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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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CNVkit Antitarget Bug #471

Open Muyiyuan opened 5 years ago

Muyiyuan commented 5 years ago

The antitarget module has bug that the bed produce by this module include some target region. I review the code and find the bug come from the iter_ranges function (intersect.py from skgenome). The original code like this: subtable = table.iloc[region_idx] The table dataframe do not reset index and region_idx is calculate by reseting index, therefore, when chromsome number increase, subtable will get empty dataframe. I change the code like this, and it worked out. subtable = table.reset_index(drop=True).iloc[region_idx]

etal commented 4 years ago

Thanks for letting me know! I'll check it out.