Open inodb opened 3 years ago
@inodb I mentioned in the PR that user as1000
is not yet registered in git as a user in the development team and so the jenkins unit tests for this code base [which run inside our firewall] are refusing to run. If this PR needs to be merged at some point down the road, we will need to adjust the development team or re-open the PR from a trusted developer account.
We have had a lot of issues trying to reproduce the original chrom/pos/ref/alt1/alt2 after normalizing it in the genome nexus annotation pipeline. Basically imagine the use case of running genome-nexus-annotation-pipeline twice in a row on the same MAF file. When there is an error in the normalization of chrom/pos/ref/alt1/alt2, we are not able to reproduce the original chrom/pos/ref/alt1/alt2. Let's store a copy as a separate column that's immutable to get around this issue
We could have the following logic:
If the columns prefixed with
genome_nexus_ignore_original
are missing (genome_nexus_ignore_original_Chromosome genome_nexus_ignore_original_Start_Position genome_nexus_ignore_original_End_Position genome_nexus_ignore_original_Reference_Allele genome_nexus_ignore_original_Tumor_Seq_Allele1 genome_nexus_ignore_original_Tumor_Seq_Allele2
) then create these columns and copy over the values from the inputted MAFChromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1
If they are not missing then use the columns prefixed with
genome_nexus_ignore_original
to annotate them instead of the inputtedChromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2
. We do this because we might have normalized the non-prefixed ones incorrectly before.Bonus points: note that if we really want to manually change some
genome_nexus_ignore_original
ones, we can add another column prefix likegenome_nexus_ignore_original_manual_override
. That one would be preferred overgenome_nexus_ignore_original
. That way we can continue to keep the immutable column truly immutable and also see which records we manually override.