output unused rsids

diff --git a/vcf_rs_grep b/vcf_rs_grep
index 56aef856b514d4ca83f94a160650b316e1a4bb60..4c89281f037abea871e4209f95f92c52a94bca0f 100755 (executable)
--- a/vcf_rs_grep
+++ b/vcf_rs_grep
@@ -126,7 +126,20 @@ while (<$vcf>) {
     $_ =~ /^\S+\s+\S+\s+(\S+)/o;
     next unless $1;
     next unless exists $rsids{$1} and $rsids{$1};
     $_ =~ /^\S+\s+\S+\s+(\S+)/o;
     next unless $1;
     next unless exists $rsids{$1} and $rsids{$1};

+    $rsids{$1}++;

     print $_;
 }
 
     print $_;
 }
 

+my @unused_rsids;
+for my $rsid (keys %rsids) {
+    if ($rsids{$rsid} == 1) {
+        push @unused_rsids,$rsid;
+    }
+}
+if (@unused_rsids) {
+    print STDERR "The following rsids were not found\n";
+    print STDERR map {$_."\n"} @unused_rsids;
+}
+
+

 __END__
 __END__