Updated description of the -f parameter.

syri/scripts/syri.py

@@ -285,7 +285,7 @@ def main(cmd):
 
     other = parser.add_argument_group("Additional arguments")
     other.add_argument('-F', dest="ftype", help="Input file type. T: Table, S: SAM, B: BAM, P: PAF", default="T", choices=['T', 'S', 'B', 'P'])
-    other.add_argument('-f', dest='f', help='Filter out low quality alignments', default=True, action='store_false')
+    other.add_argument('-f', dest='f', help='As a default, syri filters out low quality and small alignments. Use this parameter to use the full list of alignments without any filtering.', default=True, action='store_false')
     other.add_argument('-k', dest="keep", help="Keep intermediate output files", default=False, action="store_true")
     other.add_argument('--dir', dest='dir', help="path to working directory (if not current directory). All files must be in this directory.", action='store')
     other.add_argument("--prefix", dest="prefix", help="Prefix to add before the output file Names", type=str, default="")