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Merged
ANRudrapatna merged 2 commits into from
Sep 14, 2026
Merged

Update parser.py #156

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7f496ee
Update parser.py
ANRudrapatna Mar 19, 2026
1679e0f
Merge branch 'main' into ANRudrapatna-patch-4
ANRudrapatna Sep 14, 2026
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33 changes: 20 additions & 13 deletions maxatac/utilities/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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",
Expand Down