npm - @jbrowse/plugin-alignments - Versions diffs - 2.4.1 → 2.5.0 - Mend

@jbrowse/plugin-alignments 2.4.1 → 2.5.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (193) hide show

package/esm/PileupRenderer/PileupRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/PileupRenderer/configSchema.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/esm/SNPCoverageAdapter/configSchema.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js CHANGED Viewed

@@ -83,7 +83,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
             const score = feature.get('score');
             const snpinfo = feature.get('snpinfo');
-            const w = Math.max(rightPx - leftPx + fudgeFactor, 1);
+            const w = Math.max(rightPx - leftPx, 1);
             const totalScore = snpinfo.total;
             const keys = Object.keys(snpinfo.cov).sort();
             let curr = 0;

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/esm/SNPCoverageRenderer/configSchema.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

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

package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "2.4.1",
+  "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": "747c50c4edc0184827efa4f8dfc576ca9a72caeb"
+  "gitHead": "d1ca073996d008f0fe9a52f7c1a47ae649dcfdaf"
 }