#sampleMapping in own file not working

[Malcolm Cook]

Hello,

By my reading of https://software.broadinstitute.org/software/igv/SampleInformation#samplemappingfile sampleMapping can either

 - be added at the end of an attributes .txt file, or

 - stand alone in its own .txt file

However, I find the following to work in the first case but not in the second:

#sampleMapping

data2/R1_WT_N.Log R1_WT_N

data2/R1_WT_N.Log.final R1_WT_N

data2/R1_WT_N.Log.progress R1_WT_N

data2/R1_WT_N.ReadsPerGene.tab R1_WT_N

        Unexpected error: An error occurred while accessing: /n/core/Genomics/Analysis/Si/younshim_park/yop2/mec/data2/SampleMapping.txt
        Could not determine file type. Does file have proper extension? .
        

Further, I get the same error trying the example file:

       https://dm.genomespace.org/datamanager/file/Home/Public/SpaceCadet/IGV%20Sample%20Information%20Files/BLCA_SampleMapping_3sets.txt

    

Again, if I append my sampleMapping to the end of my sampleAttribute.txt file, it works fine.

Any suggestions out there?

Thanks,

Malcolm

[James Robinson]

I was not actually aware you can add this as a stand-alone file.   It looks like the documentation is wrong here.   If that is a desirable feature please open a git issue.    Thanks.

Jim

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