From cfbaa397354d8f82e220cd05fc8de837412d8908 Mon Sep 17 00:00:00 2001
From: Shashank B R <shashank.b.r.gowda45587@gmail.com>
Date: Wed, 25 Oct 2023 21:00:22 +0100
Subject: [PATCH] Fix crash with very long features (#282)

* limit feature min max to 500000 bp

* feature min max limit

* change
---
 .../LinearApolloDisplay/stateModel/layouts.ts | 24 +++++++++++++++----
 1 file changed, 19 insertions(+), 5 deletions(-)

diff --git a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts
index 84349c72..4232e9ac 100644
--- a/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts
+++ b/packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts
@@ -16,6 +16,9 @@ export function layoutsModelFactory(
   const BaseLinearApolloDisplay = baseModelFactory(pluginManager, configSchema)
 
   return BaseLinearApolloDisplay.named('LinearApolloDisplayLayouts')
+    .props({
+      featuresMinMaxLimit: 500_000,
+    })
     .volatile(() => ({
       seenFeatures: observable.map<string, AnnotationFeatureI>(),
     }))
@@ -31,7 +34,8 @@ export function layoutsModelFactory(
           for (const [, feature] of self.seenFeatures) {
             if (
               refName !== assembly?.getCanonicalRefName(feature.refSeq) ||
-              !doesIntersect2(start, end, feature.min, feature.max)
+              !doesIntersect2(start, end, feature.min, feature.max) ||
+              feature.length > self.featuresMinMaxLimit
             ) {
               continue
             }
@@ -118,9 +122,13 @@ export function layoutsModelFactory(
                       feature.max - feature.min === 0
                         ? feature.min + 1
                         : feature.max
-                    return rowForFeature
-                      .slice(feature.min - min, featureMax - min)
-                      .some(Boolean)
+                    let start = feature.min - min,
+                      end = featureMax - min
+                    if (feature.min - min < 0) {
+                      start = 0
+                      end = featureMax - feature.min
+                    }
+                    return rowForFeature.slice(start, end).some(Boolean)
                   })
                   .some(Boolean)
               ) {
@@ -133,7 +141,13 @@ export function layoutsModelFactory(
                 rowNum++
               ) {
                 const row = rows[rowNum]
-                row.fill(true, feature.min - min, feature.max - min)
+                let start = feature.min - min,
+                  end = feature.max - min
+                if (feature.min - min < 0) {
+                  start = 0
+                  end = feature.max - feature.min
+                }
+                row.fill(true, start, end)
                 const layoutRow = featureLayout.get(rowNum)
                 layoutRow?.push([rowNum - startingRow, feature])
               }