Sample chromosome ploidy support for RWB Echo [VS-1500] #9051
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| # the standard `sample_chromosome_ploidy` schema by the addition of the `genotype` column. At the time of this writing | ||
| # it is not expected that any additional samples will be loaded into the `echo` dataset, but if there are additional | ||
| # samples then this code will match the actual `echo` schema. | ||
| String sample_chromosome_ploidy_schema_json = '[{"name": "sample_id","type": "INTEGER","mode": "REQUIRED"},{"name": "chromosome","type": "INTEGER","mode": "REQUIRED"},{"name":"genotype","type":"STRING","mode":"NULLABLE"},{"name": "ploidy","type": "INTEGER","mode": "REQUIRED"}]' |
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These changes aren't actually necessary for supporting RWB extract. They likely won't hurt, but they are not necessary for this PR as RWB does not run this wdl.
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Yeah that's kinda what I was trying to say with the comment. 🙂 It was bugging me that this was out of sync with SchemaUtils.java, even if we're super unlikely to ever need these changes.
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Looks good. I had the same comment/question as Aaron. I'm a little concerned about what we will do if we copy the sample_ploidy table from Echo->Foxtrot and then have to deal with that genotype column as we add more samples. But that's not in the scope of this ticket
I was assuming we would not have a |
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Yeah, that makes sense. So, would we delete that column from the copied table? Or just regenerate it? |
Differs from the "stock"
sample_chromosome_ploidytable in having a "bonus"genotypecolumn.