Hide small indels

GMOD · Dec 19, 2024 · 3b35cd5 · 3b35cd5
1 parent 818b059
commit 3b35cd5
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Showing 5 changed files with 84 additions and 26 deletions.
diff --git a/plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts b/plugins/alignments/src/LinearPileupDisplay/SharedLinearPileupDisplayMixin.ts
@@ -98,6 +98,10 @@ export function SharedLinearPileupDisplayMixin(
          * #property
          */
         jexlFilters: types.optional(types.array(types.string), []),
+        /**
+         * #property
+         */
+        hideSmallIndelsSetting: types.maybe(types.boolean),
       }),
     )
     .volatile(() => ({
@@ -130,10 +134,20 @@ export function SharedLinearPileupDisplayMixin(
       },
     }))
     .views(self => ({
+      /**
+       * #getter
+       */
       get autorunReady() {
         const view = getContainingView(self) as LGV
         return view.initialized && self.statsReadyAndRegionNotTooLarge
       },
+
+      /**
+       * #getter
+       */
+      get hideSmallIndels() {
+        return self.hideSmallIndelsSetting
+      },
     }))
     .actions(self => ({
       /**
@@ -265,24 +279,35 @@ export function SharedLinearPileupDisplayMixin(
       setJexlFilters(filters: string[]) {
         self.jexlFilters = cast(filters)
       },
+
+      /**
+       * #action
+       */
+      setHideSmallIndels(arg: boolean) {
+        self.hideSmallIndelsSetting = arg
+      },
     }))
 
     .views(self => ({
       /**
        * #getter
        */
       get rendererConfig() {
-        const { featureHeight, noSpacing, trackMaxHeight, rendererTypeName } =
-          self
+        const {
+          featureHeight: height,
+          noSpacing,
+          hideSmallIndels,
+          trackMaxHeight: maxHeight,
+          rendererTypeName,
+        } = self
         const configBlob = getConf(self, ['renderers', rendererTypeName]) || {}
         return self.rendererType.configSchema.create(
           {
             ...configBlob,
-            ...(featureHeight !== undefined ? { height: featureHeight } : {}),
+            ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
+            ...(height !== undefined ? { height } : {}),
             ...(noSpacing !== undefined ? { noSpacing } : {}),
-            ...(trackMaxHeight !== undefined
-              ? { maxHeight: trackMaxHeight }
-              : {}),
+            ...(maxHeight !== undefined ? { maxHeight } : {}),
           },
           getEnv(self),
         )
@@ -561,6 +586,15 @@ export function SharedLinearPileupDisplayMixin(
                 },
               ],
             },
+            {
+              label: 'Hide small indels (<10bp)',
+              priority: -1,
+              type: 'checkbox',
+              checked: self.hideSmallIndels,
+              onClick: () => {
+                self.setHideSmallIndels(!self.hideSmallIndels)
+              },
+            },
             {
               label: 'Set max height...',
               priority: -1,

diff --git a/plugins/alignments/src/LinearPileupDisplay/model.ts b/plugins/alignments/src/LinearPileupDisplay/model.ts
@@ -208,12 +208,14 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
           trackMaxHeight,
           mismatchAlpha,
           rendererTypeName,
+          hideSmallIndels,
         } = self
         const configBlob = getConf(self, ['renderers', rendererTypeName]) || {}
         return self.rendererType.configSchema.create(
           {
             ...configBlob,
             ...(featureHeight !== undefined ? { height: featureHeight } : {}),
+            ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
             ...(noSpacing !== undefined ? { noSpacing } : {}),
             ...(mismatchAlpha !== undefined ? { mismatchAlpha } : {}),
             ...(trackMaxHeight !== undefined

diff --git a/plugins/alignments/src/PileupRenderer/configSchema.ts b/plugins/alignments/src/PileupRenderer/configSchema.ts
@@ -52,6 +52,15 @@ const PileupRenderer = ConfigurationSchema(
         '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,
     },
+    /**
+     * #slot
+     */
+    hideSmallIndels: {
+      type: 'boolean',
+      description:
+        'Hides small indels, sometimes occurring in long read sequencing',
+      defaultValue: false,
+    },
     /**
      * #slot
      */

diff --git a/plugins/alignments/src/PileupRenderer/makeImageData.ts b/plugins/alignments/src/PileupRenderer/makeImageData.ts
@@ -46,6 +46,7 @@ export function makeImageData({
     config,
     'largeInsertionIndicatorScale',
   )
+  const hideSmallIndels = readConfObject(config, 'hideSmallIndels') as boolean
   const defaultColor = readConfObject(config, 'color') === '#f0f'
   const theme = createJBrowseTheme(configTheme)
   const colorForBase = getColorBaseMap(theme)
@@ -76,6 +77,7 @@ export function makeImageData({
       ctx,
       feat,
       renderArgs,
+      hideSmallIndels,
       mismatchAlpha,
       drawSNPsMuted,
       drawIndels,

diff --git a/plugins/alignments/src/PileupRenderer/renderMismatches.ts b/plugins/alignments/src/PileupRenderer/renderMismatches.ts
@@ -18,6 +18,7 @@ export function renderMismatches({
   charHeight,
   colorForBase,
   contrastForBase,
+  hideSmallIndels,
   canvasWidth,
   drawSNPsMuted,
   drawIndels = true,
@@ -32,6 +33,7 @@ export function renderMismatches({
   drawSNPsMuted?: boolean
   minSubfeatureWidth: number
   largeInsertionIndicatorScale: number
+  hideSmallIndels: boolean
   charWidth: number
   charHeight: number
   canvasWidth: number
@@ -100,32 +102,41 @@ export function renderMismatches({
         )
       }
     } else if (mismatch.type === 'deletion' && drawIndels) {
-      fillRect(
-        ctx,
-        leftPx,
-        topPx,
-        Math.abs(leftPx - rightPx),
-        heightPx,
-        canvasWidth,
-        colorForBase.deletion,
-      )
-      const txt = `${mismatch.length}`
-      const rwidth = measureText(txt, 10)
-      if (widthPx >= rwidth && heightPx >= heightLim) {
-        ctx.fillStyle = contrastForBase.deletion!
-        ctx.fillText(txt, (leftPx + rightPx) / 2 - rwidth / 2, topPx + heightPx)
+      const len = mismatch.length
+      if (!hideSmallIndels || len >= 10) {
+        fillRect(
+          ctx,
+          leftPx,
+          topPx,
+          Math.abs(leftPx - rightPx),
+          heightPx,
+          canvasWidth,
+          colorForBase.deletion,
+        )
+        const txt = `${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) {
       const pos = leftPx + extraHorizontallyFlippedOffset
       const len = +mismatch.base || mismatch.length
       const insW = Math.max(minSubfeatureWidth, 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 = Math.round(pos - insW)
-          fillRect(ctx, l, topPx, insW * 3, 1, canvasWidth)
-          fillRect(ctx, l, topPx + heightPx - 1, insW * 3, 1, canvasWidth)
-          ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx)
+        if (!hideSmallIndels) {
+          fillRect(ctx, pos, topPx, insW, heightPx, canvasWidth, 'purple')
+          if (1 / bpPerPx >= charWidth && heightPx >= heightLim) {
+            const l = Math.round(pos - insW)
+            fillRect(ctx, l, topPx, insW * 3, 1, canvasWidth)
+            fillRect(ctx, l, topPx + heightPx - 1, insW * 3, 1, canvasWidth)
+            ctx.fillText(`(${mismatch.base})`, pos + 3, topPx + heightPx)
+          }
         }
       }
     } else if (mismatch.type === 'hardclip' || mismatch.type === 'softclip') {