@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/dist/LinearReadCloudDisplay/drawFeats.js

@@ -1,145 +1,29 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
+exports.drawFeats = void 0;
 const util_1 = require("@jbrowse/core/util");
-// locals
-const color_1 = require("../shared/color");
-// avoid drawing negative width features for SVG exports
-function fillRectCtx(x, y, width, height, ctx, color) {
-    if (width < 0) {
-        x += width;
-        width = -width;
-    }
-    if (height < 0) {
-        y += height;
-        height = -height;
-    }
-    if (color) {
-        ctx.fillStyle = color;
-    }
-    ctx.fillRect(x, y, width, height);
-}
-async function drawFeats(self, ctx) {
-    var _a;
+const util_2 = require("../shared/util");
+const drawPairChains_1 = require("./drawPairChains");
+const drawLongReadChains_1 = require("./drawLongReadChains");
+function drawFeats(self, ctx) {
     const { chainData } = self;
     if (!chainData) {
         return;
     }
     const { assemblyManager } = (0, util_1.getSession)(self);
-    const featureHeight = (0, configuration_1.getConf)(self, 'featureHeight');
-    const displayHeight = self.height;
     const view = (0, util_1.getContainingView)(self);
     const assemblyName = view.assemblyNames[0];
     const asm = assemblyManager.get(assemblyName);
     if (!asm) {
         return;
     }
-    self.setLastDrawnOffsetPx(view.offsetPx);
-    const { chains, stats } = chainData;
-    const coords = [];
-    for (let i = 0; i < chains.length; i++) {
-        const chain = chains[i];
-        // if we're looking at a paired read (flag 1) then assume it is just two
-        // reads (some small cases may defy this assumption such as secondary
-        // alignments but this may be uncommon)
-        if (chain[0].flags & 1 && chain.length > 1) {
-            const v0 = chain[0];
-            const v1 = chain[1];
-            const ra1 = asm.getCanonicalRefName(v0.refName);
-            const ra2 = asm.getCanonicalRefName(v1.refName);
-            const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
-            const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
-            const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
-            const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
-            let distance = 0;
-            if (r1s !== undefined &&
-                r1e !== undefined &&
-                r2s !== undefined &&
-                r2e !== undefined) {
-                if (v0.refName === v1.refName) {
-                    const s = Math.min(v0.start, v1.start);
-                    const e = Math.max(v0.end, v1.end);
-                    distance = Math.abs(e - s);
-                }
-                coords.push({
-                    r1s: r1s.offsetPx,
-                    r1e: r1e.offsetPx,
-                    r2s: r2s.offsetPx,
-                    r2e: r2e.offsetPx,
-                    v0,
-                    v1,
-                    distance,
-                });
-            }
-        }
-        else {
-            // if we're not looking at pairs, then it could be a multiply-split-long
-            // read, so traverse chain
-            for (let i = 1; i < chain.length; i++) {
-                const v0 = chain[i - 1];
-                const v1 = chain[i];
-                const ra1 = asm.getCanonicalRefName(v0.refName);
-                const ra2 = asm.getCanonicalRefName(v1.refName);
-                const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
-                const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
-                const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
-                const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
-                let distance = 0;
-                if (r1s !== undefined &&
-                    r1e !== undefined &&
-                    r2s !== undefined &&
-                    r2e !== undefined) {
-                    if (v0.refName === v1.refName) {
-                        const s = Math.min(v0.start, v1.start);
-                        const e = Math.max(v0.end, v1.end);
-                        distance = Math.abs(e - s);
-                    }
-                    coords.push({
-                        r1s: r1s.offsetPx,
-                        r1e: r1e.offsetPx,
-                        r2s: r2s.offsetPx,
-                        r2e: r2e.offsetPx,
-                        v0,
-                        v1,
-                        distance,
-                    });
-                }
-            }
-        }
-    }
-    let max = 0;
-    for (let i = 0; i < coords.length; i++) {
-        const { distance } = coords[i];
-        max = Math.max(max, distance);
+    const hasPaired = (0, util_2.hasPairedReads)(chainData);
+    if (hasPaired) {
+        (0, drawPairChains_1.drawPairChains)({ self, view, asm, ctx, chainData });
     }
-    const halfHeight = featureHeight / 2 - 0.5;
-    const scaler = (displayHeight - 20) / Math.log(max);
-    for (let i = 0; i < coords.length; i++) {
-        const { r1s, r1e, r2s, r2e, v0, v1, distance } = coords[i];
-        const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
-        const top = Math.log(distance) * scaler;
-        ctx.fillStyle = 'black';
-        const w = r2s - r1e;
-        fillRectCtx(r1e - view.offsetPx, top + halfHeight, w, 1, ctx);
-        if (type === 'insertSizeAndOrientation') {
-            ctx.fillStyle = (0, color_1.getInsertSizeAndOrientationColor)(v0, v1, stats);
-        }
-        else if (type === 'orientation') {
-            ctx.fillStyle = (0, color_1.getOrientationColor)(v0);
-        }
-        else if (type === 'insertSize') {
-            ctx.fillStyle = (0, color_1.getInsertSizeColor)(v0, v1, stats) || 'grey';
-        }
-        else if (type === 'gradient') {
-            const s = Math.min(v0.start, v1.start);
-            const e = Math.max(v0.end, v1.end);
-            ctx.fillStyle = `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`;
-        }
-        const w1 = Math.max(r1e - r1s, 2);
-        const w2 = Math.max(r2e - r2s, 2);
-        fillRectCtx(r1s - view.offsetPx, top, w1, featureHeight, ctx);
-        fillRectCtx(r2s - view.offsetPx, top, w2, featureHeight, ctx);
+    else {
+        (0, drawLongReadChains_1.drawLongReadChains)({ self, view, asm, ctx, chainData });
     }
 }
-exports.default = drawFeats;
+exports.drawFeats = drawFeats;
 //# sourceMappingURL=drawFeats.js.map

package/dist/LinearReadCloudDisplay/drawFeats.js.map

@@ -1 +1 @@
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package/dist/LinearReadCloudDisplay/drawLongReadChains.d.ts

@@ -0,0 +1,11 @@
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import { ChainData } from '../shared/fetchChains';
+import { LinearReadCloudDisplayModel } from './model';
+export declare function drawLongReadChains({ ctx, self, chainData, view, asm, }: {
+    ctx: CanvasRenderingContext2D;
+    self: LinearReadCloudDisplayModel;
+    chainData: ChainData;
+    view: LinearGenomeViewModel;
+    asm: Assembly;
+}): void;

package/dist/LinearReadCloudDisplay/drawLongReadChains.js

@@ -0,0 +1,69 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.drawLongReadChains = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const color_1 = require("../shared/color");
+const util_2 = require("./util");
+function drawLongReadChains({ ctx, self, chainData, view, asm, }) {
+    var _a, _b, _c, _d, _e;
+    const distances = [];
+    const minXs = [];
+    const { chains } = chainData;
+    const { height } = self;
+    const featureHeight = (0, configuration_1.getConf)(self, 'featureHeight');
+    // get bounds on the 'distances' (pixel span that a particular split long
+    // read 'chain' would have in view)
+    for (const chain of chains) {
+        let minX = Number.MAX_VALUE;
+        let maxX = Number.MIN_VALUE;
+        for (const elt of chain) {
+            const refName = asm.getCanonicalRefName(elt.refName) || elt.refName;
+            const rs = (_a = view.bpToPx({ refName, coord: elt.start })) === null || _a === void 0 ? void 0 : _a.offsetPx;
+            const re = (_b = view.bpToPx({ refName, coord: elt.end })) === null || _b === void 0 ? void 0 : _b.offsetPx;
+            if (rs !== undefined && re !== undefined) {
+                minX = Math.min(minX, rs);
+                maxX = Math.max(maxX, re);
+            }
+        }
+        const distance = Math.abs(maxX - minX);
+        distances.push(distance);
+        minXs.push(minX);
+    }
+    const maxD = Math.log((0, util_1.max)(distances));
+    const minD = Math.max(Math.log((0, util_1.min)(distances)) - 1, 0);
+    const scaler = (height - 20) / (maxD - minD);
+    const halfHeight = featureHeight / 2 - 0.5;
+    // draw split long read 'chains' as connected entities
+    for (let i = 0; i < chains.length; i++) {
+        const chain = chains[i];
+        const w = distances[i];
+        const top = (Math.log(w) - minD) * scaler;
+        const min = minXs[i];
+        (0, util_2.fillRectCtx)(min - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
+        const c1 = chain[0];
+        let primaryStrand;
+        if (!(c1.flags & 2048)) {
+            primaryStrand = c1.strand;
+        }
+        else {
+            const res = (_c = c1.SA) === null || _c === void 0 ? void 0 : _c.split(';')[0].split(',')[2];
+            primaryStrand = res === '-' ? -1 : 1;
+        }
+        for (const v0 of chain) {
+            const ra = asm.getCanonicalRefName(v0.refName) || v0.refName;
+            const rs = (_d = view.bpToPx({ refName: ra, coord: v0.start })) === null || _d === void 0 ? void 0 : _d.offsetPx;
+            const re = (_e = view.bpToPx({ refName: ra, coord: v0.end })) === null || _e === void 0 ? void 0 : _e.offsetPx;
+            if (rs !== undefined && re !== undefined) {
+                const w = Math.max(re - rs, 2);
+                const l = rs - view.offsetPx;
+                const effectiveStrand = v0.strand * primaryStrand;
+                const c = effectiveStrand === -1 ? 'color_rev_strand' : 'color_fwd_strand';
+                (0, util_2.strokeRectCtx)(l, top, w, featureHeight, ctx, color_1.strokeColor[c]);
+                (0, util_2.fillRectCtx)(l, top, w, featureHeight, ctx, color_1.fillColor[c]);
+            }
+        }
+    }
+}
+exports.drawLongReadChains = drawLongReadChains;
+//# sourceMappingURL=drawLongReadChains.js.map

package/dist/LinearReadCloudDisplay/drawLongReadChains.js.map

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package/dist/LinearReadCloudDisplay/drawPairChains.d.ts

@@ -0,0 +1,17 @@
+import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import { ChainData, ChainStats, ReducedFeature } from '../shared/fetchChains';
+import { LinearReadCloudDisplayModel } from './model';
+export declare function drawPairChains({ ctx, self, chainData, view, asm, }: {
+    ctx: CanvasRenderingContext2D;
+    self: LinearReadCloudDisplayModel;
+    chainData: ChainData;
+    view: LinearGenomeViewModel;
+    asm: Assembly;
+}): void;
+export declare function getPairedColor({ type, v0, v1, stats, }: {
+    type: string;
+    v0: ReducedFeature;
+    v1: ReducedFeature;
+    stats?: ChainStats;
+}): readonly [string, string] | undefined;

package/dist/LinearReadCloudDisplay/drawPairChains.js

@@ -0,0 +1,100 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getPairedColor = exports.drawPairChains = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./util");
+const color_1 = require("../shared/color");
+function drawPairChains({ ctx, self, chainData, view, asm, }) {
+    var _a, _b, _c, _d, _e, _f, _g;
+    const coords = [];
+    const featureHeight = (0, configuration_1.getConf)(self, 'featureHeight');
+    const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
+    const { chains, stats } = chainData;
+    for (const chain of chains) {
+        // if we're looking at a paired read (flag 1) then assume it is just
+        // two reads (some small cases may defy this assumption such as
+        // secondary alignments but this may be uncommon)
+        if (chain.length > 1) {
+            const v0 = chain[0];
+            const v1 = chain[1];
+            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
+            const ra2 = asm.getCanonicalRefName(v1.refName) || v1.refName;
+            const r1s = (_b = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _b === void 0 ? void 0 : _b.offsetPx;
+            const r1e = (_c = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _c === void 0 ? void 0 : _c.offsetPx;
+            const r2s = (_d = view.bpToPx({ refName: ra2, coord: v1.start })) === null || _d === void 0 ? void 0 : _d.offsetPx;
+            const r2e = (_e = view.bpToPx({ refName: ra2, coord: v1.end })) === null || _e === void 0 ? void 0 : _e.offsetPx;
+            let distance = 0;
+            if (r1s !== undefined &&
+                r1e !== undefined &&
+                r2s !== undefined &&
+                r2e !== undefined) {
+                if (v0.refName === v1.refName) {
+                    const s = Math.min(v0.start, v1.start);
+                    const e = Math.max(v0.end, v1.end);
+                    distance = Math.abs(e - s);
+                }
+                coords.push({
+                    r1s,
+                    r1e,
+                    r2s,
+                    r2e,
+                    v0,
+                    v1,
+                    distance,
+                });
+            }
+        }
+        else if (self.drawSingletons) {
+            const v0 = chain[0];
+            const ra1 = asm.getCanonicalRefName(v0.refName) || v0.refName;
+            const r1s = (_f = view.bpToPx({ refName: ra1, coord: v0.start })) === null || _f === void 0 ? void 0 : _f.offsetPx;
+            const r1e = (_g = view.bpToPx({ refName: ra1, coord: v0.end })) === null || _g === void 0 ? void 0 : _g.offsetPx;
+            if (r1s !== undefined && r1e !== undefined) {
+                const w1 = Math.max(r1e - r1s, 2);
+                (0, util_2.fillRectCtx)(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#f00');
+                (0, util_2.strokeRectCtx)(r1s - view.offsetPx, 0, w1, featureHeight, ctx, '#a00');
+            }
+        }
+    }
+    const maxD = Math.log((0, util_1.max)(coords.map(c => c.distance)));
+    const minD = Math.max(Math.log((0, util_1.min)(coords.map(c => c.distance))) - 1, 0);
+    const scaler = (self.height - 20) / (maxD - minD);
+    for (let i = 0; i < coords.length; i++) {
+        const { r1e, r1s, r2e, r2s, distance, v0, v1 } = coords[i];
+        const w1 = Math.max(r1e - r1s, 2);
+        const w2 = Math.max(r2e - r2s, 2);
+        const [fill, stroke] = getPairedColor({ type, v0, v1, stats }) || [];
+        const top = (Math.log(distance) - minD) * scaler;
+        const halfHeight = featureHeight / 2 - 0.5;
+        const w = r2s - r1e;
+        (0, util_2.fillRectCtx)(r1e - view.offsetPx, top + halfHeight, w, 1, ctx, 'black');
+        (0, util_2.strokeRectCtx)(r1s - view.offsetPx, top, w1, featureHeight, ctx, stroke);
+        (0, util_2.strokeRectCtx)(r2s - view.offsetPx, top, w2, featureHeight, ctx, stroke);
+        (0, util_2.fillRectCtx)(r1s - view.offsetPx, top, w1, featureHeight, ctx, fill);
+        (0, util_2.fillRectCtx)(r2s - view.offsetPx, top, w2, featureHeight, ctx, fill);
+    }
+}
+exports.drawPairChains = drawPairChains;
+function getPairedColor({ type, v0, v1, stats, }) {
+    if (type === 'insertSizeAndOrientation') {
+        return (0, color_1.getPairedInsertSizeAndOrientationColor)(v0, v1, stats);
+    }
+    else if (type === 'orientation') {
+        return (0, color_1.getPairedOrientationColor)(v0);
+    }
+    else if (type === 'insertSize') {
+        return (0, color_1.getPairedInsertSizeColor)(v0, v1, stats);
+    }
+    else if (type === 'gradient') {
+        const s = Math.min(v0.start, v1.start);
+        const e = Math.max(v0.end, v1.end);
+        return [
+            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,50%)`,
+            `hsl(${Math.log10(Math.abs(e - s)) * 10},50%,30%)`,
+        ];
+    }
+    return undefined;
+}
+exports.getPairedColor = getPairedColor;
+//# sourceMappingURL=drawPairChains.js.map

package/dist/LinearReadCloudDisplay/drawPairChains.js.map

@@ -0,0 +1 @@
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