGxC,4EAA4E;AAC5E,eAAe;AACf,MAAM,UAAU,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC5C,CAAC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,MAAM,UAAU,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;IAClE,OAAO,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAED,gDAAgD;AAChD,kFAAkF;AAClF,MAAM,CAAC,MAAM,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAED,MAAM,UAAU,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEhD,MAAM,KAAK,GAAG,MAAM,OAAO;SACxB,WAAW,CAAC;QACX,GAAG,MAAM;QACT,OAAO,EAAE,eAAe,IAAI,OAAO;QACnC,GAAG,EAAE,GAAG,GAAG,CAAC;KACb,CAAC;SACD,IAAI,CAAC,OAAO,EAAE,CAAC;SACf,SAAS,EAAE,CAAA;IACd,OAAO,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,CAAA;AAC7B,CAAC;AAED,kEAAkE;AAClE,MAAM,UAAU,4BAA4B,CAAC,IAAa;IACxD,OAAO,IAAI,KAAK,aAAa,CAAA;AAC/B,CAAC"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AAGxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AACrC,4EAA4E;AAC5E,eAAe;AACf,MAAM,UAAU,MAAM,CAAC,OAAgB,EAAE,GAAW;IAClD,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;IAChC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;AAC5C,CAAC;AAED,4EAA4E;AAC5E,0CAA0C;AAC1C,MAAM,UAAU,SAAS,CAAC,OAAgB,EAAE,GAAW,EAAE,GAAW;IAClE,OAAO,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,GAAG,CAAC,CAAA;AACrD,CAAC;AAED,gDAAgD;AAChD,kFAAkF;AAClF,MAAM,CAAC,MAAM,gBAAgB,GAAG;IAC9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;IAE9B,EAAE,EAAE;QACF,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;QAEV,IAAI,EAAE,IAAI;QACV,IAAI,EAAE,IAAI;KACkB;CAC/B,CAAA;AAED,MAAM,UAAU,YAAY,CAAC,MAAc,EAAE,IAAY;IACvD,IAAI,MAAM,KAAK,CAAC,EAAE;QAChB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;SAAM,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE;QACxB,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;QACD,IAAI,IAAI,KAAK,GAAG,EAAE;YAChB,OAAO,MAAM,CAAA;SACd;KACF;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,aAAa,CACjC,MAAuB,EACvB,OAA+B;;IAE/B,MAAM,EAAE,GAAG,EAAE,eAAe,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;IAEhD,MAAM,KAAK,GAAG,MAAM,cAAc,CAChC,OAAO;SACJ,WAAW,CAAC;QACX,GAAG,MAAM;QACT,OAAO,EAAE,eAAe,IAAI,OAAO;QACnC,GAAG,EAAE,GAAG,GAAG,CAAC;KACb,CAAC;SACD,IAAI,CAAC,OAAO,EAAE,CAAC,CACnB,CAAA;IACD,OAAO,MAAA,KAAK,CAAC,CAAC,CAAC,0CAAE,GAAG,CAAC,KAAK,CAAC,CAAA;AAC7B,CAAC;AAED,kEAAkE;AAClE,MAAM,UAAU,4BAA4B,CAAC,IAAa;IACxD,OAAO,IAAI,KAAK,aAAa,CAAA;AAC/B,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.3.1",
+  "version": "2.3.3",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -56,7 +56,7 @@
     "mobx-react": "^7.0.0",
     "mobx-state-tree": "^5.0.0",
     "react": ">=16.8.0",
-    "rxjs": "^6.0.0",
+    "rxjs": "^7.0.0",
     "tss-react": "^4.0.0"
   },
   "publishConfig": {
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "75c4cba2f50c626c62881abd5851dbf2435c2401"
+  "gitHead": "283e0387ccd5acc9f092cf00804d1fcac212e68d"
 }

package/src/AlignmentsFeatureDetail/{index.test.js → index.test.tsx}

@@ -1,13 +1,14 @@
+import React from 'react'
 import { render } from '@testing-library/react'
 import { types } from 'mobx-state-tree'
-import React from 'react'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
+
+// locals
 import { stateModelFactory } from '.'
 import ReactComponent from './AlignmentsFeatureDetail'
 
 test('open up a widget', () => {
-  console.warn = jest.fn()
   const pluginManager = new PluginManager([])
 
   const Session = types.model({
@@ -17,6 +18,7 @@ test('open up a widget', () => {
   })
   const session = Session.create(
     {
+      // @ts-ignore
       widget: { type: 'AlignmentsFeatureWidget' },
     },
     { pluginManager },

package/src/BamAdapter/BamAdapter.test.ts

@@ -1,4 +1,5 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import Adapter from './BamAdapter'
 import configSchema from './configSchema'
 
@@ -25,7 +26,7 @@ test('adapter can fetch features from volvox.bam', async () => {
     end: 20000,
   })
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   expect(featuresArray[0].get('refName')).toBe('ctgA')
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.length).toEqual(3809)
@@ -58,7 +59,7 @@ test('adapter can fetch features from volvox.bam', async () => {
     start: 0,
     end: 20000,
   })
-  const featuresArrayCSI = await featuresCSI.pipe(toArray()).toPromise()
+  const featuresArrayCSI = await firstValueFrom(featuresCSI.pipe(toArray()))
   const featuresJsonArrayCSI = featuresArrayCSI.map(f => f.toJSON())
   expect(featuresJsonArrayCSI).toEqual(featuresJsonArray)
 })
@@ -86,7 +87,7 @@ test('test usage of BamSlightlyLazyFeature toJSON (used in the widget)', async (
     start: 0,
     end: 100,
   })
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const f = featuresArray[0].toJSON()
   expect(f.refName).toBe('ctgA')
   expect(f.start).toBe(2)
@@ -117,7 +118,7 @@ test('test usage of BamSlightlyLazyFeature for extended CIGAR', async () => {
     start: 13260,
     end: 13340,
   })
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const f = featuresArray[0]
   expect(f.get('mismatches')).toMatchSnapshot()
 })

package/src/BamAdapter/BamAdapter.ts

@@ -11,6 +11,7 @@ import { toArray } from 'rxjs/operators'
 
 // locals
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature'
+import { firstValueFrom } from 'rxjs'
 
 interface Header {
   idToName: string[]
@@ -138,7 +139,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
       assemblyName: '',
     })
 
-    const seqChunks = await features.pipe(toArray()).toPromise()
+    const seqChunks = await firstValueFrom(features.pipe(toArray()))
 
     let sequence = ''
     seqChunks

package/src/CombinationTest.test.ts

@@ -9,6 +9,7 @@ import { SequenceAdapter } from './CramAdapter/CramTestAdapters'
 
 import cramConfigSchema from './CramAdapter/configSchema'
 import bamConfigSchema from './BamAdapter/configSchema'
+import { firstValueFrom } from 'rxjs'
 
 const pluginManager = new PluginManager()
 
@@ -55,8 +56,8 @@ async function getFeats(f1: string, f2: string) {
   }
   const bamFeatures = bamAdapter.getFeatures(query)
   const cramFeatures = cramAdapter.getFeatures(query)
-  const bamFeaturesArray = await bamFeatures.pipe(toArray()).toPromise()
-  const cramFeaturesArray = await cramFeatures.pipe(toArray()).toPromise()
+  const bamFeaturesArray = await firstValueFrom(bamFeatures.pipe(toArray()))
+  const cramFeaturesArray = await firstValueFrom(cramFeatures.pipe(toArray()))
   return { bamFeaturesArray, cramFeaturesArray }
 }
 

package/src/CramAdapter/CramAdapter.test.ts

@@ -1,4 +1,5 @@
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import { LocalFile } from 'generic-filehandle'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
@@ -40,7 +41,7 @@ test('adapter can fetch features from volvox-sorted.cram', async () => {
     end: 20000,
   })
 
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   expect(featuresArray[0].get('refName')).toBe('ctgA')
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray.length).toEqual(3809)
@@ -74,7 +75,7 @@ test('test usage of cramSlightlyLazyFeature toJSON (used in the widget)', async
     start: 0,
     end: 100,
   })
-  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresArray = await firstValueFrom(features.pipe(toArray()))
   const f = featuresArray[0].toJSON()
   expect(f.refName).toBe('ctgA')
   expect(f.start).toBe(2)

package/src/CramAdapter/CramAdapter.ts

@@ -8,6 +8,7 @@ import { checkAbortSignal, Region, Feature } from '@jbrowse/core/util'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { toArray } from 'rxjs/operators'
+import { firstValueFrom } from 'rxjs'
 import CramSlightlyLazyFeature from './CramSlightlyLazyFeature'
 
 interface Header {
@@ -103,15 +104,16 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
       throw new Error('unknown')
     }
 
-    const seqChunks = await sequenceAdapter
-      .getFeatures({
-        refName,
-        start,
-        end,
-        assemblyName: '',
-      })
-      .pipe(toArray())
-      .toPromise()
+    const seqChunks = await firstValueFrom(
+      sequenceAdapter
+        .getFeatures({
+          refName,
+          start,
+          end,
+          assemblyName: '',
+        })
+        .pipe(toArray()),
+    )
 
     const sequence = seqChunks
       .sort((a, b) => a.get('start') - b.get('start'))

package/src/LinearAlignmentsDisplay/models/{configSchema.test.js → configSchema.test.ts}

@@ -5,6 +5,8 @@ import {
   svgFeatureRendererConfigSchema,
   SvgFeatureRendererReactComponent,
 } from '@jbrowse/plugin-svg'
+
+// locals
 import PileupRenderer from '../../PileupRenderer'
 import SNPCoverageRenderer from '../../SNPCoverageRenderer'
 import LinearPileupDisplay from '../../LinearPileupDisplay'
@@ -17,11 +19,13 @@ beforeEach(() => {
 })
 
 afterEach(() => {
+  // @ts-ignore
   console.warn.mockRestore()
 })
 
 class AlignmentsPlugin extends Plugin {
-  install(pluginManager) {
+  name = 'AlignmentsPlugin'
+  install(pluginManager: PluginManager) {
     PileupRenderer(pluginManager)
 
     pluginManager.addRendererType(

package/src/LinearReadArcsDisplay/configSchema.ts

@@ -28,6 +28,16 @@ function configSchemaF(pluginManager: PluginManager) {
         defaultValue: 1,
       },
 
+      /**
+       * #slot
+       */
+      jitter: {
+        type: 'number',
+        description:
+          'jitters the x position so e.g. if many reads map to exact same x position, jittering makes it easy to see that there are many of them',
+        defaultValue: 0,
+      },
+
       /**
        * #slot
        */

package/src/LinearReadArcsDisplay/drawFeats.ts

@@ -9,6 +9,7 @@ import {
 } from '../shared/color'
 import { ChainData } from '../shared/fetchChains'
 import { featurizeSA } from '../MismatchParser'
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 
 export function hasPairedReads(features: ChainData) {
   for (const f of features.chains.values()) {
@@ -21,6 +22,17 @@ export function hasPairedReads(features: ChainData) {
 
 type LGV = LinearGenomeViewModel
 
+function jitter(n: number) {
+  return Math.random() * 2 * n - n
+}
+
+interface CoreFeat {
+  strand: number
+  refName: string
+  start: number
+  end: number
+}
+
 export default async function drawFeats(
   self: {
     setLastDrawnOffsetPx: (n: number) => void
@@ -31,34 +43,48 @@ export default async function drawFeats(
     height: number
     chainData?: ChainData
     lineWidthSetting: number
+    jitterVal: number
   },
   ctx: CanvasRenderingContext2D,
 ) {
-  const { chainData } = self
+  const {
+    chainData,
+    height,
+    colorBy,
+    drawInter,
+    drawLongRange,
+    lineWidthSetting,
+    jitterVal,
+  } = self
   if (!chainData) {
     return
   }
-  const displayHeight = self.height
   const view = getContainingView(self) as LGV
   const { assemblyManager } = getSession(self)
   self.setLastDrawnOffsetPx(view.offsetPx)
-  ctx.lineWidth = self.lineWidthSetting
+  ctx.lineWidth = lineWidthSetting
   const { chains, stats } = chainData
   const hasPaired = hasPairedReads(chainData)
   const assemblyName = view.assemblyNames[0]
   const asm = assemblyManager.get(assemblyName)
-  const type = self.colorBy?.type || 'insertSizeAndOrientation'
+  const type = colorBy?.type || 'insertSizeAndOrientation'
+  if (!asm) {
+    return
+  }
+
+  function drawLineAtOffset(p: number, c: string) {
+    // draws a vertical line off to middle of nowhere if the second end not found
+    ctx.strokeStyle = c
+    ctx.beginPath()
+    ctx.moveTo(p, 0)
+    ctx.lineTo(p, height)
+    ctx.stroke()
+  }
 
   function draw(
-    k1: {
-      strand: number
-      refName: string
-      start: number
-      end: number
-      tlen?: number
-      pair_orientation?: string
-    },
-    k2: { strand: number; refName: string; start: number; end: number },
+    k1: CoreFeat & { tlen?: number; pair_orientation?: string },
+    k2: CoreFeat,
+    assembly: Assembly,
     longRange?: boolean,
   ) {
     const s1 = k1.strand
@@ -68,14 +94,16 @@ export default async function drawFeats(
 
     const p1 = f1 ? k1.start : k1.end
     const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start
-
-    const r1 = view.bpToPx({ refName: k1.refName, coord: p1 })
-    const r2 = view.bpToPx({ refName: k2.refName, coord: p2 })
+    const ra1 = assembly.getCanonicalRefName(k1.refName)
+    const ra2 = assembly.getCanonicalRefName(k2.refName)
+    const r1 = view.bpToPx({ refName: ra1, coord: p1 })
+    const r2 = view.bpToPx({ refName: ra2, coord: p2 })
 
     if (r1 && r2) {
       const radius = (r2.offsetPx - r1.offsetPx) / 2
       const absrad = Math.abs(radius)
       const p = r1.offsetPx - view.offsetPx
+      const p2 = r2.offsetPx - view.offsetPx
 
       // bezier (used for non-long-range arcs) requires moveTo before beginPath
       // arc (used for long-range) requires moveTo after beginPath (or else a
@@ -99,9 +127,7 @@ export default async function drawFeats(
           } else if (type === 'insertSize') {
             ctx.strokeStyle = getInsertSizeColor(k1, k2, stats) || 'grey'
           } else if (type === 'gradient') {
-            ctx.strokeStyle = `hsl(${
-              Math.log10(Math.abs(p1 - p2)) * 10
-            },50%,50%)`
+            ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`
           }
         } else {
           if (type === 'orientation' || type === 'insertSizeAndOrientation') {
@@ -113,53 +139,55 @@ export default async function drawFeats(
               ctx.strokeStyle = 'grey'
             }
           } else if (type === 'gradient') {
-            ctx.strokeStyle = `hsl(${
-              Math.log10(Math.abs(p1 - p2)) * 10
-            },50%,50%)`
+            ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`
           }
         }
       }
 
       const destX = p + radius * 2
-      const destY = Math.min(displayHeight, absrad)
+      const destY = Math.min(height + jitter(jitterVal), absrad)
       if (longRange) {
-        ctx.arc(p + radius, 0, absrad, 0, Math.PI)
+        // avoid drawing gigantic circles that glitch out the rendering,
+        // instead draw vertical lines
+        if (absrad > 100_000) {
+          drawLineAtOffset(p + jitter(jitterVal), 'red')
+          drawLineAtOffset(p2 + jitter(jitterVal), 'red')
+        } else {
+          ctx.arc(p + radius + jitter(jitterVal), 0, absrad, 0, Math.PI)
+          ctx.stroke()
+        }
       } else {
-        ctx.bezierCurveTo(p, destY, destX, destY, destX, 0)
+        ctx.bezierCurveTo(
+          p + jitter(jitterVal),
+          destY,
+          destX,
+          destY,
+          destX + jitter(jitterVal),
+          0,
+        )
+        ctx.stroke()
       }
-      ctx.stroke()
-    } else if (r1 && self.drawInter) {
-      // draws a vertical line off to middle of nowhere if the second end not found
-      const p = r1.offsetPx - view.offsetPx
-      ctx.strokeStyle = 'purple'
-      ctx.beginPath()
-      ctx.moveTo(p, 0)
-      ctx.lineTo(p, displayHeight)
-      ctx.stroke()
+    } else if (r1 && drawInter) {
+      drawLineAtOffset(r1.offsetPx - view.offsetPx, 'purple')
     }
   }
 
   for (let i = 0; i < chains.length; i++) {
     let chain = chains[i]
-
-    if (chain.length === 1 && self.drawLongRange) {
+    if (chain.length === 1 && drawLongRange) {
       // singleton feature
       const f = chain[0]
 
       // special case where we look at RPOS/RNEXT
       if (hasPaired) {
         // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
-        const refName = asm?.getCanonicalRefName(f.next_ref!) || f.next_ref!
+        const refName = f.next_ref!
         // eslint-disable-next-line @typescript-eslint/no-non-null-assertion
         const coord = f.next_pos!
         draw(
           f,
-          {
-            refName,
-            start: coord,
-            end: coord,
-            strand: f.strand,
-          },
+          { refName, start: coord, end: coord, strand: f.strand },
+          asm,
           true,
         )
       }
@@ -171,16 +199,7 @@ export default async function drawFeats(
         for (let i = 0; i < features.length - 1; i++) {
           const f = features[i]
           const v1 = features[i + 1]
-          draw(
-            f,
-            {
-              refName: asm?.getCanonicalRefName(v1.refName) || v1.refName,
-              start: v1.start,
-              end: v1.end,
-              strand: v1.strand,
-            },
-            true,
-          )
+          draw(f, v1, asm, true)
         }
       }
     } else {
@@ -192,7 +211,7 @@ export default async function drawFeats(
         chain = chain.filter(f => !(f.flags & 2048))
       }
       for (let i = 0; i < chain.length - 1; i++) {
-        draw(chain[i], chain[i + 1], false)
+        draw(chain[i], chain[i + 1], asm, false)
       }
     }
   }