@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/MismatchParser/index.js

@@ -1,4 +1,5 @@
 import { revcom } from '@jbrowse/core/util';
+import { getTagAlt } from '../util';
 const mdRegex = new RegExp(/(\d+|\^[a-z]+|[a-z])/gi);
 const modificationRegex = new RegExp(/([A-Z])([-+])([^,.?]+)([.?])?/);
 const cigarRegex = new RegExp(/([MIDNSHPX=])/);
@@ -98,17 +99,17 @@ export function cigarToMismatches(ops, seq, ref, qual) {
     return mismatches;
 }
 /**
- * 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 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
@@ -223,6 +224,42 @@ export function* getNextRefPos(cigarOps, positions) {
         }
     }
 }
+export function getModificationProbabilities(feature) {
+    var _a;
+    const m = getTagAlt(feature, 'ML', 'Ml') || [];
+    return m
+        ? (typeof m === 'string' ? m.split(',').map(e => +e) : m).map(e => e / 255)
+        : (_a = 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));
+}
+export function getMethBins(feature) {
+    const fstart = feature.get('start');
+    const fend = feature.get('end');
+    const fstrand = feature.get('strand');
+    const flen = fend - fstart;
+    const mm = 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 };
+}
 export function getModificationPositions(mm, fseq, fstrand) {
     const seq = fstrand === -1 ? revcom(fseq) : fseq;
     const mods = mm.split(';').filter(mod => !!mod);

package/esm/MismatchParser/index.js.map

@@ -1 +1 @@
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package/esm/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/esm/PileupRPC/methods/GetReducedFeatures.js

@@ -1,5 +1,5 @@
 import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
-import { dedupe } from '@jbrowse/core/util';
+import { dedupe, groupBy } from '@jbrowse/core/util';
 import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
 // locals
@@ -34,14 +34,7 @@ export default class PileupGetReducedFeatures extends PileupBaseRPC {
         })), f => f.id);
         const filtered = filterForPairs(reduced);
         const stats = filtered.length ? getInsertSizeStats(filtered) : undefined;
-        const chains = {};
-        // pair features
-        reduced.forEach(f => {
-            if (!chains[f.name]) {
-                chains[f.name] = [];
-            }
-            chains[f.name].push(f);
-        });
+        const chains = groupBy(reduced, f => f.name);
         return {
             chains: Object.values(chains),
             stats,

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

@@ -1 +1 @@
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package/esm/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/esm/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>;