@jbrowse/plugin-alignments 2.16.0 → 2.17.0

package/esm/SNPCoverageAdapter/generateCoverageBins.js

@@ -1,6 +1,8 @@
-import { getTag, getTagAlt, shouldFetchReferenceSequence } from '../util';
-import { parseCigar, getNextRefPos, getModificationPositions, getMethBins, } from '../MismatchParser';
-import { doesIntersect2 } from '@jbrowse/core/util';
+import { doesIntersect2, max, sum } from '@jbrowse/core/util';
+// locals
+import { parseCigar } from '../MismatchParser';
+import { getMethBins } from '../ModificationParser';
+import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
 function mismatchLen(mismatch) {
     return !isInterbase(mismatch.type) ? mismatch.length : 1;
 }
@@ -11,192 +13,293 @@ function inc(bin, strand, type, field) {
     let thisBin = bin[type][field];
     if (thisBin === undefined) {
         thisBin = bin[type][field] = {
-            total: 0,
+            entryDepth: 0,
+            probabilities: [],
             '-1': 0,
             '0': 0,
             '1': 0,
         };
     }
-    thisBin.total++;
+    thisBin.entryDepth++;
     thisBin[strand]++;
 }
-export default async function generateCoverageBins(features, region, opts, fetchSequence) {
-    var _a, _b, _c;
-    const { colorBy } = opts;
-    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 regionSequence = features.length && shouldFetchReferenceSequence((_a = opts.colorBy) === null || _a === void 0 ? void 0 : _a.type)
-        ? await fetchSequence(region)
-        : undefined;
-    const bins = [];
-    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) {
-                if (bins[i] === undefined) {
-                    bins[i] = {
-                        total: 0,
-                        all: 0,
-                        ref: 0,
+function processDepth({ feature, bins, region, regionSequence, }) {
+    const fstart = feature.get('start');
+    const fend = feature.get('end');
+    const fstrand = feature.get('strand');
+    const regionLength = region.end - region.start;
+    for (let j = fstart; j < fend + 1; j++) {
+        const i = j - region.start;
+        if (i >= 0 && i < regionLength) {
+            if (bins[i] === undefined) {
+                bins[i] = {
+                    depth: 0,
+                    readsCounted: 0,
+                    refbase: regionSequence[i],
+                    ref: {
+                        probabilities: [],
+                        entryDepth: 0,
                         '-1': 0,
-                        '0': 0,
-                        '1': 0,
-                        lowqual: {},
-                        cov: {},
-                        delskips: {},
-                        noncov: {},
-                    };
-                }
-                if (j !== fend) {
-                    bins[i].total++;
-                    bins[i].all++;
-                    bins[i].ref++;
-                    bins[i][fstrand]++;
-                }
+                        0: 0,
+                        1: 0,
+                    },
+                    snps: {},
+                    mods: {},
+                    nonmods: {},
+                    delskips: {},
+                    noncov: {},
+                };
+            }
+            if (j !== fend) {
+                bins[i].depth++;
+                bins[i].readsCounted++;
+                bins[i].ref.entryDepth++;
+                bins[i].ref[fstrand]++;
             }
         }
-        if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-            const seq = feature.get('seq');
-            const mm = getTagAlt(feature, 'MM', 'Mm') || '';
-            const ops = parseCigar(feature.get('CIGAR'));
-            const fend = feature.get('end');
-            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];
-                            inc(bin, fstrand, 'cov', mod);
-                        }
-                    }
+    }
+}
+function processSNPs({ feature, region, bins, skipmap, }) {
+    var _a;
+    const fstart = feature.get('start');
+    const fstrand = feature.get('strand');
+    const mismatches = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
+    // normal SNP based coloring
+    for (const mismatch of mismatches) {
+        const mstart = fstart + mismatch.start;
+        const mlen = mismatchLen(mismatch);
+        const mend = mstart + mlen;
+        for (let j = mstart; j < mstart + mlen; j++) {
+            const epos = j - region.start;
+            if (epos >= 0 && epos < bins.length) {
+                const bin = bins[epos];
+                const { base, type } = mismatch;
+                const interbase = isInterbase(type);
+                if (type === 'deletion' || type === 'skip') {
+                    inc(bin, fstrand, 'delskips', type);
+                    bin.depth--;
+                }
+                else if (!interbase) {
+                    inc(bin, fstrand, 'snps', base);
+                    bin.ref.entryDepth--;
+                    bin.ref[fstrand]--;
+                }
+                else {
+                    inc(bin, fstrand, 'noncov', type);
                 }
             }
         }
-        if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
-            if (!regionSequence) {
-                throw new Error('no region sequence detected, need sequenceAdapter configuration');
+        if (mismatch.type === 'skip') {
+            // for upper case XS and TS: reports the literal strand of the genomic
+            // transcript
+            const tags = feature.get('tags');
+            const xs = (tags === null || tags === void 0 ? void 0 : tags.XS) || (tags === null || tags === void 0 ? void 0 : tags.TS);
+            // for lower case ts from minimap2: genomic transcript flipped by read
+            // strand
+            const ts = tags === null || tags === void 0 ? void 0 : tags.ts;
+            const effectiveStrand = xs === '+'
+                ? 1
+                : xs === '-'
+                    ? -1
+                    : (ts === '+' ? 1 : xs === '-' ? -1 : 0) * fstrand;
+            const hash = `${mstart}_${mend}_${effectiveStrand}`;
+            if (skipmap[hash] === undefined) {
+                skipmap[hash] = {
+                    feature: feature,
+                    start: mstart,
+                    end: mend,
+                    strand: fstrand,
+                    effectiveStrand,
+                    score: 0,
+                };
             }
-            const seq = feature.get('seq');
-            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 ((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');
-                            bin1.ref--;
-                            bin1[fstrand]--;
-                        }
+            skipmap[hash].score++;
+        }
+    }
+}
+function processReferenceCpGs({ feature, region, bins, regionSequence, }) {
+    var _a;
+    const fstart = feature.get('start');
+    const fend = feature.get('end');
+    const fstrand = feature.get('strand');
+    const seq = feature.get('seq');
+    const mismatches = (_a = feature.get('mismatches')) !== null && _a !== void 0 ? _a : [];
+    const r = regionSequence.toLowerCase();
+    if (seq) {
+        const cigarOps = parseCigar(feature.get('CIGAR'));
+        const { methBins, methProbs } = getMethBins(feature, cigarOps);
+        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 = r[j - region.start + 1];
+            const l2 = r[j - region.start + 2];
+            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 ((b0 && (p0 !== undefined ? p0 > 0.5 : true)) ||
+                    (b1 && (p1 !== undefined ? p1 > 0.5 : true))) {
+                    if (bin0) {
+                        incWithProbabilities(bin0, fstrand, 'mods', 'cpg_meth', p0 || 0);
+                        bin0.ref.entryDepth--;
+                        bin0.ref[fstrand]--;
                     }
-                    else {
-                        if (bin0) {
-                            if (!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) {
+                        incWithProbabilities(bin1, fstrand, 'mods', 'cpg_meth', p1 || 0);
+                        bin1.ref.entryDepth--;
+                        bin1.ref[fstrand]--;
+                    }
+                }
+                else {
+                    if (bin0) {
+                        if (!dels.some(d => doesIntersect2(j, j + 1, d.start + fstart, d.start + fstart + d.length))) {
+                            incWithProbabilities(bin0, fstrand, 'nonmods', 'cpg_unmeth', 1 - (p0 || 0));
+                            bin0.ref.entryDepth--;
+                            bin0.ref[fstrand]--;
                         }
-                        if (bin1) {
-                            if (!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]--;
-                            }
+                    }
+                    if (bin1) {
+                        if (!dels.some(d => doesIntersect2(j + 1, j + 2, d.start + fstart, d.start + fstart + d.length))) {
+                            incWithProbabilities(bin1, fstrand, 'nonmods', 'cpg_unmeth', 1 - (p1 || 0));
+                            bin1.ref.entryDepth--;
+                            bin1.ref[fstrand]--;
                         }
                     }
                 }
             }
         }
-        // normal SNP based coloring
-        const colorSNPs = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'modifications' && (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) !== 'methylation';
-        for (const mismatch of mismatches) {
-            const mstart = fstart + mismatch.start;
-            const mlen = mismatchLen(mismatch);
-            const mend = mstart + mlen;
-            for (let j = mstart; j < mstart + mlen; j++) {
-                const epos = j - region.start;
-                if (epos >= 0 && epos < bins.length) {
-                    const bin = bins[epos];
-                    const { base, type } = mismatch;
-                    const interbase = isInterbase(type);
-                    if (!interbase) {
-                        bin.ref--;
-                        bin[fstrand]--;
-                    }
-                    else {
-                        inc(bin, fstrand, 'noncov', type);
-                    }
-                    if (type === 'deletion' || type === 'skip') {
-                        inc(bin, fstrand, 'delskips', type);
-                        bin.total--;
-                    }
-                    else if (!interbase && colorSNPs) {
-                        inc(bin, fstrand, 'cov', base);
-                        bin.refbase = mismatch.altbase;
-                    }
-                }
+    }
+}
+function processModification({ feature, colorBy, region, bins, regionSequence, }) {
+    var _a, _b, _c;
+    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 = getMaxProbModAtEachPosition(feature)) === null || _c === void 0 ? void 0 : _c.forEach(({ type, prob, allProbs }, pos) => {
+        if (isolatedModification && type !== isolatedModification) {
+            return;
+        }
+        const epos = pos + fstart - region.start;
+        if (epos >= 0 && epos < bins.length && pos + fstart < fend) {
+            if (bins[epos] === undefined) {
+                bins[epos] = {
+                    depth: 0,
+                    readsCounted: 0,
+                    refbase: regionSequence[epos],
+                    snps: {},
+                    ref: {
+                        probabilities: [],
+                        entryDepth: 0,
+                        '-1': 0,
+                        0: 0,
+                        1: 0,
+                    },
+                    mods: {},
+                    nonmods: {},
+                    delskips: {},
+                    noncov: {},
+                };
             }
-            if (mismatch.type === 'skip') {
-                const hash = `${mstart}_${mend}_${fstrand}`;
-                if (skipmap[hash] === undefined) {
-                    skipmap[hash] = {
-                        feature: feature,
-                        start: mstart,
-                        end: mend,
-                        strand: fstrand,
-                        xs: getTag(feature, 'XS') || getTag(feature, 'TS'),
-                        score: 0,
-                    };
-                }
-                skipmap[hash].score++;
+            const s = 1 - sum(allProbs);
+            const bin = bins[epos];
+            if (twoColor && s > max(allProbs)) {
+                incWithProbabilities(bin, fstrand, 'nonmods', `nonmod_${type}`, s);
+            }
+            else {
+                incWithProbabilities(bin, fstrand, 'mods', `mod_${type}`, prob);
             }
         }
+    });
+}
+function incWithProbabilities(bin, strand, type, field, probability) {
+    let thisBin = bin[type][field];
+    if (thisBin === undefined) {
+        thisBin = bin[type][field] = {
+            entryDepth: 0,
+            probabilities: [],
+            '-1': 0,
+            '0': 0,
+            '1': 0,
+        };
     }
-    return { bins, skipmap };
+    thisBin.entryDepth++;
+    thisBin.probabilities.push(probability);
+    thisBin[strand]++;
+}
+export async function generateCoverageBins({ fetchSequence, features, region, opts, }) {
+    const { colorBy } = opts;
+    const skipmap = {};
+    const bins = [];
+    const start2 = Math.max(0, region.start - 1);
+    const diff = region.start - start2;
+    const regionSequence = (await fetchSequence({
+        ...region,
+        start: start2,
+        end: region.end + 1,
+    })) || '';
+    for (const feature of features) {
+        processDepth({
+            feature,
+            bins,
+            region,
+            regionSequence: regionSequence.slice(diff),
+        });
+        if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
+            processModification({
+                feature,
+                colorBy,
+                bins,
+                region,
+                regionSequence: regionSequence.slice(diff),
+            });
+        }
+        else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
+            processReferenceCpGs({
+                feature,
+                bins,
+                region,
+                regionSequence,
+            });
+        }
+        processSNPs({ feature, skipmap, bins, region });
+    }
+    for (const bin of bins) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        if (bin) {
+            bin.mods = Object.fromEntries(Object.entries(bin.mods).map(([key, val]) => {
+                return [
+                    key,
+                    {
+                        ...val,
+                        avgProbability: val.probabilities.length
+                            ? sum(val.probabilities) / val.probabilities.length
+                            : undefined,
+                    },
+                ];
+            }));
+            bin.nonmods = Object.fromEntries(Object.entries(bin.nonmods).map(([key, val]) => {
+                return [
+                    key,
+                    {
+                        ...val,
+                        avgProbability: val.probabilities.length
+                            ? sum(val.probabilities) / val.probabilities.length
+                            : undefined,
+                    },
+                ];
+            }));
+        }
+    }
+    return {
+        bins,
+        skipmap,
+    };
 }

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -1,6 +1,7 @@
 import { Feature } from '@jbrowse/core/util';
 import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
 import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
+import { ModificationTypeWithColor } from '../shared/types';
 export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
     bpPerPx: number;
     height: number;
@@ -13,7 +14,7 @@ export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserializ
         values: number[];
     };
     displayCrossHatches: boolean;
-    modificationTagMap?: Record<string, string>;
+    visibleModifications?: Record<string, ModificationTypeWithColor>;
 }
 export default class SNPCoverageRenderer extends WiggleBaseRenderer {
     draw(ctx: CanvasRenderingContext2D, props: RenderArgsDeserializedWithFeatures): Promise<undefined>;