npm - @jbrowse/plugin-alignments - Versions diffs - 2.4.2 → 2.5.0 - Mend

@jbrowse/plugin-alignments 2.4.2 → 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 (147) hide show

package/dist/SNPCoverageAdapter/generateCoverageBins.js CHANGED Viewed

@@ -66,21 +66,23 @@ async function generateCoverageBins(features, region, opts, fetchSequence) {
             const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
             const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
             const fend = feature.get('end');
-            (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
-                const mod = `mod_${type}`;
-                for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
-                    const epos = pos + fstart - region.start;
-                    if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-                        const bin = bins[epos];
-                        if (bin) {
-                            inc(bin, fstrand, 'cov', mod);
-                        }
-                        else {
-                            console.warn('Undefined position in modifications snpcoverage encountered');
+            if (seq) {
+                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
+                    const mod = `mod_${type}`;
+                    for (const pos of (0, MismatchParser_1.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
@@ -92,41 +94,43 @@ async function generateCoverageBins(features, region, opts, fetchSequence) {
             const mm = (0, util_1.getTagAlt)(feature, 'MM', 'Mm') || '';
             const methBins = new Array(region.end - region.start).fill(0);
             const ops = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-            (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
-                // we are processing methylation
-                if (type === 'm') {
-                    for (const pos of (0, MismatchParser_1.getNextRefPos)(ops, positions)) {
-                        const epos = pos + fstart - region.start;
-                        if (epos >= 0 && epos < methBins.length) {
-                            methBins[epos] = 1;
+            if (seq) {
+                (0, MismatchParser_1.getModificationPositions)(mm, seq, fstrand).forEach(({ type, positions }) => {
+                    // we are processing methylation
+                    if (type === 'm') {
+                        for (const pos of (0, MismatchParser_1.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/dist/SNPCoverageAdapter/generateCoverageBins.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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package/dist/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/dist/shared/FilterByTag.d.ts CHANGED Viewed

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

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 declare const _default: (props: {
     model: IAnyStateTreeNode;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureFlags.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 export default function AlignmentFlags(props: {
     feature: {
         flags: number;

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureSuppAligns.d.ts CHANGED Viewed

@@ -1,4 +1,3 @@
-/// <reference types="react" />
 import { IAnyStateTreeNode } from 'mobx-state-tree';
 export default function SupplementaryAlignments(props: {
     tag: string;

package/esm/AlignmentsFeatureDetail/index.d.ts CHANGED Viewed

@@ -1,5 +1,5 @@
 import PluginManager from '@jbrowse/core/PluginManager';
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
@@ -13,10 +13,13 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & {
     type: import("mobx-state-tree").ISimpleType<"AlignmentsFeatureWidget">;
 }, {
+    error: unknown;
+} & {
     setFeatureData(featureData: Record<string, unknown>): void;
     clearFeatureData(): void;
     setFormattedData(feat: Record<string, unknown>): void;
     setExtra(type?: string | undefined, trackId?: string | undefined): void;
+    setError(e: unknown): void;
 } & {
     afterCreate(): void;
 }, {

package/esm/AlignmentsTrack/configSchemaF.d.ts ADDED Viewed

@@ -0,0 +1,74 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+export default function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    name: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    assemblyNames: {
+        description: string;
+        type: string;
+        defaultValue: string[];
+    };
+    description: {
+        description: string;
+        type: string;
+        defaultValue: string;
+    };
+    category: {
+        description: string;
+        type: string;
+        defaultValue: never[];
+    };
+    metadata: {
+        type: string;
+        description: string;
+        defaultValue: {};
+    };
+    adapter: import("mobx-state-tree").IAnyModelType;
+    textSearching: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        indexingAttributes: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        indexingFeatureTypesToExclude: {
+            type: string;
+            description: string;
+            defaultValue: string[];
+        };
+        textSearchAdapter: import("mobx-state-tree").IAnyModelType;
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    displays: import("mobx-state-tree").IArrayType<import("mobx-state-tree").IAnyModelType>;
+    formatDetails: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        feature: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        subfeatures: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        depth: {
+            type: string;
+            defaultValue: number;
+            description: string;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    formatAbout: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        config: {
+            type: string;
+            description: string;
+            defaultValue: {};
+            contextVariable: string[];
+        };
+        hideUris: {
+            type: string;
+            defaultValue: boolean;
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "trackId">>, undefined>>;

package/esm/AlignmentsTrack/configSchemaF.js ADDED Viewed

@@ -0,0 +1,16 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+import { createBaseTrackConfig } from '@jbrowse/core/pluggableElementTypes';
+/**
+ * #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) {
+    return ConfigurationSchema('AlignmentsTrack', {}, {
+        /**
+         * #baseConfiguration
+         */
+        baseConfiguration: createBaseTrackConfig(pluginManager),
+    });
+}
+//# sourceMappingURL=configSchemaF.js.map

package/esm/AlignmentsTrack/configSchemaF.js.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"configSchemaF.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/configSchemaF.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,qCAAqC,CAAA;AAG3E;;;GAGG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,CAAC,OAAO,UAAU,mBAAmB,CAAC,aAA4B;IACtE,OAAO,mBAAmB,CACxB,iBAAiB,EACjB,EAAE,EACF;QACE;;WAEG;QACH,iBAAiB,EAAE,qBAAqB,CAAC,aAAa,CAAC;KACxD,CACF,CAAA;AACH,CAAC"}

package/esm/AlignmentsTrack/index.js CHANGED Viewed

@@ -1,22 +1,9 @@
 import TrackType from '@jbrowse/core/pluggableElementTypes/TrackType';
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-import { createBaseTrackConfig, createBaseTrackModel, } from '@jbrowse/core/pluggableElementTypes/models';
-/**
- * #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) {
-    return ConfigurationSchema('AlignmentsTrack', {}, {
-        /**
-         * #baseConfiguration
-         */
-        baseConfiguration: createBaseTrackConfig(pluginManager),
-    });
-}
+import { createBaseTrackModel } from '@jbrowse/core/pluggableElementTypes/models';
+import configSchemaF from './configSchemaF';
 export default function register(pm) {
     pm.addTrackType(() => {
-        const configSchema = configSchemaFactory(pm);
+        const configSchema = configSchemaF(pm);
         const track = new TrackType({
             name: 'AlignmentsTrack',
             displayName: 'Alignments track',

package/esm/AlignmentsTrack/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/AlignmentsTrack/index.ts"],"names":[],"mappings":"AACA,OAAO,SAAS,MAAM,+CAA+C,CAAA;AACrE,OAAO,EAAE,oBAAoB,EAAE,MAAM,4CAA4C,CAAA;AACjF,OAAO,aAAa,MAAM,iBAAiB,CAAA;AAE3C,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,EAAiB;IAChD,EAAE,CAAC,YAAY,CAAC,GAAG,EAAE;QACnB,MAAM,YAAY,GAAG,aAAa,CAAC,EAAE,CAAC,CAAA;QACtC,MAAM,KAAK,GAAG,IAAI,SAAS,CAAC;YAC1B,IAAI,EAAE,iBAAiB;YACvB,WAAW,EAAE,kBAAkB;YAC/B,YAAY;YACZ,UAAU,EAAE,oBAAoB,CAAC,EAAE,EAAE,iBAAiB,EAAE,YAAY,CAAC;SACtE,CAAC,CAAA;QACF,MAAM,uBAAuB,GAAG,EAAE,CAAC,cAAc,CAAC,yBAAyB,CAAC,CAAA;QAC5E,0EAA0E;QAC1E,yEAAyE;QACzE,qDAAqD;QACrD,KAAK,CAAC,cAAc,CAAC,uBAAuB,CAAC,CAAA;QAC7C,OAAO,KAAK,CAAA;IACd,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/BamAdapter/BamAdapter.d.ts CHANGED Viewed

@@ -39,7 +39,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             readName: string;
         };
     }): 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 | {
         bytes: number;
         fetchSizeLimit: any;
     }>;

package/esm/BamAdapter/BamAdapter.js CHANGED Viewed

@@ -156,7 +156,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, signal);
     }
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const { bam } = await this.configure();
         // this is a method to avoid calling on htsget adapters
         // @ts-expect-error
@@ -166,7 +166,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
             return { bytes, fetchSizeLimit };
         }
         else {
-            return super.estimateRegionsStats(regions, opts);
+            return super.getMultiRegionFeatureDensityStats(regions, opts);
         }
     }
     freeResources( /* { region } */) { }

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

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

@@ -1,2 +1,51 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     */
+    bamLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    index: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+        /**
+         * #slot index.indexType
+         */
+        indexType: {
+            model: import("mobx-state-tree").ISimpleType<string>;
+            type: string;
+            defaultValue: string;
+        };
+        /**
+         * #slot index.location
+         */
+        location: {
+            type: string;
+            defaultValue: {
+                uri: string;
+                locationType: string;
+            };
+        };
+    }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    /**
+     * #slot
+     */
+    fetchSizeLimit: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/CramAdapter/CramAdapter.d.ts CHANGED Viewed

@@ -45,7 +45,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
     }): import("rxjs").Observable<Feature>;
     freeResources(): void;
     cramRecordToFeature(record: CramRecord): CramSlightlyLazyFeature;
-    estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<{
+    getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<{
         bytes: number;
         fetchSizeLimit: any;
     }>;

package/esm/CramAdapter/CramAdapter.js CHANGED Viewed

@@ -195,7 +195,7 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         return new CramSlightlyLazyFeature(record, this);
     }
     // we return the configured fetchSizeLimit, and the bytes for the region
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const bytes = await this.bytesForRegions(regions, opts);
         const fetchSizeLimit = this.getConf('fetchSizeLimit');
         return {

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

	@@ -1 +1 @@
1	- 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package/esm/CramAdapter/CramTestAdapters.js CHANGED Viewed

@@ -1,7 +1,7 @@
 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) {
     return text

package/esm/CramAdapter/CramTestAdapters.js.map CHANGED Viewed

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

@@ -1,2 +1,41 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot fetchSizeLimit
+     */
+    fetchSizeLimit: {
+        type: string;
+        description: string;
+        defaultValue: number;
+    };
+    /**
+     * #slot cramLocation
+     */
+    cramLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot craiLocation
+     */
+    craiLocation: {
+        type: string;
+        defaultValue: {
+            uri: string;
+            locationType: string;
+        };
+    };
+    /**
+     * #slot sequenceAdapter
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+        type: string;
+        description: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;