From c526ab7d313416bee9bb0e66c2c404f56b931df9 Mon Sep 17 00:00:00 2001 From: chaklim Date: Mon, 23 Dec 2019 16:15:51 +0800 Subject: [PATCH] Rename haploid_mode to haploid --- clair/callVarBam.py | 4 ++-- clair/callVarBamParallel.py | 4 ++-- clair/call_var.py | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/clair/callVarBam.py b/clair/callVarBam.py index f81dc8e..6d91aa7 100644 --- 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 index 453cda3..f8a94df 100644 --- 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 index b95544a..6dc09de 100644 --- 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()