@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/dist/PileupRenderer/makeImageData.js

@@ -0,0 +1,64 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.makeImageData = void 0;
+const configuration_1 = require("@jbrowse/core/configuration");
+const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("./util");
+const renderAlignment_1 = require("./renderAlignment");
+const renderMismatches_1 = require("./renderMismatches");
+const renderSoftClipping_1 = require("./renderSoftClipping");
+function makeImageData({ ctx, layoutRecords, canvasWidth, renderArgs, }) {
+    const { config, showSoftClip, colorBy, theme: configTheme } = renderArgs;
+    const mismatchAlpha = (0, configuration_1.readConfObject)(config, 'mismatchAlpha');
+    const minSubfeatureWidth = (0, configuration_1.readConfObject)(config, 'minSubfeatureWidth');
+    const largeInsertionIndicatorScale = (0, configuration_1.readConfObject)(config, 'largeInsertionIndicatorScale');
+    const defaultColor = (0, configuration_1.readConfObject)(config, 'color') === '#f0f';
+    const theme = (0, ui_1.createJBrowseTheme)(configTheme);
+    const colorForBase = (0, util_1.getColorBaseMap)(theme);
+    const contrastForBase = (0, util_1.getContrastBaseMap)(theme);
+    ctx.font = 'bold 10px Courier New,monospace';
+    const { charWidth, charHeight } = (0, util_1.getCharWidthHeight)();
+    const drawSNPsMuted = (0, util_1.shouldDrawSNPsMuted)(colorBy === null || colorBy === void 0 ? void 0 : colorBy.type);
+    const drawIndels = (0, util_1.shouldDrawIndels)();
+    for (const feat of layoutRecords) {
+        (0, renderAlignment_1.renderAlignment)({
+            ctx,
+            feat,
+            renderArgs,
+            defaultColor,
+            colorForBase,
+            contrastForBase,
+            charWidth,
+            charHeight,
+            canvasWidth,
+        });
+        (0, renderMismatches_1.renderMismatches)({
+            ctx,
+            feat,
+            renderArgs,
+            mismatchAlpha,
+            drawSNPsMuted,
+            drawIndels,
+            largeInsertionIndicatorScale,
+            minSubfeatureWidth,
+            charWidth,
+            charHeight,
+            colorForBase,
+            contrastForBase,
+            canvasWidth,
+        });
+        if (showSoftClip) {
+            (0, renderSoftClipping_1.renderSoftClipping)({
+                ctx,
+                feat,
+                renderArgs,
+                colorForBase,
+                config,
+                theme,
+                canvasWidth,
+            });
+        }
+    }
+}
+exports.makeImageData = makeImageData;
+//# sourceMappingURL=makeImageData.js.map

package/dist/PileupRenderer/makeImageData.js.map

@@ -0,0 +1 @@
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package/dist/PileupRenderer/renderAlignment.d.ts

@@ -0,0 +1,13 @@
+import { LayoutFeature } from './util';
+import { RenderArgsWithColor } from './makeImageData';
+export declare function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }: {
+    ctx: CanvasRenderingContext2D;
+    feat: LayoutFeature;
+    renderArgs: RenderArgsWithColor;
+    colorForBase: Record<string, string>;
+    contrastForBase: Record<string, string>;
+    charWidth: number;
+    charHeight: number;
+    defaultColor: boolean;
+    canvasWidth: number;
+}): void;

package/dist/PileupRenderer/renderAlignment.js

@@ -0,0 +1,72 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderAlignment = void 0;
+const getAlignmentShapeColor_1 = require("./getAlignmentShapeColor");
+const renderAlignmentShape_1 = require("./renderAlignmentShape");
+const renderPerBaseQuality_1 = require("./renderPerBaseQuality");
+const renderPerBaseLettering_1 = require("./renderPerBaseLettering");
+const renderModifications_1 = require("./renderModifications");
+const renderMethylation_1 = require("./renderMethylation");
+function renderAlignment({ ctx, feat, renderArgs, colorForBase, contrastForBase, charWidth, charHeight, defaultColor, canvasWidth, }) {
+    const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs;
+    const { tag = '', type: colorType = '' } = colorBy || {};
+    const { feature } = feat;
+    const region = regions[0];
+    ctx.fillStyle = (0, getAlignmentShapeColor_1.getAlignmentShapeColor)({
+        feature,
+        config,
+        tag,
+        defaultColor,
+        colorType,
+        colorTagMap,
+    });
+    (0, renderAlignmentShape_1.renderAlignmentShape)({ ctx, feat, renderArgs });
+    // second pass for color types that render per-base things that go over the
+    // existing drawing
+    switch (colorType) {
+        case 'perBaseQuality':
+            (0, renderPerBaseQuality_1.renderPerBaseQuality)({
+                ctx,
+                feat,
+                region,
+                bpPerPx,
+                canvasWidth,
+            });
+            break;
+        case 'perBaseLettering':
+            (0, renderPerBaseLettering_1.renderPerBaseLettering)({
+                ctx,
+                feat,
+                region,
+                bpPerPx,
+                colorForBase,
+                contrastForBase,
+                charWidth,
+                charHeight,
+                canvasWidth,
+            });
+            break;
+        case 'modifications':
+            (0, renderModifications_1.renderModifications)({
+                ctx,
+                feat,
+                region,
+                bpPerPx,
+                renderArgs,
+                canvasWidth,
+            });
+            break;
+        case 'methylation':
+            (0, renderMethylation_1.renderMethylation)({
+                ctx,
+                feat,
+                region,
+                bpPerPx,
+                renderArgs,
+                canvasWidth,
+            });
+            break;
+    }
+}
+exports.renderAlignment = renderAlignment;
+//# sourceMappingURL=renderAlignment.js.map

package/dist/PileupRenderer/renderAlignment.js.map

@@ -0,0 +1 @@
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package/dist/PileupRenderer/renderAlignmentShape.d.ts

@@ -0,0 +1,7 @@
+import { RenderArgsDeserialized } from './PileupRenderer';
+import { LayoutFeature } from './util';
+export declare function renderAlignmentShape({ ctx, feat, renderArgs, }: {
+    ctx: CanvasRenderingContext2D;
+    feat: LayoutFeature;
+    renderArgs: RenderArgsDeserialized;
+}): void;

package/dist/PileupRenderer/renderAlignmentShape.js

@@ -0,0 +1,41 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderAlignmentShape = void 0;
+const util_1 = require("@jbrowse/core/util");
+function renderAlignmentShape({ ctx, feat, renderArgs, }) {
+    const { regions, bpPerPx } = renderArgs;
+    const { heightPx, topPx, feature } = feat;
+    const [region] = regions;
+    const s = feature.get('start');
+    const e = feature.get('end');
+    const [leftPx, rightPx] = (0, util_1.bpSpanPx)(s, e, region, bpPerPx);
+    const flip = region.reversed ? -1 : 1;
+    const strand = feature.get('strand') * flip;
+    if (bpPerPx < 10) {
+        if (strand === -1) {
+            ctx.beginPath();
+            ctx.moveTo(leftPx - 5, topPx + heightPx / 2);
+            ctx.lineTo(leftPx, topPx + heightPx);
+            ctx.lineTo(rightPx, topPx + heightPx);
+            ctx.lineTo(rightPx, topPx);
+            ctx.lineTo(leftPx, topPx);
+            ctx.closePath();
+            ctx.fill();
+        }
+        else {
+            ctx.beginPath();
+            ctx.moveTo(leftPx, topPx);
+            ctx.lineTo(leftPx, topPx + heightPx);
+            ctx.lineTo(rightPx, topPx + heightPx);
+            ctx.lineTo(rightPx + 5, topPx + heightPx / 2);
+            ctx.lineTo(rightPx, topPx);
+            ctx.closePath();
+            ctx.fill();
+        }
+    }
+    else {
+        ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx);
+    }
+}
+exports.renderAlignmentShape = renderAlignmentShape;
+//# sourceMappingURL=renderAlignmentShape.js.map

package/dist/PileupRenderer/renderAlignmentShape.js.map

@@ -0,0 +1 @@
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package/dist/PileupRenderer/renderMethylation.d.ts

@@ -0,0 +1,11 @@
+import { Region } from '@jbrowse/core/util';
+import { LayoutFeature } from './util';
+import { RenderArgsWithColor } from './makeImageData';
+export declare function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }: {
+    ctx: CanvasRenderingContext2D;
+    feat: LayoutFeature;
+    region: Region;
+    bpPerPx: number;
+    renderArgs: RenderArgsWithColor;
+    canvasWidth: number;
+}): void;

package/dist/PileupRenderer/renderMethylation.js

@@ -0,0 +1,63 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderMethylation = void 0;
+const util_1 = require("@jbrowse/core/util");
+const MismatchParser_1 = require("../MismatchParser");
+const util_2 = require("./util");
+// Color by methylation is slightly modified version of color by
+// modifications that focuses on CpG sites, with non-methylated CpG colored
+function renderMethylation({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }) {
+    var _a, _b;
+    const { regionSequence, Color } = renderArgs;
+    const { feature, topPx, heightPx } = feat;
+    if (!regionSequence) {
+        throw new Error('region sequence required for methylation');
+    }
+    const seq = feature.get('seq');
+    if (!seq) {
+        return;
+    }
+    const fstart = feature.get('start');
+    const fend = feature.get('end');
+    const { methBins, methProbs } = (0, MismatchParser_1.getMethBins)(feature);
+    function getCol(k) {
+        if (methBins[k]) {
+            const p = methProbs[k] || 0;
+            return p > 0.5
+                ? Color('red')
+                    .alpha((p - 0.5) * 2)
+                    .hsl()
+                    .string()
+                : Color('blue')
+                    .alpha(1 - p * 2)
+                    .hsl()
+                    .string();
+        }
+        return undefined;
+    }
+    for (let i = 0; i < fend - fstart; i++) {
+        const j = i + fstart;
+        const l1 = (_a = regionSequence[j - region.start + 1]) === null || _a === void 0 ? void 0 : _a.toLowerCase();
+        const l2 = (_b = regionSequence[j - region.start + 2]) === null || _b === void 0 ? void 0 : _b.toLowerCase();
+        if (l1 === 'c' && l2 === 'g') {
+            if (bpPerPx > 2) {
+                const [leftPx, rightPx] = (0, util_1.bpSpanPx)(j, j + 2, region, bpPerPx);
+                const w = rightPx - leftPx + 0.5;
+                const c = getCol(i) || getCol(i + 1) || 'blue';
+                (0, util_2.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+            }
+            else {
+                const [leftPx, rightPx] = (0, util_1.bpSpanPx)(j, j + 1, region, bpPerPx);
+                const w = rightPx - leftPx + 0.5;
+                const c = getCol(i) || 'blue';
+                (0, util_2.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+                const [leftPx2, rightPx2] = (0, util_1.bpSpanPx)(j + 1, j + 2, region, bpPerPx);
+                const w2 = rightPx2 - leftPx2 + 0.5;
+                const c2 = getCol(i + 1) || 'blue';
+                (0, util_2.fillRect)(ctx, leftPx2, topPx, w2, heightPx, canvasWidth, c2);
+            }
+        }
+    }
+}
+exports.renderMethylation = renderMethylation;
+//# sourceMappingURL=renderMethylation.js.map

package/dist/PileupRenderer/renderMethylation.js.map

@@ -0,0 +1 @@
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package/dist/PileupRenderer/renderMismatches.d.ts

@@ -0,0 +1,21 @@
+import { LayoutFeature } from './util';
+import { RenderArgsWithColor } from './makeImageData';
+export declare function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels, }: {
+    ctx: CanvasRenderingContext2D;
+    feat: LayoutFeature;
+    renderArgs: RenderArgsWithColor;
+    colorForBase: {
+        [key: string]: string;
+    };
+    contrastForBase: {
+        [key: string]: string;
+    };
+    mismatchAlpha?: boolean;
+    drawIndels?: boolean;
+    drawSNPsMuted?: boolean;
+    minSubfeatureWidth: number;
+    largeInsertionIndicatorScale: number;
+    charWidth: number;
+    charHeight: number;
+    canvasWidth: number;
+}): void;

package/dist/PileupRenderer/renderMismatches.js

@@ -0,0 +1,135 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderMismatches = void 0;
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./util");
+function renderMismatches({ ctx, feat, renderArgs, minSubfeatureWidth, largeInsertionIndicatorScale, mismatchAlpha, charWidth, charHeight, colorForBase, contrastForBase, canvasWidth, drawSNPsMuted, drawIndels = true, }) {
+    const { Color, bpPerPx, regions } = renderArgs;
+    const { heightPx, topPx, feature } = feat;
+    const [region] = regions;
+    const start = feature.get('start');
+    const pxPerBp = Math.min(1 / bpPerPx, 2);
+    const mismatches = feature.get('mismatches');
+    const heightLim = charHeight - 2;
+    // extraHorizontallyFlippedOffset is used to draw interbase items, which
+    // are located to the left when forward and right when reversed
+    const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx + 1 : -1;
+    if (!mismatches) {
+        return;
+    }
+    // two pass rendering: first pass, draw all the mismatches except wide
+    // insertion markers
+    for (let i = 0; i < mismatches.length; i += 1) {
+        const mismatch = mismatches[i];
+        const mstart = start + mismatch.start;
+        const mlen = mismatch.length;
+        const mbase = mismatch.base;
+        const [leftPx, rightPx] = (0, util_1.bpSpanPx)(mstart, mstart + mlen, region, bpPerPx);
+        const widthPx = Math.max(minSubfeatureWidth, Math.abs(leftPx - rightPx));
+        if (mismatch.type === 'mismatch') {
+            if (!drawSNPsMuted) {
+                const baseColor = colorForBase[mismatch.base] || '#888';
+                const c = mismatchAlpha
+                    ? mismatch.qual === undefined
+                        ? baseColor
+                        : Color(baseColor)
+                            .alpha(Math.min(1, mismatch.qual / 50))
+                            .hsl()
+                            .string()
+                    : baseColor;
+                (0, util_2.fillRect)(ctx, Math.round(leftPx), topPx, widthPx, heightPx, canvasWidth, c);
+            }
+            if (widthPx >= charWidth && heightPx >= heightLim) {
+                // normal SNP coloring
+                const contrastColor = drawSNPsMuted
+                    ? 'black'
+                    : contrastForBase[mismatch.base] || 'black';
+                ctx.fillStyle = mismatchAlpha
+                    ? mismatch.qual === undefined
+                        ? contrastColor
+                        : Color(contrastColor)
+                            .alpha(Math.min(1, mismatch.qual / 50))
+                            .hsl()
+                            .string()
+                    : contrastColor;
+                ctx.fillText(mbase, leftPx + (widthPx - charWidth) / 2 + 1, topPx + heightPx);
+            }
+        }
+        else if (mismatch.type === 'deletion' && drawIndels) {
+            (0, util_2.fillRect)(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorForBase.deletion);
+            const txt = `${mismatch.length}`;
+            const rwidth = (0, util_1.measureText)(txt, 10);
+            if (widthPx >= rwidth && heightPx >= heightLim) {
+                ctx.fillStyle = contrastForBase.deletion;
+                ctx.fillText(txt, (leftPx + rightPx) / 2 - rwidth / 2, topPx + heightPx);
+            }
+        }
+        else if (mismatch.type === 'insertion' && drawIndels) {
+            ctx.fillStyle = 'purple';
+            const pos = leftPx + extraHorizontallyFlippedOffset;
+            const len = +mismatch.base || mismatch.length;
+            const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx));
+            if (len < 10) {
+                (0, util_2.fillRect)(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple');
+                if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
+                    const l = pos - insW;
+                    (0, util_2.fillRect)(ctx, l, topPx, insW * 3, 1, canvasWidth);
+                    (0, util_2.fillRect)(ctx, l, topPx + heightPx - 1, insW * 3, 1, canvasWidth);
+                    ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx);
+                }
+            }
+        }
+        else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {
+            const pos = leftPx + extraHorizontallyFlippedOffset;
+            const c = mismatch.type === 'hardclip' ? 'red' : 'blue';
+            const clipW = Math.max(minSubfeatureWidth, pxPerBp);
+            (0, util_2.fillRect)(ctx, pos, topPx, clipW, heightPx, canvasWidth, c);
+            if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
+                const l = pos - clipW;
+                (0, util_2.fillRect)(ctx, l, topPx, clipW * 3, 1, canvasWidth);
+                (0, util_2.fillRect)(ctx, l, topPx + heightPx - 1, clipW * 3, 1, canvasWidth);
+                ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx);
+            }
+        }
+        else if (mismatch.type === 'skip') {
+            // fix to avoid bad rendering note that this was also related to chrome
+            // bug https://bugs.chromium.org/p/chromium/issues/detail?id=1131528
+            // also affected firefox ref #1236 #2750
+            if (leftPx + widthPx > 0) {
+                // make small exons more visible when zoomed far out
+                const adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0);
+                ctx.clearRect(leftPx, topPx, adjustPx, heightPx);
+                (0, util_2.fillRect)(ctx, Math.max(0, leftPx), topPx + heightPx / 2 - 1, adjustPx + (leftPx < 0 ? leftPx : 0), 2, canvasWidth, '#333');
+            }
+        }
+    }
+    // second pass, draw wide insertion markers on top
+    if (drawIndels) {
+        for (let i = 0; i < mismatches.length; i += 1) {
+            const mismatch = mismatches[i];
+            const mstart = start + mismatch.start;
+            const mlen = mismatch.length;
+            const [leftPx] = (0, util_1.bpSpanPx)(mstart, mstart + mlen, region, bpPerPx);
+            const len = +mismatch.base || mismatch.length;
+            const txt = `${len}`;
+            if (mismatch.type === 'insertion' && len >= 10) {
+                if (bpPerPx > largeInsertionIndicatorScale) {
+                    (0, util_2.fillRect)(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, 'purple');
+                }
+                else if (heightPx > charHeight) {
+                    const rwidth = (0, util_1.measureText)(txt);
+                    const padding = 5;
+                    (0, util_2.fillRect)(ctx, leftPx - rwidth / 2 - padding, topPx, rwidth + 2 * padding, heightPx, canvasWidth, 'purple');
+                    ctx.fillStyle = 'white';
+                    ctx.fillText(txt, leftPx - rwidth / 2, topPx + heightPx);
+                }
+                else {
+                    const padding = 2;
+                    (0, util_2.fillRect)(ctx, leftPx - padding, topPx, 2 * padding, heightPx, canvasWidth, 'purple');
+                }
+            }
+        }
+    }
+}
+exports.renderMismatches = renderMismatches;
+//# sourceMappingURL=renderMismatches.js.map

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package/dist/PileupRenderer/renderModifications.d.ts

@@ -0,0 +1,11 @@
+import { Region } from '@jbrowse/core/util';
+import { LayoutFeature } from './util';
+import { RenderArgsWithColor } from './makeImageData';
+export declare function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }: {
+    ctx: CanvasRenderingContext2D;
+    feat: LayoutFeature;
+    region: Region;
+    bpPerPx: number;
+    renderArgs: RenderArgsWithColor;
+    canvasWidth: number;
+}): void;

package/dist/PileupRenderer/renderModifications.js

@@ -0,0 +1,54 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderModifications = void 0;
+const util_1 = require("@jbrowse/core/util");
+const MismatchParser_1 = require("../MismatchParser");
+const util_2 = require("../util");
+const util_3 = require("./util");
+// 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
+function renderModifications({ ctx, feat, region, bpPerPx, renderArgs, canvasWidth, }) {
+    const { feature, topPx, heightPx } = feat;
+    const { Color, modificationTagMap = {} } = renderArgs;
+    const seq = feature.get('seq');
+    if (!seq) {
+        return;
+    }
+    const mm = (0, util_2.getTagAlt)(feature, 'MM', 'Mm') || '';
+    const cigar = feature.get('CIGAR');
+    const start = feature.get('start');
+    const strand = feature.get('strand');
+    const cigarOps = (0, MismatchParser_1.parseCigar)(cigar);
+    const probabilities = (0, MismatchParser_1.getModificationProbabilities)(feature);
+    const modifications = (0, MismatchParser_1.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 = Color(col);
+        for (const readPos of (0, MismatchParser_1.getNextRefPos)(cigarOps, positions)) {
+            const r = start + readPos;
+            const [leftPx, rightPx] = (0, util_1.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)
+                    .hsl()
+                    .string()
+                : col;
+            const w = rightPx - leftPx + 0.5;
+            (0, util_3.fillRect)(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+            probIndex++;
+        }
+    }
+}
+exports.renderModifications = renderModifications;
+//# sourceMappingURL=renderModifications.js.map

package/dist/PileupRenderer/renderModifications.js.map

@@ -0,0 +1 @@
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package/dist/PileupRenderer/renderPerBaseLettering.d.ts

@@ -0,0 +1,13 @@
+import { Region } from '@jbrowse/core/util';
+import { LayoutFeature } from './util';
+export declare function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, }: {
+    ctx: CanvasRenderingContext2D;
+    feat: LayoutFeature;
+    region: Region;
+    bpPerPx: number;
+    colorForBase: Record<string, string>;
+    contrastForBase: Record<string, string>;
+    charWidth: number;
+    charHeight: number;
+    canvasWidth: number;
+}): void;

package/dist/PileupRenderer/renderPerBaseLettering.js

@@ -0,0 +1,47 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderPerBaseLettering = void 0;
+const util_1 = require("@jbrowse/core/util");
+const MismatchParser_1 = require("../MismatchParser");
+const util_2 = require("./util");
+function renderPerBaseLettering({ ctx, feat, region, bpPerPx, colorForBase, contrastForBase, charWidth, charHeight, canvasWidth, }) {
+    const heightLim = charHeight - 2;
+    const { feature, topPx, heightPx } = feat;
+    const seq = feature.get('seq');
+    const cigarOps = (0, MismatchParser_1.parseCigar)(feature.get('CIGAR'));
+    const w = 1 / bpPerPx;
+    const start = feature.get('start');
+    let soffset = 0;
+    let roffset = 0;
+    if (!seq) {
+        return;
+    }
+    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 letter = seq[soffset + m];
+                const r = start + roffset + m;
+                const [leftPx] = (0, util_1.bpSpanPx)(r, r + 1, region, bpPerPx);
+                const c = colorForBase[letter];
+                (0, util_2.fillRect)(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c);
+                if (w >= charWidth && heightPx >= heightLim) {
+                    // normal SNP coloring
+                    ctx.fillStyle = contrastForBase[letter];
+                    ctx.fillText(letter, leftPx + (w - charWidth) / 2 + 1, topPx + heightPx);
+                }
+            }
+            soffset += len;
+            roffset += len;
+        }
+    }
+}
+exports.renderPerBaseLettering = renderPerBaseLettering;
+//# sourceMappingURL=renderPerBaseLettering.js.map

package/dist/PileupRenderer/renderPerBaseLettering.js.map

@@ -0,0 +1 @@
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package/dist/PileupRenderer/renderPerBaseQuality.d.ts

@@ -0,0 +1,9 @@
+import { Region } from '@jbrowse/core/util';
+import { LayoutFeature } from './util';
+export declare function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }: {
+    ctx: CanvasRenderingContext2D;
+    feat: LayoutFeature;
+    region: Region;
+    bpPerPx: number;
+    canvasWidth: number;
+}): void;