add support for merged rs numbers

diff --git a/vcf_rs_grep b/vcf_rs_grep
index 8021b036b41cc6e235a1b20852a3a9e32941e953..56aef856b514d4ca83f94a160650b316e1a4bb60 100755 (executable)
--- a/vcf_rs_grep
+++ b/vcf_rs_grep
@@ -58,6 +58,7 @@ my %options = (debug           => 0,
               );
 
 GetOptions(\%options,
               );
 
 GetOptions(\%options,

+           'merge=s',

            'debug|d+','help|h|?','man|m');
 
 pod2usage() if $options{help};
            'debug|d+','help|h|?','man|m');
 
 pod2usage() if $options{help};


@@ -103,6 +104,20 @@ while (<STDIN>) {
     $rsids{$_} = 1;
 }
 
     $rsids{$_} = 1;
 }
 

+my %merge_rsids;
+if (defined $options{merge}) {
+    my $merge = open_compressed_file($options{merge})
+        or die "Unable to open file $options{merge}: $!";
+    while (<$merge>) {
+        chomp;
+        my ($old,$new,undef) = split /\t/;
+        next unless exists $rsids{'rs'.$old};
+        $merge_rsids{'rs'.$old} = 'rs'.$new;
+        $rsids{'rs'.$new} = 1;
+    }
+    close ($merge);
+}
+

 while (<$vcf>) {
     if (/^#/o) {
         print $_;
 while (<$vcf>) {
     if (/^#/o) {
         print $_;