@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/PileupRenderer/renderSoftClipping.js

@@ -0,0 +1,44 @@
+import { readConfObject, } from '@jbrowse/core/configuration';
+import { bpSpanPx } from '@jbrowse/core/util';
+import { fillRect, getCharWidthHeight } from './util';
+export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }) {
+    const { feature, topPx, heightPx } = feat;
+    const { regions, bpPerPx } = renderArgs;
+    const [region] = regions;
+    const minFeatWidth = readConfObject(config, 'minSubfeatureWidth');
+    const mismatches = feature.get('mismatches');
+    const seq = feature.get('seq');
+    const { charWidth, charHeight } = getCharWidthHeight();
+    // Display all bases softclipped off in lightened colors
+    if (!(seq && mismatches)) {
+        return;
+    }
+    mismatches
+        .filter(mismatch => mismatch.type === 'softclip')
+        .forEach(mismatch => {
+        const len = mismatch.cliplen || 0;
+        const s = feature.get('start');
+        const start = mismatch.start === 0 ? s - len : s + mismatch.start;
+        for (let k = 0; k < len; k += 1) {
+            const base = seq.charAt(k + mismatch.start);
+            // If softclip length+start is longer than sequence, no need to
+            // continue showing base
+            if (!base) {
+                return;
+            }
+            const s0 = start + k;
+            const [leftPx, rightPx] = bpSpanPx(s0, s0 + 1, region, bpPerPx);
+            const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
+            // Black accounts for IUPAC ambiguity code bases such as N that
+            // show in soft clipping
+            const baseColor = colorForBase[base] || '#000000';
+            ctx.fillStyle = baseColor;
+            fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
+            if (widthPx >= charWidth && heightPx >= charHeight - 5) {
+                ctx.fillStyle = theme.palette.getContrastText(baseColor);
+                ctx.fillText(base, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
+            }
+        }
+    });
+}
+//# sourceMappingURL=renderSoftClipping.js.map

package/esm/PileupRenderer/renderSoftClipping.js.map

@@ -0,0 +1 @@
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package/esm/PileupRenderer/sortUtil.js

@@ -72,10 +72,9 @@ export const sortFeature = (features, sortedBy) => {
             break;
         }
     }
-    const sortedMap = new Map([...featuresInCenterLine, ...featuresOutsideCenter].map(feature => [
+    return new Map([...featuresInCenterLine, ...featuresOutsideCenter].map(feature => [
         feature.id(),
         feature,
     ]));
-    return sortedMap;
 };
 //# sourceMappingURL=sortUtil.js.map

package/esm/PileupRenderer/sortUtil.js.map

@@ -1 +1 @@
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package/esm/PileupRenderer/util.d.ts

@@ -0,0 +1,24 @@
+import { Feature } from '@jbrowse/core/util';
+import { Theme } from '@mui/material';
+export declare function fillRect(ctx: CanvasRenderingContext2D, l: number, t: number, w: number, h: number, cw: number, color?: string): void;
+export declare function getColorBaseMap(theme: Theme): {
+    A: string;
+    C: string;
+    G: string;
+    T: string;
+    deletion: string;
+};
+export declare function getContrastBaseMap(theme: Theme): {
+    [k: string]: string;
+};
+export declare function shouldDrawSNPsMuted(type?: string): boolean;
+export declare function shouldDrawIndels(): boolean;
+export interface LayoutFeature {
+    heightPx: number;
+    topPx: number;
+    feature: Feature;
+}
+export declare function getCharWidthHeight(): {
+    charWidth: number;
+    charHeight: number;
+};

package/esm/PileupRenderer/util.js

@@ -0,0 +1,42 @@
+import { measureText } from '@jbrowse/core/util';
+export function fillRect(ctx, l, t, w, h, cw, color) {
+    if (l + w < 0 || l > cw) {
+        return;
+    }
+    else {
+        if (color) {
+            ctx.fillStyle = color;
+        }
+        ctx.fillRect(l, t, w, h);
+    }
+}
+export function getColorBaseMap(theme) {
+    const { bases } = theme.palette;
+    return {
+        A: bases.A.main,
+        C: bases.C.main,
+        G: bases.G.main,
+        T: bases.T.main,
+        deletion: '#808080', // gray
+    };
+}
+export function getContrastBaseMap(theme) {
+    return Object.fromEntries(Object.entries(getColorBaseMap(theme)).map(([key, value]) => [
+        key,
+        theme.palette.getContrastText(value),
+    ]));
+}
+export function shouldDrawSNPsMuted(type) {
+    return ['methylation', 'modifications'].includes(type || '');
+}
+export function shouldDrawIndels() {
+    return true;
+}
+// get width and height of chars the height is an approximation: width letter M
+// is approximately the height
+export function getCharWidthHeight() {
+    const charWidth = measureText('A');
+    const charHeight = measureText('M') - 2;
+    return { charWidth, charHeight };
+}
+//# sourceMappingURL=util.js.map

package/esm/PileupRenderer/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/PileupRenderer/util.ts"],"names":[],"mappings":"AAAA,OAAO,EAAW,WAAW,EAAE,MAAM,oBAAoB,CAAA;AAGzD,MAAM,UAAU,QAAQ,CACtB,GAA6B,EAC7B,CAAS,EACT,CAAS,EACT,CAAS,EACT,CAAS,EACT,EAAU,EACV,KAAc;IAEd,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,EAAE,EAAE;QACvB,OAAM;KACP;SAAM;QACL,IAAI,KAAK,EAAE;YACT,GAAG,CAAC,SAAS,GAAG,KAAK,CAAA;SACtB;QACD,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,CAAC,CAAA;KACzB;AACH,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,KAAY;IAC1C,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,OAAO,CAAA;IAC/B,OAAO;QACL,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;QACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;QACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;QACf,CAAC,EAAE,KAAK,CAAC,CAAC,CAAC,IAAI;QACf,QAAQ,EAAE,SAAS,EAAE,OAAO;KAC7B,CAAA;AACH,CAAC;AAED,MAAM,UAAU,kBAAkB,CAAC,KAAY;IAC7C,OAAO,MAAM,CAAC,WAAW,CACvB,MAAM,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC;QAC3D,GAAG;QACH,KAAK,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC;KACrC,CAAC,CACH,CAAA;AACH,CAAC;AAED,MAAM,UAAU,mBAAmB,CAAC,IAAa;IAC/C,OAAO,CAAC,aAAa,EAAE,eAAe,CAAC,CAAC,QAAQ,CAAC,IAAI,IAAI,EAAE,CAAC,CAAA;AAC9D,CAAC;AAED,MAAM,UAAU,gBAAgB;IAC9B,OAAO,IAAI,CAAA;AACb,CAAC;AAQD,+EAA+E;AAC/E,8BAA8B;AAC9B,MAAM,UAAU,kBAAkB;IAChC,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAA;IAClC,MAAM,UAAU,GAAG,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;IACvC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,CAAA;AAClC,CAAC"}

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.d.ts

@@ -8,9 +8,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     }>;
     fetchSequence(region: Region): Promise<any>;
     getFeatures(region: Region, opts?: BaseOptions): 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>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     freeResources(): void;
 }
-declare const capabilities: string[];
-export { capabilities };

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -65,9 +65,9 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
             observer.complete();
         }, opts.signal);
     }
-    async estimateRegionsStats(regions, opts) {
+    async getMultiRegionFeatureDensityStats(regions, opts) {
         const { subadapter } = await this.configure();
-        return subadapter.estimateRegionsStats(regions, opts);
+        return subadapter.getMultiRegionFeatureDensityStats(regions, opts);
     }
     async getRefNames(opts = {}) {
         const { subadapter } = await this.configure();
@@ -75,6 +75,4 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     }
     freeResources( /* { region } */) { }
 }
-const { capabilities } = SNPCoverageAdapter;
-export { capabilities };
 //# sourceMappingURL=SNPCoverageAdapter.js.map

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js.map

@@ -1 +1 @@
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+{"version":3,"file":"SNPCoverageAdapter.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/SNPCoverageAdapter.ts"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,GAEvB,MAAM,yCAAyC,CAAA;AAEhD,OAAO,aAA0B,MAAM,kCAAkC,CAAA;AACzE,OAAO,EAAE,gBAAgB,EAAE,MAAM,yBAAyB,CAAA;AAC1D,OAAO,EAAE,OAAO,EAAE,MAAM,gBAAgB,CAAA;AACxC,OAAO,EAAE,cAAc,EAAE,MAAM,MAAM,CAAA;AAErC,SAAS;AACT,OAAO,oBAAoB,MAAM,wBAAwB,CAAA;AACzD,OAAO,EAAE,aAAa,EAAE,MAAM,SAAS,CAAA;AAEvC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,sBAAsB;IAC1D,KAAK,CAAC,SAAS;;QACvB,MAAM,gBAAgB,GAAG,IAAI,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACnD,MAAM,YAAY,GAAG,gBAAgB,CAAC,eAAe,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,gBAAgB,CAAC,CAAA,CAAA;QAEhE,MAAM,eAAe,GAAG,YAAY;YAClC,CAAC,CAAC,MAAM,CAAA,MAAA,IAAI,CAAC,aAAa,qDAAG,YAAY,CAAC,CAAA;YAC1C,CAAC,CAAC,SAAS,CAAA;QAEb,IAAI,CAAC,WAAW,EAAE;YAChB,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;SAC5C;QAED,OAAO;YACL,UAAU,EAAE,WAAW,CAAC,WAAqC;YAC7D,eAAe,EAAE,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,WAErB;SACd,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa,CAAC,MAAc;QAChC,MAAM,EAAE,eAAe,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAClD,IAAI,CAAC,eAAe,EAAE;YACpB,OAAO,SAAS,CAAA;SACjB;QAED,OAAO,aAAa,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC/C,CAAC;IAED,WAAW,CAAC,MAAc,EAAE,OAAoB,EAAE;QAChD,OAAO,gBAAgB,CAAU,KAAK,EAAC,QAAQ,EAAC,EAAE;YAChD,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC7C,MAAM,KAAK,GAAG,MAAM,cAAc,CAChC,UAAU,CAAC,WAAW,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC,CACrD,CAAA;YAED,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,MAAM,oBAAoB,CAClD,KAAK,EACL,MAAM,EACN,IAAI,EACJ,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAC/B,CAAA;YAED,IAAI,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,KAAK,EAAE,EAAE;gBAC1B,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,GAAG,KAAK,CAAA;gBAClC,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG,IAAI,CAAC,EAAE,IAAI,KAAK,EAAE;oBACzB,IAAI,EAAE;wBACJ,KAAK,EAAE,GAAG,CAAC,KAAK;wBAChB,OAAO,EAAE,GAAG;wBACZ,KAAK;wBACL,GAAG,EAAE,KAAK,GAAG,CAAC;wBACd,OAAO,EAAE,MAAM,CAAC,OAAO;qBACxB;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,uCAAuC;YACvC,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,EAAE,IAAI,CAAC,EAAE,EAAE;gBAC9C,QAAQ,CAAC,IAAI,CACX,IAAI,aAAa,CAAC;oBAChB,EAAE,EAAE,GAAG;oBACP,IAAI,EAAE;wBACJ,IAAI,EAAE,MAAM;wBACZ,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,GAAG,EAAE,IAAI,CAAC,GAAG;wBACb,MAAM,EAAE,IAAI,CAAC,MAAM;wBACnB,KAAK,EAAE,IAAI,CAAC,KAAK;wBACjB,EAAE,EAAE,IAAI,CAAC,EAAE;qBACZ;iBACF,CAAC,CACH,CAAA;YACH,CAAC,CAAC,CAAA;YAEF,QAAQ,CAAC,QAAQ,EAAE,CAAA;QACrB,CAAC,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACjB,CAAC;IAED,KAAK,CAAC,iCAAiC,CACrC,OAAiB,EACjB,IAAkB;QAElB,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,iCAAiC,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IACpE,CAAC;IAED,KAAK,CAAC,WAAW,CAAC,OAAoB,EAAE;QACtC,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC7C,OAAO,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,aAAa,EAAC,gBAAgB,IAAS,CAAC;CACzC"}

package/esm/SNPCoverageAdapter/configSchema.d.ts

@@ -1,2 +1,11 @@
-declare const configSchema: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    /**
+     * #slot
+     * normally refers to a BAM or CRAM adapter
+     */
+    subadapter: {
+        type: string;
+        defaultValue: null;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default configSchema;

package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts

@@ -1,5 +1,6 @@
 import { AugmentedRegion as Region } from '@jbrowse/core/util/types';
 import { Feature } from '@jbrowse/core/util/simpleFeature';
+import { Bin, SkipMap } from './util';
 export default function generateCoverageBins(features: Feature[], region: Region, opts: {
     bpPerPx?: number;
     colorBy?: {
@@ -7,47 +8,6 @@ export default function generateCoverageBins(features: Feature[], region: Region
         tag?: string;
     };
 }, fetchSequence: (arg: Region) => Promise<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;
-        };
-    };
+    bins: Bin[];
+    skipmap: SkipMap;
 }>;

package/esm/SNPCoverageAdapter/generateCoverageBins.js

@@ -1,5 +1,6 @@
 import { getTag, getTagAlt, shouldFetchReferenceSequence } from '../util';
-import { parseCigar, getNextRefPos, getModificationPositions, } from '../MismatchParser';
+import { parseCigar, getNextRefPos, getModificationPositions, getMethBins, } from '../MismatchParser';
+import { doesIntersect2 } from '@jbrowse/core/util';
 function mismatchLen(mismatch) {
     return !isInterbase(mismatch.type) ? mismatch.length : 1;
 }
@@ -21,19 +22,24 @@ function inc(bin, strand, type, field) {
     thisBin[strand]++;
 }
 export default async function generateCoverageBins(features, region, opts, fetchSequence) {
-    var _a;
+    var _a, _b, _c;
     const { colorBy } = opts;
-    const binMax = Math.ceil(region.end - region.start);
+    const extendedRegion = {
+        ...region,
+        start: Math.max(0, region.start - 1),
+        end: region.end + 1,
+    };
+    const binMax = Math.ceil(extendedRegion.end - extendedRegion.start);
     const skipmap = {};
-    const regionSeq = features.length && shouldFetchReferenceSequence((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
+    const regionSequence = features.length && shouldFetchReferenceSequence((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
         ? await fetchSequence(region)
         : undefined;
     const bins = [];
-    for (let i = 0; i < features.length; i++) {
-        const feature = features[i];
+    for (const feature of features) {
         const fstart = feature.get('start');
         const fend = feature.get('end');
         const fstrand = feature.get('strand');
+        const mismatches = feature.get('mismatches') || [];
         for (let j = fstart; j < fend + 1; j++) {
             const i = j - region.start;
             if (i >= 0 && i < binMax) {
@@ -64,77 +70,98 @@ export default async function generateCoverageBins(features, region, opts, fetch
             const mm = getTagAlt(feature, 'MM', 'Mm') || '';
             const ops = parseCigar(feature.get('CIGAR'));
             const fend = feature.get('end');
-            getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
-                const mod = `mod_${type}`;
-                for (const pos of getNextRefPos(ops, positions)) {
-                    const epos = pos + fstart - region.start;
-                    if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
-                        const bin = bins[epos];
-                        if (bin) {
-                            inc(bin, fstrand, 'cov', mod);
-                        }
-                        else {
-                            console.warn('Undefined position in modifications snpcoverage encountered');
+            if (seq) {
+                const modifications = getModificationPositions(mm, seq, fstrand);
+                for (const { type, positions } of modifications) {
+                    const mod = `mod_${type}`;
+                    for (const pos of getNextRefPos(ops, positions)) {
+                        const epos = pos + fstart - region.start;
+                        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+                            if (bins[epos] === undefined) {
+                                bins[epos] = {
+                                    total: 0,
+                                    all: 0,
+                                    ref: 0,
+                                    '-1': 0,
+                                    '0': 0,
+                                    '1': 0,
+                                    lowqual: {},
+                                    cov: {},
+                                    delskips: {},
+                                    noncov: {},
+                                };
+                            }
+                            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
-        else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
-            if (!regionSeq) {
+        if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
+            if (!regionSequence) {
                 throw new Error('no region sequence detected, need sequenceAdapter configuration');
             }
             const seq = feature.get('seq');
-            const mm = getTagAlt(feature, 'MM', 'Mm') || '';
-            const methBins = new Array(region.end - region.start).fill(0);
-            const ops = parseCigar(feature.get('CIGAR'));
-            getModificationPositions(mm, seq, fstrand).forEach(({ type, positions }) => {
-                // we are processing methylation
-                if (type === 'm') {
-                    for (const pos of 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];
+            if (!seq) {
+                continue;
+            }
+            const { methBins, methProbs } = getMethBins(feature);
+            const dels = mismatches.filter(f => f.type === 'deletion');
+            // methylation based coloring takes into account both reference sequence
+            // CpG detection and reads
+            for (let i = 0; i < fend - fstart; i++) {
+                const j = i + fstart;
+                const l1 = (_b = regionSequence[j - region.start + 1]) === null || _b === void 0 ? void 0 : _b.toLowerCase();
+                const l2 = (_c = regionSequence[j - region.start + 2]) === null || _c === void 0 ? void 0 : _c.toLowerCase();
+                if (l1 === 'c' && l2 === 'g') {
+                    const bin0 = bins[j - region.start];
+                    const bin1 = bins[j - region.start + 1];
+                    const b0 = methBins[i];
+                    const b1 = methBins[i + 1];
+                    const p0 = methProbs[i];
+                    const p1 = methProbs[i + 1];
                     // color
-                    if (l1 === 'c' && l2 === 'g') {
-                        if (methBins[i] || methBins[i + 1]) {
-                            inc(bin, fstrand, 'cov', 'meth');
+                    if ((b0 && (p0 !== undefined ? p0 > 0.5 : true)) ||
+                        (b1 && (p1 !== undefined ? p1 > 0.5 : true))) {
+                        if (bin0) {
+                            inc(bin0, fstrand, 'cov', 'meth');
+                            bin0.ref--;
+                            bin0[fstrand]--;
+                        }
+                        if (bin1) {
                             inc(bin1, fstrand, 'cov', 'meth');
-                            bins[i].ref--;
-                            bins[i][fstrand]--;
-                            bins[i + 1].ref--;
-                            bins[i + 1][fstrand]--;
+                            bin1.ref--;
+                            bin1[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]--;
+                    }
+                    else {
+                        if (bin0) {
+                            if (!(dels === null || dels === void 0 ? void 0 : dels.some(d => doesIntersect2(j, j + 1, d.start + fstart, d.start + fstart + d.length)))) {
+                                inc(bin0, fstrand, 'cov', 'unmeth');
+                                bin0.ref--;
+                                bin0[fstrand];
+                            }
+                        }
+                        if (bin1) {
+                            if (!(dels === null || dels === void 0 ? void 0 : dels.some(d => doesIntersect2(j + 1, j + 2, d.start + fstart, d.start + fstart + d.length)))) {
+                                inc(bin1, fstrand, 'cov', 'unmeth');
+                                bin1.ref--;
+                                bin1[fstrand]--;
+                            }
                         }
                     }
                 }
             }
         }
         // normal SNP based coloring
-        const mismatches = feature.get('mismatches') || [];
         const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
-        for (let i = 0; i < mismatches.length; i++) {
-            const mismatch = mismatches[i];
+        for (const mismatch of mismatches) {
             const mstart = fstart + mismatch.start;
             const mlen = mismatchLen(mismatch);
             const mend = mstart + mlen;

package/esm/SNPCoverageAdapter/generateCoverageBins.js.map

@@ -1 +1 @@
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package/esm/SNPCoverageAdapter/index.js

@@ -1,6 +1,5 @@
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
 import configSchema from './configSchema';
-import { capabilities } from './SNPCoverageAdapter';
 export default function (pluginManager) {
     pluginManager.addAdapterType(() => {
         return new AdapterType({
@@ -11,7 +10,6 @@ export default function (pluginManager) {
             },
             getAdapterClass: () => import('./SNPCoverageAdapter').then(r => r.default),
             configSchema,
-            adapterCapabilities: capabilities,
         });
     });
 }

package/esm/SNPCoverageAdapter/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,WAAW,MAAM,iDAAiD,CAAA;AACzE,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,WAAW,aAA4B;IACnD,aAAa,CAAC,cAAc,CAAC,GAAG,EAAE;QAChC,OAAO,IAAI,WAAW,CAAC;YACrB,IAAI,EAAE,oBAAoB;YAC1B,WAAW,EAAE,qBAAqB;YAClC,eAAe,EAAE;gBACf,aAAa,EAAE,IAAI;aACpB;YACD,eAAe,EAAE,GAAG,EAAE,CACpB,MAAM,CAAC,sBAAsB,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;YACrD,YAAY;SACb,CAAC,CAAA;IACJ,CAAC,CAAC,CAAA;AACJ,CAAC"}

package/esm/SNPCoverageAdapter/util.d.ts

@@ -0,0 +1,29 @@
+export interface SkipMap {
+    [key: string]: {
+        score: number;
+        feature: unknown;
+        start: number;
+        end: number;
+        strand: number;
+        xs: string;
+    };
+}
+export interface BinType {
+    total?: number;
+    strands?: {
+        [key: string]: number;
+    };
+}
+export interface Bin {
+    refbase?: string;
+    total: number;
+    all: number;
+    ref: number;
+    '-1': number;
+    '0': number;
+    '1': number;
+    lowqual: BinType;
+    cov: BinType;
+    delskips: BinType;
+    noncov: BinType;
+}

package/esm/SNPCoverageAdapter/util.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=util.js.map

package/esm/SNPCoverageAdapter/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/SNPCoverageAdapter/util.ts"],"names":[],"mappings":""}

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -13,7 +13,7 @@ export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserializ
         values: number[];
     };
     displayCrossHatches: boolean;
-    modificationTagMap?: Record<string, string>;
+    modificationTagMap?: Record<string, string | undefined>;
 }
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<void>;

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.js

@@ -46,10 +46,10 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
             C: bases.C.main,
             G: bases.G.main,
             T: bases.T.main,
-            total: 'lightgrey',
             insertion: 'purple',
             softclip: 'blue',
             hardclip: 'red',
+            total: readConfObject(cfg, 'color'),
             meth: 'red',
             unmeth: 'blue',
         };
@@ -93,7 +93,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
                 ctx.fillStyle =
                     colorForBase[base] ||
                         modificationTagMap[base.replace('mod_', '')] ||
-                        '#888';
+                        'black';
                 const height = toHeight(score);
                 const bottom = toY(score) + height;
                 ctx.fillRect(Math.round(leftPx), bottom - ((total + curr) / score) * height, w, (total / score) * height);