From 930a0ae8b59e3ebfca471ab38c2b971441b03124 Mon Sep 17 00:00:00 2001
From: Bryce Lorenz Kille <brycekille@gmail.com>
Date: Tue, 19 Nov 2024 14:59:18 -0600
Subject: [PATCH] Add back xtrafast and fix capitalization

---
 parsnp | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/parsnp b/parsnp
index fb7c126..22e17a3 100755
--- a/parsnp
+++ b/parsnp
@@ -556,6 +556,7 @@ def parse_args():
     misc_args.add_argument(
         "-x",
         "--recomb-filter",
+        "--xtrafast",
         action = "store_true",
         help="Run recombination filter (phipack)")
     misc_args.add_argument(
@@ -1348,7 +1349,7 @@ SETTINGS:
     mumi_dict = {}
     finalfiles = []
     auto_ref = ""
-    if not curated and not args.skip_ANI_filter:
+    if not curated and not args.skip_ani_filter:
         logger.info("Filtering genomes...")
         if use_parsnp_mumi:
             if not inifile_exists:
@@ -1469,7 +1470,7 @@ SETTINGS:
             allfiles.extend(finalfiles)
 
     # If "curateD" then anything that was removed gets added back.
-    if curated or args.skip_ANI_filter:
+    if curated or args.skip_ani_filter:
         for f in fnafiles:
             if f not in finalfiles:
                 finalfiles.append(f)