Insure "fetch" in vcf.py returns a list of variants. Fixes #76

igvteam · Sep 22, 2023 · 1788db9 · 1788db9
1 parent 5fbbf6f
commit 1788db9
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diff --git a/igv_reports/vcf.py b/igv_reports/vcf.py
@@ -58,7 +58,7 @@ def fetch(self, chr, start, end):
         vcf = self.file
         if vcf.index is not None:
             try:
-                return vcf.fetch(chr, start, end)
+                return list(vcf.fetch(chr, start, end))
             except ValueError:
 
                 # Possible chr alias error (e.g. 1 vs chr1)

diff --git a/test/data/variants/SKBR3_Sniffles_variants_tra.vcf.gz b/test/data/variants/SKBR3_Sniffles_variants_tra.vcf.gz
diff --git a/test/data/variants/SKBR3_Sniffles_variants_tra.vcf.gz.tbi b/test/data/variants/SKBR3_Sniffles_variants_tra.vcf.gz.tbi