--- a/CSP2/bin/runSNPPipeline.py	Tue Dec 03 16:35:35 2024 -0500
+++ b/CSP2/bin/runSNPPipeline.py	Wed Dec 04 12:50:59 2024 -0500
@@ -636,17 +636,17 @@
 parser.add_argument('--output_directory', type=str, help='Output Directory')
 parser.add_argument('--log_directory', type=str, help='Log Directory')
 parser.add_argument('--snpdiffs_file', type=str, help='Path to SNPdiffs file')
-parser.add_argument('--min_cov', type=float, help='Minimum coverage')
-parser.add_argument('--min_len', type=int, help='Minimum length')
-parser.add_argument('--min_iden', type=float, help='Minimum identity')
-parser.add_argument('--ref_edge', type=int, help='Reference edge')
-parser.add_argument('--query_edge', type=int, help='Query edge')
-parser.add_argument('--density_windows', type=str, help='Density windows')
-parser.add_argument('--max_snps', type=str, help='Maximum SNPs')
-parser.add_argument('--trim_name', type=str, help='Trim name')
-parser.add_argument('--max_missing', type=float, help='Maximum missing')
-parser.add_argument('--tmp_dir', type=str, help='Temporary directory')
-parser.add_argument('--rescue', type=str, help='Rescue edge SNPs (rescue/norescue)')
+parser.add_argument('--min_cov', default=85,type=float, help='Minimum coverage')
+parser.add_argument('--min_len', default=500,type=int, help='Minimum length')
+parser.add_argument('--min_iden', default=99,type=float, help='Minimum identity')
+parser.add_argument('--ref_edge', default=150,type=int, help='Reference edge')
+parser.add_argument('--query_edge', default=150,type=int, help='Query edge')
+parser.add_argument('--density_windows', default="1000,125,15",type=str, help='Density windows')
+parser.add_argument('--max_snps', default="3,2,1", type=str, help='Maximum SNPs')
+parser.add_argument('--trim_name', type=str, default="", help='trim name')
+parser.add_argument('--max_missing',default=50, type=float, help='Maximum missing')
+parser.add_argument('--tmp_dir',default="", type=str, help='Temporary directory')
+parser.add_argument('--rescue', default="norescue",type=str, help='Rescue edge SNPs (rescue/norescue)')
 args = parser.parse_args()
 
 reference_id = args.reference_id