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saigegit / SAIGE

Development for SAIGE and SAIGE-GENE(+)
GNU General Public License v3.0
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the --vcfFileIndex option seems to be ignored #38

Closed pettyalex closed 1 year ago

pettyalex commented 2 years ago

I noticed that the --vcfFileIndex option does not actually seem to be used at any point during the analysis. Instead, I see that the VCF file path is being passed into savvy without any reference to the index. When using VCFs or BCFs, it seems hard coded to require a .csi index that's right next to the file in the same directory.

Can the documentation be updated to indicate this? Also, I'd be willing to help remove everything about --vcfFileIndex from the code, because right now it's being passed all the way through R into the VcfClass::setVcfObj method where it is completely unused. I also see it's in SAIGE-GENE unused in setvcfDosageMatrix. It would simplify the code if all references to --vcfFileIndex were removed, given that it isn't used.

saigegit commented 2 years ago

Hi Alex,

Thanks so much for catching this and offering help to remove codes with vcfFileIndex! Please feel free to do so.

Thanks, Wei