@jbrowse/plugin-alignments 2.3.1 → 2.3.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/LinearReadArcsDisplay/configSchema.js +8 -0
- package/dist/LinearReadArcsDisplay/configSchema.js.map +1 -1
- package/dist/LinearReadArcsDisplay/drawFeats.d.ts +1 -0
- package/dist/LinearReadArcsDisplay/drawFeats.js +45 -37
- package/dist/LinearReadArcsDisplay/drawFeats.js.map +1 -1
- package/dist/LinearReadArcsDisplay/model.d.ts +46 -15
- package/dist/LinearReadArcsDisplay/model.js +42 -0
- package/dist/LinearReadArcsDisplay/model.js.map +1 -1
- package/dist/LinearReadCloudDisplay/drawFeats.js +18 -32
- package/dist/LinearReadCloudDisplay/drawFeats.js.map +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js +1 -1
- package/dist/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/esm/LinearReadArcsDisplay/configSchema.js +8 -0
- package/esm/LinearReadArcsDisplay/configSchema.js.map +1 -1
- package/esm/LinearReadArcsDisplay/drawFeats.d.ts +1 -0
- package/esm/LinearReadArcsDisplay/drawFeats.js +45 -37
- package/esm/LinearReadArcsDisplay/drawFeats.js.map +1 -1
- package/esm/LinearReadArcsDisplay/model.d.ts +46 -15
- package/esm/LinearReadArcsDisplay/model.js +42 -0
- package/esm/LinearReadArcsDisplay/model.js.map +1 -1
- package/esm/LinearReadCloudDisplay/drawFeats.js +19 -33
- package/esm/LinearReadCloudDisplay/drawFeats.js.map +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.d.ts +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js +1 -1
- package/esm/LinearSNPCoverageDisplay/components/Tooltip.js.map +1 -1
- package/package.json +2 -2
- package/src/LinearReadArcsDisplay/configSchema.ts +10 -0
- package/src/LinearReadArcsDisplay/drawFeats.ts +73 -54
- package/src/LinearReadArcsDisplay/model.tsx +45 -0
- package/src/LinearReadCloudDisplay/drawFeats.ts +21 -33
- package/src/LinearSNPCoverageDisplay/components/Tooltip.tsx +76 -73
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@@ -24,6 +24,14 @@ function configSchemaF(pluginManager) {
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description: 'set arc line width',
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defaultValue: 1,
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},
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+
/**
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* #slot
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*/
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jitter: {
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type: 'number',
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description: 'jitters the x position so e.g. if many reads map to exact same x position, jittering makes it easy to see that there are many of them',
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defaultValue: 0,
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},
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/**
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* #slot
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*/
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/configSchema.ts"],"names":[],"mappings":";;AACA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAuC;AAEvC;;GAEG;AACH,SAAS,aAAa,CAAC,aAA4B;IACjD,OAAO,IAAA,mCAAmB,EACxB,uBAAuB,EACvB;QACE;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,oBAAoB;YACjC,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,kBAAe,aAAa,CAAA"}
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{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/configSchema.ts"],"names":[],"mappings":";;AACA,+DAAiE;AACjE,kFAA0F;AAC1F,qDAAuC;AAEvC;;GAEG;AACH,SAAS,aAAa,CAAC,aAA4B;IACjD,OAAO,IAAA,mCAAmB,EACxB,uBAAuB,EACvB;QACE;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,oBAAoB;YACjC,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,MAAM,EAAE;YACN,IAAI,EAAE,QAAQ;YACd,WAAW,EACT,uIAAuI;YACzI,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,uBAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,IAAA,iEAAqC,EAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,kBAAe,aAAa,CAAA"}
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@@ -14,35 +14,50 @@ function hasPairedReads(features) {
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return false;
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}
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exports.hasPairedReads = hasPairedReads;
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function jitter(n) {
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return Math.random() * 2 * n - n;
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}
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async function drawFeats(self, ctx) {
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-
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const { chainData } = self;
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const { chainData, height, colorBy, drawInter, drawLongRange, lineWidthSetting, jitterVal, } = self;
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if (!chainData) {
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return;
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}
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const displayHeight = self.height;
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const view = (0, util_1.getContainingView)(self);
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const { assemblyManager } = (0, util_1.getSession)(self);
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self.setLastDrawnOffsetPx(view.offsetPx);
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ctx.lineWidth =
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ctx.lineWidth = lineWidthSetting;
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const { chains, stats } = chainData;
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const hasPaired = hasPairedReads(chainData);
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const assemblyName = view.assemblyNames[0];
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const asm = assemblyManager.get(assemblyName);
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const type = (
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-
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const type = (colorBy === null || colorBy === void 0 ? void 0 : colorBy.type) || 'insertSizeAndOrientation';
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if (!asm) {
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return;
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}
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function drawLineAtOffset(p, c) {
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// draws a vertical line off to middle of nowhere if the second end not found
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ctx.strokeStyle = c;
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ctx.beginPath();
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ctx.moveTo(p, 0);
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ctx.lineTo(p, height);
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ctx.stroke();
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}
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function draw(k1, k2, assembly, longRange) {
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const s1 = k1.strand;
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const s2 = k2.strand;
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const f1 = s1 === -1;
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const f2 = s2 === -1;
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const p1 = f1 ? k1.start : k1.end;
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const p2 = hasPaired ? (f2 ? k2.start : k2.end) : f2 ? k2.end : k2.start;
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const
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const
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const ra1 = assembly.getCanonicalRefName(k1.refName);
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const ra2 = assembly.getCanonicalRefName(k2.refName);
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const r1 = view.bpToPx({ refName: ra1, coord: p1 });
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const r2 = view.bpToPx({ refName: ra2, coord: p2 });
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if (r1 && r2) {
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const radius = (r2.offsetPx - r1.offsetPx) / 2;
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const absrad = Math.abs(radius);
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const p = r1.offsetPx - view.offsetPx;
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const p2 = r2.offsetPx - view.offsetPx;
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// bezier (used for non-long-range arcs) requires moveTo before beginPath
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// arc (used for long-range) requires moveTo after beginPath (or else a
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// unwanted line at y=0 is rendered along with the arc)
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@@ -69,7 +84,7 @@ async function drawFeats(self, ctx) {
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ctx.strokeStyle = (0, color_1.getInsertSizeColor)(k1, k2, stats) || 'grey';
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}
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else if (type === 'gradient') {
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ctx.strokeStyle = `hsl(${Math.log10(
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ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`;
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}
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}
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else {
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}
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}
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else if (type === 'gradient') {
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ctx.strokeStyle = `hsl(${Math.log10(
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ctx.strokeStyle = `hsl(${Math.log10(absrad) * 10},50%,50%)`;
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}
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}
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}
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const destX = p + radius * 2;
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const destY = Math.min(
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const destY = Math.min(height + jitter(jitterVal), absrad);
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if (longRange) {
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// avoid drawing gigantic circles that glitch out the rendering,
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// instead draw vertical lines
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if (absrad > 100000) {
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drawLineAtOffset(p + jitter(jitterVal), 'red');
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drawLineAtOffset(p2 + jitter(jitterVal), 'red');
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}
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else {
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ctx.arc(p + radius + jitter(jitterVal), 0, absrad, 0, Math.PI);
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ctx.stroke();
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}
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}
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else {
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ctx.bezierCurveTo(p, destY, destX, destY, destX, 0);
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ctx.bezierCurveTo(p + jitter(jitterVal), destY, destX, destY, destX + jitter(jitterVal), 0);
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ctx.stroke();
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}
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ctx.stroke();
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}
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else if (r1 &&
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const p = r1.offsetPx - view.offsetPx;
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ctx.strokeStyle = 'purple';
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ctx.beginPath();
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ctx.moveTo(p, 0);
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ctx.lineTo(p, displayHeight);
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ctx.stroke();
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else if (r1 && drawInter) {
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drawLineAtOffset(r1.offsetPx - view.offsetPx, 'purple');
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}
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}
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for (let i = 0; i < chains.length; i++) {
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let chain = chains[i];
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if (chain.length === 1 &&
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if (chain.length === 1 && drawLongRange) {
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// singleton feature
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const f = chain[0];
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// special case where we look at RPOS/RNEXT
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if (hasPaired) {
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// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
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const refName =
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const refName = f.next_ref;
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// eslint-disable-next-line @typescript-eslint/no-non-null-assertion
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const coord = f.next_pos;
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draw(f, {
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refName,
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start: coord,
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end: coord,
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strand: f.strand,
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}, true);
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draw(f, { refName, start: coord, end: coord, strand: f.strand }, asm, true);
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}
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// special case where we look at SA
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else {
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@@ -134,12 +147,7 @@ async function drawFeats(self, ctx) {
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for (let i = 0; i < features.length - 1; i++) {
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const f = features[i];
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const v1 = features[i + 1];
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draw(f,
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refName: (asm === null || asm === void 0 ? void 0 : asm.getCanonicalRefName(v1.refName)) || v1.refName,
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start: v1.start,
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end: v1.end,
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strand: v1.strand,
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}, true);
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draw(f, v1, asm, true);
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}
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}
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}
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chain = chain.filter(f => !(f.flags & 2048));
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}
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for (let i = 0; i < chain.length - 1; i++) {
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draw(chain[i], chain[i + 1], false);
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draw(chain[i], chain[i + 1], asm, false);
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}
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}
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}
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{"version":3,"file":"drawFeats.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/drawFeats.ts"],"names":[],"mappings":";;;AAAA,6CAAkE;AAGlE,SAAS;AACT,2CAIwB;AAExB,sDAA+C;
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icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
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-
muiName: string;
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+
muiName: string; /**
|
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+
* #action
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345
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+
* used during tests to detect when we can complete a snapshot test
|
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|
+
*/
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316
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|
};
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|
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348
|
subMenu: {
|
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318
349
|
label: string;
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@@ -64,6 +64,10 @@ function stateModelFactory(configSchema) {
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64
64
|
* #property
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65
65
|
*/
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|
66
66
|
lineWidth: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
|
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67
|
+
/**
|
|
68
|
+
* #property
|
|
69
|
+
*/
|
|
70
|
+
jitter: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.number),
|
|
67
71
|
/**
|
|
68
72
|
* #property
|
|
69
73
|
*/
|
|
@@ -160,6 +164,14 @@ function stateModelFactory(configSchema) {
|
|
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160
164
|
setLineWidth(n) {
|
|
161
165
|
self.lineWidth = n;
|
|
162
166
|
},
|
|
167
|
+
/**
|
|
168
|
+
* #action
|
|
169
|
+
* jitter val, helpful to jitter the x direction so you see better evidence when e.g. 100
|
|
170
|
+
* long reads map to same x position
|
|
171
|
+
*/
|
|
172
|
+
setJitter(n) {
|
|
173
|
+
self.jitter = n;
|
|
174
|
+
},
|
|
163
175
|
}))
|
|
164
176
|
.views(self => {
|
|
165
177
|
const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
|
|
@@ -171,6 +183,13 @@ function stateModelFactory(configSchema) {
|
|
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171
183
|
var _a;
|
|
172
184
|
return (_a = self.lineWidth) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'lineWidth');
|
|
173
185
|
},
|
|
186
|
+
/**
|
|
187
|
+
* #getter
|
|
188
|
+
*/
|
|
189
|
+
get jitterVal() {
|
|
190
|
+
var _a;
|
|
191
|
+
return (_a = self.jitter) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'jitter');
|
|
192
|
+
},
|
|
174
193
|
/**
|
|
175
194
|
* #getter
|
|
176
195
|
*/
|
|
@@ -225,6 +244,29 @@ function stateModelFactory(configSchema) {
|
|
|
225
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|
},
|
|
226
245
|
],
|
|
227
246
|
},
|
|
247
|
+
{
|
|
248
|
+
label: 'Jitter x-positions',
|
|
249
|
+
subMenu: [
|
|
250
|
+
{
|
|
251
|
+
type: 'checkbox',
|
|
252
|
+
checked: this.jitterVal === 0,
|
|
253
|
+
label: 'None',
|
|
254
|
+
onClick: () => self.setJitter(0),
|
|
255
|
+
},
|
|
256
|
+
{
|
|
257
|
+
type: 'checkbox',
|
|
258
|
+
checked: this.jitterVal === 2,
|
|
259
|
+
label: 'Small',
|
|
260
|
+
onClick: () => self.setJitter(2),
|
|
261
|
+
},
|
|
262
|
+
{
|
|
263
|
+
type: 'checkbox',
|
|
264
|
+
checked: this.jitterVal === 10,
|
|
265
|
+
label: 'Large',
|
|
266
|
+
onClick: () => self.setJitter(10),
|
|
267
|
+
},
|
|
268
|
+
],
|
|
269
|
+
},
|
|
228
270
|
{
|
|
229
271
|
label: 'Draw inter-region vertical lines',
|
|
230
272
|
type: 'checkbox',
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/model.tsx"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,+CAAmC;AACnC,+BAA8B;AAC9B,qDAAoE;AACpE,+DAKoC;AACpC,6CAAkE;AAElE,kFAG2C;AAE3C,QAAQ;AACR,0EAAqD;AACrD,4EAAyD;AAEzD,SAAS;AACT,sCAAuC;AACvC,4DAAmC;AACnC,uDAA8D;AAG9D,QAAQ;AACR,MAAM,cAAc,GAAG,IAAA,YAAI,EAAC,GAAG,EAAE,mDAAQ,uBAAuB,GAAC,CAAC,CAAA;AAWlE;;;GAGG;AACH,SAAS,iBAAiB,CAAC,YAAwC;IACjE,OAAO,uBAAK;SACT,OAAO,CACN,uBAAuB,EACvB,6CAAiB,EACjB,uBAAK,CAAC,KAAK,CAAC;QACV;;WAEG;QACH,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,uBAAuB,CAAC;QAC5C;;WAEG;QACH,aAAa,EAAE,IAAA,sCAAsB,EAAC,YAAY,CAAC;QAEnD;;WAEG;QACH,QAAQ,EAAE,uBAAK,CAAC,QAAQ,CAAC,oBAAW,EAAE,EAAE,CAAC;QAEzC;;WAEG;QACH,SAAS,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QAEpC;;WAEG;QACH,MAAM,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;QAEjC;;WAEG;QACH,OAAO,EAAE,uBAAK,CAAC,KAAK,CAClB,uBAAK,CAAC,KAAK,CAAC;YACV,IAAI,EAAE,uBAAK,CAAC,MAAM;YAClB,GAAG,EAAE,uBAAK,CAAC,KAAK,CAAC,uBAAK,CAAC,MAAM,CAAC;YAC9B,KAAK,EAAE,uBAAK,CAAC,MAAM,EAAE;SACtB,CAAC,CACH;QAED;;WAEG;QACH,SAAS,EAAE,IAAI;QAEf;;WAEG;QACH,aAAa,EAAE,IAAI;KACpB,CAAC,CACH;SACA,QAAQ,CAAC,GAAG,EAAE,CAAC,CAAC;QACf,OAAO,EAAE,KAAK;QACd,KAAK,EAAE,KAAK;QACZ,SAAS,EAAE,SAAkC;QAC7C,GAAG,EAAE,IAAgC;QACrC,iBAAiB,EAAE,CAAC;KACrB,CAAC,CAAC;SACF,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAChB;;;WAGG;QACH,MAAM;YACJ,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;QACxB,CAAC;QACD;;;WAGG;QACH,MAAM,CAAC,GAA6B;YAClC,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QAChB,CAAC;QAED;;WAEG;QACH,cAAc,CAAC,CAAmB;YAChC,IAAI,CAAC,OAAO,GAAG,IAAA,sBAAI,EAAC,CAAC,CAAC,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,YAAY,CAAC,IAAe;YAC1B,IAAI,CAAC,SAAS,GAAG,IAAI,CAAA;QACvB,CAAC;QAED;;WAEG;QACH,YAAY,CAAC,CAAU;YACrB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;QACpB,CAAC;QAED;;WAEG;QACH,gBAAgB,CAAC,CAAU;YACzB,IAAI,CAAC,aAAa,GAAG,CAAC,CAAA;QACxB,CAAC;QAED;;WAEG;QACH,UAAU,CAAC,CAAU;YACnB,IAAI,CAAC,OAAO,GAAG,CAAC,CAAA;QAClB,CAAC;QAED;;;WAGG;QACH,QAAQ,CAAC,CAAU;YACjB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QAChB,CAAC;QAED;;WAEG;QACH,WAAW,CAAC,MAAc;YACxB,IAAI,CAAC,QAAQ,GAAG,IAAA,sBAAI,EAAC,MAAM,CAAC,CAAA;QAC9B,CAAC;QAED;;;WAGG;QACH,oBAAoB,CAAC,CAAS;YAC5B,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAA;QAC5B,CAAC;QAED;;;WAGG;QACH,YAAY,CAAC,CAAS;YACpB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;QACpB,CAAC;QAED;;;;WAIG;QACH,SAAS,CAAC,CAAS;YACjB,IAAI,CAAC,MAAM,GAAG,CAAC,CAAA;QACjB,CAAC;KACF,CAAC,CAAC;SAEF,KAAK,CAAC,IAAI,CAAC,EAAE;QACZ,MAAM,EACJ,cAAc,EAAE,mBAAmB,EACnC,WAAW,EAAE,gBAAgB,GAC9B,GAAG,IAAI,CAAA;QAER,OAAO;YACL;;eAEG;YACH,IAAI,gBAAgB;;gBAClB,OAAO,MAAA,IAAI,CAAC,SAAS,mCAAI,IAAA,uBAAO,EAAC,IAAI,EAAE,WAAW,CAAC,CAAA;YACrD,CAAC;YAED;;eAEG;YACH,IAAI,SAAS;;gBACX,OAAO,MAAA,IAAI,CAAC,MAAM,mCAAI,IAAA,uBAAO,EAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;YAC/C,CAAC;YACD;;eAEG;YACH,IAAI,KAAK;gBACP,OAAO,CAAC,CAAC,IAAI,CAAC,SAAS,CAAA;YACzB,CAAC;YACD,mEAAmE;YACnE,0CAA0C;YAC1C,IAAI,gBAAgB;gBAClB,OAAO,gBAAgB,CAAA;YACzB,CAAC;YACD,gEAAgE;YAChE,0BAA0B;YAC1B,WAAW;gBACT,OAAO;oBACL,GAAG,gBAAgB,EAAE;oBACrB,uDAAuD;oBACvD,QAAQ,EAAE,IAAI;oBACd,MAAM,EAAE,IAAA,mCAAmB,EAAC,OAAO,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE;iBAClD,CAAA;YACH,CAAC;YAED;;eAEG;YACH,cAAc;gBACZ,OAAO;oBACL,GAAG,mBAAmB,EAAE;oBACxB;wBACE,KAAK,EAAE,WAAW;wBAClB,IAAI,EAAE,kBAAc;wBACpB,OAAO,EAAE,GAAG,EAAE;4BACZ,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAC,WAAW,CAAC,WAAW,CAAC,EAAE,CAAC;gCAC1C,cAAc;gCACd,EAAE,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE;6BAC7B,CAAC,CAAA;wBACJ,CAAC;qBACF;oBACD;wBACE,KAAK,EAAE,YAAY;wBACnB,OAAO,EAAE;4BACP;gCACE,KAAK,EAAE,MAAM;gCACb,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC;6BACpC;4BACD;gCACE,KAAK,EAAE,MAAM;gCACb,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC;6BACpC;4BACD;gCACE,KAAK,EAAE,YAAY;gCACnB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC;6BACpC;yBACF;qBACF;oBACD;wBACE,KAAK,EAAE,oBAAoB;wBAC3B,OAAO,EAAE;4BACP;gCACE,IAAI,EAAE,UAAU;gCAChB,OAAO,EAAE,IAAI,CAAC,SAAS,KAAK,CAAC;gCAC7B,KAAK,EAAE,MAAM;gCACb,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC;6BACjC;4BACD;gCACE,IAAI,EAAE,UAAU;gCAChB,OAAO,EAAE,IAAI,CAAC,SAAS,KAAK,CAAC;gCAC7B,KAAK,EAAE,OAAO;gCACd,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC;6BACjC;4BACD;gCACE,IAAI,EAAE,UAAU;gCAChB,OAAO,EAAE,IAAI,CAAC,SAAS,KAAK,EAAE;gCAC9B,KAAK,EAAE,OAAO;gCACd,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;6BAClC;yBACF;qBACF;oBAED;wBACE,KAAK,EAAE,kCAAkC;wBACzC,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,SAAS;wBACvB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC;qBAClD;oBACD;wBACE,KAAK,EAAE,6BAA6B;wBACpC,IAAI,EAAE,UAAU;wBAChB,OAAO,EAAE,IAAI,CAAC,aAAa;wBAC3B,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC;qBAC1D;oBACD;wBACE,KAAK,EAAE,cAAc;wBACrB,IAAI,EAAE,iBAAW;wBACjB,OAAO,EAAE;4BACP;gCACE,KAAK,EAAE,kCAAkC;gCACzC,OAAO,EAAE,GAAG,EAAE,CACZ,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,0BAA0B,EAAE,CAAC;6BAC5D;4BACD;gCACE,KAAK,EAAE,kBAAkB;gCACzB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC;6BAC3D;4BACD;gCACE,KAAK,EAAE,aAAa;gCACpB,OAAO,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,cAAc,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC;6BAC5D;4BACD;gCACE,KAAK,EAAE,sBAAsB;gCAC7B,OAAO,EAAE,GAAG,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@@ -25,9 +25,15 @@ async function drawFeats(self, ctx) {
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if (!chainData) {
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return;
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const { assemblyManager } = (0, util_1.getSession)(self);
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|
const featureHeight = (0, configuration_1.getConf)(self, 'featureHeight');
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const displayHeight = self.height;
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const view = (0, util_1.getContainingView)(self);
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const assemblyName = view.assemblyNames[0];
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const asm = assemblyManager.get(assemblyName);
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if (!asm) {
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return;
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}
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self.setLastDrawnOffsetPx(view.offsetPx);
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const { chains, stats } = chainData;
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const coords = [];
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@@ -39,22 +45,12 @@ async function drawFeats(self, ctx) {
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if (chain[0].flags & 1 && chain.length > 1) {
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const v0 = chain[0];
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const v1 = chain[1];
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const
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});
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const
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coord: v0.end,
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});
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const r2s = view.bpToPx({
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refName: v1.refName,
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coord: v1.start,
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});
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const r2e = view.bpToPx({
|
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refName: v1.refName,
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coord: v1.end,
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});
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48
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+
const ra1 = asm.getCanonicalRefName(v0.refName);
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+
const ra2 = asm.getCanonicalRefName(v1.refName);
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const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
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const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
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+
const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
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const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
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|
let distance = 0;
|
|
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55
|
if (r1s !== undefined &&
|
|
60
56
|
r1e !== undefined &&
|
|
@@ -82,22 +78,12 @@ async function drawFeats(self, ctx) {
|
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|
82
78
|
for (let i = 1; i < chain.length; i++) {
|
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83
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|
const v0 = chain[i - 1];
|
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84
80
|
const v1 = chain[i];
|
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85
|
-
const
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|
86
|
-
|
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87
|
-
|
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|
-
});
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|
-
const
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|
|
91
|
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coord: v0.end,
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});
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|
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const r2s = view.bpToPx({
|
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refName: v1.refName,
|
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95
|
-
coord: v1.start,
|
|
96
|
-
});
|
|
97
|
-
const r2e = view.bpToPx({
|
|
98
|
-
refName: v1.refName,
|
|
99
|
-
coord: v1.end,
|
|
100
|
-
});
|
|
81
|
+
const ra1 = asm.getCanonicalRefName(v0.refName);
|
|
82
|
+
const ra2 = asm.getCanonicalRefName(v1.refName);
|
|
83
|
+
const r1s = view.bpToPx({ refName: ra1, coord: v0.start });
|
|
84
|
+
const r1e = view.bpToPx({ refName: ra1, coord: v0.end });
|
|
85
|
+
const r2s = view.bpToPx({ refName: ra2, coord: v1.start });
|
|
86
|
+
const r2e = view.bpToPx({ refName: ra2, coord: v1.end });
|
|
101
87
|
let distance = 0;
|
|
102
88
|
if (r1s !== undefined &&
|
|
103
89
|
r1e !== undefined &&
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"drawFeats.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/drawFeats.ts"],"names":[],"mappings":";;AAAA,+DAAqD;AACrD,
|
|
1
|
+
{"version":3,"file":"drawFeats.js","sourceRoot":"","sources":["../../src/LinearReadCloudDisplay/drawFeats.ts"],"names":[],"mappings":";;AAAA,+DAAqD;AACrD,6CAAkE;AAGlE,SAAS;AACT,2CAIwB;AAexB,wDAAwD;AACxD,SAAS,WAAW,CAClB,CAAS,EACT,CAAS,EACT,KAAa,EACb,MAAc,EACd,GAA6B,EAC7B,KAAc;IAEd,IAAI,KAAK,GAAG,CAAC,EAAE;QACb,CAAC,IAAI,KAAK,CAAA;QACV,KAAK,GAAG,CAAC,KAAK,CAAA;KACf;IACD,IAAI,MAAM,GAAG,CAAC,EAAE;QACd,CAAC,IAAI,MAAM,CAAA;QACX,MAAM,GAAG,CAAC,MAAM,CAAA;KACjB;IAED,IAAI,KAAK,EAAE;QACT,GAAG,CAAC,SAAS,GAAG,KAAK,CAAA;KACtB;IACD,GAAG,CAAC,QAAQ,CAAC,CAAC,EAAE,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,CAAA;AACnC,CAAC;AAEc,KAAK,UAAU,SAAS,CACrC,IAMC,EACD,GAA6B;;IAE7B,MAAM,EAAE,SAAS,EAAE,GAAG,IAAI,CAAA;IAC1B,IAAI,CAAC,SAAS,EAAE;QACd,OAAM;KACP;IACD,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;IAC5C,MAAM,aAAa,GAAG,IAAA,uBAAO,EAAC,IAAI,EAAE,eAAe,CAAC,CAAA;IACpD,MAAM,aAAa,GAAG,IAAI,CAAC,MAAM,CAAA;IACjC,MAAM,IAAI,GAAG,IAAA,wBAAiB,EAAC,IAAI,CAAQ,CAAA;IAC3C,MAAM,YAAY,GAAG,IAAI,CAAC,aAAa,CAAC,CAAC,CAAC,CAAA;IAC1C,MAAM,GAAG,GAAG,eAAe,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;IAC7C,IAAI,CAAC,GAAG,EAAE;QACR,OAAM;KACP;IAED,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;IAExC,MAAM,EAAE,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAA;IACnC,MAAM,MAAM,GAAiB,EAAE,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACtC,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QACvB,wEAAwE;QACxE,qEAAqE;QACrE,uCAAuC;QACvC,IAAI,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE;YAC1C,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;YACnB,MAAM,GAAG,GAAG,GAAG,CAAC,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;YAC/C,MAAM,GAAG,GAAG,GAAG,CAAC,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;YAC/C,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAA;YAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;YACxD,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAA;YAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;YAExD,IAAI,QAAQ,GAAG,CAAC,CAAA;YAEhB,IACE,GAAG,KAAK,SAAS;gBACjB,GAAG,KAAK,SAAS;gBACjB,GAAG,KAAK,SAAS;gBACjB,GAAG,KAAK,SAAS,EACjB;gBACA,IAAI,EAAE,CAAC,OAAO,KAAK,EAAE,CAAC,OAAO,EAAE;oBAC7B,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,CAAA;oBACtC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,CAAA;oBAClC,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;iBAC3B;gBACD,MAAM,CAAC,IAAI,CAAC;oBACV,GAAG,EAAE,GAAG,CAAC,QAAQ;oBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;oBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;oBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;oBACjB,EAAE;oBACF,EAAE;oBACF,QAAQ;iBACT,CAAC,CAAA;aACH;SACF;aAAM;YACL,wEAAwE;YACxE,0BAA0B;YAC1B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;gBACrC,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;gBACvB,MAAM,EAAE,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBACnB,MAAM,GAAG,GAAG,GAAG,CAAC,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;gBAC/C,MAAM,GAAG,GAAG,GAAG,CAAC,mBAAmB,CAAC,EAAE,CAAC,OAAO,CAAC,CAAA;gBAC/C,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAA;gBAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;gBACxD,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,KAAK,EAAE,CAAC,CAAA;gBAC1D,MAAM,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,EAAE,OAAO,EAAE,GAAG,EAAE,KAAK,EAAE,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;gBAExD,IAAI,QAAQ,GAAG,CAAC,CAAA;gBAEhB,IACE,GAAG,KAAK,SAAS;oBACjB,GAAG,KAAK,SAAS;oBACjB,GAAG,KAAK,SAAS;oBACjB,GAAG,KAAK,SAAS,EACjB;oBACA,IAAI,EAAE,CAAC,OAAO,KAAK,EAAE,CAAC,OAAO,EAAE;wBAC7B,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,CAAA;wBAClC,QAAQ,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;qBAC3B;oBACD,MAAM,CAAC,IAAI,CAAC;wBACV,GAAG,EAAE,GAAG,CAAC,QAAQ;wBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;wBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;wBACjB,GAAG,EAAE,GAAG,CAAC,QAAQ;wBACjB,EAAE;wBACF,EAAE;wBACF,QAAQ;qBACT,CAAC,CAAA;iBACH;aACF;SACF;KACF;IAED,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACtC,MAAM,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAC9B,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,QAAQ,CAAC,CAAA;KAC9B;IACD,MAAM,UAAU,GAAG,aAAa,GAAG,CAAC,GAAG,GAAG,CAAA;IAC1C,MAAM,MAAM,GAAG,CAAC,aAAa,GAAG,EAAE,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;IAEnD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE;QACtC,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,EAAE,EAAE,EAAE,QAAQ,EAAE,GAAG,MAAM,CAAC,CAAC,CAAC,CAAA;QAC1D,MAAM,IAAI,GAAG,CAAA,MAAA,IAAI,CAAC,OAAO,0CAAE,IAAI,KAAI,0BAA0B,CAAA;QAE7D,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,GAAG,MAAM,CAAA;QACvC,GAAG,CAAC,SAAS,GAAG,OAAO,CAAA;QACvB,MAAM,CAAC,GAAG,GAAG,GAAG,GAAG,CAAA;QACnB,WAAW,CAAC,GAAG,GAAG,IAAI,CAAC,QAAQ,EAAE,GAAG,GAAG,UAAU,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;QAE7D,IAAI,IAAI,KAAK,0BAA0B,EAAE;YACvC,GAAG,CAAC,SAAS,GAAG,IAAA,wCAAgC,EAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,CAAA;SAChE;aAAM,IAAI,IAAI,KAAK,aAAa,EAAE;YACjC,GAAG,CAAC,SAAS,GAAG,IAAA,2BAAmB,EAAC,EAAE,CAAC,CAAA;SACxC;aAAM,IAAI,IAAI,KAAK,YAAY,EAAE;YAChC,GAAG,CAAC,SAAS,GAAG,IAAA,0BAAkB,EAAC,EAAE,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,MAAM,CAAA;SAC5D;aAAM,IAAI,IAAI,KAAK,UAAU,EAAE;YAC9B,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,CAAA;YACtC,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,EAAE,CAAC,GAAG,CAAC,CAAA;YAClC,GAAG,CAAC,SAAS,GAAG,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,WAAW,CAAA;SACnE;QAED,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;QACjC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,GAAG,EAAE,CAAC,CAAC,CAAA;QACjC,WAAW,CAAC,GAAG,GAAG,IAAI,CAAC,QAAQ,EAAE,GAAG,EAAE,EAAE,EAAE,aAAa,EAAE,GAAG,CAAC,CAAA;QAC7D,WAAW,CAAC,GAAG,GAAG,IAAI,CAAC,QAAQ,EAAE,GAAG,EAAE,EAAE,EAAE,aAAa,EAAE,GAAG,CAAC,CAAA;KAC9D;AACH,CAAC;AA5ID,4BA4IC"}
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@@ -9,7 +9,7 @@ const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
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9
9
|
const en = (n) => n.toLocaleString('en-US');
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const toP = (s = 0) => +(+s).toFixed(1);
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11
|
const pct = (n, total) => `${toP((n / (total || 1)) * 100)}%`;
|
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12
|
-
const TooltipContents = react_1.default.forwardRef(({ feature }, reactRef)
|
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12
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+
const TooltipContents = react_1.default.forwardRef(function ({ feature }, reactRef) {
|
|
13
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|
const start = feature.get('start');
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14
14
|
const end = feature.get('end');
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15
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|
const name = feature.get('refName');
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@@ -1 +1 @@
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|
|
1
|
-
{"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/components/Tooltip.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAErC,0DAAgD;AAyBhD,MAAM,EAAE,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AACnD,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;AACvC,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,KAAa,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAA;
|
|
1
|
+
{"version":3,"file":"Tooltip.js","sourceRoot":"","sources":["../../../src/LinearSNPCoverageDisplay/components/Tooltip.tsx"],"names":[],"mappings":";;;;;AAAA,kDAAyB;AACzB,2CAAqC;AAErC,0DAAgD;AAyBhD,MAAM,EAAE,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,CAAC,cAAc,CAAC,OAAO,CAAC,CAAA;AACnD,MAAM,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAA;AACvC,MAAM,GAAG,GAAG,CAAC,CAAS,EAAE,KAAa,EAAE,EAAE,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,GAAG,CAAA;AAI7E,MAAM,eAAe,GAAG,eAAK,CAAC,UAAU,CAAwB,UAC9D,EAAE,OAAO,EAAE,EACX,QAAQ;IAER,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;IAClC,MAAM,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;IAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAC,CAAA;IACnC,MAAM,EACJ,OAAO,EACP,GAAG,EACH,KAAK,EACL,GAAG,EACH,IAAI,EAAE,GAAG,EACT,GAAG,EAAE,EAAE,EACP,GAAG,EAAE,EAAE,EACP,GAAG,IAAI,EACR,GAAG,OAAO,CAAC,GAAG,CAAC,SAAS,CAAY,CAAA;IACrC,MAAM,GAAG,GAAG,CAAC,IAAI,EAAE,KAAK,KAAK,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,KAAK,CAAC,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC;SACvE,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC;SAChB,IAAI,CAAC,GAAG,CAAC,CAAA;IAEZ,OAAO,CACL,uCAAK,GAAG,EAAE,QAAQ;QAChB;YACE,+CAAU,GAAG,CAAW;YACxB;gBACE;oBACE,iDAAa;oBACb,kDAAc;oBACd,uDAAmB;oBACnB,oDAAgB;oBAChB,mDAAe,CACZ,CACC;YACR;gBACE;oBACE,kDAAc;oBACd,0CAAK,GAAG,CAAM,CACX;gBACL;oBACE;;wBAAS,OAAO,CAAC,CAAC,CAAC,IAAI,OAAO,CAAC,WAAW,EAAE,GAAG,CAAC,CAAC,CAAC,EAAE,CAAM;oBAC1D,0CAAK,GAAG,CAAM;oBACd,0CAAK,GAAG,CAAC,GAAG,EAAE,GAAG,CAAC,CAAM;oBACxB;wBACG,GAAG,CAAC,CAAC,CAAC,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE;wBACtB,EAAE,CAAC,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,EAAE,CAClB;oBACL,yCAAM,CACH;gBAEJ,MAAM,CAAC,OAAO,CAAC,IAAwC,CAAC,CAAC,GAAG,CAC3D,CAAC,CAAC,GAAG,EAAE,KAAK,CAAC,EAAE,EAAE,CACf,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE,KAAK,CAAC,EAAE,EAAE,CAAC,CAC3C,sCAAI,GAAG,EAAE,IAAI;oBACX,0CAAK,IAAI,CAAC,WAAW,EAAE,CAAM;oBAC7B,0CAAK,KAAK,CAAC,KAAK,CAAM;oBACtB,0CACG,IAAI,KAAK,OAAO,IAAI,IAAI,KAAK,MAAM;wBAClC,CAAC,CAAC,KAAK;wBACP,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CACtB;oBACL;wBACG,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;wBACtC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAClC;oBACL,0CAAK,GAAG,CAAM,CACX,CACN,CAAC,CACL,CACK,CACF,CACJ,CACP,CAAA;AACH,CAAC,CAAC,CAAA;AAIF,MAAM,kBAAkB,GAAG,IAAA,qBAAQ,EACjC,CAAC,KAMA,EAAE,EAAE;IACH,MAAM,EAAE,KAAK,EAAE,GAAG,KAAK,CAAA;IACvB,MAAM,EAAE,iBAAiB,EAAE,IAAI,EAAE,GAAG,KAAK,CAAA;IACzC,OAAO,IAAI,IAAI,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,KAAK,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAClD,8BAAC,uBAAO,IAAC,eAAe,EAAE,eAAe,KAAM,KAAK,GAAI,CACzD,CAAA;AACH,CAAC,CACF,CAAA;AAED,kBAAe,kBAAkB,CAAA"}
|
|
@@ -22,6 +22,14 @@ function configSchemaF(pluginManager) {
|
|
|
22
22
|
description: 'set arc line width',
|
|
23
23
|
defaultValue: 1,
|
|
24
24
|
},
|
|
25
|
+
/**
|
|
26
|
+
* #slot
|
|
27
|
+
*/
|
|
28
|
+
jitter: {
|
|
29
|
+
type: 'number',
|
|
30
|
+
description: 'jitters the x position so e.g. if many reads map to exact same x position, jittering makes it easy to see that there are many of them',
|
|
31
|
+
defaultValue: 0,
|
|
32
|
+
},
|
|
25
33
|
/**
|
|
26
34
|
* #slot
|
|
27
35
|
*/
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"configSchema.js","sourceRoot":"","sources":["../../src/LinearReadArcsDisplay/configSchema.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,mBAAmB,EAAE,MAAM,6BAA6B,CAAA;AACjE,OAAO,EAAE,qCAAqC,EAAE,MAAM,oCAAoC,CAAA;AAC1F,OAAO,EAAE,KAAK,EAAE,MAAM,iBAAiB,CAAA;AAEvC;;GAEG;AACH,SAAS,aAAa,CAAC,aAA4B;IACjD,OAAO,mBAAmB,CACxB,uBAAuB,EACvB;QACE;;WAEG;QACH,uBAAuB,EAAE;YACvB,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,0DAA0D;YACvE,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,SAAS,EAAE;YACT,IAAI,EAAE,QAAQ;YACd,WAAW,EAAE,oBAAoB;YACjC,YAAY,EAAE,CAAC;SAChB;QAED;;WAEG;QACH,WAAW,EAAE;YACX,IAAI,EAAE,YAAY;YAClB,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,aAAa,EAAE;gBACtC,QAAQ;gBACR,QAAQ;gBACR,YAAY;gBACZ,0BAA0B;gBAC1B,gBAAgB;gBAChB,KAAK;aACN,CAAC;YACF,WAAW,EAAE,qBAAqB;YAClC,YAAY,EAAE,QAAQ;SACvB;KACF,EACD;QACE;;WAEG;QACH,iBAAiB,EAAE,qCAAqC,CAAC,aAAa,CAAC;QACvE,eAAe,EAAE,IAAI;KACtB,CACF,CAAA;AACH,CAAC;AAED,eAAe,aAAa,CAAA"}
|
|
1
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+
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