Lines Matching refs:csq

268         my ($pos,$ref,$alt,$csq) = split(/\t/,$line);
269         my @csq = split(/,/,$csq);
270         chomp($csq[-1]);
271         for my $csq (@csq)
273             if ( $csq=~/Transcript\|$$opts{tscript}/ ) { push @out,$csq; }
276         $csq = join(',',@out);
277         print $out join("\t",($pos,$ref,$alt,$csq))."\n";
298         my ($pos,$ref,$alt,$csq) = split(/\t/,$line);
299         my @csq = split(/,/,$csq);
300         chomp($csq[-1]);
301         for my $csq (@csq)
303             if ( !($csq=~/Transcript/) or $csq=~/Transcript\|$$opts{tscript}/ ) { push @out,$csq; }
306         $csq = join(',',@out);
307         print $out join("\t",($pos,$ref,$alt,$csq))."\n";