@jbrowse/plugin-alignments 2.16.1 → 2.17.0

package/esm/PileupRenderer/renderModifications.js

@@ -1,45 +1,42 @@
-import { bpSpanPx } from '@jbrowse/core/util';
-import { getModificationPositions, getModificationProbabilities, getNextRefPos, parseCigar, } from '../MismatchParser';
-import { getTagAlt } from '../util';
+import { bpSpanPx, max, sum } from '@jbrowse/core/util';
+// locals
 import { fillRect } from './util';
-import { colord } from '@jbrowse/core/util/colord';
+import { alphaColor } from '../shared/util';
+import { getMaxProbModAtEachPosition } from '../shared/getMaximumModificationAtEachPosition';
 // render modifications stored in MM tag in BAM
-//
-// ML stores probabilities as array of numerics and MP is scaled phred scores
-// https://github.com/samtools/hts-specs/pull/418/files#diff-e765c6479316309f56b636f88189cdde8c40b854c7bdcce9ee7fe87a4e76febcR596
-//
-// if we have ML or Ml, it is an 8bit probability, divide by 255
-//
-// if we have MP or Mp it is phred scaled ASCII, which can go up to 90 but
-// has very high likelihood basecalls at that point, we really only care
-// about low qual calls <20 approx
-export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }) {
+export function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, cigarOps, }) {
+    var _a, _b, _c;
     const { feature, topPx, heightPx } = feat;
-    const { modificationTagMap = {} } = renderArgs;
+    const { colorBy, visibleModifications = {} } = renderArgs;
     const seq = feature.get('seq');
     if (!seq) {
         return;
     }
-    const mm = getTagAlt(feature, 'MM', 'Mm') || '';
-    const cigar = feature.get('CIGAR');
     const start = feature.get('start');
-    const strand = feature.get('strand');
-    const cigarOps = parseCigar(cigar);
-    const probabilities = getModificationProbabilities(feature);
-    const modifications = getModificationPositions(mm, seq, strand);
-    // probIndex applies across multiple modifications e.g.
-    let probIndex = 0;
-    for (const { type, positions } of modifications) {
-        const col = modificationTagMap[type] || 'black';
-        const base = colord(col);
-        for (const readPos of getNextRefPos(cigarOps, positions)) {
-            const r = start + readPos;
-            const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx);
-            const prob = (probabilities === null || probabilities === void 0 ? void 0 : probabilities[probIndex]) || 0;
-            const c = prob !== 1 ? base.alpha(prob + 0.1).toHslString() : col;
+    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;
+    (_c = getMaxProbModAtEachPosition(feature, cigarOps)) === null || _c === void 0 ? void 0 : _c.forEach(({ allProbs, prob, type }, pos) => {
+        const r = start + pos;
+        const [leftPx, rightPx] = 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;
+        }
+        const col = mod.color || 'black';
+        const s = 1 - sum(allProbs);
+        if (twoColor && s > max(allProbs)) {
+            const c = alphaColor('blue', s);
             const w = rightPx - leftPx + 0.5;
             fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
-            probIndex++;
         }
-    }
+        else {
+            const c = alphaColor(col, prob);
+            const w = rightPx - leftPx + 0.5;
+            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+        }
+    });
 }

package/esm/PileupRenderer/renderPerBaseLettering.d.ts

@@ -1,6 +1,6 @@
 import { Region } from '@jbrowse/core/util';
 import { LayoutFeature } from './util';
-export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, }: {
+export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     region: Region;
@@ -10,4 +10,5 @@ export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, col
     charWidth: number;
     charHeight: number;
     canvasWidth: number;
+    cigarOps: string[];
 }): void;

package/esm/PileupRenderer/renderPerBaseLettering.js

@@ -1,11 +1,9 @@
 import { bpSpanPx } from '@jbrowse/core/util';
-import { parseCigar } from '../MismatchParser';
 import { fillRect } from './util';
-export function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, }) {
+export function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, cigarOps, }) {
     const heightLim = charHeight - 2;
     const { feature, topPx, heightPx } = feat;
     const seq = feature.get('seq');
-    const cigarOps = parseCigar(feature.get('CIGAR'));
     const w = 1 / bpPerPx;
     const start = feature.get('start');
     let soffset = 0;

package/esm/PileupRenderer/renderPerBaseQuality.d.ts

@@ -1,9 +1,10 @@
 import { Region } from '@jbrowse/core/util';
 import { LayoutFeature } from './util';
-export declare function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }: {
+export declare function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, cigarOps, }: {
     ctx: CanvasRenderingContext2D;
     feat: LayoutFeature;
     region: Region;
     bpPerPx: number;
     canvasWidth: number;
+    cigarOps: string[];
 }): void;

package/esm/PileupRenderer/renderPerBaseQuality.js

@@ -1,11 +1,9 @@
 import { bpSpanPx } from '@jbrowse/core/util';
-import { parseCigar } from '../MismatchParser';
 import { fillRect } from './util';
-export function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }) {
+export function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, cigarOps, }) {
     const { feature, topPx, heightPx } = feat;
     const qual = feature.get('qual') || '';
     const scores = qual.split(' ').map(val => +val);
-    const cigarOps = parseCigar(feature.get('CIGAR'));
     const w = 1 / bpPerPx;
     const start = feature.get('start');
     let soffset = 0; // sequence offset

package/esm/PileupRenderer/renderSoftClipping.js

@@ -1,8 +1,7 @@
 import { readConfObject, } from '@jbrowse/core/configuration';
 import { bpSpanPx } from '@jbrowse/core/util';
-// locals
-import { parseCigar } from '../MismatchParser';
 import { fillRect, getCharWidthHeight } from './util';
+import { parseCigar } from '../MismatchParser';
 export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }) {
     const { feature, topPx, heightPx } = feat;
     const { regions, bpPerPx } = renderArgs;
@@ -16,12 +15,13 @@ export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, color
         return;
     }
     const heightLim = charHeight - 2;
-    const CIGAR = parseCigar(feature.get('CIGAR'));
     let seqOffset = 0;
     let refOffset = 0;
-    for (let i = 0; i < CIGAR.length; i += 2) {
-        const op = CIGAR[i + 1];
-        const len = +CIGAR[i];
+    const CIGAR = feature.get('CIGAR');
+    const cigarOps = parseCigar(CIGAR);
+    for (let i = 0; i < cigarOps.length; i += 2) {
+        const op = cigarOps[i + 1];
+        const len = +cigarOps[i];
         if (op === 'S') {
             for (let k = 0; k < len; k++) {
                 const base = seq[seqOffset + k];

package/esm/PileupRenderer/sortUtil.d.ts

@@ -1,8 +1,3 @@
 import { Feature } from '@jbrowse/core/util';
-interface SortObject {
-    pos: number;
-    type: string;
-    tag?: string;
-}
-export declare const sortFeature: (features: Map<string, Feature>, sortedBy: SortObject) => Map<string, Feature>;
-export {};
+import { SortedBy } from '../shared/types';
+export declare const sortFeature: (features: Map<string, Feature>, sortedBy: SortedBy) => Map<string, Feature>;

package/esm/PileupRenderer/sortUtil.js

@@ -40,29 +40,29 @@ export const sortFeature = (features, sortedBy) => {
         // first sort all mismatches, then all reference bases at the end
         case 'Base pair': {
             const baseSortArray = [];
-            featuresInCenterLine.forEach(feature => {
+            for (const feature of featuresInCenterLine) {
                 const mismatches = feature.get('mismatches');
-                mismatches.forEach(mismatch => {
+                for (const m of mismatches) {
                     const start = feature.get('start');
-                    const offset = start + mismatch.start + 1;
-                    const consuming = mismatch.type === 'insertion' || mismatch.type === 'softclip';
-                    const len = consuming ? 0 : mismatch.length;
+                    const offset = start + m.start + 1;
+                    const consuming = m.type === 'insertion' || m.type === 'softclip';
+                    const len = consuming ? 0 : m.length;
                     if (pos >= offset && pos < offset + len) {
-                        baseSortArray.push([feature.id(), mismatch]);
+                        baseSortArray.push([feature.id(), m]);
                     }
-                });
-            });
+                }
+            }
             const baseMap = new Map(baseSortArray);
             featuresInCenterLine.sort((a, b) => {
                 const aMismatch = baseMap.get(a.id());
                 const bMismatch = baseMap.get(b.id());
                 const acode = bMismatch === null || bMismatch === void 0 ? void 0 : bMismatch.base.toUpperCase();
                 const bcode = aMismatch === null || aMismatch === void 0 ? void 0 : aMismatch.base.toUpperCase();
-                if (acode === bcode && acode === '*') {
-                    // @ts-expect-error
-                    return aMismatch.length - bMismatch.length;
-                }
-                return ((acode ? acode.charCodeAt(0) : 0) - (bcode ? bcode.charCodeAt(0) : 0));
+                return acode === bcode && acode === '*'
+                    ? // @ts-expect-error
+                        aMismatch.length - bMismatch.length
+                    : (acode ? acode.charCodeAt(0) : 0) -
+                        (bcode ? bcode.charCodeAt(0) : 0);
             });
             break;
         }

package/esm/SNPCoverageAdapter/SNPCoverageAdapter.js

@@ -4,8 +4,8 @@ import { ObservableCreate } from '@jbrowse/core/util/rxjs';
 import { toArray } from 'rxjs/operators';
 import { firstValueFrom } from 'rxjs';
 // locals
-import generateCoverageBins from './generateCoverageBins';
 import { fetchSequence } from '../util';
+import { generateCoverageBins } from './generateCoverageBins';
 export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     async configure() {
         var _a, _b;
@@ -33,14 +33,19 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
     getFeatures(region, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { subadapter } = await this.configure();
-            const feats = await firstValueFrom(subadapter.getFeatures(region, opts).pipe(toArray()));
-            const { bins, skipmap } = await generateCoverageBins(feats, region, opts, arg => this.fetchSequence(arg));
+            const features = await firstValueFrom(subadapter.getFeatures(region, opts).pipe(toArray()));
+            const { bins, skipmap } = await generateCoverageBins({
+                features,
+                region,
+                opts,
+                fetchSequence: (region) => this.fetchSequence(region),
+            });
             bins.forEach((bin, index) => {
                 const start = region.start + index;
                 observer.next(new SimpleFeature({
                     id: `${this.id}-${start}`,
                     data: {
-                        score: bin.total,
+                        score: bin.depth,
                         snpinfo: bin,
                         start,
                         end: start + 1,
@@ -58,7 +63,7 @@ export default class SNPCoverageAdapter extends BaseFeatureDataAdapter {
                         end: skip.end,
                         strand: skip.strand,
                         score: skip.score,
-                        xs: skip.xs,
+                        effectiveStrand: skip.effectiveStrand,
                     },
                 }));
             });

package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts

@@ -1,13 +1,17 @@
 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: {
+import { Feature } from '@jbrowse/core/util';
+import { ColorBy, PreBaseCoverageBin, SkipMap } from '../shared/types';
+interface Opts {
     bpPerPx?: number;
-    colorBy?: {
-        type: string;
-        tag?: string;
-    };
-}, fetchSequence: (arg: Region) => Promise<string>): Promise<{
-    bins: Bin[];
+    colorBy?: ColorBy;
+}
+export declare function generateCoverageBins({ fetchSequence, features, region, opts, }: {
+    features: Feature[];
+    region: Region;
+    opts: Opts;
+    fetchSequence: (arg: Region) => Promise<string>;
+}): Promise<{
+    bins: PreBaseCoverageBin[];
     skipmap: SkipMap;
 }>;
+export {};