add -ci0 to the intersect for #15. still no dice

dkoslicki · Mar 31, 2020 · 3dcd8a2 · 3dcd8a2
1 parent ac6e6b2
commit 3dcd8a2
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/CMash/Query.py b/CMash/Query.py
@@ -275,9 +275,9 @@ def intersect(self):
 
 		# intersect kmers
 		if self.verbose:
-			res = subprocess.run(f"{self.kmc_tools} simple {db_kmers_loc} {in_path} -ci0 intersect {out_path} -ci0 ", shell=True)
+			res = subprocess.run(f"{self.kmc_tools} simple {db_kmers_loc} -ci0 {in_path} -ci0 intersect {out_path} -ci0 ", shell=True)
 		else:
-			res = subprocess.run(f"{self.kmc_tools} simple {db_kmers_loc} {in_path} -ci0 intersect {out_path} -ci0 ", shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
+			res = subprocess.run(f"{self.kmc_tools} simple {db_kmers_loc} -ci0 {in_path} -ci0 intersect {out_path} -ci0 ", shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)
 		if res.returncode != 0:
 			raise Exception(f"The command {res.args} failed to run and returned the returncode={res.returncode}")