@jbrowse/plugin-alignments 2.4.2 → 2.6.0

package/esm/PileupRenderer/makeImageData.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"makeImageData.js","sourceRoot":"","sources":["../../src/PileupRenderer/makeImageData.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAA;AAC5D,OAAO,EAAE,kBAAkB,EAAE,MAAM,kBAAkB,CAAA;AACrD,OAAO,EACL,kBAAkB,EAClB,eAAe,EACf,kBAAkB,EAClB,gBAAgB,EAChB,mBAAmB,GACpB,MAAM,QAAQ,CAAA;AACf,OAAO,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAA;AACnD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAA;AACrD,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAA;AAazD,MAAM,UAAU,aAAa,CAAC,EAC5B,GAAG,EACH,aAAa,EACb,WAAW,EACX,UAAU,GAMX;IACC,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,KAAK,EAAE,WAAW,EAAE,GAAG,UAAU,CAAA;IACxE,MAAM,aAAa,GAAG,cAAc,CAAC,MAAM,EAAE,eAAe,CAAC,CAAA;IAC7D,MAAM,kBAAkB,GAAG,cAAc,CAAC,MAAM,EAAE,oBAAoB,CAAC,CAAA;IACvE,MAAM,4BAA4B,GAAG,cAAc,CACjD,MAAM,EACN,8BAA8B,CAC/B,CAAA;IACD,MAAM,YAAY,GAAG,cAAc,CAAC,MAAM,EAAE,OAAO,CAAC,KAAK,MAAM,CAAA;IAC/D,MAAM,KAAK,GAAG,kBAAkB,CAAC,WAAW,CAAC,CAAA;IAC7C,MAAM,YAAY,GAAG,eAAe,CAAC,KAAK,CAAC,CAAA;IAC3C,MAAM,eAAe,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAA;IACjD,GAAG,CAAC,IAAI,GAAG,iCAAiC,CAAA;IAE5C,MAAM,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,kBAAkB,EAAE,CAAA;IACtD,MAAM,aAAa,GAAG,mBAAmB,CAAC,OAAO,aAAP,OAAO,uBAAP,OAAO,CAAE,IAAI,CAAC,CAAA;IACxD,MAAM,UAAU,GAAG,gBAAgB,EAAE,CAAA;IACrC,KAAK,MAAM,IAAI,IAAI,aAAa,EAAE;QAChC,eAAe,CAAC;YACd,GAAG;YACH,IAAI;YACJ,UAAU;YACV,YAAY;YACZ,YAAY;YACZ,eAAe;YACf,SAAS;YACT,UAAU;YACV,WAAW;SACZ,CAAC,CAAA;QACF,gBAAgB,CAAC;YACf,GAAG;YACH,IAAI;YACJ,UAAU;YACV,aAAa;YACb,aAAa;YACb,UAAU;YACV,4BAA4B;YAC5B,kBAAkB;YAClB,SAAS;YACT,UAAU;YACV,YAAY;YACZ,eAAe;YACf,WAAW;SACZ,CAAC,CAAA;QACF,IAAI,YAAY,EAAE;YAChB,kBAAkB,CAAC;gBACjB,GAAG;gBACH,IAAI;gBACJ,UAAU;gBACV,YAAY;gBACZ,MAAM;gBACN,KAAK;gBACL,WAAW;aACZ,CAAC,CAAA;SACH;KACF;AACH,CAAC"}

package/esm/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/esm/PileupRenderer/renderAlignment.js

@@ -0,0 +1,68 @@
+import { getAlignmentShapeColor } from './getAlignmentShapeColor';
+import { renderAlignmentShape } from './renderAlignmentShape';
+import { renderPerBaseQuality } from './renderPerBaseQuality';
+import { renderPerBaseLettering } from './renderPerBaseLettering';
+import { renderModifications } from './renderModifications';
+import { renderMethylation } from './renderMethylation';
+export 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 = getAlignmentShapeColor({
+        feature,
+        config,
+        tag,
+        defaultColor,
+        colorType,
+        colorTagMap,
+    });
+    renderAlignmentShape({ ctx, feat, renderArgs });
+    // second pass for color types that render per-base things that go over the
+    // existing drawing
+    switch (colorType) {
+        case 'perBaseQuality':
+            renderPerBaseQuality({
+                ctx,
+                feat,
+                region,
+                bpPerPx,
+                canvasWidth,
+            });
+            break;
+        case 'perBaseLettering':
+            renderPerBaseLettering({
+                ctx,
+                feat,
+                region,
+                bpPerPx,
+                colorForBase,
+                contrastForBase,
+                charWidth,
+                charHeight,
+                canvasWidth,
+            });
+            break;
+        case 'modifications':
+            renderModifications({
+                ctx,
+                feat,
+                region,
+                bpPerPx,
+                renderArgs,
+                canvasWidth,
+            });
+            break;
+        case 'methylation':
+            renderMethylation({
+                ctx,
+                feat,
+                region,
+                bpPerPx,
+                renderArgs,
+                canvasWidth,
+            });
+            break;
+    }
+}
+//# sourceMappingURL=renderAlignment.js.map

package/esm/PileupRenderer/renderAlignment.js.map

@@ -0,0 +1 @@
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package/esm/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/esm/PileupRenderer/renderAlignmentShape.js

@@ -0,0 +1,37 @@
+import { bpSpanPx } from '@jbrowse/core/util';
+export 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] = 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);
+    }
+}
+//# sourceMappingURL=renderAlignmentShape.js.map

package/esm/PileupRenderer/renderAlignmentShape.js.map

@@ -0,0 +1 @@
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package/esm/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/esm/PileupRenderer/renderMethylation.js

@@ -0,0 +1,59 @@
+import { bpSpanPx } from '@jbrowse/core/util';
+import { getMethBins } from '../MismatchParser';
+import { fillRect } from './util';
+// Color by methylation is slightly modified version of color by
+// modifications that focuses on CpG sites, with non-methylated CpG colored
+export 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 } = 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] = bpSpanPx(j, j + 2, region, bpPerPx);
+                const w = rightPx - leftPx + 0.5;
+                const c = getCol(i) || getCol(i + 1) || 'blue';
+                fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+            }
+            else {
+                const [leftPx, rightPx] = bpSpanPx(j, j + 1, region, bpPerPx);
+                const w = rightPx - leftPx + 0.5;
+                const c = getCol(i) || 'blue';
+                fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+                const [leftPx2, rightPx2] = bpSpanPx(j + 1, j + 2, region, bpPerPx);
+                const w2 = rightPx2 - leftPx2 + 0.5;
+                const c2 = getCol(i + 1) || 'blue';
+                fillRect(ctx, leftPx2, topPx, w2, heightPx, canvasWidth, c2);
+            }
+        }
+    }
+}
+//# sourceMappingURL=renderMethylation.js.map

package/esm/PileupRenderer/renderMethylation.js.map

@@ -0,0 +1 @@
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package/esm/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/esm/PileupRenderer/renderMismatches.js

@@ -0,0 +1,131 @@
+import { bpSpanPx, measureText } from '@jbrowse/core/util';
+import { fillRect } from './util';
+export 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] = 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;
+                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) {
+            fillRect(ctx, leftPx, topPx, Math.abs(leftPx - rightPx), heightPx, canvasWidth, colorForBase.deletion);
+            const txt = `${mismatch.length}`;
+            const rwidth = measureText(txt, 10);
+            if (widthPx >= rwidth && heightPx >= heightLim) {
+                ctx.fillStyle = contrastForBase.deletion;
+                ctx.fillText(txt, (leftPx + rightPx) / 2 - rwidth / 2, topPx + heightPx);
+            }
+        }
+        else if (mismatch.type === 'insertion' && drawIndels) {
+            ctx.fillStyle = 'purple';
+            const pos = leftPx + extraHorizontallyFlippedOffset;
+            const len = +mismatch.base || mismatch.length;
+            const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx));
+            if (len < 10) {
+                fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple');
+                if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
+                    const l = pos - insW;
+                    fillRect(ctx, l, topPx, insW * 3, 1, canvasWidth);
+                    fillRect(ctx, l, topPx + heightPx - 1, insW * 3, 1, canvasWidth);
+                    ctx.fillText(`(${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);
+            fillRect(ctx, pos, topPx, clipW, heightPx, canvasWidth, c);
+            if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
+                const l = pos - clipW;
+                fillRect(ctx, l, topPx, clipW * 3, 1, canvasWidth);
+                fillRect(ctx, l, topPx + heightPx - 1, clipW * 3, 1, canvasWidth);
+                ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx);
+            }
+        }
+        else if (mismatch.type === 'skip') {
+            // fix to avoid bad rendering note that this was also related to chrome
+            // bug https://bugs.chromium.org/p/chromium/issues/detail?id=1131528
+            // also affected firefox ref #1236 #2750
+            if (leftPx + widthPx > 0) {
+                // make small exons more visible when zoomed far out
+                const adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0);
+                ctx.clearRect(leftPx, topPx, adjustPx, heightPx);
+                fillRect(ctx, Math.max(0, leftPx), topPx + heightPx / 2 - 1, adjustPx + (leftPx < 0 ? leftPx : 0), 2, canvasWidth, '#333');
+            }
+        }
+    }
+    // second pass, draw wide insertion markers on top
+    if (drawIndels) {
+        for (let i = 0; i < mismatches.length; i += 1) {
+            const mismatch = mismatches[i];
+            const mstart = start + mismatch.start;
+            const mlen = mismatch.length;
+            const [leftPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx);
+            const len = +mismatch.base || mismatch.length;
+            const txt = `${len}`;
+            if (mismatch.type === 'insertion' && len >= 10) {
+                if (bpPerPx > largeInsertionIndicatorScale) {
+                    fillRect(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, 'purple');
+                }
+                else if (heightPx > charHeight) {
+                    const rwidth = measureText(txt);
+                    const padding = 5;
+                    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;
+                    fillRect(ctx, leftPx - padding, topPx, 2 * padding, heightPx, canvasWidth, 'purple');
+                }
+            }
+        }
+    }
+}
+//# sourceMappingURL=renderMismatches.js.map

package/esm/PileupRenderer/renderMismatches.js.map

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package/esm/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/esm/PileupRenderer/renderModifications.js

@@ -0,0 +1,50 @@
+import { bpSpanPx } from '@jbrowse/core/util';
+import { getModificationPositions, getModificationProbabilities, getNextRefPos, parseCigar, } from '../MismatchParser';
+import { getTagAlt } from '../util';
+import { fillRect } from './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
+export 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 = 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 = Color(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)
+                    .hsl()
+                    .string()
+                : col;
+            const w = rightPx - leftPx + 0.5;
+            fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c);
+            probIndex++;
+        }
+    }
+}
+//# sourceMappingURL=renderModifications.js.map

package/esm/PileupRenderer/renderModifications.js.map

@@ -0,0 +1 @@
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package/esm/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/esm/PileupRenderer/renderPerBaseLettering.js

@@ -0,0 +1,43 @@
+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, }) {
+    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;
+    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] = bpSpanPx(r, r + 1, region, bpPerPx);
+                const c = colorForBase[letter];
+                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;
+        }
+    }
+}
+//# sourceMappingURL=renderPerBaseLettering.js.map

package/esm/PileupRenderer/renderPerBaseLettering.js.map

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package/esm/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;

package/esm/PileupRenderer/renderPerBaseQuality.js

@@ -0,0 +1,35 @@
+import { bpSpanPx } from '@jbrowse/core/util';
+import { parseCigar } from '../MismatchParser';
+import { fillRect } from './util';
+export function renderPerBaseQuality({ ctx, feat, region, bpPerPx, canvasWidth, }) {
+    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
+    let roffset = 0; // reference offset
+    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;
+        }
+    }
+}
+//# sourceMappingURL=renderPerBaseQuality.js.map

package/esm/PileupRenderer/renderPerBaseQuality.js.map

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package/esm/PileupRenderer/renderSoftClipping.d.ts

@@ -0,0 +1,13 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import { Theme } from '@mui/material';
+import { RenderArgsDeserializedWithFeaturesAndLayout } from './PileupRenderer';
+import { LayoutFeature } from './util';
+export declare function renderSoftClipping({ ctx, feat, renderArgs, config, theme, colorForBase, canvasWidth, }: {
+    ctx: CanvasRenderingContext2D;
+    feat: LayoutFeature;
+    renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+    config: AnyConfigurationModel;
+    colorForBase: Record<string, string>;
+    theme: Theme;
+    canvasWidth: number;
+}): void;