Rename haploid_mode to haploid

KewinOgink · Dec 23, 2019 · c526ab7 · c526ab7
1 parent b9caffe
commit c526ab7
Show file tree

Hide file tree

Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/clair/callVarBam.py b/clair/callVarBam.py
@@ -87,7 +87,7 @@ def Run(args):
     stop_consider_left_edge = command_option_from(args.stop_consider_left_edge, 'stop_consider_left_edge')
     log_path = command_option_from(args.log_path, 'log_path', option_value=args.log_path)
     pysam_for_all_indel_bases = command_option_from(args.pysam_for_all_indel_bases, 'pysam_for_all_indel_bases')
-    haploid_mode = command_option_from(args.haploid_mode, 'haploid_mode')
+    haploid_mode = command_option_from(args.haploid, 'haploid')
     debug = command_option_from(args.debug, 'debug')
     qual = command_option_from(args.qual, 'qual', option_value=args.qual)
     fast_plotting = command_option_from(args.fast_plotting, 'fast_plotting')
@@ -295,7 +295,7 @@ def main():
     parser.add_argument('--pysam_for_all_indel_bases', action='store_true',
                         help="Always using pysam for outputting indel bases, optional")
 
-    parser.add_argument('--haploid_mode', action='store_true',
+    parser.add_argument('--haploid', action='store_true',
                         help="call haploid instead of diploid")
 
     parser.add_argument('--activation_only', action='store_true',

diff --git a/clair/callVarBamParallel.py b/clair/callVarBamParallel.py
@@ -45,7 +45,7 @@ def Run(args):
     stop_consider_left_edge = command_option_from(args.stop_consider_left_edge, 'stop_consider_left_edge')
     log_path = command_option_from(args.log_path, 'log_path', option_value=args.log_path)
     pysam_for_all_indel_bases = command_option_from(args.pysam_for_all_indel_bases, 'pysam_for_all_indel_bases')
-    haploid_mode = command_option_from(args.haploid_mode, 'haploid_mode')
+    haploid_mode = command_option_from(args.haploid, 'haploid')
     debug = command_option_from(args.debug, 'debug')
     qual = command_option_from(args.qual, 'qual', option_value=args.qual)
     fast_plotting = command_option_from(args.fast_plotting, 'fast_plotting')
@@ -176,7 +176,7 @@ def main():
     parser.add_argument('--pysam_for_all_indel_bases', action='store_true',
                         help="Always using pysam for outputting indel bases, optional")
 
-    parser.add_argument('--haploid_mode', action='store_true',
+    parser.add_argument('--haploid', action='store_true',
                         help="call haploid instead of diploid")
 
     parser.add_argument('--activation_only', action='store_true',

diff --git a/clair/call_var.py b/clair/call_var.py
@@ -1165,7 +1165,7 @@ def call_variants(args, m):
     output_config = OutputConfig(
         is_show_reference=args.showRef,
         is_debug=args.debug,
-        is_haploid_mode_enabled=args.haploid_mode,
+        is_haploid_mode_enabled=args.haploid,
         quality_score_for_pass=args.qual,
     )
     output_utilities = output_utilties_from(
@@ -1282,7 +1282,7 @@ def main():
     parser.add_argument('--pysam_for_all_indel_bases', action='store_true',
                         help="Always using pysam for outputting indel bases, optional")
 
-    parser.add_argument('--haploid_mode', action='store_true',
+    parser.add_argument('--haploid', action='store_true',
                         help="call haploid instead of diploid")
 
     args = parser.parse_args()