Add option to save single mapped counts by side #248
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agalitsyna
reviewed
Sep 6, 2024
| @@ -739,6 +787,19 @@ def add_pairs_from_dataframe(self, df, unmapped_chrom="!"): | |||
| self._stat[key]["total_single_sided_mapped"] += int( | |||
| total_count - (mapped_count + unmapped_count) | |||
| ) | |||
| if self.single_mapped_by_side: | |||
| left_only_mapped_count = np.logical_and( | |||
| df_filtered["chrom1"] != unmapped_chrom, | |||
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Hmmm, this definition of "one-sided mapped" won't work for chimeric reads originating from R1. It will count them as "two-sided" although they factually come from R1 oly. This looks like a re-implementation of single-end mapped pairs.
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Ummm is there a way to account for those properly at all at this stage? I think without some extra arguments this information is just lost...
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Yeah, you need walk_pair_type column for that
https://pairtools.readthedocs.io/en/latest/parsing.html#rescuing-complex-walks section walk_pair_types
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