@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/dist/LinearSNPCoverageDisplay/models/model.js

@@ -4,7 +4,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const mobx_state_tree_1 = require("mobx-state-tree");
-const clone_1 = __importDefault(require("clone"));
 const mobx_1 = require("mobx");
 const configuration_1 = require("@jbrowse/core/configuration");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
@@ -12,6 +11,8 @@ const util_1 = require("@jbrowse/core/util");
 // locals
 const Tooltip_1 = __importDefault(require("../components/Tooltip"));
 const shared_1 = require("../../shared");
+const util_2 = require("../../util");
+const util_3 = require("../../util");
 // using a map because it preserves order
 const rendererTypes = new Map([['snpcoverage', 'SNPCoverageRenderer']]);
 /**
@@ -50,7 +51,8 @@ function stateModelFactory(pluginManager, configSchema) {
         })),
     }))
         .volatile(() => ({
-        modificationTagMap: undefined,
+        modificationTagMap: mobx_1.observable.map({}),
+        modificationsReady: false,
     }))
         .actions(self => ({
         /**
@@ -75,16 +77,11 @@ function stateModelFactory(pluginManager, configSchema) {
          * #action
          */
         updateModificationColorMap(uniqueModifications) {
-            const colorPalette = ['red', 'blue', 'green', 'orange', 'purple'];
-            let i = 0;
-            const newMap = (0, clone_1.default)(self.modificationTagMap) || {};
             uniqueModifications.forEach(value => {
-                if (!newMap[value]) {
-                    const newColor = colorPalette[i++];
-                    newMap[value] = newColor;
+                if (!self.modificationTagMap.has(value)) {
+                    self.modificationTagMap.set(value, util_2.modificationColors[value] || (0, util_3.randomColor)());
                 }
             });
-            self.modificationTagMap = newMap;
         },
     }))
         .views(self => {
@@ -127,11 +124,19 @@ function stateModelFactory(pluginManager, configSchema) {
             /**
              * #getter
              */
-            get modificationsReady() {
-                var _a;
-                return ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) === 'modifications'
-                    ? self.modificationTagMap !== undefined
-                    : true;
+            get autorunReady() {
+                const view = (0, util_1.getContainingView)(self);
+                return (view.initialized &&
+                    self.featureDensityStatsReady &&
+                    !self.regionTooLarge &&
+                    !self.error);
+            },
+            get renderReady() {
+                const superProps = superRenderProps();
+                return !superProps.notReady && self.modificationsReady;
+            },
+            get ready() {
+                return this.renderReady;
             },
             /**
              * #method
@@ -141,8 +146,8 @@ function stateModelFactory(pluginManager, configSchema) {
                 const { colorBy, filterBy, modificationTagMap } = self;
                 return {
                     ...superProps,
-                    notReady: superProps.notReady || !this.modificationsReady,
-                    modificationTagMap: modificationTagMap,
+                    notReady: !this.ready,
+                    modificationTagMap: Object.fromEntries(modificationTagMap.toJSON()),
                     // must use getSnapshot because otherwise changes to e.g. just the
                     // colorBy.type are not read
                     colorBy: colorBy ? (0, mobx_state_tree_1.getSnapshot)(colorBy) : undefined,
@@ -152,6 +157,12 @@ function stateModelFactory(pluginManager, configSchema) {
         };
     })
         .actions(self => ({
+        /**
+         * #action
+         */
+        setModificationsReady(flag) {
+            self.modificationsReady = flag;
+        },
         /**
          * #action
          */
@@ -170,27 +181,29 @@ function stateModelFactory(pluginManager, configSchema) {
         toggleDrawArcs() {
             self.drawArcs = !self.drawArcsSetting;
         },
+    }))
+        .actions(self => ({
         afterAttach() {
-            (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-                try {
-                    const { colorBy } = self;
-                    const view = (0, util_1.getContainingView)(self);
-                    if (!view.initialized ||
-                        !self.estimatedStatsReady ||
-                        self.regionTooLarge) {
-                        return;
-                    }
-                    const { staticBlocks } = view;
-                    if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-                        const adapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
-                        self.updateModificationColorMap(await (0, shared_1.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks));
+            (0, util_2.createAutorun)(self, async () => {
+                self.setModificationsReady(false);
+                if (!self.autorunReady) {
+                    return;
+                }
+                const view = (0, util_1.getContainingView)(self);
+                const { staticBlocks } = view;
+                const { colorBy } = self;
+                if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+                    const adapter = (0, configuration_1.getConf)(self.parentTrack, 'adapter');
+                    const vals = await (0, shared_1.getUniqueModificationValues)(self, adapter, colorBy, staticBlocks);
+                    if ((0, mobx_state_tree_1.isAlive)(self)) {
+                        self.updateModificationColorMap(vals);
+                        self.setModificationsReady(true);
                     }
                 }
-                catch (error) {
-                    console.error(error);
-                    self.setError(error);
+                else {
+                    self.setModificationsReady(true);
                 }
-            }, { delay: 1000 }));
+            }, { delay: 1000 });
         },
     }))
         .views(self => {

package/dist/LinearSNPCoverageDisplay/models/model.js.map

@@ -1 +1 @@
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package/dist/MismatchParser/index.d.ts

@@ -13,12 +13,17 @@ export interface Mismatch {
 export declare function parseCigar(cigar?: string): string[];
 export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 /**
- * parse a SAM MD tag to find mismatching bases of the template versus the reference
- * @returns array of mismatches and their positions
+ * parse a SAM MD tag to find mismatching bases of the template versus the
+ * reference @returns array of mismatches and their positions
  */
 export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer): Mismatch[];
 export declare function getMismatches(cigar: string, md?: string, seq?: string, ref?: string, qual?: Buffer): Mismatch[];
 export declare function getNextRefPos(cigarOps: string[], positions: number[]): Generator<number, void, unknown>;
+export declare function getModificationProbabilities(feature: Feature): number[] | undefined;
+export declare function getMethBins(feature: Feature): {
+    methBins: number[];
+    methProbs: number[];
+};
 export declare function getModificationPositions(mm: string, fseq: string, fstrand: number): {
     type: string;
     positions: number[];

package/dist/MismatchParser/index.js

@@ -1,7 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.featurizeSA = exports.getTag = exports.getClip = exports.getLengthSansClipping = exports.getLength = exports.getLengthOnRef = exports.getOrientedMismatches = exports.getOrientedCigar = exports.getModificationTypes = exports.getModificationPositions = exports.getNextRefPos = exports.getMismatches = exports.mdToMismatches = exports.cigarToMismatches = exports.parseCigar = void 0;
+exports.featurizeSA = exports.getTag = exports.getClip = exports.getLengthSansClipping = exports.getLength = exports.getLengthOnRef = exports.getOrientedMismatches = exports.getOrientedCigar = exports.getModificationTypes = exports.getModificationPositions = exports.getMethBins = exports.getModificationProbabilities = exports.getNextRefPos = exports.getMismatches = exports.mdToMismatches = exports.cigarToMismatches = exports.parseCigar = void 0;
 const util_1 = require("@jbrowse/core/util");
+const util_2 = require("../util");
 const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
 const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
 const cigarRegex = new RegExp(/([MIDNSHPX=])/);
@@ -103,17 +104,17 @@ function cigarToMismatches(ops, seq, ref, qual) {
 }
 exports.cigarToMismatches = cigarToMismatches;
 /**
- * parse a SAM MD tag to find mismatching bases of the template versus the reference
- * @returns array of mismatches and their positions
+ * parse a SAM MD tag to find mismatching bases of the template versus the
+ * reference @returns array of mismatches and their positions
  */
 function mdToMismatches(mdstring, ops, cigarMismatches, seq, qual) {
-    const mismatchRecords = [];
     let curr = { start: 0, base: '', length: 0, type: 'mismatch' };
-    const skips = cigarMismatches.filter(cigar => cigar.type === 'skip');
     let lastCigar = 0;
     let lastTemplateOffset = 0;
     let lastRefOffset = 0;
     let lastSkipPos = 0;
+    const mismatchRecords = [];
+    const skips = cigarMismatches.filter(cigar => cigar.type === 'skip');
     // convert a position on the reference sequence to a position
     // on the template sequence, taking into account hard and soft
     // clipping of reads
@@ -231,6 +232,44 @@ function* getNextRefPos(cigarOps, positions) {
     }
 }
 exports.getNextRefPos = getNextRefPos;
+function getModificationProbabilities(feature) {
+    var _a;
+    const m = (0, util_2.getTagAlt)(feature, 'ML', 'Ml') || [];
+    return m
+        ? (typeof m === 'string' ? m.split(',').map(e => +e) : m).map(e => e / 255)
+        : (_a = (0, util_2.getTagAlt)(feature, 'MP', 'Mp')) === null || _a === void 0 ? void 0 : _a.split('').map(s => s.charCodeAt(0) - 33).map(elt => Math.min(1, elt / 50));
+}
+exports.getModificationProbabilities = getModificationProbabilities;
+function getMethBins(feature) {
+    const fstart = feature.get('start');
+    const fend = feature.get('end');
+    const fstrand = feature.get('strand');
+    const flen = fend - fstart;
+    const mm = (0, util_2.getTagAlt)(feature, 'MM', 'Mm') || '';
+    const methBins = new Array(flen);
+    const methProbs = new Array(flen);
+    const seq = feature.get('seq');
+    if (seq) {
+        const ops = parseCigar(feature.get('CIGAR'));
+        const probabilities = getModificationProbabilities(feature);
+        const modifications = getModificationPositions(mm, seq, fstrand);
+        let probIndex = 0;
+        for (const { type, positions } of modifications) {
+            if (type === 'm') {
+                for (const ref of getNextRefPos(ops, positions)) {
+                    const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[probIndex]) || 0;
+                    probIndex++;
+                    if (ref >= 0 && ref < flen) {
+                        methBins[ref] = 1;
+                        methProbs[ref] = prob;
+                    }
+                }
+            }
+        }
+    }
+    return { methBins, methProbs };
+}
+exports.getMethBins = getMethBins;
 function getModificationPositions(mm, fseq, fstrand) {
     const seq = fstrand === -1 ? (0, util_1.revcom)(fseq) : fseq;
     const mods = mm.split(';').filter(mod => !!mod);

package/dist/MismatchParser/index.js.map

@@ -1 +1 @@
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package/dist/PileupRPC/methods/GetReducedFeatures.d.ts

@@ -1,6 +1,5 @@
 import { Region } from '@jbrowse/core/util';
 import { RemoteAbortSignal } from '@jbrowse/core/rpc/remoteAbortSignals';
-import { ReducedFeature } from '../../shared/fetchChains';
 import PileupBaseRPC from '../base';
 export default class PileupGetReducedFeatures extends PileupBaseRPC {
     name: string;
@@ -12,7 +11,21 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC {
         sessionId: string;
         tag: string;
     }, rpcDriver: string): Promise<{
-        chains: ReducedFeature[][];
+        chains: {
+            id: string;
+            refName: string;
+            name: any;
+            start: number;
+            strand: any;
+            end: number;
+            flags: any;
+            tlen: any;
+            pair_orientation: any;
+            next_ref: any;
+            next_pos: any;
+            clipPos: any;
+            SA: any;
+        }[][];
         stats: {
             upper: number;
             lower: number;

package/dist/PileupRPC/methods/GetReducedFeatures.js

@@ -39,14 +39,7 @@ class PileupGetReducedFeatures extends base_1.default {
         })), f => f.id);
         const filtered = (0, util_2.filterForPairs)(reduced);
         const stats = filtered.length ? (0, util_2.getInsertSizeStats)(filtered) : undefined;
-        const chains = {};
-        // pair features
-        reduced.forEach(f => {
-            if (!chains[f.name]) {
-                chains[f.name] = [];
-            }
-            chains[f.name].push(f);
-        });
+        const chains = (0, util_1.groupBy)(reduced, f => f.name);
         return {
             chains: Object.values(chains),
             stats,

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

@@ -1 +1 @@
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package/dist/PileupRenderer/PileupLayoutSession.d.ts

@@ -1,5 +1,5 @@
 import { LayoutSession } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
 import GranularRectLayout from '@jbrowse/core/util/layouts/GranularRectLayout';
 import MultiLayout from '@jbrowse/core/util/layouts/MultiLayout';

package/dist/PileupRenderer/PileupRenderer.d.ts

@@ -1,9 +1,7 @@
 /// <reference types="react" />
-import { Theme } from '@mui/material/styles';
 import BoxRendererType, { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
-import { Region, Feature } from '@jbrowse/core/util';
+import { Feature, Region } from '@jbrowse/core/util';
 import { BaseLayout } from '@jbrowse/core/util/layouts/BaseLayout';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import { PileupLayoutSession, PileupLayoutSessionProps } from './PileupLayoutSession';
 export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
     colorBy?: {
@@ -11,7 +9,7 @@ export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
         tag?: string;
     };
     colorTagMap?: Record<string, string>;
-    modificationTagMap?: Record<string, string>;
+    modificationTagMap?: Record<string, string | undefined>;
     sortedBy?: {
         type: string;
         pos: number;
@@ -27,33 +25,9 @@ export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsD
     layout: BaseLayout<Feature>;
     regionSequence?: string;
 }
-interface LayoutRecord {
-    feature: Feature;
-    leftPx: number;
-    rightPx: number;
-    topPx: number;
-    heightPx: number;
-}
-interface LayoutFeature {
-    heightPx: number;
-    topPx: number;
-    feature: Feature;
-}
 export default class PileupRenderer extends BoxRendererType {
     supportsSVG: boolean;
-    getCharWidthHeight(): {
-        charWidth: number;
-        charHeight: number;
-    };
-    layoutFeature({ feature, layout, bpPerPx, region, showSoftClip, heightPx, displayMode, }: {
-        feature: Feature;
-        layout: BaseLayout<Feature>;
-        bpPerPx: number;
-        region: Region;
-        showSoftClip?: boolean;
-        heightPx: number;
-        displayMode: string;
-    }): LayoutRecord | null;
+    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
     getExpandedRegion(region: Region, renderArgs: RenderArgsDeserialized): {
         start: number;
         end: number;
@@ -61,93 +35,6 @@ export default class PileupRenderer extends BoxRendererType {
         reversed?: boolean | undefined;
         assemblyName: string;
     };
-    colorByOrientation(feature: Feature, config: AnyConfigurationModel): string;
-    getOrientation(feature: Feature, config: AnyConfigurationModel): string;
-    colorByInsertSize(feature: Feature, _config: AnyConfigurationModel): string;
-    colorByStranded(feature: Feature, _config: AnyConfigurationModel): "color_rev_strand" | "color_fwd_strand" | "color_rev_missing_mate" | "color_fwd_missing_mate" | "color_rev_strand_not_proper" | "color_fwd_strand_not_proper" | "color_fwd_diff_chr" | "color_rev_diff_chr";
-    colorByPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, }: {
-        ctx: CanvasRenderingContext2D;
-        feat: LayoutFeature;
-        region: Region;
-        bpPerPx: number;
-        colorForBase: Record<string, string>;
-        contrastForBase: Record<string, string>;
-        charWidth: number;
-        charHeight: number;
-        canvasWidth: number;
-    }): void;
-    colorByPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }: {
-        ctx: CanvasRenderingContext2D;
-        feat: LayoutFeature;
-        region: Region;
-        bpPerPx: number;
-        canvasWidth: number;
-    }): void;
-    colorByModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }: {
-        ctx: CanvasRenderingContext2D;
-        feat: LayoutFeature;
-        region: Region;
-        bpPerPx: number;
-        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-        canvasWidth: number;
-    }): void;
-    colorByMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }: {
-        ctx: CanvasRenderingContext2D;
-        feat: LayoutFeature;
-        region: Region;
-        bpPerPx: number;
-        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-        canvasWidth: number;
-    }): void;
-    drawRect(ctx: CanvasRenderingContext2D, feat: LayoutFeature, props: RenderArgsDeserialized): void;
-    drawAlignmentRect({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, theme, canvasWidth, }: {
-        ctx: CanvasRenderingContext2D;
-        feat: LayoutFeature;
-        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-        colorForBase: Record<string, string>;
-        contrastForBase: Record<string, string>;
-        charWidth: number;
-        charHeight: number;
-        defaultColor: boolean;
-        canvasWidth: number;
-        theme: Theme;
-    }): void;
-    drawMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, }: {
-        ctx: CanvasRenderingContext2D;
-        feat: LayoutFeature;
-        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-        colorForBase: {
-            [key: string]: string;
-        };
-        contrastForBase: {
-            [key: string]: string;
-        };
-        mismatchAlpha?: boolean;
-        drawIndels?: boolean;
-        drawSNPsMuted?: boolean;
-        minSubfeatureWidth: number;
-        largeInsertionIndicatorScale: number;
-        charWidth: number;
-        charHeight: number;
-        canvasWidth: number;
-        theme: Theme;
-    }): void;
-    drawSoftClipping({ ctx, feat, renderArgs, config, theme, canvasWidth, }: {
-        ctx: CanvasRenderingContext2D;
-        feat: LayoutFeature;
-        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-        config: AnyConfigurationModel;
-        theme: Theme;
-        canvasWidth: number;
-    }): void;
-    makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }: {
-        ctx: CanvasRenderingContext2D;
-        canvasWidth: number;
-        layoutRecords: (LayoutFeature | null)[];
-        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
-    }): void;
-    layoutFeats(props: RenderArgsDeserializedWithFeaturesAndLayout): (LayoutRecord | null)[];
-    fetchSequence(renderProps: RenderArgsDeserialized): Promise<any>;
     render(renderProps: RenderArgsDeserialized): Promise<{
         features: Map<any, any>;
         layout: import("@jbrowse/core/util/layouts").GranularRectLayout<unknown>;
@@ -163,7 +50,7 @@ export default class PileupRenderer extends BoxRendererType {
         height: number;
         width: number;
         maxHeightReached: boolean;
-        reactElement: JSX.Element;
+        reactElement: import("react").JSX.Element;
         html?: string | undefined;
     } | {
         features: Map<any, any>;