@jbrowse/plugin-alignments 3.6.5 → 4.0.0

package/esm/PileupRenderer/renderPerBaseQuality.js

@@ -1,32 +0,0 @@
-import { bpSpanPx } from '@jbrowse/core/util';
-import { fillRect } from './util';
-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 w = 1 / bpPerPx;
-    const start = feature.get('start');
-    let soffset = 0;
-    let roffset = 0;
-    for (let i = 0; i < cigarOps.length; i += 2) {
-        const len = +cigarOps[i];
-        const op = cigarOps[i + 1];
-        if (op === 'S' || op === 'I') {
-            soffset += len;
-        }
-        else if (op === 'D' || op === 'N') {
-            roffset += len;
-        }
-        else if (op === 'M' || op === 'X' || op === '=') {
-            for (let m = 0; m < len; m++) {
-                const score = scores[soffset + m];
-                const start0 = start + roffset + m;
-                const leftPx = bpSpanPx(start0, start0 + 1, region, bpPerPx)[0];
-                const c = `hsl(${score === 255 ? 150 : score * 1.5},55%,50%)`;
-                fillRect(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c);
-            }
-            soffset += len;
-            roffset += len;
-        }
-    }
-}

package/esm/PileupRenderer/renderSoftClipping.d.ts

@@ -1,13 +0,0 @@
-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, }: {
-    ctx: CanvasRenderingContext2D;
-    feat: LayoutFeature;
-    renderArgs: ProcessedRenderArgs;
-    config: AnyConfigurationModel;
-    colorMap: Record<string, string>;
-    theme: Theme;
-    canvasWidth: number;
-}): void;

package/esm/PileupRenderer/renderSoftClipping.js

@@ -1,56 +0,0 @@
-import { readConfObject } from '@jbrowse/core/configuration';
-import { bpSpanPx } from '@jbrowse/core/util';
-import { fillRect, getCharWidthHeight } from './util';
-import { parseCigar } from '../MismatchParser';
-export function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorMap, canvasWidth, }) {
-    const { feature, topPx, heightPx } = feat;
-    const { regions, bpPerPx } = renderArgs;
-    const region = regions[0];
-    const minFeatWidth = readConfObject(config, 'minSubfeatureWidth');
-    const mismatches = feature.get('mismatches');
-    const seq = feature.get('seq');
-    const { charWidth, charHeight } = getCharWidthHeight();
-    if (!(seq && mismatches)) {
-        return;
-    }
-    const heightLim = charHeight - 2;
-    let seqOffset = 0;
-    let refOffset = 0;
-    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];
-                const s0 = feature.get('start') - (i === 0 ? len : 0) + refOffset + k;
-                const [leftPx, rightPx] = bpSpanPx(s0, s0 + 1, region, bpPerPx);
-                const widthPx = Math.max(minFeatWidth, rightPx - leftPx);
-                const baseColor = colorMap[base] || '#000000';
-                ctx.fillStyle = baseColor;
-                fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth);
-                if (widthPx >= charWidth && heightPx >= heightLim) {
-                    ctx.fillStyle = theme.palette.getContrastText(baseColor);
-                    ctx.fillText(base, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
-                }
-            }
-            seqOffset += len;
-        }
-        if (op === 'N') {
-            refOffset += len;
-        }
-        if (op === 'M' || op === '=' || op === 'X') {
-            refOffset += len;
-            seqOffset += len;
-        }
-        if (op === 'H') {
-        }
-        if (op === 'D') {
-            refOffset += len;
-        }
-        if (op === 'I') {
-            seqOffset += len;
-        }
-    }
-}

package/esm/SNPCoverageAdapter/generateCoverageBins.d.ts

@@ -1,13 +0,0 @@
-import type { Opts } from './util';
-import type { PreBaseCoverageBin, SkipMap } from '../shared/types';
-import type { Feature } from '@jbrowse/core/util';
-import type { AugmentedRegion as Region } from '@jbrowse/core/util/types';
-export declare function generateCoverageBins({ fetchSequence, features, region, opts, }: {
-    features: Feature[];
-    region: Region;
-    opts: Opts;
-    fetchSequence: (arg: Region) => Promise<string>;
-}): Promise<{
-    bins: PreBaseCoverageBin[];
-    skipmap: SkipMap;
-}>;

package/esm/SNPCoverageAdapter/generateCoverageBins.js

@@ -1,83 +0,0 @@
-import { sum } from '@jbrowse/core/util';
-import { checkStopToken } from '@jbrowse/core/util/stopToken';
-import { processDepth } from './processDepth';
-import { processMismatches } from './processMismatches';
-import { processModifications } from './processModifications';
-import { processReferenceCpGs } from './processReferenceCpGs';
-export async function generateCoverageBins({ fetchSequence, features, region, opts, }) {
-    const { stopToken, colorBy } = opts;
-    const skipmap = {};
-    const bins = [];
-    const start2 = Math.max(0, region.start - 1);
-    const diff = region.start - start2;
-    let start = performance.now();
-    for (const feature of features) {
-        if (performance.now() - start > 400) {
-            checkStopToken(stopToken);
-            start = performance.now();
-        }
-        processDepth({
-            feature,
-            bins,
-            region,
-        });
-        if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'modifications') {
-            const regionSequence = (await fetchSequence({
-                ...region,
-                start: start2,
-                end: region.end + 1,
-            })) || '';
-            processModifications({
-                feature,
-                colorBy,
-                bins,
-                region,
-                regionSequence: regionSequence.slice(diff),
-            });
-        }
-        else if ((colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) === 'methylation') {
-            const regionSequence = (await fetchSequence({
-                ...region,
-                start: start2,
-                end: region.end + 1,
-            })) || '';
-            processReferenceCpGs({
-                feature,
-                bins,
-                region,
-                regionSequence,
-            });
-        }
-        processMismatches({ feature, skipmap, bins, region });
-    }
-    for (const bin of bins) {
-        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/SNPCoverageAdapter/processDepth.d.ts

@@ -1,8 +0,0 @@
-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

@@ -1,35 +0,0 @@
-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

@@ -1,9 +0,0 @@
-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

@@ -1,55 +0,0 @@
-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/shared/components/BaseDisplayComponent.d.ts

@@ -1,7 +0,0 @@
-import type { LinearReadArcsDisplayModel } from '../../LinearReadArcsDisplay/model';
-import type { LinearReadCloudDisplayModel } from '../../LinearReadCloudDisplay/model';
-declare const BaseDisplayComponent: ({ model, children, }: {
-    model: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel;
-    children?: React.ReactNode;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default BaseDisplayComponent;

package/esm/shared/components/BaseDisplayComponent.js

@@ -1,42 +0,0 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { LoadingEllipses } from '@jbrowse/core/ui';
-import { getContainingView } from '@jbrowse/core/util';
-import { BlockMsg } from '@jbrowse/plugin-linear-genome-view';
-import { Button, Tooltip } from '@mui/material';
-import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(theme => ({
-    loading: {
-        backgroundColor: theme.palette.background.default,
-        backgroundImage: `repeating-linear-gradient(45deg, transparent, transparent 5px, ${theme.palette.action.disabledBackground} 5px, ${theme.palette.action.disabledBackground} 10px)`,
-        position: 'absolute',
-        bottom: 0,
-        height: 50,
-        width: 300,
-        right: 0,
-        pointerEvents: 'none',
-        textAlign: 'center',
-    },
-}));
-const BlockError = observer(function ({ model, }) {
-    const { error } = model;
-    return (_jsx(BlockMsg, { message: `${error}`, severity: "error", action: _jsx(Tooltip, { title: "Reload", children: _jsx(Button, { "data-testid": "reload_button", onClick: () => {
-                    model.reload();
-                }, children: "Reload" }) }) }));
-});
-const BaseDisplayComponent = observer(function ({ model, children, }) {
-    const { error, regionTooLarge } = model;
-    return error ? (_jsx(BlockError, { model: model })) : regionTooLarge ? (model.regionCannotBeRendered()) : (_jsx(DataDisplay, { model: model, children: children }));
-});
-const DataDisplay = observer(function ({ model, children, }) {
-    const { drawn, loading } = model;
-    const view = getContainingView(model);
-    const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx;
-    return (_jsxs("div", { "data-testid": `drawn-${drawn}`, children: [_jsx("div", { style: { position: 'absolute', left }, children: children }), left !== 0 || loading ? _jsx(LoadingBar, { model: model }) : null] }));
-});
-const LoadingBar = observer(function ({ model, }) {
-    const { classes } = useStyles();
-    const { message } = model;
-    return (_jsx("div", { className: classes.loading, children: _jsx(LoadingEllipses, { message: message }) }));
-});
-export default BaseDisplayComponent;

package/esm/shared/fetchChains.d.ts

@@ -1,28 +0,0 @@
-import type { LinearReadArcsDisplayModel } from '../LinearReadArcsDisplay/model';
-import type { LinearReadCloudDisplayModel } from '../LinearReadCloudDisplay/model';
-export interface ReducedFeature {
-    name: string;
-    strand: number;
-    refName: string;
-    start: number;
-    end: number;
-    id: string;
-    flags: number;
-    tlen: number;
-    pair_orientation: string;
-    next_ref?: string;
-    next_pos?: number;
-    clipPos: number;
-    SA?: string;
-}
-export interface ChainStats {
-    max: number;
-    min: number;
-    upper: number;
-    lower: number;
-}
-export interface ChainData {
-    chains: ReducedFeature[][];
-    stats?: ChainStats;
-}
-export declare function fetchChains(self: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel): Promise<void>;

package/esm/shared/fetchChains.js

@@ -1,19 +0,0 @@
-import { getContainingView, getSession } from '@jbrowse/core/util';
-import { getRpcSessionId } from '@jbrowse/core/util/tracks';
-export async function fetchChains(self) {
-    const sessionId = getRpcSessionId(self);
-    const { rpcManager } = getSession(self);
-    const view = getContainingView(self);
-    if (!view.initialized || self.error || !self.statsReadyAndRegionNotTooLarge) {
-        return;
-    }
-    self.setLoading(true);
-    const ret = (await rpcManager.call(sessionId, 'PileupGetReducedFeatures', {
-        sessionId,
-        regions: view.staticBlocks.contentBlocks,
-        filterBy: self.filterBy,
-        adapterConfig: self.adapterConfig,
-    }));
-    self.setChainData(ret);
-    self.setLoading(false);
-}