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fix: avoid adding duplicate CSQ/ANN fields via --retain-ann #366

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fix: avoid adding duplicate CSQ/ANN fields via --retain-ann #366

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8 changes: 7 additions & 1 deletion vcf2maf.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -553,7 +553,13 @@ sub GetBiotypePriority {

# push any requested custom VEP annotations from the CSQ/ANN section into @ann_cols
if ($retain_ann) {
push @ann_cols, split(',',$retain_ann);
my @extra_ann = split(',',$retain_ann);
for my $ann (@extra_ann) {
# make sure not to add duplicates to @ann_cols
if ( !($ann ~~ @ann_cols) ) {
push @ann_cols, $ann;
}
}
}

my @ann_cols_format; # To store the actual order of VEP data, that may differ between runs
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