#!/usr/bin/perl -w
###
# But : ajout ou modif de couleur d'un gff
# 
# Entrees : fichier gff
#
# Sortie : gff affiche a l'ecran
#
###------------------------------------------------------

#!/usr/bin/perl -w                                                                                                                                                     
              
use vars qw($USAGE);                      
use strict;                               

=head1 NAME

sortGff.pl - sort a gff file

=head1 SYNOPSIS

% sortGff.pl -i file.gff [-h] 

=head1 DESCRIPTION
This script will sort a gff file (only when inversion of two successive lines).

    -i|--input fileName  gff input file name
    -o|--output fileName  gff3 output file name
   [-h|--help]           help mode then die                              

=head1 AUTHOR - Claire Toffano-Nioche - mar.11

=cut

#-----------------------
my ($fileName, $colourGff, $outFileName) = ("", "", "sortOut.gff3") ;
   # command line check
    foreach my $num (0 .. $#ARGV) {
        SWITCH: for ($ARGV[$num]) {
        /--input|-i/ && do { 
		$fileName=$ARGV[$num+1]; 
		open ( fichierGff, "< $fileName" ) or die "Can't open gff file: \"$fileName\"\n" ; 
		last };
#		/--output|-o/ && do { 
#		$outFileName=$ARGV[$num+1]; 
#		last };
        /--help|-h/ && do { exec("pod2text $0\n") ; die };
        }
    }
    # informations retrieval
#    open(OUT,">$outFileName") or die "Error can't $outFileName open for output. $!\n";
    my @lines = <fichierGff> ; 
    close fichierGff ;
    # treatment
	#print "gff file read ; number of lines : $#lines\n";
    my $previous = 0;
    my $i = 0;
	#print "$#lines\n" ;
    while ($i <= $#lines) {
	my @infos = split('\t', $lines[$i]) ;
	#print "info[3]:$infos[3]; prv:$previous!\n";
	if ($infos[3] < $previous) {
	    &exchange($i, $infos[3]) ;
	    $previous=$infos[3] ; 
	    $i--;
	} 
	$previous=$infos[3];
	$i++;	
    }
    for (my $i=0 ; $i <= $#lines ; $i++) {
#	print OUT $lines[$i] ;	
	print $lines[$i] ;
    }
#close OUT ;
exit(0);
#-----------------------
sub exchange {
	my ($index, $position) = @_ ;
	my @info_col = split("\t", $lines[$index-1]) ;
	if ($info_col[3] > $position) {
		#print "$lines[$index]";
		my $line_to_push = $lines[$index-1] ;
		$lines[$index-1] = $lines[$index] ;
		$lines[$index] = $line_to_push ;
	} else {
		print "TODO : push > one line\n" ;
	}
}