force vcf indexing

Stops annoying crashes when recreating results in a not perfectly cleaned output directory
ACEnglish · Oct 6, 2023 · e1aa7b5 · e1aa7b5
1 parent 79a342d
commit e1aa7b5
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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)