Larger SNPs

GMOD · Feb 22, 2023 · ec77170 · ec77170
1 parent e514a51
commit ec77170
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Showing 23 changed files with 98 additions and 98 deletions.
diff --git a/plugins/alignments/src/PileupRenderer/PileupRenderer.ts b/plugins/alignments/src/PileupRenderer/PileupRenderer.ts
@@ -743,7 +743,7 @@ export default class PileupRenderer extends BoxRendererType {
       default:
         if (defaultColor) {
           // avoid a readConfObject call here
-          ctx.fillStyle = '#ccc'
+          ctx.fillStyle = 'lightgrey'
         } else {
           ctx.fillStyle = readConfObject(config, 'color', { feature })
         }

diff --git a/plugins/alignments/src/PileupRenderer/configSchema.ts b/plugins/alignments/src/PileupRenderer/configSchema.ts
@@ -50,7 +50,7 @@ const PileupRenderer = ConfigurationSchema(
       type: 'number',
       description:
         'the minimum width in px for a pileup mismatch feature. use for increasing/decreasing mismatch marker widths when zoomed out, e.g. 0 or 1',
-      defaultValue: 1,
+      defaultValue: 1.5,
     },
     /**
      * #slot

diff --git a/plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts b/plugins/alignments/src/SNPCoverageRenderer/SNPCoverageRenderer.ts
@@ -100,7 +100,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
       C: bases.C.main,
       G: bases.G.main,
       T: bases.T.main,
-      total: '#ccc',
+      total: 'lightgrey',
       insertion: 'purple',
       softclip: 'blue',
       hardclip: 'red',
@@ -144,7 +144,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
 
       const score = feature.get('score') as number
       const snpinfo = feature.get('snpinfo') as SNPInfo
-      const w = Math.max(rightPx - leftPx + fudgeFactor, 1)
+      const w = Math.max(rightPx - leftPx + fudgeFactor, 1.5)
       const totalScore = snpinfo.total
       const keys = Object.keys(snpinfo.cov).sort()
 
@@ -160,7 +160,7 @@ export default class SNPCoverageRenderer extends WiggleBaseRenderer {
         const height = toHeight(score)
         const bottom = toY(score) + height
         ctx.fillRect(
-          Math.floor(leftPx),
+          Math.round(leftPx),
           bottom - ((total + curr) / score) * height,
           w,
           (total / score) * height,

diff --git a/.../src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.tsx.snap b/.../src/ConfigurationEditorWidget/components/__snapshots__/ConfigurationEditor.test.tsx.snap
@@ -1571,7 +1571,7 @@ exports[`ConfigurationEditor widget renders with defaults of the PileupTrack sch
                                     class="MuiInputBase-input MuiOutlinedInput-input css-1t8l2tu-MuiInputBase-input-MuiOutlinedInput-input"
                                     id="mui-21"
                                     type="number"
-                                    value="0.7"
+                                    value="1.5"
                                   />
                                   <fieldset
                                     aria-hidden="true"

diff --git a/...uence/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.tsx.snap b/...uence/src/DivSequenceRenderer/components/__snapshots__/DivSequenceRendering.test.tsx.snap
@@ -169,7 +169,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
       B
     </text>
     <rect
-      fill="#ffc107"
+      fill="#ff9800"
       height="20"
       stroke="#555"
       width="20"
@@ -178,7 +178,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
     />
     <text
       dominant-baseline="middle"
-      fill="black"
+      fill="white"
       text-anchor="middle"
       x="19930"
       y="70"
@@ -390,7 +390,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
       F
     </text>
     <rect
-      fill="#ffc107"
+      fill="#ff9800"
       height="20"
       stroke="#555"
       width="20"
@@ -399,7 +399,7 @@ exports[`renders with one feature reversed with a correct seq, zoomed in, should
     />
     <text
       dominant-baseline="middle"
-      fill="black"
+      fill="white"
       text-anchor="middle"
       x="19850"
       y="90"
@@ -807,7 +807,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
       F
     </text>
     <rect
-      fill="#ffc107"
+      fill="#ff9800"
       height="20"
       stroke="#555"
       width="20"
@@ -816,7 +816,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
     />
     <text
       dominant-baseline="middle"
-      fill="black"
+      fill="white"
       text-anchor="middle"
       x="150"
       y="70"
@@ -892,7 +892,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
       B
     </text>
     <rect
-      fill="#ffc107"
+      fill="#ff9800"
       height="20"
       stroke="#555"
       width="20"
@@ -901,7 +901,7 @@ exports[`renders with one feature with a correct seq, zoomed in, should render n
     />
     <text
       dominant-baseline="middle"
-      fill="black"
+      fill="white"
       text-anchor="middle"
       x="70"
       y="90"
@@ -1276,7 +1276,7 @@ exports[`renders with one feature with an incorrect seq, zoomed in, should throw
       B
     </text>
     <rect
-      fill="#ffc107"
+      fill="#ff9800"
       height="20"
       stroke="#555"
       width="20"
@@ -1285,7 +1285,7 @@ exports[`renders with one feature with an incorrect seq, zoomed in, should throw
     />
     <text
       dominant-baseline="middle"
-      fill="black"
+      fill="white"
       text-anchor="middle"
       x="70"
       y="90"