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Changed default value of ignore_diags to auto instead of None in coverage #402

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Changed default value of ignore_diags to auto instead of None in coverage #402

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6 changes: 3 additions & 3 deletions cooltools/api/coverage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ def _get_chunk_coverage(chunk, pixel_weight_key="count"):

def coverage(
clr,
ignore_diags=None,
ignore_diags="auto",
chunksize=int(1e7),
map=map,
use_lock=False,
Expand Down Expand Up @@ -95,7 +95,7 @@ def coverage(
ignore_diags : int, optional
Drop elements occurring on the first ``ignore_diags`` diagonals of the
matrix (including the main diagonal).
If None, equals the number of diagonals ignored during IC balancing.
If auto, equals the number of diagonals ignored during IC balancing.
store : bool, optional
If True, store the results in the input cooler file when finished. If clr_weight_name=None,
also stores total cis counts in the cooler info. Default is False.
Expand All @@ -113,7 +113,7 @@ def coverage(
try:
ignore_diags = (
ignore_diags
if ignore_diags is not None
if ignore_diags != "auto"
else clr._load_attrs(clr.root.rstrip("/") + "/bins/weight")["ignore_diags"]
)
except:
Expand Down
2 changes: 0 additions & 2 deletions cooltools/cli/coverage.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,6 @@
help="The number of diagonals to ignore. By default, equals"
" the number of diagonals ignored during IC balancing.",
type=int,
default=None,
show_default=True,
)
@click.option(
"--store",
Expand Down