Hi Monks, My issue revolves around going back to a do{}while loop in my code, I thought I had figured out how to label it and perlsyn corroborated my theory I thought, but I still can't get it to work, as I get the error: {0}: perl putLinesBackInVCF4.pl -1kg CEU.head.txt -knome wo127.head.txt -o output.txt Label not found for "redo LOOP" at putLinesBackInVCF4.pl line 96, <KGFILE> line 20. Here's my code, I've tried to comment it pretty extensively.

#!/usr/bin/perl
use strict;
use warnings;
use Pod::Usage;
use Getopt::Long;

my $KG_FILE;
my $OUTFILE;
my $KNOME_FILE;

GetOptions(
    '1kg=s'    =>\$KG_FILE,
    'knome=s'    =>\$KNOME_FILE,
    'o=s'    =>\$OUTFILE,
    'help'    =>sub{pod2usage(1);}
) or pod2usage(2);

=head SYNOPSIS

putLinesBackinVCF.pl

Options:

     -1kg      1000 genomes input vcf file
     -knome    knome file with sites
     -o        output file
     -help     display this message

=cut

if (!$KG_FILE){
    pod2usage(2);
    die "Please supply an input 1000 genomes file\n";
}
if(!$KNOME_FILE){
    pod2usage(2);
    die "Please supply our sites file\n";
}
if(!$OUTFILE){
    pod2usage(2);
    die "Please supply an output file\n";
}
unless(open( KGFILE, $KG_FILE)){
    die "Couldn't create link to 1kg file: $!\n";
}
unless(open( KNOME, $KNOME_FILE)){
    die "Couldn't create link to knome input file: $!\n";
}
unless (open( OUTFILE,">", $OUTFILE)){
    die "Couldn't create link to output file: $!\n";
}

my $pos = 0;
while (<KGFILE>){
    if ($_ =~ /^#/){
        next;
    }  # skip header lines...
    my ($kgLine) = $_;
    chomp $kgLine;
    my @kgArr = (split("\t", $kgLine))[0,1]; #grab the chrom and posit
+ion columns
    my $chr;
    my @arr;
LOOP: { 
    do{
    # go through the KNOME file;
    # print out the positions till we reach (or exceed) the position f
+rom the KGFILE

        my $line = <KNOME>;
        if (not defined $line) {
            last;
        }
        chomp $line;
        @arr = (split("\t", $line))[0,1];
        $arr[0] =~ s/^0//;
        $chr = $arr[0];     #remove leading 0's from chromosome number
        $pos = $arr[1]+1;   #to adjust positions to base 1 rather than
+ base 0
        if ($pos < $kgArr[1]){
            print OUTFILE "$chr\t$pos\n";  #probably unncessary if sta
+tement but shouldn't hurt anything even if so
        }

    } while $pos < $kgArr[1];
}
    if($kgArr[1] < $pos){    #at this point the position from KNOME is
+ no longer LESS THAN position from KGFILE
        print OUTFILE $kgLine,"\n";
        while ($kgArr[1] < $pos){  
#if last position from KNOME is GREATER THAN position from KGFILE we n
+ow need to loop through
#and print all the lines from KGFILE until we catch back up to KNOME's
+ position!
            my $catchup = (<KGFILE>);
            chomp $catchup;
            @kgArr = (split("\t", $catchup))[0,1];
            if ($kgArr[1] == $pos){   #If we get to the point where th
+ey're equal, good... just print, this while loop will end, and we'll 
+start the whole process over
                print OUTFILE $catchup,"\n";
            }
            elsif($kgArr[1] > $pos){
                print OUTFILE "$chr\t$pos\n";
                redo LOOP ;
                last;
                #print OUTFILE "$catchup\n"; 
#if KGFILE's position has become GREATER than the KNOME $pos again, ho
+wever, it gets tricky...
# but now we need to go through KNOME file positions again and see if 
+that position matches later on...
# can't just quit the loop or this line will be lost, but we don't rea
+lly want to print it here either... 
# 
            }
        }
    }
    elsif($kgArr[1] == $pos){
        print OUTFILE $kgLine,"\n";
    }
}

#if we get to the end of the KGFILE and there's still lines left in th
+e KNOME file, just print the rest of those lines chr and pos values;
while (<KNOME>){
    chomp;
    my @remainingArr = (split("\t", $_))[0,1];
    $remainingArr[0] =~ s/^0//;
    my $remChr = $remainingArr[0];
    my $remPos = $remainingArr[1]+1;
    print OUTFILE "$remChr\t$remPos\n";
}
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