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fix yaml parse RG ID bug #69

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fix yaml parse RG ID bug #69

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4 changes: 1 addition & 3 deletions lib/PCAP/Bwa/Meta.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -200,7 +200,6 @@ sub _validate_yaml {
my $yaml_obj = LoadFile( $meta_yaml );
# if all ID's aren't unique we generate time based UUID and take the first section as the new ID
# this will not prevent universal clash but will within a BAM file.
my %ids;
for my $rg_key(keys %{$yaml_obj->{'READGRPS'}}) {
my $rg_rec = $yaml_obj->{'READGRPS'}->{$rg_key};

Expand All @@ -224,10 +223,9 @@ sub _validate_yaml {
$rg_rec->{'PL'} = uc $rg_rec->{'PL'};
}

if(! exists $rg_rec->{'ID'} || exists $ids{$rg_rec->{'ID'}} ) {
if(! exists $rg_rec->{'ID'}) {
$rg_rec->{'ID'} = _getuuid_for_rg();
}
$ids{$rg_rec->{'ID'}} = 1;
}
return $yaml_obj;
}
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