fix: raise ValueError on empty CNV HMM data instead of IndexError#1258
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ADAMSmugwe wants to merge 1 commit intomalariagen:masterfrom
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fix: raise ValueError on empty CNV HMM data instead of IndexError#1258ADAMSmugwe wants to merge 1 commit intomalariagen:masterfrom
ADAMSmugwe wants to merge 1 commit intomalariagen:masterfrom
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Problem
Two plotting functions in
cnv_data.pycrash with a crypticIndexError: index 0 is out of bounds for axis 0 with size 0when a requested region or sample has no valid CNV HMM data:
plot_cnv_hmm_coverage— afterdata.query("call_CN >= 0")filtersout all uncalled windows, accessing
values[0]/values[-1]on theempty DataFrame crashes.
plot_cnv_hmm_heatmap_track— ifn_windows == 0for the requestedregion, accessing
start[0]andend[-1]crashes.Fix
Added an early
ValueErrorguard in both functions before the unsafeindex access, with a descriptive message that names the sample/region
so the user knows exactly what produced no data.
Follows the existing pattern used in
frq_base.pyand elsewhere inthe codebase.
Files Changed
malariagen_data/anoph/cnv_data.py