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[vds/combiner] Teach VDS combiner how to handle custom call fields - #13385
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Add the call_fields argument. Much like refrence entries, when passing a VDS to the combiner, we check it's call fields to ensure that there is a match between the passed argument and the VDS's call fields.
| @@ -156,7 +157,7 @@ class VariantDatasetCombiner: # pylint: disable=too-many-instance-attributes | |||
| for all GVCF files. Finer partitioning yields more parallelism but less work per task. | |||
| gvcf_info_to_keep : :class:`list` of :class:`str` or :obj:`None` | |||
| GVCF ``INFO`` fields to keep in the ``gvcf_info`` entry field. By default, all fields are | |||
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need to remove the are on the previous line
| call_fields_tmp = (call_fields_tmp - {'LPGT'}) | {'PGT'} | ||
| if set(call_fields) != call_fields_tmp: | ||
| warning("Mismatch between 'call_fields' and VDS call fields. " | ||
| "Overwriting with types from supplied VDS") |
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Include the mismatch. In particular, the user should know the call_fields argument but might not know what's in the dataset.
What do you mean by "overwriting with types ..."? It's not the types that are taken from the VDS but the call fields that are taken from it, right?
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Will do. Also will clarify.
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| all_entry_types = chain(vds.reference_data._type.entry.items(), | ||
| vds.variant_data._type.entry.items()) | ||
| call_fields_tmp = {name for name, typ in all_entry_types if typ == hl.tcall} - {'LGT', 'GT'} |
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These are the call fields from the vds, right? Let's use a descriptive name. Maybe vds_call_fields?
| vds.variant_data._type.entry.items()) | ||
| call_fields_tmp = {name for name, typ in all_entry_types if typ == hl.tcall} - {'LGT', 'GT'} | ||
| if 'LPGT' in call_fields_tmp: | ||
| call_fields_tmp = (call_fields_tmp - {'LPGT'}) | {'PGT'} |
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I don't understand why this is here. If the VDS has LPGT, why would we rename that to PGT? Why doesn't that cause a problem later when the VDS is lacking PGT (it has LPGT instead)?
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We transform certain fields from their 'normal' gvcf versions to the VDS 'local' ones, PGT is one of them and is also the only VCF field we parse as a call field by default.
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Mostly me not knowing how this code works, so, my apologies for slowing you down. |
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Add the call_fields argument.
Much like refrence entries, when passing a VDS to the combiner, we check it's call fields to ensure that there is a match between the passed argument and the VDS's call fields.