Enable more checks in HIVIntact

cfe-lab · Jul 21, 2023 · 6b77cac · 6b77cac
1 parent 1d54987
commit 6b77cac
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/gene_splicer/primer_finder.py b/gene_splicer/primer_finder.py
@@ -537,6 +537,12 @@ def run(contigs_csv,
                     subprocess.run(['proviral',
                                     'intact',
                                     '--subtype=B',
+                                    '--run-hypermut',
+                                    '--check-long-deletion',
+                                    '--check-nonhiv',
+                                    '--check-scramble',
+                                    '--check-internal-inversion',
+                                    '--include-small-orfs',
                                     str(no_primers_fasta)],
                                    check=True,
                                    stdout=log_file,