@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/esm/SNPCoverageAdapter/processDepth.d.ts

@@ -0,0 +1,8 @@
+import type { PreBaseCoverageBin } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion } from '@jbrowse/core/util/types';
+export declare function processDepth({ feature, bins, region, }: {
+    feature: Feature;
+    bins: PreBaseCoverageBin[];
+    region: AugmentedRegion;
+}): void;

package/esm/SNPCoverageAdapter/processDepth.js

@@ -0,0 +1,35 @@
+export function processDepth({ feature, bins, region, }) {
+    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,
+                    ref: {
+                        probabilities: [],
+                        entryDepth: 0,
+                        '-1': 0,
+                        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]++;
+            }
+        }
+    }
+}

package/esm/SNPCoverageAdapter/processMismatches.d.ts

@@ -0,0 +1,9 @@
+import type { PreBaseCoverageBin, SkipMap } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion } from '@jbrowse/core/util/types';
+export declare function processMismatches({ feature, region, bins, skipmap, }: {
+    region: AugmentedRegion;
+    bins: PreBaseCoverageBin[];
+    feature: Feature;
+    skipmap: SkipMap;
+}): void;

package/esm/SNPCoverageAdapter/processMismatches.js

@@ -0,0 +1,55 @@
+import { inc, isInterbase, mismatchLen } from './util';
+export function processMismatches({ 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 : [];
+    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, altbase, 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]--;
+                    bin.refbase = altbase;
+                }
+                else {
+                    inc(bin, fstrand, 'noncov', type);
+                }
+            }
+        }
+        if (mismatch.type === 'skip') {
+            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);
+            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,
+                };
+            }
+            skipmap[hash].score++;
+        }
+    }
+}

package/esm/SNPCoverageAdapter/processModifications.d.ts

@@ -0,0 +1,10 @@
+import type { ColorBy, PreBaseCoverageBin } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
+export declare function processModifications({ feature, colorBy, region, bins, regionSequence, }: {
+    bins: PreBaseCoverageBin[];
+    feature: Feature;
+    region: Region;
+    colorBy?: ColorBy;
+    regionSequence: string;
+}): void;

package/esm/SNPCoverageAdapter/processModifications.js

@@ -0,0 +1,46 @@
+import { max, sum } from '@jbrowse/core/util';
+import { incWithProbabilities } from './util';
+import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
+export function processModifications({ 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: {},
+                };
+            }
+            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);
+            }
+        }
+    });
+}

package/esm/SNPCoverageAdapter/processReferenceCpGs.d.ts

@@ -0,0 +1,9 @@
+import type { PreBaseCoverageBin } from '../shared/types';
+import type { Feature } from '@jbrowse/core/util';
+import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
+export declare function processReferenceCpGs({ feature, region, bins, regionSequence, }: {
+    bins: PreBaseCoverageBin[];
+    feature: Feature;
+    region: Region;
+    regionSequence: string;
+}): void;

package/esm/SNPCoverageAdapter/processReferenceCpGs.js

@@ -0,0 +1,60 @@
+import { doesIntersect2 } from '@jbrowse/core/util';
+import { parseCigar } from '../MismatchParser';
+import { getMethBins } from '../ModificationParser';
+import { incWithProbabilities } from './util';
+export 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');
+        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];
+                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]--;
+                    }
+                    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))) {
+                            incWithProbabilities(bin1, fstrand, 'nonmods', 'cpg_unmeth', 1 - (p1 || 0));
+                            bin1.ref.entryDepth--;
+                            bin1.ref[fstrand]--;
+                        }
+                    }
+                }
+            }
+        }
+    }
+}

package/esm/SNPCoverageAdapter/util.d.ts

@@ -1,25 +1,10 @@
-export type SkipMap = Record<string, {
-    score: number;
-    feature: unknown;
-    start: number;
-    end: number;
-    strand: number;
-    xs: string;
-}>;
-export interface BinType {
-    total?: number;
-    strands?: Record<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;
+import type { ColorBy, Mismatch, PreBaseCoverageBin, PreBaseCoverageBinSubtypes } from '../shared/types';
+export interface Opts {
+    bpPerPx?: number;
+    colorBy?: ColorBy;
+    stopToken?: string;
 }
+export declare function mismatchLen(mismatch: Mismatch): number;
+export declare function isInterbase(type: string): type is "insertion" | "hardclip" | "softclip";
+export declare function inc(bin: PreBaseCoverageBin, strand: -1 | 0 | 1, type: keyof PreBaseCoverageBinSubtypes, field: string): void;
+export declare function incWithProbabilities(bin: PreBaseCoverageBin, strand: -1 | 0 | 1, type: keyof PreBaseCoverageBinSubtypes, field: string, probability: number): void;

package/esm/SNPCoverageAdapter/util.js

@@ -1 +1,35 @@
-export {};
+export function mismatchLen(mismatch) {
+    return !isInterbase(mismatch.type) ? mismatch.length : 1;
+}
+export function isInterbase(type) {
+    return type === 'softclip' || type === 'hardclip' || type === 'insertion';
+}
+export function inc(bin, strand, type, field) {
+    let thisBin = bin[type][field];
+    if (thisBin === undefined) {
+        thisBin = bin[type][field] = {
+            entryDepth: 0,
+            probabilities: [],
+            '-1': 0,
+            '0': 0,
+            '1': 0,
+        };
+    }
+    thisBin.entryDepth++;
+    thisBin[strand]++;
+}
+export 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,
+        };
+    }
+    thisBin.entryDepth++;
+    thisBin.probabilities.push(probability);
+    thisBin[strand]++;
+}

package/esm/SNPCoverageRenderer/SNPCoverageRenderer.d.ts

@@ -1,6 +1,8 @@
-import { Feature } from '@jbrowse/core/util';
-import { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import { ScaleOpts, WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
+import { WiggleBaseRenderer } from '@jbrowse/plugin-wiggle';
+import type { ModificationTypeWithColor } from '../shared/types';
+import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Feature } from '@jbrowse/core/util';
+import type { ScaleOpts } from '@jbrowse/plugin-wiggle';
 export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
     bpPerPx: number;
     height: number;
@@ -13,7 +15,7 @@ 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>;