From: Don Armstrong <don@donarmstrong.com>
Date: Mon, 27 Feb 2017 18:29:13 +0000 (-0800)
Subject: add support for merged rs numbers
X-Git-Url: https://git.donarmstrong.com/?p=bin.git;a=commitdiff_plain;h=05dbb78bfedc7d9de2c0fc7ba70ea93ff9847af4

add support for merged rs numbers
---

diff --git a/vcf_rs_grep b/vcf_rs_grep
index 8021b03..56aef85 100755
--- a/vcf_rs_grep
+++ b/vcf_rs_grep
@@ -58,6 +58,7 @@ my %options = (debug           => 0,
               );
 
 GetOptions(\%options,
+           'merge=s',
            'debug|d+','help|h|?','man|m');
 
 pod2usage() if $options{help};
@@ -103,6 +104,20 @@ while (<STDIN>) {
     $rsids{$_} = 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 $_;