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 '*' )