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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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Asks for .tbi, expects .csi #315

Closed mferreiradasilva closed 2 years ago

mferreiradasilva commented 3 years ago

The SPA function argument vfFileIndex asks for a .tbi tabix index file, but as it is provided it gives an error because it's expecting a .csi file:

if(!grepl("\\.sav$", vcfFile) && !file.exists(paste(vcfFile,".csi", sep=""))){
      stop("ERROR! vcfFileIndex ", paste(vcfFile,".csi", sep=""), " does not exist\n")
    }
mferreiradasilva commented 3 years ago

Yeah. It works fine with a .csi, but the info and manual are wrong because they specifically mention a tabix tbi.

rbutleriii commented 3 years ago

Notably, it used to work with a .tbi, but now it does not.

medinacarolina commented 2 years ago

Hi, I am running into the same problem I think is something that would be handy to be solved

MWendorff commented 2 years ago

Same problem here by calling step2_SPAtests.R for saige_gene. Also in the walkthrough (https://github.com/weizhouUMICH/SAIGE/wiki/Genetic-association-tests-using-SAIGE#running-saige-and-saige-gene) it is presented with tbi.

Hint for other users: It works with csi (tabix -C)

weizhouUMICH commented 2 years ago

We have just released a new version 1.0.0. It has substantial computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests and clearer log output. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/ The program will be maintained by multiple SAIGE developers there. The docker image has been updated. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei