bcftools --help instead of -h, no_sort store_false is an _action_, not a _default_

Author: lordzappo

bin/cmo_bcftools

@@ -9,7 +9,7 @@ LPAD_CONFIG_LOC = "/opt/common/CentOS_6-dev/cmo/fireworks_config_files/"
 
 def find_bcftools_options(bcftools_version, subcommand):
     bcftools_cmd = cmo.util.programs['bcftools'][bcftools_version]
-    bcftools_help = subprocess.Popen(" ".join([bcftools_cmd, subcommand, "-h"]), shell=True, stderr=subprocess.PIPE).communicate()[1]
+    bcftools_help = subprocess.Popen(" ".join([bcftools_cmd, subcommand, "--help"]), shell=True, stderr=subprocess.PIPE).communicate()[1]
     lines = bcftools_help.split("\n")
     last_sarg=''
     last_larg=''

bin/cmo_list2bed

@@ -24,7 +24,7 @@ if __name__ =='__main__':
     #he's a very mean individual
     parser.add_argument("-i", "--input_file", help="picard interval list", required=True)
     parser.add_argument("-o", "--output_file", help="output bed file", required=True)
-    parser.add_argument("-ns", "--no_sort", help="sort bed file output", default='store_false')
+    parser.add_argument("-ns", "--no_sort", help="sort bed file output", action='store_false')
     args = parser.parse_args()
     args_dict = vars(args)
     cmd = [script]