diff --git a/maxatac/utilities/parser.py b/maxatac/utilities/parser.py index 43dccdb..abce03c 100644 --- a/maxatac/utilities/parser.py +++ b/maxatac/utilities/parser.py @@ -175,6 +175,14 @@ def get_parser(): default=AUTOSOMAL_CHRS, help="Chromosomes for averaging. Default: 1-22" ) + + average_parser.add_argument("--genome", + dest="genome", + type=str, + default="hg38", + required=False, + help="The reference genome build to use." + ) average_parser.add_argument("--genome", dest="genome", @@ -255,6 +263,13 @@ def get_parser(): help="The number of zoom levels that should be computed for the output bigWig file." ) + predict_parser.add_argument("--genome", + dest="genome", + type=str, + default="hg38", + required=False, + help="The reference genome build to use.") + predict_parser.add_argument("-i", "-s", "--signal", dest="signal", type=str, @@ -639,24 +654,16 @@ def get_parser(): type=str, nargs="+", default=AUTOSOMAL_CHRS, - help="Chromosomes for normalization. Default: 1-22" - ) - + help="Chromosomes for normalization. Default: 1-22 from the hg38 genome" + ) + normalize_parser.add_argument("--genome", dest="genome", type=str, default="hg38", required=False, - help="The reference genome build to which the input file was aligned." - ) - - normalize_parser.add_argument("--max_zooms", - dest="max_zooms", - type=int, - default=5, - required=False, - help="The number of zoom levels that should be computed for the normalized bigWig file." - ) + help="The reference genome build to use." + ) normalize_parser.add_argument("-o", "--output", "--output_dir", dest="output_dir",