Update README.md

README.md

@@ -107,21 +107,29 @@ You can control the number of parallel computations using this parameter. By def
 ### options
 
 ````
+
+optional arguments:
   -h, --help            show this help message and exit
   -i INPUT, --input INPUT
                         path to input file
   -o OUTPUT, --output OUTPUT
-                        path to output file
-  -f [FORMAT], --format [FORMAT]
-                        input file format, default: fasta ('genbank','fasta')
-  --stride [STRIDE]     stride of the sliding window. default:2048
-  --batch [BATCH]       parallel batch size, set to a lower value if your gpu runs out of memory. default:2048
+                        path to output directory
+  -of OFASTA, --ofasta OFASTA
+                        path to output fasta file
+  --cutoff CUTOFF       fasta output cutoff score
+  --fsize [FSIZE]       length of the sliding window (value must be 2^n). default:2048
+  --stride [STRIDE]     stride of the sliding window. default:2048 (stride==fsize)
+  --batch [BATCH]       parallel batch size, set to a lower value if your gpu runs out of memory. default:128
   --cpu                 Number of threads to use for inference. default:False
   --gpu                 run on gpu, runs on all gpus on the system by default: default: True
   --getalllabels        get predicted labels for Non-Viral contigs. default:False
   --meanscore           output mean predictive score per contig. deafault:True
   --fragscore           output percentage of perclass predictions per contig. deafault:True
-  -v, --verbose         increase output verbosity
+
+Misc. Options:
+  -v, --verbose         Verbosity level : -v warning, -vv info, -vvv debug, (default info)
+  -f, --overwrite       Overwrite existing files
+
   
 
 ````