#!/usr/bin/perl -w

#usage : perl sm_gatk_1_addrg_index
#sarah maman - 12/09/2012

use strict;
use File::Basename;


my $RG = $ARGV[0];
my $SM = $ARGV[1];
my $PF = $ARGV[2];
my $input = $ARGV[3];
my $output = $ARGV[4];
my $name = $RG."_".$SM ;


#pour connaître le path du tool cuadapt, utiliser la commande which cutadapt
my $ADDRG = '/usr/local/bioinfo/bin/addReadGroup.pl';
my $SAMTOOLS = '/usr/local/bioinfo/bin/samtools';
my $cmd = '';

$cmd = "($SAMTOOLS view -h $input | perl $ADDRG -i - -r $RG -s $SM -p $PF | $SAMTOOLS view -bS - -o $name.bam) >& ./addrg.log";
system $cmd;

#Fournir la ligne de commande aux biologistes via le stdout
print STDOUT "La ligne de commande utilisee est : \n\n $SAMTOOLS view -h $input | perl $ADDRG -i - -r $RG -s $SM -p $PF | $SAMTOOLS view -bS - -o $name.bam \n\n";


if (! -e "$name.bam")
{
print STDERR "Echec lors de la generation du BAM sortant apres addRG\n";
}
else
{
#indexation du BAM SORTANT
#$cmd = "($SAMTOOLS index $name.bam ) >& ./indexBAM.log";
#system $cmd;
`(cp -a \"$name.bam\" $output) >& ./cpaddrg.log 2>&1`
}