Mercurial > repos > fubar > jbrowse2
view x/static/js/4060.8757dbe8.chunk.js.map @ 125:49f3d3878413 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 5ea1f9c1eef1de76232e69aa6d34cda77d90d566
| author | fubar |
|---|---|
| date | Sat, 05 Oct 2024 23:58:05 +0000 |
| parents | |
| children |
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{ Feature, measureText } from '@jbrowse/core/util'\nimport { Theme } from '@mui/material'\n\nexport function fillRect(\n ctx: CanvasRenderingContext2D,\n l: number,\n t: number,\n w: number,\n h: number,\n cw: number,\n color?: string,\n) {\n if (l + w < 0 || l > cw) {\n return\n }\n if (color) {\n ctx.fillStyle = color\n }\n ctx.fillRect(l, t, w, h)\n}\n\nexport function getColorBaseMap(theme: Theme) {\n const { bases } = theme.palette\n return {\n A: bases.A.main,\n C: bases.C.main,\n G: bases.G.main,\n T: bases.T.main,\n deletion: '#808080', // gray\n }\n}\n\nexport function getContrastBaseMap(theme: Theme) {\n return Object.fromEntries(\n Object.entries(getColorBaseMap(theme)).map(([key, value]) => [\n key,\n theme.palette.getContrastText(value),\n ]),\n )\n}\n\nexport function shouldDrawSNPsMuted(type?: string) {\n return ['methylation', 'modifications'].includes(type || '')\n}\n\nexport function shouldDrawIndels() {\n return true\n}\n\nexport interface LayoutFeature {\n heightPx: number\n topPx: number\n feature: Feature\n}\n\n// get width and height of chars the height is an approximation: width letter M\n// is approximately the height\nexport function getCharWidthHeight() {\n const charWidth = measureText('A')\n const charHeight = measureText('M') - 2\n return { charWidth, charHeight }\n}\n","import {\n AnyConfigurationModel,\n readConfObject,\n} from '@jbrowse/core/configuration'\nimport { Feature } from '@jbrowse/core/util'\nimport { fillColor } from '../shared/color'\nimport {\n colorByInsertSize,\n colorByMappingQuality,\n colorByOrientation,\n colorByStrand,\n colorByStrandedRnaSeq,\n} from './colorBy'\n\nexport function getAlignmentShapeColor({\n colorType,\n tag,\n feature,\n config,\n defaultColor,\n colorTagMap,\n}: {\n colorType: string\n tag: string\n feature: Feature\n defaultColor: boolean\n config: AnyConfigurationModel\n colorTagMap: Record<string, string>\n}) {\n // first pass for simple color changes that change the color of the\n // alignment\n switch (colorType) {\n case 'insertSize':\n return colorByInsertSize(feature)\n case 'strand':\n return colorByStrand(feature)\n case 'mappingQuality':\n return colorByMappingQuality(feature)\n case 'pairOrientation':\n return colorByOrientation(feature, config)\n case 'stranded':\n return colorByStrandedRnaSeq(feature)\n case 'xs':\n case 'tag': {\n const tags = feature.get('tags')\n const val = tags ? tags[tag] : feature.get(tag)\n\n if (tag === 'XS' || tag === 'TS') {\n if (val === '-') {\n return fillColor.color_rev_strand\n } else if (val === '+') {\n return fillColor.color_fwd_strand\n } else {\n return fillColor.color_nostrand\n }\n }\n if (tag === 'ts') {\n if (val === '-') {\n return feature.get('strand') === -1\n ? fillColor.color_fwd_strand\n : fillColor.color_rev_strand\n } else if (val === '+') {\n return feature.get('strand') === -1\n ? fillColor.color_rev_strand\n : fillColor.color_fwd_strand\n } else {\n return fillColor.color_nostrand\n }\n }\n return colorTagMap[val] || fillColor.color_nostrand\n }\n case 'insertSizeAndPairOrientation':\n break\n\n case 'modifications':\n case 'methylation':\n // this coloring is similar to igv.js, and is helpful to color negative\n // strand reads differently because their c-g will be flipped (e.g. g-c\n // read right to left)\n return feature.get('flags') & 16 ? '#c8dcc8' : '#c8c8c8'\n\n default:\n return defaultColor\n ? 'lightgrey'\n : readConfObject(config, 'color', { feature })\n }\n}\n","import {\n AnyConfigurationModel,\n readConfObject,\n} from '@jbrowse/core/configuration'\nimport { Feature } from '@jbrowse/core/util'\nimport { fillColor } from '../shared/color'\nimport { orientationTypes } from '../util'\n\nexport function colorByInsertSize(feature: Feature) {\n return feature.get('is_paired') &&\n feature.get('refName') !== feature.get('next_ref')\n ? '#555'\n : `hsl(${Math.abs(feature.get('template_length')) / 10},50%,50%)`\n}\n\nexport function colorByMappingQuality(feature: Feature) {\n return `hsl(${feature.get('score')},50%,50%)`\n}\n\nfunction getOrientation(feature: Feature, config: AnyConfigurationModel) {\n const orientationType = readConfObject(config, 'orientationType') as\n | 'fr'\n | 'ff'\n | 'rf'\n const type = orientationTypes[orientationType]\n const orientation = type[feature.get('pair_orientation') as string]!\n return {\n LR: 'color_pair_lr' as const,\n RR: 'color_pair_rr' as const,\n RL: 'color_pair_rl' as const,\n LL: 'color_pair_ll' as const,\n }[orientation]\n}\n\nexport function colorByStrand(feature: Feature) {\n return feature.get('strand') === -1 ? '#8F8FD8' : '#EC8B8B'\n}\n\nexport function colorByOrientation(\n feature: Feature,\n config: AnyConfigurationModel,\n) {\n return fillColor[getOrientation(feature, config) || 'color_nostrand']\n}\nfunction getStranded(feature: Feature) {\n const flags = feature.get('flags')\n const strand = feature.get('strand')\n\n // is paired\n if (flags & 1) {\n // first-of-pair?\n const flipper = flags & 64 ? -1 : 1\n\n // proper pairing\n if (flags & 2) {\n return strand * flipper === 1 ? 'color_rev_strand' : 'color_fwd_strand'\n }\n // mate missing, separate color\n if (flags & 8) {\n return strand * flipper === 1\n ? 'color_rev_missing_mate'\n : 'color_fwd_missing_mate'\n }\n // same chrom without proper pairing gets separate color\n if (feature.get('refName') === feature.get('next_ref')) {\n return strand * flipper === 1\n ? 'color_rev_strand_not_proper'\n : 'color_fwd_strand_not_proper'\n }\n // abberant chrom\n\n return strand === 1 ? 'color_fwd_diff_chr' : 'color_rev_diff_chr'\n }\n return 'color_unknown'\n}\n\nexport function colorByStrandedRnaSeq(feature: Feature) {\n return fillColor[getStranded(feature)]\n}\n","import { LayoutFeature } from './util'\n\nimport { getAlignmentShapeColor } from './getAlignmentShapeColor'\nimport { renderAlignmentShape } from './renderAlignmentShape'\nimport { renderPerBaseQuality } from './renderPerBaseQuality'\nimport { renderPerBaseLettering } from './renderPerBaseLettering'\nimport { renderModifications } from './renderModifications'\nimport { renderMethylation } from './renderMethylation'\nimport { RenderArgsWithColor } from './makeImageData'\n\nexport function renderAlignment({\n ctx,\n feat,\n renderArgs,\n colorForBase,\n contrastForBase,\n charWidth,\n charHeight,\n defaultColor,\n canvasWidth,\n}: {\n ctx: CanvasRenderingContext2D\n feat: LayoutFeature\n renderArgs: RenderArgsWithColor\n colorForBase: Record<string, string>\n contrastForBase: Record<string, string>\n charWidth: number\n charHeight: number\n defaultColor: boolean\n canvasWidth: number\n}) {\n const { config, bpPerPx, regions, colorBy, colorTagMap = {} } = renderArgs\n const { tag = '', type: colorType = '' } = colorBy || {}\n const { feature } = feat\n const region = regions[0]!\n\n ctx.fillStyle = getAlignmentShapeColor({\n feature,\n config,\n tag,\n defaultColor,\n colorType,\n colorTagMap,\n })\n\n renderAlignmentShape({ ctx, feat, renderArgs })\n\n // second pass for color types that render per-base things that go over the\n // existing drawing\n switch (colorType) {\n case 'perBaseQuality':\n renderPerBaseQuality({\n ctx,\n feat,\n region,\n bpPerPx,\n canvasWidth,\n })\n break\n\n case 'perBaseLettering':\n renderPerBaseLettering({\n ctx,\n feat,\n region,\n bpPerPx,\n colorForBase,\n contrastForBase,\n charWidth,\n charHeight,\n canvasWidth,\n })\n break\n\n case 'modifications':\n renderModifications({\n ctx,\n feat,\n region,\n bpPerPx,\n renderArgs,\n canvasWidth,\n })\n break\n\n case 'methylation':\n renderMethylation({\n ctx,\n feat,\n region,\n bpPerPx,\n renderArgs,\n canvasWidth,\n })\n break\n }\n}\n","import { bpSpanPx } from '@jbrowse/core/util'\nimport { RenderArgsDeserialized } from './PileupRenderer'\nimport { LayoutFeature } from './util'\n\nexport function renderAlignmentShape({\n ctx,\n feat,\n renderArgs,\n}: {\n ctx: CanvasRenderingContext2D\n feat: LayoutFeature\n renderArgs: RenderArgsDeserialized\n}) {\n const { regions, bpPerPx } = renderArgs\n const { heightPx, topPx, feature } = feat\n const region = regions[0]!\n const s = feature.get('start')\n const e = feature.get('end')\n const [leftPx, rightPx] = bpSpanPx(s, e, region, bpPerPx)\n const flip = region.reversed ? -1 : 1\n const strand = feature.get('strand') * flip\n if (bpPerPx < 10 && heightPx > 5) {\n if (strand === -1) {\n ctx.beginPath()\n ctx.moveTo(leftPx - 5, topPx + heightPx / 2)\n ctx.lineTo(leftPx, topPx + heightPx)\n ctx.lineTo(rightPx, topPx + heightPx)\n ctx.lineTo(rightPx, topPx)\n ctx.lineTo(leftPx, topPx)\n ctx.closePath()\n ctx.fill()\n } else {\n ctx.beginPath()\n ctx.moveTo(leftPx, topPx)\n ctx.lineTo(leftPx, topPx + heightPx)\n ctx.lineTo(rightPx, topPx + heightPx)\n ctx.lineTo(rightPx + 5, topPx + heightPx / 2)\n ctx.lineTo(rightPx, topPx)\n ctx.closePath()\n ctx.fill()\n }\n } else {\n ctx.fillRect(leftPx, topPx, rightPx - leftPx, heightPx)\n }\n}\n","import { bpSpanPx, Region } from '@jbrowse/core/util'\nimport { parseCigar } from '../MismatchParser'\nimport { fillRect, LayoutFeature } from './util'\n\nexport function renderPerBaseQuality({\n ctx,\n feat,\n region,\n bpPerPx,\n canvasWidth,\n}: {\n ctx: CanvasRenderingContext2D\n feat: LayoutFeature\n region: Region\n bpPerPx: number\n canvasWidth: number\n}) {\n const { feature, topPx, heightPx } = feat\n const qual: string = feature.get('qual') || ''\n const scores = qual.split(' ').map(val => +val)\n const cigarOps = parseCigar(feature.get('CIGAR'))\n const w = 1 / bpPerPx\n const start = feature.get('start')\n let soffset = 0 // sequence offset\n let roffset = 0 // reference offset\n\n for (let i = 0; i < cigarOps.length; i += 2) {\n const len = +cigarOps[i]!\n const op = cigarOps[i + 1]!\n if (op === 'S' || op === 'I') {\n soffset += len\n } else if (op === 'D' || op === 'N') {\n roffset += len\n } else if (op === 'M' || op === 'X' || op === '=') {\n for (let m = 0; m < len; m++) {\n const score = scores[soffset + m]!\n const start0 = start + roffset + m\n const leftPx = bpSpanPx(start0, start0 + 1, region, bpPerPx)[0]\n const c = `hsl(${score === 255 ? 150 : score * 1.5},55%,50%)`\n fillRect(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c)\n }\n soffset += len\n roffset += len\n }\n }\n}\n","import { bpSpanPx, Region } from '@jbrowse/core/util'\nimport { parseCigar } from '../MismatchParser'\nimport { fillRect, LayoutFeature } from './util'\n\nexport function renderPerBaseLettering({\n ctx,\n feat,\n region,\n bpPerPx,\n colorForBase,\n contrastForBase,\n charWidth,\n charHeight,\n canvasWidth,\n}: {\n ctx: CanvasRenderingContext2D\n feat: LayoutFeature\n region: Region\n bpPerPx: number\n colorForBase: Record<string, string>\n contrastForBase: Record<string, string>\n charWidth: number\n charHeight: number\n canvasWidth: number\n}) {\n const heightLim = charHeight - 2\n const { feature, topPx, heightPx } = feat\n const seq = feature.get('seq') as string | undefined\n const cigarOps = parseCigar(feature.get('CIGAR'))\n const w = 1 / bpPerPx\n const start = feature.get('start')\n let soffset = 0\n let roffset = 0\n\n if (!seq) {\n return\n }\n for (let i = 0; i < cigarOps.length; i += 2) {\n const len = +cigarOps[i]!\n const op = cigarOps[i + 1]!\n if (op === 'S' || op === 'I') {\n soffset += len\n } else if (op === 'D' || op === 'N') {\n roffset += len\n } else if (op === 'M' || op === 'X' || op === '=') {\n for (let m = 0; m < len; m++) {\n const letter = seq[soffset + m]!\n const r = start + roffset + m\n const [leftPx] = bpSpanPx(r, r + 1, region, bpPerPx)\n const c = colorForBase[letter]\n fillRect(ctx, leftPx, topPx, w + 0.5, heightPx, canvasWidth, c)\n\n if (w >= charWidth && heightPx >= heightLim) {\n // normal SNP coloring\n ctx.fillStyle = contrastForBase[letter]!\n ctx.fillText(\n letter,\n leftPx + (w - charWidth) / 2 + 1,\n topPx + heightPx,\n )\n }\n }\n soffset += len\n roffset += len\n }\n }\n}\n","import { bpSpanPx, Region } from '@jbrowse/core/util'\nimport {\n getModificationPositions,\n getModificationProbabilities,\n getNextRefPos,\n parseCigar,\n} from '../MismatchParser'\nimport { getTagAlt } from '../util'\nimport { fillRect, LayoutFeature } from './util'\nimport { RenderArgsWithColor } from './makeImageData'\nimport { colord } from '@jbrowse/core/util/colord'\n\n// render modifications stored in MM tag in BAM\n//\n// ML stores probabilities as array of numerics and MP is scaled phred scores\n// https://github.com/samtools/hts-specs/pull/418/files#diff-e765c6479316309f56b636f88189cdde8c40b854c7bdcce9ee7fe87a4e76febcR596\n//\n// if we have ML or Ml, it is an 8bit probability, divide by 255\n//\n// if we have MP or Mp it is phred scaled ASCII, which can go up to 90 but\n// has very high likelihood basecalls at that point, we really only care\n// about low qual calls <20 approx\nexport function renderModifications({\n ctx,\n feat,\n region,\n bpPerPx,\n renderArgs,\n canvasWidth,\n}: {\n ctx: CanvasRenderingContext2D\n feat: LayoutFeature\n region: Region\n bpPerPx: number\n renderArgs: RenderArgsWithColor\n canvasWidth: number\n}) {\n const { feature, topPx, heightPx } = feat\n const { modificationTagMap = {} } = renderArgs\n\n const seq = feature.get('seq') as string | undefined\n\n if (!seq) {\n return\n }\n const mm = (getTagAlt(feature, 'MM', 'Mm') as string) || ''\n const cigar = feature.get('CIGAR')\n const start = feature.get('start')\n const strand = feature.get('strand')\n const cigarOps = parseCigar(cigar)\n const probabilities = getModificationProbabilities(feature)\n const modifications = getModificationPositions(mm, seq, strand)\n\n // probIndex applies across multiple modifications e.g.\n let probIndex = 0\n for (const { type, positions } of modifications) {\n const col = modificationTagMap[type] || 'black'\n const base = colord(col)\n for (const readPos of getNextRefPos(cigarOps, positions)) {\n const r = start + readPos\n const [leftPx, rightPx] = bpSpanPx(r, r + 1, region, bpPerPx)\n const prob = probabilities?.[probIndex] || 0\n const c = prob !== 1 ? base.alpha(prob + 0.1).toHslString() : col\n const w = rightPx - leftPx + 0.5\n fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c)\n probIndex++\n }\n }\n}\n","import { bpSpanPx, Region } from '@jbrowse/core/util'\nimport { getMethBins } from '../MismatchParser'\nimport { fillRect, LayoutFeature } from './util'\nimport { RenderArgsWithColor } from './makeImageData'\nimport { colord } from '@jbrowse/core/util/colord'\n\n// Color by methylation is slightly modified version of color by\n// modifications that focuses on CpG sites, with non-methylated CpG colored\nexport function renderMethylation({\n ctx,\n feat,\n region,\n bpPerPx,\n renderArgs,\n canvasWidth,\n}: {\n ctx: CanvasRenderingContext2D\n feat: LayoutFeature\n region: Region\n bpPerPx: number\n renderArgs: RenderArgsWithColor\n canvasWidth: number\n}) {\n const { regionSequence } = renderArgs\n const { feature, topPx, heightPx } = feat\n if (!regionSequence) {\n throw new Error('region sequence required for methylation')\n }\n\n const seq = feature.get('seq') as string | undefined\n if (!seq) {\n return\n }\n const fstart = feature.get('start')\n const fend = feature.get('end')\n const { methBins, methProbs } = getMethBins(feature)\n\n function getCol(k: number) {\n if (methBins[k]) {\n const p = methProbs[k] || 0\n return (\n p > 0.5\n ? colord('red').alpha((p - 0.5) * 2)\n : colord('blue').alpha(1 - p * 2)\n ).toHslString()\n }\n return undefined\n }\n for (let i = 0; i < fend - fstart; i++) {\n const j = i + fstart\n const l1 = regionSequence[j - region.start + 1]?.toLowerCase()\n const l2 = regionSequence[j - region.start + 2]?.toLowerCase()\n\n if (l1 === 'c' && l2 === 'g') {\n if (bpPerPx > 2) {\n const [leftPx, rightPx] = bpSpanPx(j, j + 2, region, bpPerPx)\n const w = rightPx - leftPx + 0.5\n const c = getCol(i) || getCol(i + 1) || 'blue'\n fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c)\n } else {\n const [leftPx, rightPx] = bpSpanPx(j, j + 1, region, bpPerPx)\n const w = rightPx - leftPx + 0.5\n const c = getCol(i) || 'blue'\n fillRect(ctx, leftPx, topPx, w, heightPx, canvasWidth, c)\n const [leftPx2, rightPx2] = bpSpanPx(j + 1, j + 2, region, bpPerPx)\n const w2 = rightPx2 - leftPx2 + 0.5\n const c2 = getCol(i + 1) || 'blue'\n fillRect(ctx, leftPx2, topPx, w2, heightPx, canvasWidth, c2)\n }\n }\n }\n}\n","import { bpSpanPx, measureText } from '@jbrowse/core/util'\nimport { Mismatch } from '../MismatchParser'\nimport { fillRect, LayoutFeature } from './util'\nimport { RenderArgsWithColor } from './makeImageData'\nimport { colord } from '@jbrowse/core/util/colord'\n\nexport function renderMismatches({\n ctx,\n feat,\n renderArgs,\n minSubfeatureWidth,\n largeInsertionIndicatorScale,\n mismatchAlpha,\n charWidth,\n charHeight,\n colorForBase,\n contrastForBase,\n canvasWidth,\n drawSNPsMuted,\n drawIndels = true,\n}: {\n ctx: CanvasRenderingContext2D\n feat: LayoutFeature\n renderArgs: RenderArgsWithColor\n colorForBase: Record<string, string>\n contrastForBase: Record<string, string>\n mismatchAlpha?: boolean\n drawIndels?: boolean\n drawSNPsMuted?: boolean\n minSubfeatureWidth: number\n largeInsertionIndicatorScale: number\n charWidth: number\n charHeight: number\n canvasWidth: number\n}) {\n const { bpPerPx, regions } = renderArgs\n const { heightPx, topPx, feature } = feat\n const region = regions[0]!\n const start = feature.get('start')\n\n const pxPerBp = Math.min(1 / bpPerPx, 2)\n const mismatches = feature.get('mismatches') as Mismatch[] | undefined\n const heightLim = charHeight - 2\n\n // extraHorizontallyFlippedOffset is used to draw interbase items, which\n // are located to the left when forward and right when reversed\n const extraHorizontallyFlippedOffset = region.reversed ? 1 / bpPerPx + 1 : -1\n\n if (!mismatches) {\n return\n }\n\n // two pass rendering: first pass, draw all the mismatches except wide\n // insertion markers\n for (const mismatch of mismatches) {\n const mstart = start + mismatch.start\n const mlen = mismatch.length\n const mbase = mismatch.base\n const [leftPx, rightPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx)\n const widthPx = Math.max(minSubfeatureWidth, Math.abs(leftPx - rightPx))\n if (mismatch.type === 'mismatch') {\n if (!drawSNPsMuted) {\n const baseColor = colorForBase[mismatch.base] || '#888'\n const c = mismatchAlpha\n ? mismatch.qual === undefined\n ? baseColor\n : colord(baseColor)\n .alpha(Math.min(1, mismatch.qual / 50))\n .toHslString()\n : baseColor\n\n fillRect(\n ctx,\n Math.round(leftPx),\n topPx,\n widthPx,\n heightPx,\n canvasWidth,\n c,\n )\n }\n\n if (widthPx >= charWidth && heightPx >= heightLim) {\n // normal SNP coloring\n const contrastColor = drawSNPsMuted\n ? 'black'\n : contrastForBase[mismatch.base] || 'black'\n ctx.fillStyle = mismatchAlpha\n ? mismatch.qual === undefined\n ? contrastColor\n : colord(contrastColor)\n .alpha(Math.min(1, mismatch.qual / 50))\n .toHslString()\n : contrastColor\n ctx.fillText(\n mbase,\n leftPx + (widthPx - charWidth) / 2 + 1,\n topPx + heightPx,\n )\n }\n } else if (mismatch.type === 'deletion' && drawIndels) {\n fillRect(\n ctx,\n leftPx,\n topPx,\n Math.abs(leftPx - rightPx),\n heightPx,\n canvasWidth,\n colorForBase.deletion,\n )\n const txt = `${mismatch.length}`\n const rwidth = measureText(txt, 10)\n if (widthPx >= rwidth && heightPx >= heightLim) {\n ctx.fillStyle = contrastForBase.deletion!\n ctx.fillText(txt, (leftPx + rightPx) / 2 - rwidth / 2, topPx + heightPx)\n }\n } else if (mismatch.type === 'insertion' && drawIndels) {\n ctx.fillStyle = 'purple'\n const pos = leftPx + extraHorizontallyFlippedOffset\n const len = +mismatch.base || mismatch.length\n const insW = Math.max(0, Math.min(1.2, 1 / bpPerPx))\n if (len < 10) {\n fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple')\n if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {\n const l = pos - insW\n fillRect(ctx, l, topPx, insW * 3, 1, canvasWidth)\n fillRect(ctx, l, topPx + heightPx - 1, insW * 3, 1, canvasWidth)\n ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx)\n }\n }\n } else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {\n const pos = leftPx + extraHorizontallyFlippedOffset\n const c = mismatch.type === 'hardclip' ? 'red' : 'blue'\n const clipW = Math.max(minSubfeatureWidth, pxPerBp)\n fillRect(ctx, pos, topPx, clipW, heightPx, canvasWidth, c)\n if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {\n const l = pos - clipW\n fillRect(ctx, l, topPx, clipW * 3, 1, canvasWidth)\n fillRect(ctx, l, topPx + heightPx - 1, clipW * 3, 1, canvasWidth)\n ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx)\n }\n } else if (mismatch.type === 'skip') {\n // fix to avoid bad rendering note that this was also related to chrome\n // bug https://bugs.chromium.org/p/chromium/issues/detail?id=1131528\n // also affected firefox ref #1236 #2750\n if (leftPx + widthPx > 0) {\n // make small exons more visible when zoomed far out\n const adjustPx = widthPx - (bpPerPx > 10 ? 1.5 : 0)\n ctx.clearRect(leftPx, topPx, adjustPx, heightPx)\n fillRect(\n ctx,\n Math.max(0, leftPx),\n topPx + heightPx / 2 - 1,\n adjustPx + (leftPx < 0 ? leftPx : 0),\n 2,\n canvasWidth,\n '#333',\n )\n }\n }\n }\n\n // second pass, draw wide insertion markers on top\n if (drawIndels) {\n for (const mismatch of mismatches) {\n const mstart = start + mismatch.start\n const mlen = mismatch.length\n const [leftPx] = bpSpanPx(mstart, mstart + mlen, region, bpPerPx)\n const len = +mismatch.base || mismatch.length\n const txt = `${len}`\n if (mismatch.type === 'insertion' && len >= 10) {\n if (bpPerPx > largeInsertionIndicatorScale) {\n fillRect(ctx, leftPx - 1, topPx, 2, heightPx, canvasWidth, 'purple')\n } else if (heightPx > charHeight) {\n const rwidth = measureText(txt)\n const padding = 5\n fillRect(\n ctx,\n leftPx - rwidth / 2 - padding,\n topPx,\n rwidth + 2 * padding,\n heightPx,\n canvasWidth,\n 'purple',\n )\n ctx.fillStyle = 'white'\n ctx.fillText(txt, leftPx - rwidth / 2, topPx + heightPx)\n } else {\n const padding = 2\n fillRect(\n ctx,\n leftPx - padding,\n topPx,\n 2 * padding,\n heightPx,\n canvasWidth,\n 'purple',\n )\n }\n }\n }\n }\n}\n","import {\n AnyConfigurationModel,\n readConfObject,\n} from '@jbrowse/core/configuration'\nimport { bpSpanPx } from '@jbrowse/core/util'\nimport { Theme } from '@mui/material'\n\n// locals\nimport { Mismatch, parseCigar } from '../MismatchParser'\nimport { RenderArgsDeserializedWithFeaturesAndLayout } from './PileupRenderer'\nimport { fillRect, getCharWidthHeight, LayoutFeature } from './util'\n\nexport function renderSoftClipping({\n ctx,\n feat,\n renderArgs,\n config,\n theme,\n colorForBase,\n canvasWidth,\n}: {\n ctx: CanvasRenderingContext2D\n feat: LayoutFeature\n renderArgs: RenderArgsDeserializedWithFeaturesAndLayout\n config: AnyConfigurationModel\n colorForBase: Record<string, string>\n theme: Theme\n canvasWidth: number\n}) {\n const { feature, topPx, heightPx } = feat\n const { regions, bpPerPx } = renderArgs\n const region = regions[0]!\n const minFeatWidth = readConfObject(config, 'minSubfeatureWidth')\n const mismatches = feature.get('mismatches') as Mismatch[] | undefined\n const seq = feature.get('seq') as string | undefined\n const { charWidth, charHeight } = getCharWidthHeight()\n\n // Display all bases softclipped off in lightened colors\n if (!(seq && mismatches)) {\n return\n }\n\n const heightLim = charHeight - 2\n const CIGAR = parseCigar(feature.get('CIGAR'))\n let seqOffset = 0\n let refOffset = 0\n for (let i = 0; i < CIGAR.length; i += 2) {\n const op = CIGAR[i + 1]!\n const len = +CIGAR[i]!\n if (op === 'S') {\n for (let k = 0; k < len; k++) {\n const base = seq[seqOffset + k]!\n const s0 = feature.get('start') - (i === 0 ? len : 0) + refOffset + k\n const [leftPx, rightPx] = bpSpanPx(s0, s0 + 1, region, bpPerPx)\n const widthPx = Math.max(minFeatWidth, rightPx - leftPx)\n\n // Black accounts for IUPAC ambiguity code bases such as N that\n // show in soft clipping\n const baseColor = colorForBase[base] || '#000000'\n ctx.fillStyle = baseColor\n fillRect(ctx, leftPx, topPx, widthPx, heightPx, canvasWidth)\n\n if (widthPx >= charWidth && heightPx >= heightLim) {\n ctx.fillStyle = theme.palette.getContrastText(baseColor)\n ctx.fillText(\n base,\n leftPx + (widthPx - charWidth) / 2 + 1,\n topPx + heightPx,\n )\n }\n }\n seqOffset += len\n }\n if (op === 'N') {\n refOffset += len\n }\n if (op === 'M' || op === '=' || op === 'X') {\n refOffset += len\n seqOffset += len\n }\n if (op === 'H') {\n // do nothing\n }\n if (op === 'D') {\n refOffset += len\n }\n if (op === 'I') {\n seqOffset += len\n }\n }\n}\n","import { Feature } from '@jbrowse/core/util'\nimport { RenderArgsDeserializedWithFeaturesAndLayout } from './PileupRenderer'\nimport { readConfObject } from '@jbrowse/core/configuration'\nimport { createJBrowseTheme } from '@jbrowse/core/ui'\nimport {\n getCharWidthHeight,\n getColorBaseMap,\n getContrastBaseMap,\n shouldDrawIndels,\n shouldDrawSNPsMuted,\n} from './util'\nimport { renderAlignment } from './renderAlignment'\nimport { renderMismatches } from './renderMismatches'\nimport { renderSoftClipping } from './renderSoftClipping'\n\nexport type RenderArgsWithColor = RenderArgsDeserializedWithFeaturesAndLayout\n\ninterface LayoutFeature {\n heightPx: number\n topPx: number\n feature: Feature\n}\n\nexport function makeImageData({\n ctx,\n layoutRecords,\n canvasWidth,\n renderArgs,\n}: {\n ctx: CanvasRenderingContext2D\n canvasWidth: number\n layoutRecords: LayoutFeature[]\n renderArgs: RenderArgsWithColor\n}) {\n const { config, showSoftClip, colorBy, theme: configTheme } = renderArgs\n const mismatchAlpha = readConfObject(config, 'mismatchAlpha')\n const minSubfeatureWidth = readConfObject(config, 'minSubfeatureWidth')\n const largeInsertionIndicatorScale = readConfObject(\n config,\n 'largeInsertionIndicatorScale',\n )\n const defaultColor = readConfObject(config, 'color') === '#f0f'\n const theme = createJBrowseTheme(configTheme)\n const colorForBase = getColorBaseMap(theme)\n const contrastForBase = getContrastBaseMap(theme)\n ctx.font = 'bold 10px Courier New,monospace'\n\n const { charWidth, charHeight } = getCharWidthHeight()\n const drawSNPsMuted = shouldDrawSNPsMuted(colorBy?.type)\n const drawIndels = shouldDrawIndels()\n for (const feat of layoutRecords) {\n renderAlignment({\n ctx,\n feat,\n renderArgs,\n defaultColor,\n colorForBase,\n contrastForBase,\n charWidth,\n charHeight,\n canvasWidth,\n })\n renderMismatches({\n ctx,\n feat,\n renderArgs,\n mismatchAlpha,\n drawSNPsMuted,\n drawIndels,\n largeInsertionIndicatorScale,\n minSubfeatureWidth,\n charWidth,\n charHeight,\n colorForBase,\n contrastForBase,\n canvasWidth,\n })\n if (showSoftClip) {\n renderSoftClipping({\n ctx,\n feat,\n renderArgs,\n colorForBase,\n config,\n theme,\n canvasWidth,\n })\n }\n }\n return 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