Fix BND singletons in ensemble VCF#18
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sci-kai wants to merge 2 commits into
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… switched, not just CHROM POS (including ALT field)
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As mentioned in issue #17 this is a fix for single notated breakends having the wrong ALT column definition in the ensembl VCF file.
It ahs 2 changes:
Fixing ALT cols for single breakends
After copying the single breakend and altering CHROM and POS, it also replaces the ALT column with the corresponding chrom pos so that both entries are representing the opposite breakpoints.
Swap whole row in _check_df_order function
Additionally, I also fixed the _check_df_order function that only swaps CHROM and POS column for reordering the df. Now it also swaps the whole row including the ALT column, which ensures the different ALT cols are also replaced.