From 10a6cca0de13e1c2f4f36c1ccdd157d88daa6381 Mon Sep 17 00:00:00 2001
From: Colin <colin.diesh@gmail.com>
Date: Mon, 25 Sep 2023 12:47:11 -0400
Subject: [PATCH] Updates

---
 .../models/components/SaveTrackData.tsx                | 10 ++++++----
 .../variants/src/VariantTrack/saveTrackFormats/vcf.ts  | 10 +++++++++-
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx b/packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx
index 4ad64eb1bf8..7105a4882de 100644
--- a/packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx
+++ b/packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx
@@ -15,7 +15,7 @@ import { IAnyStateTreeNode } from 'mobx-state-tree'
 import { makeStyles } from 'tss-react/mui'
 import { saveAs } from 'file-saver'
 import { observer } from 'mobx-react'
-import { Dialog, ErrorMessage, LoadingEllipses } from '@jbrowse/core/ui'
+import { Dialog, ErrorMessage } from '@jbrowse/core/ui'
 import {
   getSession,
   getContainingView,
@@ -96,9 +96,11 @@ const SaveTrackDataDialog = observer(function ({
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
-        const view = getContainingView(model)
+        const { visibleRegions } = getContainingView(model) as {
+          visibleRegions?: Region[]
+        }
         const session = getSession(model)
-        if (!features) {
+        if (!features || !visibleRegions) {
           return
         }
         const generator = options[type] || {
@@ -108,7 +110,7 @@ const SaveTrackDataDialog = observer(function ({
           await generator.callback({
             features,
             session,
-            assemblyName: view.visibleRegions[0].assemblyName,
+            assemblyName: visibleRegions[0].assemblyName,
           }),
         )
       } catch (e) {
diff --git a/plugins/variants/src/VariantTrack/saveTrackFormats/vcf.ts b/plugins/variants/src/VariantTrack/saveTrackFormats/vcf.ts
index 3bcf751ab83..59a927efbb7 100644
--- a/plugins/variants/src/VariantTrack/saveTrackFormats/vcf.ts
+++ b/plugins/variants/src/VariantTrack/saveTrackFormats/vcf.ts
@@ -1,9 +1,17 @@
 import { Feature } from '@jbrowse/core/util'
 
+function generateINFO(feature: Feature) {
+  return Object.entries(feature.get('INFO'))
+    .map(([key, value]) => `${key}=${value}`)
+    .join(';')
+}
 export function stringifyVCF({ features }: { features: Feature[] }) {
+  const fields = ['refName', 'start', 'name', 'REF', 'ALT', 'QUAL', 'FILTER']
   return features
     .map(feature => {
-      return `hello ${feature.get('name')}`
+      return `${fields
+        .map(field => feature.get(field) || '.')
+        .join('\t')}\t${generateINFO(feature)}`
     })
     .join('\n')
 }