From e1aa7b5bd5c6b9eac0a9cb5603138a3336c4c5b1 Mon Sep 17 00:00:00 2001
From: Adam English <ACEnglish@gmail.com>
Date: Fri, 6 Oct 2023 09:42:58 -0400
Subject: [PATCH] force vcf indexing

Stops annoying crashes when recreating results in a not perfectly
cleaned output directory
---
 truvari/utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/truvari/utils.py b/truvari/utils.py
index d7d4c2e3..f0a63fb9 100644
--- a/truvari/utils.py
+++ b/truvari/utils.py
@@ -433,7 +433,7 @@ def compress_index_vcf(fn, fout=None, remove=True):
     with open(m_tmp, 'w') as out_hdlr:
         out_hdlr.write(bcftools.sort(fn))
     pysam.tabix_compress(m_tmp, fout)
-    pysam.tabix_index(fout, preset="vcf")
+    pysam.tabix_index(fout, force=True, preset="vcf")
     if remove:
         os.remove(fn)
     os.remove(m_tmp)