From d04b701130b7766900e0c2a810fac6fb62c31a8e Mon Sep 17 00:00:00 2001
From: Petr Danecek <pd3@sanger.ac.uk>
Date: Fri, 12 Feb 2010 09:52:37 +0000
Subject: [PATCH] Print an error for pileups in simple format

---
 misc/sam2vcf.pl | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/misc/sam2vcf.pl b/misc/sam2vcf.pl
index c2644f5..e722e74 100755
--- a/misc/sam2vcf.pl
+++ b/misc/sam2vcf.pl
@@ -117,7 +117,12 @@ sub do_pileup_to_vcf
     while (my $line=<$fh_in>)
     {
         chomp($line);
-        my ($chr,$pos,$ref,$cons,$cons_qual,$snp_qual,$rms_qual,$depth,@items) = split(/\t/,$line);
+        my (@items) = split(/\t/,$line);
+        if ( scalar @items<8 ) 
+        { 
+            error("\nToo few columns, does not look like output of 'samtools pileup -c': $line\n"); 
+        }
+        my ($chr,$pos,$ref,$cons,$cons_qual,$snp_qual,$rms_qual,$depth) = @items;
 
         my ($alt,$gt);
         if ( $ref eq '*' )
-- 
2.39.2