From 20f9575f918f137545ec00beff5d77dd41ce8f46 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 15 Feb 2021 14:02:59 -0700
Subject: [PATCH] Display a quality track for the read vs ref

---
 .../src/FromConfigAdapter/configSchema.ts     |  4 ++
 plugins/linear-comparative-view/src/index.tsx | 37 +++++++++++++++++++
 2 files changed, 41 insertions(+)

diff --git a/plugins/config/src/FromConfigAdapter/configSchema.ts b/plugins/config/src/FromConfigAdapter/configSchema.ts
index c09bd4d914..a0fa43f5ce 100644
--- a/plugins/config/src/FromConfigAdapter/configSchema.ts
+++ b/plugins/config/src/FromConfigAdapter/configSchema.ts
@@ -11,6 +11,10 @@ export const configSchema = ConfigurationSchema(
       type: 'string',
       defaultValue: 'SimpleFeature',
     },
+    noAssemblyManager: {
+      type: 'boolean',
+      defaultValue: false,
+    },
   },
   { explicitlyTyped: true },
 )
diff --git a/plugins/linear-comparative-view/src/index.tsx b/plugins/linear-comparative-view/src/index.tsx
index 730fdc7c22..c419b6cb13 100644
--- a/plugins/linear-comparative-view/src/index.tsx
+++ b/plugins/linear-comparative-view/src/index.tsx
@@ -166,6 +166,9 @@ function WindowSizeDlg(props: {
   const [error, setError] = useState<Error>()
   const windowSize = +window
   const [primaryFeature, setPrimaryFeature] = useState<Feature>()
+
+  // we need to fetch the primary alignment if the selected feature is 2048.
+  // this should be the first in the list of the SA tag
   useEffect(() => {
     let done = false
     ;(async () => {
@@ -363,6 +366,40 @@ function WindowSizeDlg(props: {
                   },
                 ],
               },
+              {
+                id: `${Math.random()}`,
+                type: 'QuantitativeTrack',
+                configuration: {
+                  trackId: 'qualTrack',
+                  assemblyNames: [readAssembly],
+                  name: 'Read quality',
+                  type: 'QuantitativeTrack',
+                  adapter: {
+                    type: 'FromConfigAdapter',
+                    noAssemblyManager: true,
+                    features: primaryFeature
+                      .get('qual')
+                      .split(' ')
+                      .map((qual, index) => {
+                        return {
+                          start: index,
+                          end: index + 1,
+                          refName: readName,
+                          score: +qual,
+                          assemblyName: readAssembly,
+                          uniqueId: `feat_${index}`,
+                        }
+                      }),
+                  },
+                },
+                displays: [
+                  {
+                    id: `${Math.random()}`,
+                    type: 'LinearWiggleDisplay',
+                    height: 100,
+                  },
+                ],
+              },
             ],
           },
         ],