@jbrowse/plugin-alignments 2.4.2 → 2.5.0

package/esm/PileupRenderer/configSchema.d.ts

@@ -1,2 +1,88 @@
-declare const PileupRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const PileupRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     * default magenta here is used to detect the user has not customized this
+     */
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+        contextVariable: string[];
+    };
+    /**
+     * #slot
+     */
+    orientationType: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        defaultValue: string;
+        description: string;
+    };
+    /**
+     * #slot
+     */
+    displayMode: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    minSubfeatureWidth: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    maxHeight: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    maxClippingSize: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    height: {
+        type: string;
+        description: string;
+        defaultValue: number;
+        contextVariable: string[];
+    };
+    /**
+     * #slot
+     */
+    noSpacing: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    largeInsertionIndicatorScale: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    mismatchAlpha: {
+        type: string;
+        defaultValue: boolean;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default PileupRenderer;

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -8,7 +8,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     }>;
     fetchSequence(region: Region): Promise<any>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
+    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     freeResources(): void;
 }

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -65,9 +65,9 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, opts.signal);
     }
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const { subadapter } = await this.configure();
-        return subadapter.estimateRegionsStats(regions, opts);
+        return subadapter.getMultiRegionFeatureDensityStats(regions, opts);
     }
     async getRefNames(opts = {}) {
         const { subadapter } = await this.configure();

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map

@@ -1 +1 @@
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+{"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,iCAAiC,CACrC,OAAiB,EACjB,IAAkB;QAElB,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,iCAAiC,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACpE,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/SNPCoverageAdapter/configSchema.d.ts

@@ -1,2 +1,11 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     * normally refers to a BAM or CRAM adapter
+     */
+    subadapter: {
+        type: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/SNPCoverageAdapter/generateCoverageBins.js

@@ -64,21 +64,23 @@ export default async function generateCoverageBins(features, region, opts, fetch
             const mm = getTagAlt(feature, 'MM', 'Mm') || '';
             const ops = parseCigar(feature.get('CIGAR'));
             const fend = feature.get('end');
-            getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
-                const mod = `mod_${type}`;
-                for (const pos of getNextRefPos(ops, positions)) {
-                    const epos = pos + fstart - region.start;
-                    if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-                        const bin = bins[epos];
-                        if (bin) {
-                            inc(bin, fstrand, 'cov', mod);
-                        }
-                        else {
-                            console.warn('Undefined position in modifications snpcoverage encountered');
+            if (seq) {
+                getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
+                    const mod = `mod_${type}`;
+                    for (const pos of getNextRefPos(ops, positions)) {
+                        const epos = pos + fstart - region.start;
+                        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+                            const bin = bins[epos];
+                            if (bin) {
+                                inc(bin, fstrand, 'cov', mod);
+                            }
+                            else {
+                                console.warn('Undefined position in modifications snpcoverage encountered');
+                            }
                         }
                     }
-                }
-            });
+                });
+            }
         }
         // methylation based coloring takes into account both reference
         // sequence CpG detection and reads
@@ -90,41 +92,43 @@ export default async function generateCoverageBins(features, region, opts, fetch
             const mm = getTagAlt(feature, 'MM', 'Mm') || '';
             const methBins = new Array(region.end - region.start).fill(0);
             const ops = parseCigar(feature.get('CIGAR'));
-            getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
-                // we are processing methylation
-                if (type === 'm') {
-                    for (const pos of getNextRefPos(ops, positions)) {
-                        const epos = pos + fstart - region.start;
-                        if (epos >= 0 && epos < methBins.length) {
-                            methBins[epos] = 1;
+            if (seq) {
+                getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
+                    // we are processing methylation
+                    if (type === 'm') {
+                        for (const pos of getNextRefPos(ops, positions)) {
+                            const epos = pos + fstart - region.start;
+                            if (epos >= 0 && epos < methBins.length) {
+                                methBins[epos] = 1;
+                            }
                         }
                     }
-                }
-            });
-            for (let j = fstart; j < fend; j++) {
-                const i = j - region.start;
-                if (i >= 0 && i < bins.length - 1) {
-                    const l1 = regionSeq[i].toLowerCase();
-                    const l2 = regionSeq[i + 1].toLowerCase();
-                    const bin = bins[i];
-                    const bin1 = bins[i + 1];
-                    // color
-                    if (l1 === 'c' && l2 === 'g') {
-                        if (methBins[i] || methBins[i + 1]) {
-                            inc(bin, fstrand, 'cov', 'meth');
-                            inc(bin1, fstrand, 'cov', 'meth');
-                            bins[i].ref--;
-                            bins[i][fstrand]--;
-                            bins[i + 1].ref--;
-                            bins[i + 1][fstrand]--;
-                        }
-                        else {
-                            inc(bin, fstrand, 'cov', 'unmeth');
-                            inc(bin1, fstrand, 'cov', 'unmeth');
-                            bins[i].ref--;
-                            bins[i][fstrand]--;
-                            bins[i + 1].ref--;
-                            bins[i + 1][fstrand]--;
+                });
+                for (let j = fstart; j < fend; j++) {
+                    const i = j - region.start;
+                    if (i >= 0 && i < bins.length - 1) {
+                        const l1 = regionSeq[i].toLowerCase();
+                        const l2 = regionSeq[i + 1].toLowerCase();
+                        const bin = bins[i];
+                        const bin1 = bins[i + 1];
+                        // color
+                        if (l1 === 'c' && l2 === 'g') {
+                            if (methBins[i] || methBins[i + 1]) {
+                                inc(bin, fstrand, 'cov', 'meth');
+                                inc(bin1, fstrand, 'cov', 'meth');
+                                bins[i].ref--;
+                                bins[i][fstrand]--;
+                                bins[i + 1].ref--;
+                                bins[i + 1][fstrand]--;
+                            }
+                            else {
+                                inc(bin, fstrand, 'cov', 'unmeth');
+                                inc(bin1, fstrand, 'cov', 'unmeth');
+                                bins[i].ref--;
+                                bins[i][fstrand]--;
+                                bins[i + 1].ref--;
+                                bins[i + 1][fstrand]--;
+                            }
                         }
                     }
                 }

package/esm/SNPCoverageAdapter/generateCoverageBins.js.map

@@ -1 +1 @@
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+{"version":3,"file":"generateCoverageBins.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/generateCoverageBins.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,MAAM,EAAE,SAAS,EAAE,4BAA4B,EAAE,MAAM,SAAS,CAAA;AACzE,OAAO,EACL,UAAU,EACV,aAAa,EACb,wBAAwB,GAEzB,MAAM,mBAAmB,CAAA;AAE1B,SAAS,WAAW,CAAC,QAAkB;IACrC,OAAO,CAAC,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAA;AAC1D,CAAC;AAED,SAAS,WAAW,CAAC,IAAY;IAC/B,OAAO,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,UAAU,IAAI,IAAI,KAAK,WAAW,CAAA;AAC3E,CAAC;AAED,8DAA8D;AAC9D,SAAS,GAAG,CAAC,GAAQ,EAAE,MAAc,EAAE,IAAY,EAAE,KAAa;IAChE,IAAI,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAA;IAC9B,IAAI,OAAO,KAAK,SAAS,EAAE;QACzB,OAAO,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,GAAG;YAC3B,KAAK,EAAE,CAAC;YACR,IAAI,EAAE,CAAC;YACP,GAAG,EAAE,CAAC;YACN,GAAG,EAAE,CAAC;SACP,CAAA;KACF;IACD,OAAO,CAAC,KAAK,EAAE,CAAA;IACf,OAAO,CAAC,MAAM,CAAC,EAAE,CAAA;AACnB,CAAC;AAED,MAAM,CAAC,OAAO,CAAC,KAAK,UAAU,oBAAoB,CAChD,QAAmB,EACnB,MAAc,EACd,IAAoE,EACpE,aAA+C;;IAE/C,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;IACxB,MAAM,MAAM,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAA;IAEnD,MAAM,OAAO,GAAG,EASf,CAAA;IAQD,MAAM,SAAS,GACb,QAAQ,CAAC,MAAM,IAAI,4BAA4B,CAAC,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,CAAC;QACjE,CAAC,CAAC,MAAM,aAAa,CAAC,MAAM,CAAC;QAC7B,CAAC,CAAC,SAAS,CAAA;IAEf,MAAM,IAAI,GAAG,EAYV,CAAA;IAEH,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACxC,MAAM,OAAO,GAAG,QAAQ,CAAC,CAAC,CAAC,CAAA;QAC3B,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACnC,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC/B,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,QAAQ,CAAe,CAAA;QAEnD,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;YACtC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;YAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,MAAM,EAAE;gBACxB,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE;oBACzB,IAAI,CAAC,CAAC,CAAC,GAAG;wBACR,KAAK,EAAE,CAAC;wBACR,GAAG,EAAE,CAAC;wBACN,GAAG,EAAE,CAAC;wBACN,IAAI,EAAE,CAAC;wBACP,GAAG,EAAE,CAAC;wBACN,GAAG,EAAE,CAAC;wBACN,OAAO,EAAE,EAAa;wBACtB,GAAG,EAAE,EAAa;wBAClB,QAAQ,EAAE,EAAa;wBACvB,MAAM,EAAE,EAAa;qBACtB,CAAA;iBACF;gBACD,IAAI,CAAC,KAAK,IAAI,EAAE;oBACd,IAAI,CAAC,CAAC,CAAC,CAAC,KAAK,EAAE,CAAA;oBACf,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;oBACb,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;oBACb,IAAI,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,EAAE,CAAA;iBACnB;aACF;SACF;QAED,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,eAAe,EAAE;YACrC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAuB,CAAA;YACpD,MAAM,EAAE,GAAI,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAY,IAAI,EAAE,CAAA;YAC3D,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;YAC5C,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;YAC/B,IAAI,GAAG,EAAE;gBACP,wBAAwB,CAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;oBACtB,MAAM,GAAG,GAAG,OAAO,IAAI,EAAE,CAAA;oBACzB,KAAK,MAAM,GAAG,IAAI,aAAa,CAAC,GAAG,EAAE,SAAS,CAAC,EAAE;wBAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;wBACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,IAAI,CAAC,MAAM,IAAI,GAAG,GAAG,MAAM,GAAG,IAAI,EAAE;4BAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,IAAI,CAAC,CAAA;4BACtB,IAAI,GAAG,EAAE;gCACP,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;6BAC9B;iCAAM;gCACL,OAAO,CAAC,IAAI,CACV,6DAA6D,CAC9D,CAAA;6BACF;yBACF;qBACF;gBACH,CAAC,CACF,CAAA;aACF;SACF;QAED,+DAA+D;QAC/D,mCAAmC;aAC9B,IAAI,CAAA,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,MAAK,aAAa,EAAE;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,MAAM,IAAI,KAAK,CACb,iEAAiE,CAClE,CAAA;aACF;YACD,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAuB,CAAA;YACpD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,CAAA;YAC/C,MAAM,QAAQ,GAAG,IAAI,KAAK,CAAC,MAAM,CAAC,GAAG,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;YAC7D,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC,CAAA;YAE5C,IAAI,GAAG,EAAE;gBACP,wBAAwB,CAAC,EAAE,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC,OAAO,CAChD,CAAC,EAAE,IAAI,EAAE,SAAS,EAAE,EAAE,EAAE;oBACtB,gCAAgC;oBAChC,IAAI,IAAI,KAAK,GAAG,EAAE;wBAChB,KAAK,MAAM,GAAG,IAAI,aAAa,CAAC,GAAG,EAAE,SAAS,CAAC,EAAE;4BAC/C,MAAM,IAAI,GAAG,GAAG,GAAG,MAAM,GAAG,MAAM,CAAC,KAAK,CAAA;4BACxC,IAAI,IAAI,IAAI,CAAC,IAAI,IAAI,GAAG,QAAQ,CAAC,MAAM,EAAE;gCACvC,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;6BACnB;yBACF;qBACF;gBACH,CAAC,CACF,CAAA;gBAED,KAAK,IAAI,CAAC,GAAG,MAAM,EAAE,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE;oBAClC,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAA;oBAC1B,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE;wBACjC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;wBACrC,MAAM,EAAE,GAAG,SAAS,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,CAAA;wBACzC,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;wBACnB,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;wBAExB,QAAQ;wBACR,IAAI,EAAE,KAAK,GAAG,IAAI,EAAE,KAAK,GAAG,EAAE;4BAC5B,IAAI,QAAQ,CAAC,CAAC,CAAC,IAAI,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,EAAE;gCAClC,GAAG,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;gCAChC,GAAG,CAAC,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;gCACjC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gCACb,IAAI,CAAC,CAAC,CAAC,CAAC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package/esm/SNPCoverageRenderer/configSchema.d.ts

@@ -1,2 +1,43 @@
-declare const SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const SNPCoverageRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    /**
+     * #slot
+     */
+    indicatorThreshold: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     */
+    drawArcs: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    drawInterbaseCounts: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+    /**
+     * #slot
+     */
+    drawIndicators: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default SNPCoverageRenderer;

package/esm/shared/FilterByTag.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 declare function FilterByTagDlg(props: {
     model: {
         filterBy?: {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.4.2",
+  "version": "2.5.0",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -65,5 +65,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "36e382a70e7d220343b873e7e6aba5c83e5342c8"
+  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
 }

package/src/AlignmentsFeatureDetail/__snapshots__/index.test.tsx.snap

@@ -280,7 +280,7 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="css-1upvn7b-container2"
+                class="css-1lttu3w-container"
               >
                 <button
                   class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium css-sghohy-MuiButtonBase-root-MuiButton-root"
@@ -316,7 +316,6 @@ exports[`open up a widget 1`] = `
                     />
                   </button>
                 </div>
-                <br />
               </div>
             </div>
           </div>

package/src/AlignmentsTrack/configSchemaF.ts

@@ -0,0 +1,22 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes'
+import PluginManager from '@jbrowse/core/PluginManager'
+
+/**
+ * #config AlignmentsTrack
+ * has very little config; most config and state logic is on the display
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+export default function configSchemaFactory(pluginManager: PluginManager) {
+  return ConfigurationSchema(
+    'AlignmentsTrack',
+    {},
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: createBaseTrackConfig(pluginManager),
+    },
+  )
+}

package/src/AlignmentsTrack/index.ts

@@ -1,32 +1,11 @@
 import PluginManager from '@jbrowse/core/PluginManager'
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import {
-  createBaseTrackConfig,
-  createBaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes/models'
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models'
+import configSchemaF from './configSchemaF'
 
-/**
- * #config AlignmentsTrack
- * has very little config; most config and state logic is on the display
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-function configSchemaFactory(pluginManager: PluginManager) {
-  return ConfigurationSchema(
-    'AlignmentsTrack',
-    {},
-    {
-      /**
-       * #baseConfiguration
-       */
-      baseConfiguration: createBaseTrackConfig(pluginManager),
-    },
-  )
-}
 export default function register(pm: PluginManager) {
   pm.addTrackType(() => {
-    const configSchema = configSchemaFactory(pm)
+    const configSchema = configSchemaF(pm)
     const track = new TrackType({
       name: 'AlignmentsTrack',
       displayName: 'Alignments track',

package/src/BamAdapter/BamAdapter.ts

@@ -227,7 +227,10 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     }, signal)
   }
 
-  async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {
+  async getMultiRegionFeatureDensityStats(
+    regions: Region[],
+    opts?: BaseOptions,
+  ) {
     const { bam } = await this.configure()
     // this is a method to avoid calling on htsget adapters
     // @ts-expect-error
@@ -236,7 +239,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
       const fetchSizeLimit = this.getConf('fetchSizeLimit')
       return { bytes, fetchSizeLimit }
     } else {
-      return super.estimateRegionsStats(regions, opts)
+      return super.getMultiRegionFeatureDensityStats(regions, opts)
     }
   }
 

package/src/CramAdapter/CramAdapter.ts

@@ -278,7 +278,10 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
   }
 
   // we return the configured fetchSizeLimit, and the bytes for the region
-  async estimateRegionsStats(regions: Region[], opts?: BaseOptions) {
+  async getMultiRegionFeatureDensityStats(
+    regions: Region[],
+    opts?: BaseOptions,
+  ) {
     const bytes = await this.bytesForRegions(regions, opts)
     const fetchSizeLimit = this.getConf('fetchSizeLimit')
     return {

package/src/CramAdapter/CramTestAdapters.ts

@@ -2,7 +2,7 @@ import { GenericFilehandle } from 'generic-filehandle'
 import { Observable } from 'rxjs'
 import SimpleFeature from '@jbrowse/core/util/simpleFeature'
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { ConfigurationSchema } from '@jbrowse/core/configuration/configurationSchema'
+import { ConfigurationSchema } from '@jbrowse/core/configuration'
 
 // setup for Cram Adapter Testing
 export function parseSmallFasta(text: string) {

package/src/LinearAlignmentsDisplay/models/model.tsx

@@ -20,6 +20,7 @@ import {
 import { BaseDisplay } from '@jbrowse/core/pluggableElementTypes/models'
 import PluginManager from '@jbrowse/core/PluginManager'
 import { MenuItem } from '@jbrowse/core/ui'
+import { FeatureDensityStats } from '@jbrowse/core/data_adapters/BaseAdapter'
 
 const minDisplayHeight = 20
 
@@ -161,6 +162,13 @@ function stateModelFactory(
       get height() {
         return self.heightPreConfig ?? getConf(self, 'height')
       },
+
+      get featureIdUnderMouse() {
+        return (
+          self.PileupDisplay.featureIdUnderMouse ||
+          self.SNPCoverageDisplay.featureIdUnderMouse
+        )
+      },
     }))
     .views(self => ({
       /**
@@ -234,9 +242,9 @@ function stateModelFactory(
       /**
        * #action
        */
-      updateStatsLimit(stats?: unknown) {
-        self.PileupDisplay.updateStatsLimit(stats)
-        self.SNPCoverageDisplay.updateStatsLimit(stats)
+      setFeatureDensityStatsLimit(stats?: FeatureDensityStats) {
+        self.PileupDisplay.setFeatureDensityStatsLimit(stats)
+        self.SNPCoverageDisplay.setFeatureDensityStatsLimit(stats)
       },
 
       /**

package/src/LinearPileupDisplay/components/SetMaxHeight.tsx

@@ -10,11 +10,11 @@ import {
 import { Dialog } from '@jbrowse/core/ui'
 import { makeStyles } from 'tss-react/mui'
 
-const useStyles = makeStyles()(theme => ({
+const useStyles = makeStyles()({
   root: {
     width: 500,
   },
-}))
+})
 
 function SetMaxHeightDlg(props: {
   model: {
@@ -37,9 +37,7 @@ function SetMaxHeightDlg(props: {
         </Typography>
         <TextField
           value={max}
-          onChange={event => {
-            setMax(event.target.value)
-          }}
+          onChange={event => setMax(event.target.value)}
           placeholder="Enter max height for layout"
         />
         <DialogActions>