Genotype request : filter out duplicate sample names entered by the user

[Don-Isdale]

Introduction

When requesting genotype values, the user is able to enter a list of sample names, e.g. by copy / paste into a text area.
The request is implemented by bcftools, which does not accept duplicate sample names.

The solution is to filter out duplicate sample names entered by the user before sending the request to bcftools.

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Details

There's a message in the server log indicating this has occurred :

 childProcess vcfGenotypeLookup.bash  errors : [E::bcf_hdr_subset] Duplicate sample name "AGG..."

At the same time or closely related there was also a segmentation fault in bcftools :

+ bcftools query AGG-.../Chr5A.MAF.vcf.gz -r Chr5A:70... -s AGG...71 -H -f '%ID	%POS	%REF	%ALT	%INFO[	%GT]
'

/app/lb3app/scripts/vcfGenotypeLookup.bash: line 335: 250988 Segmentation fault      (core dumped) "$bcftools" ...