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blachlylab / mucor

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split "variant_details" into respective columns #7

Open kwkroll32 opened 8 years ago

kwkroll32 commented 8 years ago

Invent a new output type like variant_details. Rather than making a comma-separated string of VF and DP for common mutations, add a new column for each duplicate. Only permits 1 sample per row.

Modify config to support new format and distinguish between variant calls. "source" will be re-named "format" to clearly identify the parsing module that should be used. The new value of "source" will be identical to "format," unless a sample has multiple VCFs from the same "format." In this case, "source" will have distinguishing values appended to it, i.e. [samtools.a, samtools.b, samtools.c] while "format" would be [samtools, samtools, samtools]. These "source" values will be used to name the specific columns in the new output mode.

jblachly commented 8 years ago

As this introduces a potentially-breaking change into the JSON config file (renaming source-> format) we should version the config file