From 03d9c410171902cfb9b4d8ed67d23e455f28b23b Mon Sep 17 00:00:00 2001
From: Douglass Turner <douglass.turner@gmail.com>
Date: Thu, 3 Nov 2022 02:20:09 -0400
Subject: [PATCH] Add bpp threshold of 10 to sequence track rendering (#1560)

* Add bpp threshold of 10 to sequence track rendering

* Update trackViewport.js

* update

Co-authored-by: Jim Robinson <933148+jrobinso@users.noreply.github.com>
---
 js/sequenceTrack.js | 10 ++++++----
 js/trackViewport.js |  4 ++--
 2 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/js/sequenceTrack.js b/js/sequenceTrack.js
index 86ff1919a..caf13cebd 100755
--- a/js/sequenceTrack.js
+++ b/js/sequenceTrack.js
@@ -111,6 +111,8 @@ const FRAME_HEIGHT = 25
 const FRAME_BORDER = 5
 const BP_PER_PIXEL_THRESHOLD = 1 / 10
 
+const bppFeatureFetchThreshold = 10
+
 class SequenceTrack {
 
     constructor(config, browser) {
@@ -163,7 +165,6 @@ class SequenceTrack {
         ]
     }
 
-
     contextMenuItemList(clickState) {
         const viewport = clickState.viewport
         if (viewport.referenceFrame.bpPerPixel <= 1) {
@@ -214,7 +215,6 @@ class SequenceTrack {
         }
     }
 
-
     translateSequence(seq) {
 
         const threeFrame = [[], [], []]
@@ -241,9 +241,11 @@ class SequenceTrack {
     }
 
     async getFeatures(chr, start, end, bpPerPixel) {
+
         start = Math.floor(start)
         end = Math.floor(end)
-        if (bpPerPixel && bpPerPixel > 1) {
+
+        if (bpPerPixel && bpPerPixel > bppFeatureFetchThreshold) {
             return null
         } else {
             const sequence = await this.browser.genome.sequence.getSequence(chr, start, end)
@@ -381,7 +383,7 @@ class SequenceTrack {
 
 }
 
-export {defaultSequenceTrackOrder}
+export {defaultSequenceTrackOrder, bppFeatureFetchThreshold}
 
 export default SequenceTrack
 
diff --git a/js/trackViewport.js b/js/trackViewport.js
index 3aa3879f5..cb0d0c563 100644
--- a/js/trackViewport.js
+++ b/js/trackViewport.js
@@ -8,6 +8,7 @@ import Viewport from "./viewport.js"
 import {DOMUtils, FileUtils} from "../node_modules/igv-utils/src/index.js"
 import C2S from "./canvas2svg.js"
 import GenomeUtils from "./genome/genome.js"
+import {bppFeatureFetchThreshold} from "./sequenceTrack.js";
 
 const NOT_LOADED_MESSAGE = 'Error loading track data'
 
@@ -90,7 +91,7 @@ class TrackViewport extends Viewport {
             }
         }
 
-        if (this.trackView.track && "sequence" === this.trackView.track.type && this.referenceFrame.bpPerPixel > 1) {
+        if (this.trackView.track && "sequence" === this.trackView.track.type && this.referenceFrame.bpPerPixel > bppFeatureFetchThreshold) {
             $(this.canvas).remove()
             this.canvas = undefined
             //this.featureCache = undefined
@@ -533,7 +534,6 @@ class TrackViewport extends Viewport {
     }
 
     async getFeatures(track, chr, start, end, bpPerPixel) {
-
         if (this.featureCache && this.featureCache.containsRange(chr, start, end, bpPerPixel)) {
             return this.featureCache.features
         } else if (typeof track.getFeatures === "function") {