From 2d3a331c78ebff92c394b5410ee3a588f0cfed01 Mon Sep 17 00:00:00 2001
From: Victor Lin <13424970+victorlin@users.noreply.github.com>
Date: Wed, 20 Nov 2024 15:32:05 -0800
Subject: [PATCH] Make JsonAnnotation.strand optional

The previous error message code indicated the possibility that this
property is unset. Express that directly in the type annotation and
simplify the error message code.
---
 src/util/entropyCreateStateFromJsons.ts | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/util/entropyCreateStateFromJsons.ts b/src/util/entropyCreateStateFromJsons.ts
index 2f67c164a..afd4b7f09 100644
--- a/src/util/entropyCreateStateFromJsons.ts
+++ b/src/util/entropyCreateStateFromJsons.ts
@@ -20,7 +20,7 @@ interface JsonAnnotation {
   end?: number
   start?: number
   segments?: JsonSegmentRange[]
-  strand: Strand
+  strand?: Strand
   gene?: string
   color?: string
   display_name?: string
@@ -225,7 +225,7 @@ function cdsFromAnnotation(
      * which are represented by augur as '?' and null, respectively. (null comes from `None` in python.)
      * In both cases it's not a good idea to make an assumption of strandedness, or to assume it's even a CDS. */
     console.error(`[Genome annotation]  ${cdsName} has strand ` + 
-      (Object.prototype.hasOwnProperty.call(annotation, "strand") ? String(annotation.strand) : '(missing)') +
+      (annotation.strand !== undefined ? annotation.strand : '(missing)') +
       ". This CDS will be ignored.");
     return invalidCds;
   }