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prevent negative start coordinate in cooler_to_bedgraph #318

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prevent negative start coordinate in cooler_to_bedgraph #318

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de8fc3b
prevent negative start coordinate
e-coral Apr 9, 2025
11d578c
fix spacing error
e-coral Apr 11, 2025
ed5446c
Merge branch 'master' into master
alsmith151 Apr 25, 2025
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9 changes: 8 additions & 1 deletion capcruncher/api/pileup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -428,7 +428,14 @@ def cooler_to_bedgraph(
if viewpoint_distance:
viewpoint_coords = cooler.Cooler(clr).info["metadata"]["viewpoint_coords"][0]
viewpoint_coords = re.split("[:-]", viewpoint_coords)
region_to_limit = f"{viewpoint_coords[0]}:{int(viewpoint_coords[1]) - viewpoint_distance}-{int(viewpoint_coords[1]) + viewpoint_distance}"
vpstart = (int(viewpoint_coords[1]) - viewpoint_distance)
vpend = (int(viewpoint_coords[1]) + viewpoint_distance)
# set start to 1 if (start - viewpoint distance) would be negative, because a negative coordinate causes
# 'ValueError: Unexpected token "-"'
if vpstart <=0:
vpstart = 1
# TODO: IF VPEND > CHR SIZE, SET TO CHR SIZE (not sure if this is needed as well?)
region_to_limit = f"{viewpoint_coords[0]}:{vpstart}-{vpend}"
else:
region_to_limit = None

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