@jbrowse/plugin-alignments 2.2.1 → 2.3.0

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

@@ -0,0 +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"}

package/esm/PileupRPC/rpcMethods.d.ts

@@ -1,34 +1,4 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { Region } from '@jbrowse/core/util';
-import { RenderArgs } from '@jbrowse/core/rpc/coreRpcMethods';
-import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-export declare class PileupGetGlobalValueForTag extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: (arg: string) => void;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
-export declare class PileupGetVisibleModifications extends RpcMethodType {
-    name: string;
-    serializeArguments(args: RenderArgs & {
-        signal?: AbortSignal;
-        statusCallback?: (arg: string) => void;
-    }, rpcDriverClassName: string): Promise<{}>;
-    execute(args: {
-        adapterConfig: {};
-        signal?: RemoteAbortSignal;
-        headers?: Record<string, string>;
-        regions: Region[];
-        sessionId: string;
-        tag: string;
-    }, rpcDriverClassName: string): Promise<string[]>;
-}
+import PileupGetReducedFeatures from './methods/GetReducedFeatures';
+import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag';
+import PileupGetVisibleModifications from './methods/GetVisibleModifications';
+export { PileupGetReducedFeatures, PileupGetVisibleModifications, PileupGetGlobalValueForTag, };

package/esm/PileupRPC/rpcMethods.js

@@ -1,75 +1,5 @@
-import RpcMethodType from '@jbrowse/core/pluggableElementTypes/RpcMethodType';
-import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { renameRegionsIfNeeded } from '@jbrowse/core/util';
-import { toArray } from 'rxjs/operators';
-// locals
-import { getTagAlt } from '../util';
-import { getModificationTypes } from '../BamAdapter/MismatchParser';
-export class PileupGetGlobalValueForTag extends RpcMethodType {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetGlobalValueForTag';
-    }
-    async serializeArguments(args, rpcDriverClassName) {
-        var _a;
-        const { rootModel } = this.pluginManager;
-        const assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
-        if (!assemblyManager) {
-            throw new Error('no assembly manager available');
-        }
-        const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args);
-        return super.serializeArguments(renamedArgs, rpcDriverClassName);
-    }
-    async execute(args, rpcDriverClassName) {
-        const pm = this.pluginManager;
-        const deArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { adapterConfig, sessionId, regions, tag } = deArgs;
-        const dataAdapter = (await getAdapter(pm, sessionId, adapterConfig))
-            .dataAdapter;
-        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
-        const featuresArray = await features.pipe(toArray()).toPromise();
-        const uniqueValues = new Set();
-        featuresArray.forEach(feature => {
-            const tags = feature.get('tags');
-            const val = tags ? tags[tag] : feature.get(tag);
-            if (val !== undefined) {
-                uniqueValues.add(`${val}`);
-            }
-        });
-        return [...uniqueValues];
-    }
-}
-export class PileupGetVisibleModifications extends RpcMethodType {
-    constructor() {
-        super(...arguments);
-        this.name = 'PileupGetVisibleModifications';
-    }
-    async serializeArguments(args, rpcDriverClassName) {
-        var _a;
-        const { rootModel } = this.pluginManager;
-        const assemblyManager = (_a = rootModel === null || rootModel === void 0 ? void 0 : rootModel.session) === null || _a === void 0 ? void 0 : _a.assemblyManager;
-        if (!assemblyManager) {
-            throw new Error('no assembly manager available');
-        }
-        const renamedArgs = await renameRegionsIfNeeded(assemblyManager, args);
-        return super.serializeArguments(renamedArgs, rpcDriverClassName);
-    }
-    async execute(args, rpcDriverClassName) {
-        const pm = this.pluginManager;
-        const deArgs = await this.deserializeArguments(args, rpcDriverClassName);
-        const { adapterConfig, sessionId, regions } = deArgs;
-        const dataAdapter = (await getAdapter(pm, sessionId, adapterConfig))
-            .dataAdapter;
-        const features = dataAdapter.getFeaturesInMultipleRegions(regions);
-        const featuresArray = await features.pipe(toArray()).toPromise();
-        const uniqueValues = new Set();
-        featuresArray.forEach(feature => {
-            const val = getTagAlt(feature, 'MM', 'Mm') || '';
-            if (val !== undefined) {
-                getModificationTypes(val).forEach(t => uniqueValues.add(t));
-            }
-        });
-        return [...uniqueValues];
-    }
-}
+import PileupGetReducedFeatures from './methods/GetReducedFeatures';
+import PileupGetGlobalValueForTag from './methods/GetGlobalValueForTag';
+import PileupGetVisibleModifications from './methods/GetVisibleModifications';
+export { PileupGetReducedFeatures, PileupGetVisibleModifications, PileupGetGlobalValueForTag, };
 //# sourceMappingURL=rpcMethods.js.map

package/esm/PileupRPC/rpcMethods.js.map

@@ -1 +1 @@
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+{"version":3,"file":"rpcMethods.js","sourceRoot":"","sources":["../../src/PileupRPC/rpcMethods.ts"],"names":[],"mappings":"AAAA,OAAO,wBAAwB,MAAM,8BAA8B,CAAA;AACnE,OAAO,0BAA0B,MAAM,gCAAgC,CAAA;AACvE,OAAO,6BAA6B,MAAM,mCAAmC,CAAA;AAE7E,OAAO,EACL,wBAAwB,EACxB,6BAA6B,EAC7B,0BAA0B,GAC3B,CAAA"}

package/esm/PileupRPC/util.d.ts

@@ -0,0 +1,8 @@
+import { ReducedFeature } from '../shared/fetchChains';
+export declare function getInsertSizeStats(features: ReducedFeature[]): {
+    upper: number;
+    lower: number;
+    avg: number;
+    sd: number;
+};
+export declare function filterForPairs(features: ReducedFeature[]): ReducedFeature[];

package/esm/PileupRPC/util.js

@@ -0,0 +1,15 @@
+export function getInsertSizeStats(features) {
+    const filtered = features.map(f => Math.abs(f.tlen));
+    const sum = filtered.reduce((a, b) => a + b, 0);
+    const sum2 = filtered.map(a => a * a).reduce((a, b) => a + b, 0);
+    const total = filtered.length;
+    const avg = sum / total;
+    const sd = Math.sqrt((total * sum2 - sum * sum) / (total * total));
+    const upper = avg + 4 * sd;
+    const lower = avg - 3 * sd;
+    return { upper, lower, avg, sd };
+}
+export function filterForPairs(features) {
+    return features.filter(f => f.flags & 2 && !(f.flags & 256) && !(f.flags & 2048));
+}
+//# sourceMappingURL=util.js.map

package/esm/PileupRPC/util.js.map

@@ -0,0 +1 @@
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package/esm/PileupRenderer/PileupRenderer.d.ts

@@ -57,8 +57,8 @@ export default class PileupRenderer extends BoxRendererType {
     getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
         start: number;
         end: number;
-        reversed?: boolean | undefined;
         refName: string;
+        reversed?: boolean | undefined;
         assemblyName: string;
     };
     colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;

package/esm/PileupRenderer/PileupRenderer.js

@@ -5,7 +5,7 @@ import { renderToAbstractCanvas } from '@jbrowse/core/util/offscreenCanvasUtils'
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
 import { readConfObject, } from '@jbrowse/core/configuration';
 // locals
-import { parseCigar, getModificationPositions, getNextRefPos, } from '../BamAdapter/MismatchParser';
+import { parseCigar, getModificationPositions, getNextRefPos, } from '../MismatchParser';
 import { sortFeature } from './sortUtil';
 import { getTagAlt, orientationTypes, fetchSequence, shouldFetchReferenceSequence, } from '../util';
 import { PileupLayoutSession, } from './PileupLayoutSession';
@@ -141,7 +141,7 @@ export default class PileupRenderer extends BoxRendererType {
     }
     colorByInsertSize(feature, _config) {
         return feature.get('is_paired') &&
-            feature.get('seq_id') !== feature.get('next_seq_id')
+            feature.get('refName') !== feature.get('next_ref')
             ? '#555'
             : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)`;
     }
@@ -161,7 +161,7 @@ export default class PileupRenderer extends BoxRendererType {
                     ? 'color_rev_missing_mate'
                     : 'color_fwd_missing_mate';
             }
-            if (feature.get('seq_id') === feature.get('next_seq_id')) {
+            if (feature.get('refName') === feature.get('next_refName')) {
                 return strand * flipper === 1
                     ? 'color_rev_strand_not_proper'
                     : 'color_fwd_strand_not_proper';
@@ -558,7 +558,7 @@ export default class PileupRenderer extends BoxRendererType {
                 }
             }
             else if (mismatch.type === 'deletion' && drawIndels) {
-                fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth, colorForBase.deletion);
+                fillRect(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorForBase.deletion);
                 const txt = `${mismatch.length}`;
                 const rwidth = measureText(txt, 10);
                 if (widthPx >= rwidth && heightPx >= heightLim) {
@@ -570,7 +570,7 @@ export default class PileupRenderer extends BoxRendererType {
                 ctx.fillStyle = 'purple';
                 const pos = leftPx + extraHorizontallyFlippedOffset;
                 const len = +mismatch.base || mismatch.length;
-                const insW = Math.max(minSubfeatureWidth / 2, Math.min(1.2, 1 / bpPerPx));
+                const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx));
                 if (len < 10) {
                     fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple');
                     if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {

package/esm/PileupRenderer/PileupRenderer.js.map

@@ -1 +1 @@
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package/esm/PileupRenderer/configSchema.js

@@ -22,7 +22,7 @@ const PileupRenderer = ConfigurationSchema('PileupRenderer', {
         type: 'stringEnum',
         model: types.enumeration('orientationType', ['fr', 'rf', 'ff']),
         defaultValue: 'fr',
-        description: 'read sequencer orienation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
+        description: 'read sequencer orientation. fr is normal "reads pointing at each other ---> <--- while some other sequencers can use other options',
     },
     /**
      * #slot

package/esm/PileupRenderer/configSchema.js.map

@@ -1 +1 @@
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+{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/PileupRenderer/configSchema.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,SAAS,CAAC,KAAI,CAAC,CAAC,wDAAwD;AAExE,MAAM,cAAc,GAAG,mBAAmB,CACxC,gBAAgB,EAChB;IACE;;;OAGG;IACH,KAAK,EAAE;QACL,IAAI,EAAE,OAAO;QACb,WAAW,EAAE,iDAAiD;QAC9D,YAAY,EAAE,MAAM;QACpB,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IAED;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,iBAAiB,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAC;QAC/D,YAAY,EAAE,IAAI;QAClB,WAAW,EACT,oIAAoI;KACvI;IACD;;OAEG;IACH,WAAW,EAAE;QACX,IAAI,EAAE,YAAY;QAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;YACtC,QAAQ;YACR,SAAS;YACT,UAAU;SACX,CAAC;QACF,WAAW,EAAE,2BAA2B;QACxC,YAAY,EAAE,QAAQ;KACvB;IACD;;OAEG;IACH,kBAAkB,EAAE;QAClB,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,0IAA0I;QAC5I,YAAY,EAAE,GAAG;KAClB;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,qDAAqD;QAClE,YAAY,EAAE,IAAI;KACnB;IACD;;OAEG;IACH,eAAe,EAAE;QACf,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,oDAAoD;QACjE,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,MAAM,EAAE;QACN,IAAI,EAAE,QAAQ;QACd,WAAW,EAAE,kDAAkD;QAC/D,YAAY,EAAE,CAAC;QACf,eAAe,EAAE,CAAC,SAAS,CAAC;KAC7B;IACD;;OAEG;IACH,SAAS,EAAE;QACT,IAAI,EAAE,SAAS;QACf,WAAW,EAAE,iCAAiC;QAC9C,YAAY,EAAE,KAAK;KACpB;IACD;;OAEG;IACH,4BAA4B,EAAE;QAC5B,IAAI,EAAE,QAAQ;QACd,WAAW,EACT,kEAAkE;QACpE,YAAY,EAAE,EAAE;KACjB;IACD;;OAEG;IACH,aAAa,EAAE;QACb,IAAI,EAAE,SAAS;QACf,YAAY,EAAE,KAAK;QACnB,WAAW,EAAE,6BAA6B;KAC3C;CACF,EACD,EAAE,eAAe,EAAE,IAAI,EAAE,CAC1B,CAAA;AACD,eAAe,cAAc,CAAA"}

package/esm/PileupRenderer/index.js

@@ -5,6 +5,7 @@ export default function register(pluginManager) {
     pluginManager.addRendererType(() => {
         return new PileupRenderer({
             name: 'PileupRenderer',
+            displayName: 'Pileup renderer',
             ReactComponent,
             configSchema,
             pluginManager,

package/esm/PileupRenderer/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/PileupRenderer/index.ts"],"names":[],"mappings":"AACA,OAAO,cAAc,MAAM,kBAAkB,CAAA;AAC7C,OAAO,cAAc,MAAM,8BAA8B,CAAA;AACzD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,QAAQ,CAAC,aAA4B;IAC3D,aAAa,CAAC,eAAe,CAAC,GAAG,EAAE;QACjC,OAAO,IAAI,cAAc,CAAC;YACxB,IAAI,EAAE,gBAAgB;YACtB,WAAW,EAAE,iBAAiB;YAC9B,cAAc;YACd,YAAY;YACZ,aAAa;SACd,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/PileupRenderer/sortUtil.d.ts

@@ -1,4 +1,4 @@
-import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Feature } from '@jbrowse/core/util';
 interface SortObject {
     pos: number;
     type: string;

package/esm/PileupRenderer/sortUtil.js

@@ -1,4 +1,4 @@
-import { doesIntersect2 } from '@jbrowse/core/util/range';
+import { doesIntersect2 } from '@jbrowse/core/util';
 export const sortFeature = (features, sortedBy) => {
     const featureArray = Array.from(features.values());
     const featuresInCenterLine = [];

package/esm/PileupRenderer/sortUtil.js.map

@@ -1 +1 @@
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package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -11,57 +11,6 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     estimateRegionsStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").Stats>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     freeResources(): void;
-    generateCoverageBins(features: Feature[], region: Region, opts: {
-        bpPerPx?: number;
-        colorBy?: {
-            type: string;
-            tag?: string;
-        };
-    }): Promise<{
-        bins: {
-            refbase?: string | undefined;
-            total: number;
-            all: number;
-            ref: number;
-            '-1': 0;
-            '0': 0;
-            '1': 0;
-            lowqual: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            cov: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            delskips: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-            noncov: {
-                total: number;
-                strands: {
-                    [key: string]: number;
-                };
-            };
-        }[];
-        skipmap: {
-            [key: string]: {
-                score: number;
-                feature: unknown;
-                start: number;
-                end: number;
-                strand: number;
-                xs: string;
-            };
-        };
-    }>;
 }
 declare const capabilities: string[];
 export { capabilities };