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DiltheyLab / HLA-LA

Fast HLA type inference from whole-genome data
GNU General Public License v3.0
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Allowing for non-alphanumeric characters in sample IDs #45

Closed tinyheero closed 11 months ago

tinyheero commented 3 years ago

Hi there,

Is it possible to allow for the --sampleID argument to accept non-alphanumeric characters? I often work with identifiers that contain a - in it and when I try to run for example something like this:

HLA-LA.pl \
        --BAM tumour-sample.bam \
        --graph PRG_MHC_GRCh38_withIMGT \
        --sampleID tumour-sample \
        --maxThreads 1 \
        --workingDir output/hla_la

I get this error:

Please use only alphanumeric characters - \w+ - for --sampleID at /projects/ace_benchmarking/miniconda3/envs/hla-la/bin/HLA-LA.pl line 147.

I could specify a --sampleID devoid of any non-alphanumeric characters, but this adds post-processing step to marry the results with the original sample identifiers, which I would like to avoid.

Kind regards,

Fong

AlexanderDilthey commented 11 months ago

Hi @tinyheero,

This is now fixed (- and _ are allowed).

Best wishes

Alex