@jbrowse/plugin-alignments 3.6.5 → 3.7.0

package/dist/PileupRenderer/{getAlignmentShapeColor.js → renderers/getAlignmentShapeColor.js}

@@ -2,8 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getAlignmentShapeColor = getAlignmentShapeColor;
 const configuration_1 = require("@jbrowse/core/configuration");
-const colorBy_1 = require("./colorBy");
-const color_1 = require("../shared/color");
+const color_1 = require("../../shared/color");
+const colorBy_1 = require("../colorBy");
 function getAlignmentShapeColor({ colorType, tag, feature, config, defaultColor, colorTagMap, }) {
     switch (colorType) {
         case 'insertSize':

package/{esm/PileupRenderer → dist/PileupRenderer/renderers}/renderAlignment.d.ts

@@ -1,5 +1,5 @@
-import type { ProcessedRenderArgs } from './types';
-import type { LayoutFeature } from './util';
+import type { FlatbushItem, ProcessedRenderArgs } from '../types';
+import type { LayoutFeature } from '../util';
 export declare function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, charWidth, charHeight, defaultColor, canvasWidth, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
@@ -10,4 +10,7 @@ export declare function renderAlignment({ ctx, feat, renderArgs, colorMap, color
     charHeight: number;
     defaultColor: boolean;
     canvasWidth: number;
-}): void;
+}): {
+    coords: number[];
+    items: FlatbushItem[];
+};

package/dist/PileupRenderer/{renderAlignment.js → renderers/renderAlignment.js}

@@ -3,12 +3,14 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderAlignment = renderAlignment;
 const getAlignmentShapeColor_1 = require("./getAlignmentShapeColor");
 const renderAlignmentShape_1 = require("./renderAlignmentShape");
+const renderMethylation_1 = require("./renderMethylation");
 const renderModifications_1 = require("./renderModifications");
 const renderPerBaseLettering_1 = require("./renderPerBaseLettering");
 const renderPerBaseQuality_1 = require("./renderPerBaseQuality");
-const MismatchParser_1 = require("../MismatchParser");
-const renderMethylation_1 = require("./renderMethylation");
+const MismatchParser_1 = require("../../MismatchParser");
 function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, charWidth, charHeight, defaultColor, canvasWidth, }) {
+    const items = [];
+    const coords = [];
     const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs;
     const { tag = '', type: colorType = '' } = colorBy || {};
     const { feature } = feat;
@@ -53,7 +55,7 @@ function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, ch
         }
         case 'modifications': {
             const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
-            (0, renderModifications_1.renderModifications)({
+            const ret = (0, renderModifications_1.renderModifications)({
                 ctx,
                 feat,
                 region,
@@ -62,6 +64,12 @@ function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, ch
                 canvasWidth,
                 cigarOps,
             });
+            for (let i = 0, l = ret.coords.length; i < l; i++) {
+                coords.push(ret.coords[i]);
+            }
+            for (let i = 0, l = ret.items.length; i < l; i++) {
+                items.push(ret.items[i]);
+            }
             break;
         }
         case 'methylation': {
@@ -78,4 +86,5 @@ function renderAlignment({ ctx, feat, renderArgs, colorMap, colorContrastMap, ch
             break;
         }
     }
+    return { coords, items };
 }

package/{esm/PileupRenderer → dist/PileupRenderer/renderers}/renderAlignmentShape.d.ts

@@ -1,5 +1,5 @@
-import type { ProcessedRenderArgs } from './types';
-import type { LayoutFeature } from './util';
+import type { ProcessedRenderArgs } from '../types';
+import type { LayoutFeature } from '../util';
 export declare function renderAlignmentShape({ ctx, feat, renderArgs, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;

package/dist/PileupRenderer/{renderAlignmentShape.js → renderers/renderAlignmentShape.js}

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderAlignmentShape = renderAlignmentShape;
 const util_1 = require("@jbrowse/core/util");
-const MismatchParser_1 = require("../MismatchParser");
+const MismatchParser_1 = require("../../MismatchParser");
 function renderAlignmentShape({ ctx, feat, renderArgs, }) {
     const { regions, bpPerPx } = renderArgs;
     const { heightPx, topPx, feature } = feat;

package/dist/PileupRenderer/{renderMethylation.d.ts → renderers/renderMethylation.d.ts}

@@ -1,5 +1,5 @@
-import type { ProcessedRenderArgs } from './types';
-import type { LayoutFeature } from './util';
+import type { ProcessedRenderArgs } from '../types';
+import type { LayoutFeature } from '../util';
 import type { Region } from '@jbrowse/core/util';
 export declare function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;

package/dist/PileupRenderer/{renderMethylation.js → renderers/renderMethylation.js}

@@ -3,8 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderMethylation = renderMethylation;
 const util_1 = require("@jbrowse/core/util");
 const colord_1 = require("@jbrowse/core/util/colord");
-const util_2 = require("./util");
-const getMethBins_1 = require("../ModificationParser/getMethBins");
+const getMethBins_1 = require("../../ModificationParser/getMethBins");
+const util_2 = require("../util");
 function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
     const { regionSequence } = renderArgs;
     const { feature, topPx, heightPx } = feat;

package/dist/PileupRenderer/{renderMismatches.d.ts → renderers/renderMismatches.d.ts}

@@ -1,5 +1,5 @@
-import type { ProcessedRenderArgs } from './types';
-import type { LayoutFeature } from './util';
+import type { FlatbushItem, ProcessedRenderArgs } from '../types';
+import type { LayoutFeature } from '../util';
 export declare function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
@@ -15,4 +15,7 @@ export declare function renderMismatches({ ctx, feat, renderArgs, minSubfeatureW
     charWidth: number;
     charHeight: number;
     canvasWidth: number;
-}): void;
+}): {
+    coords: number[];
+    items: FlatbushItem[];
+};

package/dist/PileupRenderer/{renderMismatches.js → renderers/renderMismatches.js}

@@ -3,19 +3,19 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderMismatches = renderMismatches;
 const util_1 = require("@jbrowse/core/util");
 const colord_1 = require("@jbrowse/core/util/colord");
-const util_2 = require("./util");
+const util_2 = require("../util");
 function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorMap, colorContrastMap, hideSmallIndels, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
+    var _a;
+    const items = [];
+    const coords = [];
     const { bpPerPx, regions } = renderArgs;
     const { heightPx, topPx, feature } = feat;
     const region = regions[0];
     const start = feature.get('start');
     const pxPerBp = Math.min(1 / bpPerPx, 2);
-    const mismatches = feature.get('mismatches');
+    const mismatches = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
     const heightLim = charHeight - 2;
     const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx + 1 : -1;
-    if (!mismatches) {
-        return;
-    }
     for (const mismatch of mismatches) {
         const mstart = start + mismatch.start;
         const mlen = mismatch.length;
@@ -23,6 +23,11 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
         const [leftPx, rightPx] = (0, util_1.bpSpanPx)(mstart, mstart + mlen, region, bpPerPx);
         const widthPx = Math.max(minSubfeatureWidth, rightPx - leftPx);
         if (mismatch.type === 'mismatch') {
+            items.push({
+                type: 'mismatch',
+                seq: mismatch.base,
+            });
+            coords.push(leftPx, topPx, rightPx, topPx + heightPx);
             if (!drawSNPsMuted) {
                 const baseColor = colorMap[mismatch.base] || '#888';
                 const c = mismatchAlpha && mismatch.qual !== undefined
@@ -49,6 +54,11 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
             const len = mismatch.length;
             if (!hideSmallIndels || len >= 10) {
                 (0, util_2.fillRect)(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorMap.deletion);
+                items.push({
+                    type: 'deletion',
+                    seq: `${mismatch.length}`,
+                });
+                coords.push(leftPx, topPx, rightPx, topPx + heightPx);
                 const txt = `${mismatch.length}`;
                 const rwidth = (0, util_1.measureText)(txt, 10);
                 if (widthPx >= rwidth && heightPx >= heightLim) {
@@ -65,6 +75,11 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
                 if (!hideSmallIndels) {
                     (0, util_2.fillRect)(ctx, pos, topPx, insW, heightPx, canvasWidth, colorMap.insertion);
                     if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
+                        items.push({
+                            type: 'insertion',
+                            seq: mismatch.insertedBases || 'unknown',
+                        });
+                        coords.push(leftPx - 2, topPx, leftPx + insW + 2, topPx + heightPx);
                         const l = Math.round(pos - insW);
                         (0, util_2.fillRect)(ctx, l, topPx, insW * 3, 1, canvasWidth);
                         (0, util_2.fillRect)(ctx, l, topPx + heightPx - 1, insW * 3, 1, canvasWidth);
@@ -104,6 +119,11 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
             if (mismatch.type === 'insertion' && len >= 10) {
                 const [leftPx] = (0, util_1.bpSpanPx)(mstart, mstart + mlen, region, bpPerPx);
                 const txt = `${len}`;
+                items.push({
+                    type: 'insertion',
+                    seq: mismatch.insertedBases || 'unknown',
+                });
+                coords.push(leftPx - 3, topPx, leftPx + 4, topPx + heightPx);
                 if (bpPerPx > largeInsertionIndicatorScale) {
                     (0, util_2.fillRect)(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, colorMap.insertion);
                 }
@@ -121,4 +141,8 @@ function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInse
             }
         }
     }
+    return {
+        coords,
+        items,
+    };
 }

package/dist/PileupRenderer/{renderModifications.d.ts → renderers/renderModifications.d.ts}

@@ -1,5 +1,5 @@
-import type { ProcessedRenderArgs } from './types';
-import type { LayoutFeature } from './util';
+import type { FlatbushItem, ProcessedRenderArgs } from '../types';
+import type { LayoutFeature } from '../util';
 import type { Region } from '@jbrowse/core/util';
 export declare function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;
@@ -9,4 +9,7 @@ export declare function renderModifications({ ctx, feat, region, bpPerPx, render
     renderArgs: ProcessedRenderArgs;
     canvasWidth: number;
     cigarOps: string[];
-}): void;
+}): {
+    coords: number[];
+    items: FlatbushItem[];
+};

package/dist/PileupRenderer/renderers/renderModifications.js

@@ -0,0 +1,84 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderModifications = renderModifications;
+const util_1 = require("@jbrowse/core/util");
+const MismatchParser_1 = require("../../MismatchParser");
+const getModPositions_1 = require("../../ModificationParser/getModPositions");
+const getModProbabilities_1 = require("../../ModificationParser/getModProbabilities");
+const getMaximumModificationAtEachPosition_1 = require("../../shared/getMaximumModificationAtEachPosition");
+const modificationData_1 = require("../../shared/modificationData");
+const util_2 = require("../../shared/util");
+const util_3 = require("../../util");
+const util_4 = require("../util");
+function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
+    var _a, _b, _c, _d, _e;
+    const items = [];
+    const coords = [];
+    const { feature, topPx, heightPx } = feat;
+    const { colorBy, visibleModifications = {} } = renderArgs;
+    const seq = feature.get('seq');
+    if (!seq) {
+        return { coords, items };
+    }
+    const start = feature.get('start');
+    const isolatedModification = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
+    const twoColor = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.twoColor;
+    const modificationThreshold = (_d = (_c = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _c === void 0 ? void 0 : _c.threshold) !== null && _d !== void 0 ? _d : 10;
+    const thresholdFraction = modificationThreshold / 100;
+    const fstrand = feature.get('strand');
+    const mm = (0, util_3.getTagAlt)(feature, 'MM', 'Mm') || '';
+    const modifications = (0, getModPositions_1.getModPositions)(mm, seq, fstrand);
+    const probabilities = (0, getModProbabilities_1.getModProbabilities)(feature);
+    const modsByPosition = new Map();
+    let probIndex = 0;
+    for (const { type, base, strand, positions } of modifications) {
+        for (const { ref, idx } of (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
+            const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[probIndex + (fstrand === -1 ? positions.length - 1 - idx : idx)]) || 0;
+            if (!modsByPosition.has(ref)) {
+                modsByPosition.set(ref, []);
+            }
+            modsByPosition.get(ref).push({ type, base, strand, prob });
+        }
+        probIndex += positions.length;
+    }
+    (_e = (0, getMaximumModificationAtEachPosition_1.getMaxProbModAtEachPosition)(feature, cigarOps)) === null || _e === void 0 ? void 0 : _e.forEach(({ allProbs, prob, type }, pos) => {
+        const r = start + pos;
+        const [leftPx, rightPx] = (0, util_1.bpSpanPx)(r, r + 1, region, bpPerPx);
+        const mod = visibleModifications[type];
+        if (!mod) {
+            console.warn(`${type} not known yet`);
+            return;
+        }
+        if (isolatedModification && mod.type !== isolatedModification) {
+            return;
+        }
+        if (prob < thresholdFraction) {
+            return;
+        }
+        const col = mod.color || 'black';
+        const s = 1 - (0, util_1.sum)(allProbs);
+        if (twoColor && s > (0, util_1.max)(allProbs)) {
+            const c = (0, util_2.alphaColor)('blue', s);
+            const w = rightPx - leftPx + 0.5;
+            (0, util_4.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+        }
+        else {
+            const c = (0, util_2.alphaColor)(col, prob);
+            const w = rightPx - leftPx + 0.5;
+            (0, util_4.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+        }
+        const modsAtPos = modsByPosition.get(pos) || [];
+        const strandInfo = modsAtPos
+            .map(m => `${m.base}${m.strand}${m.type} ${(0, modificationData_1.getModificationName)(m.type)} (${(m.prob * 100).toFixed(1)}%)`)
+            .join('<br/>');
+        items.push({
+            type: 'modification',
+            seq: strandInfo || mod.base,
+            modType: type,
+            probability: prob,
+        });
+        coords.push(leftPx, topPx, rightPx, topPx + heightPx);
+        pos++;
+    });
+    return { coords, items };
+}

package/dist/PileupRenderer/{renderPerBaseLettering.d.ts → renderers/renderPerBaseLettering.d.ts}

@@ -1,4 +1,4 @@
-import type { LayoutFeature } from './util';
+import type { LayoutFeature } from '../util';
 import type { Region } from '@jbrowse/core/util';
 export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorMap, colorContrastMap, charWidth, charHeight, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;

package/dist/PileupRenderer/{renderPerBaseLettering.js → renderers/renderPerBaseLettering.js}

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderPerBaseLettering = renderPerBaseLettering;
 const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
+const util_2 = require("../util");
 function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorMap, colorContrastMap, charWidth, charHeight, canvasWidth, cigarOps, }) {
     const heightLim = charHeight - 2;
     const { feature, topPx, heightPx } = feat;

package/{esm/PileupRenderer → dist/PileupRenderer/renderers}/renderPerBaseQuality.d.ts

@@ -1,4 +1,4 @@
-import type { LayoutFeature } from './util';
+import type { LayoutFeature } from '../util';
 import type { Region } from '@jbrowse/core/util';
 export declare function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;

package/dist/PileupRenderer/{renderPerBaseQuality.js → renderers/renderPerBaseQuality.js}

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderPerBaseQuality = renderPerBaseQuality;
 const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
+const util_2 = require("../util");
 function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, cigarOps, }) {
     const { feature, topPx, heightPx } = feat;
     const qual = feature.get('qual') || '';

package/dist/PileupRenderer/{renderSoftClipping.d.ts → renderers/renderSoftClipping.d.ts}

@@ -1,5 +1,5 @@
-import type { ProcessedRenderArgs } from './types';
-import type { LayoutFeature } from './util';
+import type { ProcessedRenderArgs } from '../types';
+import type { LayoutFeature } from '../util';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { Theme } from '@mui/material';
 export declare function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorMap, canvasWidth, }: {

package/dist/PileupRenderer/{renderSoftClipping.js → renderers/renderSoftClipping.js}

@@ -3,8 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderSoftClipping = renderSoftClipping;
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
-const util_2 = require("./util");
-const MismatchParser_1 = require("../MismatchParser");
+const MismatchParser_1 = require("../../MismatchParser");
+const util_2 = require("../util");
 function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorMap, canvasWidth, }) {
     const { feature, topPx, heightPx } = feat;
     const { regions, bpPerPx } = renderArgs;

package/dist/PileupRenderer/types.d.ts

@@ -7,6 +7,12 @@ export interface LayoutFeature {
     topPx: number;
     feature: Feature;
 }
+export interface FlatbushItem {
+    type: 'insertion' | 'deletion' | 'mismatch' | 'modification';
+    seq: string;
+    modType?: string;
+    probability?: number;
+}
 export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
     colorBy?: ColorBy;
     colorTagMap?: Record<string, string>;

package/dist/SNPCoverageAdapter/generateCoverageBins.js

@@ -13,6 +13,7 @@ async function generateCoverageBins({ fetchSequence, features, region, opts, })
     const bins = [];
     const start2 = Math.max(0, region.start - 1);
     const diff = region.start - start2;
+    let regionSequence;
     let start = performance.now();
     for (const feature of features) {
         if (performance.now() - start > 400) {
@@ -25,11 +26,11 @@ async function generateCoverageBins({ fetchSequence, features, region, opts, })
             region,
         });
         if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-            const regionSequence = (await fetchSequence({
+            regionSequence !== null && regionSequence !== void 0 ? regionSequence : (regionSequence = (await fetchSequence({
                 ...region,
                 start: start2,
                 end: region.end + 1,
-            })) || '';
+            })) || '');
             (0, processModifications_1.processModifications)({
                 feature,
                 colorBy,
@@ -39,11 +40,11 @@ async function generateCoverageBins({ fetchSequence, features, region, opts, })
             });
         }
         else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
-            const regionSequence = (await fetchSequence({
+            regionSequence !== null && regionSequence !== void 0 ? regionSequence : (regionSequence = (await fetchSequence({
                 ...region,
                 start: start2,
                 end: region.end + 1,
-            })) || '';
+            })) || '');
             (0, processReferenceCpGs_1.processReferenceCpGs)({
                 feature,
                 bins,

package/dist/SNPCoverageAdapter/processModifications.js

@@ -3,18 +3,29 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.processModifications = processModifications;
 const util_1 = require("@jbrowse/core/util");
 const util_2 = require("./util");
+const MismatchParser_1 = require("../MismatchParser");
 const getMaximumModificationAtEachPosition_1 = require("../shared/getMaximumModificationAtEachPosition");
 function processModifications({ feature, colorBy, region, bins, regionSequence, }) {
-    var _a, _b, _c;
+    var _a, _b, _c, _d, _e;
     const fstart = feature.get('start');
     const fstrand = feature.get('strand');
     const fend = feature.get('end');
     const twoColor = (_a = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _a === void 0 ? void 0 : _a.twoColor;
     const isolatedModification = (_b = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _b === void 0 ? void 0 : _b.isolatedModification;
-    (_c = (0, getMaximumModificationAtEachPosition_1.getMaxProbModAtEachPosition)(feature)) === null || _c === void 0 ? void 0 : _c.forEach(({ allProbs, prob, type }, pos) => {
+    const seq = feature.get('seq');
+    const modificationThreshold = (_d = (_c = colorBy === null || colorBy === void 0 ? void 0 : colorBy.modifications) === null || _c === void 0 ? void 0 : _c.threshold) !== null && _d !== void 0 ? _d : 10;
+    const thresholdFraction = modificationThreshold / 100;
+    if (!seq) {
+        return;
+    }
+    const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+    (_e = (0, getMaximumModificationAtEachPosition_1.getMaxProbModAtEachPosition)(feature, cigarOps)) === null || _e === void 0 ? void 0 : _e.forEach(({ allProbs, prob, type }, pos) => {
         if (isolatedModification && type !== isolatedModification) {
             return;
         }
+        if (prob < thresholdFraction) {
+            return;
+        }
         const epos = pos + fstart - region.start;
         if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
             if (bins[epos] === undefined) {
@@ -35,9 +46,9 @@ function processModifications({ feature, colorBy, region, bins, regionSequence,
                     noncov: {},
                 };
             }
-            const s = 1 - (0, util_1.sum)(allProbs);
             const bin = bins[epos];
             bin.refbase = regionSequence[epos];
+            const s = 1 - (0, util_1.sum)(allProbs);
             if (twoColor && s > (0, util_1.max)(allProbs)) {
                 (0, util_2.incWithProbabilities)(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
             }
@@ -45,6 +56,5 @@ function processModifications({ feature, colorBy, region, bins, regionSequence,
                 (0, util_2.incWithProbabilities)(bin, fstrand, 'mods', `mod_${type}`, prob);
             }
         }
-        pos++;
     });
 }

package/dist/SNPCoverageRenderer/makeImage.js

@@ -16,9 +16,26 @@ const complementBase = {
     T: 'A',
 };
 const fudgeFactor = 0.6;
+function calculateModificationCounts({ base, isSimplex, refbase, snps, ref, score0, }) {
+    var _a, _b, _c, _d;
+    if (base === 'N') {
+        return { modifiable: score0, detectable: score0 };
+    }
+    const cmp = complementBase[base];
+    const baseCount = (((_a = snps[base]) === null || _a === void 0 ? void 0 : _a.entryDepth) || 0) + (refbase === base ? ref.entryDepth : 0);
+    const complCount = (((_b = snps[cmp]) === null || _b === void 0 ? void 0 : _b.entryDepth) || 0) + (refbase === cmp ? ref.entryDepth : 0);
+    const modifiable = baseCount + complCount;
+    const detectable = isSimplex
+        ? (((_c = snps[base]) === null || _c === void 0 ? void 0 : _c['1']) || 0) +
+            (((_d = snps[cmp]) === null || _d === void 0 ? void 0 : _d['-1']) || 0) +
+            (refbase === base ? ref['1'] : 0) +
+            (refbase === cmp ? ref['-1'] : 0)
+        : modifiable;
+    return { modifiable, detectable };
+}
 async function makeImage(ctx, props) {
     var _a;
-    const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopToken, } = props;
+    const { features, regions, bpPerPx, colorBy, displayCrossHatches, visibleModifications = {}, simplexModifications = [], scaleOpts, height: unadjustedHeight, theme: configTheme, config: cfg, ticks, stopToken, } = props;
     const theme = (0, ui_1.createJBrowseTheme)(configTheme);
     const region = regions[0];
     const width = (region.end - region.start) / bpPerPx;
@@ -70,8 +87,9 @@ async function makeImage(ctx, props) {
     const drawingModifications = colorBy.type === 'modifications';
     const drawingMethylation = colorBy.type === 'methylation';
     const isolatedModification = (_a = colorBy.modifications) === null || _a === void 0 ? void 0 : _a.isolatedModification;
+    const simplexSet = new Set(simplexModifications);
     (0, util_1.forEachWithStopTokenCheck)(features.values(), stopToken, feature => {
-        var _a, _b, _c, _d, _e, _f, _g, _h, _j;
+        var _a;
         if (feature.get('type') === 'skip') {
             return;
         }
@@ -83,9 +101,10 @@ async function makeImage(ctx, props) {
             let curr = 0;
             const refbase = (_a = snpinfo.refbase) === null || _a === void 0 ? void 0 : _a.toUpperCase();
             const { nonmods, mods, snps, ref } = snpinfo;
-            for (const m of Object.keys(nonmods).sort().reverse()) {
-                const mod = visibleModifications[m.replace('nonmod_', '')] ||
-                    visibleModifications[m.replace('mod_', '')];
+            const nonmodKeys = Object.keys(nonmods).sort().reverse();
+            for (const m of nonmodKeys) {
+                const modKey = m.replace(/^(nonmod_|mod_)/, '');
+                const mod = visibleModifications[modKey];
                 if (!mod) {
                     console.warn(`${m} not known yet`);
                     continue;
@@ -93,19 +112,14 @@ async function makeImage(ctx, props) {
                 if (isolatedModification && mod.type !== isolatedModification) {
                     continue;
                 }
-                const cmp = complementBase[mod.base];
-                const detectable = mod.base === 'N'
-                    ? score0
-                    : (((_b = snps[mod.base]) === null || _b === void 0 ? void 0 : _b.entryDepth) || 0) +
-                        (((_c = snps[cmp]) === null || _c === void 0 ? void 0 : _c.entryDepth) || 0) +
-                        (refbase === mod.base ? ref['1'] : 0) +
-                        (refbase === cmp ? ref['-1'] : 0);
-                const modifiable = mod.base === 'N'
-                    ? score0
-                    : (((_d = snps[mod.base]) === null || _d === void 0 ? void 0 : _d.entryDepth) || 0) +
-                        (((_e = snps[cmp]) === null || _e === void 0 ? void 0 : _e.entryDepth) || 0) +
-                        (refbase === mod.base ? ref.entryDepth : 0) +
-                        (refbase === cmp ? ref.entryDepth : 0);
+                const { modifiable, detectable } = calculateModificationCounts({
+                    base: mod.base,
+                    isSimplex: simplexSet.has(mod.type),
+                    refbase,
+                    snps,
+                    ref,
+                    score0,
+                });
                 const { entryDepth, avgProbability = 0 } = snpinfo.nonmods[m];
                 const modFraction = (modifiable / score0) * (entryDepth / detectable);
                 const nonModColor = 'blue';
@@ -116,8 +130,10 @@ async function makeImage(ctx, props) {
                 ctx.fillRect(Math.round(leftPx), bottom - (curr + modFraction * height), w, modFraction * height);
                 curr += modFraction * height;
             }
-            for (const m of Object.keys(mods).sort().reverse()) {
-                const mod = visibleModifications[m.replace('mod_', '')];
+            const modKeys = Object.keys(mods).sort().reverse();
+            for (const m of modKeys) {
+                const modKey = m.replace('mod_', '');
+                const mod = visibleModifications[modKey];
                 if (!mod) {
                     console.warn(`${m} not known yet`);
                     continue;
@@ -125,19 +141,14 @@ async function makeImage(ctx, props) {
                 if (isolatedModification && mod.type !== isolatedModification) {
                     continue;
                 }
-                const cmp = complementBase[mod.base];
-                const detectable = mod.base === 'N'
-                    ? score0
-                    : (((_f = snps[mod.base]) === null || _f === void 0 ? void 0 : _f.entryDepth) || 0) +
-                        (((_g = snps[cmp]) === null || _g === void 0 ? void 0 : _g.entryDepth) || 0) +
-                        (refbase === mod.base ? ref['1'] : 0) +
-                        (refbase === cmp ? ref['-1'] : 0);
-                const modifiable = mod.base === 'N'
-                    ? score0
-                    : (((_h = snps[mod.base]) === null || _h === void 0 ? void 0 : _h.entryDepth) || 0) +
-                        (((_j = snps[cmp]) === null || _j === void 0 ? void 0 : _j.entryDepth) || 0) +
-                        (refbase === mod.base ? ref.entryDepth : 0) +
-                        (refbase === cmp ? ref.entryDepth : 0);
+                const { modifiable, detectable } = calculateModificationCounts({
+                    base: mod.base,
+                    isSimplex: simplexSet.has(mod.type),
+                    refbase,
+                    snps,
+                    ref,
+                    score0,
+                });
                 const { entryDepth, avgProbability = 0 } = mods[m];
                 const modFraction = (modifiable / score0) * (entryDepth / detectable);
                 const baseColor = mod.color || 'black';

package/dist/SNPCoverageRenderer/types.d.ts

@@ -15,6 +15,7 @@ export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserializ
     };
     displayCrossHatches: boolean;
     visibleModifications?: Record<string, ModificationTypeWithColor>;
+    simplexModifications?: string[];
     statusCallback?: (arg: string) => void;
     colorBy: ColorBy;
 }

package/dist/shared/LinearReadDisplayBaseMixin.d.ts

@@ -0,0 +1,24 @@
+import type { ChainData } from './fetchChains';
+import type { ColorBy, FilterBy } from './types';
+export declare function LinearReadDisplayBaseMixin(): import("mobx-state-tree").IModelType<{
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+}, {
+    loading: boolean;
+    chainData: ChainData | undefined;
+    lastDrawnOffsetPx: number | undefined;
+    lastDrawnBpPerPx: number;
+    ref: HTMLCanvasElement | null;
+} & {
+    setLastDrawnOffsetPx(n: number): void;
+    setLastDrawnBpPerPx(n: number): void;
+    setLoading(f: boolean): void;
+    setRef(ref: HTMLCanvasElement | null): void;
+    setColorScheme(colorBy: {
+        type: string;
+    }): void;
+    setChainData(args: ChainData): void;
+    setFilterBy(filter: FilterBy): void;
+} & {
+    readonly drawn: boolean;
+}, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;