From 015514a890109b36ca15400d5c8ad31b4f30b16c Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Mon, 27 Feb 2017 10:29:22 -0800
Subject: [PATCH] output unused rsids

---
 vcf_rs_grep | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/vcf_rs_grep b/vcf_rs_grep
index 56aef85..4c89281 100755
--- 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};
+    $rsids{$1}++;
     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__
-- 
2.39.2