#!/usr/bin/perl

use strict;
use warnings;

my($i, $j, $k);
my $parameters = {};

sub usage {
    print "\nUsage: $0 \n\n\t ";
    print "REQUIRED \n\t ";
    print "-config <config_file> \n\n";
    exit(1);
}
if(scalar(@ARGV) == 0){
    usage();
}

# Parse the Command Line
&parse_command_line($parameters, @ARGV);

# Log File
my $log_file = $parameters->{config_file} . ".log";
unless ( open(LOG_FILE, ">$log_file") ) {
    print "Cannot open file \"$log_file\" to write to!!\n\n";
    exit;
}
print LOG_FILE "config = $parameters->{config_file}\n";

# Time Stamp
my $timestamp = localtime(time);
print LOG_FILE $timestamp, "\n";

# Parse Config File
my @samples = ();
my $number_of_samples = &parse_config_file(\@samples, \$parameters);
print LOG_FILE "directory = $parameters->{directory}\n\n";

my $files = {};
# Create Target Regions File
$files->{target_regions_file} = $parameters->{directory} . "/target_regions.dat";
&create_target_regions_file(\$parameters, \$files, \*LOG_FILE);

my @tags = ();
my($reads, $tag);
my($fastq_file_1, $fastq_file_2);
my %proceed = ();
my $alignment_string = '';
my $number_of_alignment_files = 0;
my $cmd = '';

for($i = 0; $i < $number_of_samples; $i++){

    # Define Tags
    &define_tags(\@samples, \@tags, \$reads, \$tag, \$fastq_file_1, \$fastq_file_2, \$parameters, \*LOG_FILE);

    # Check if FASTQ Files Exist and are Non-empty
    $proceed{$i} = &decide_to_proceed(\$reads, \$fastq_file_1, \$fastq_file_2);

    # Create String of FASTQ Files to be Aligned by bwa_enz
    &create_alignment_string($proceed{$i}, \$reads, \$number_of_alignment_files, \$alignment_string, \$fastq_file_1, \$fastq_file_2);
}

# Align the reads with bwa_enz
# Would be better to align paired reads together??
$cmd = &align_reads(\$parameters, $number_of_alignment_files, $alignment_string);
print LOG_FILE $cmd;
system($cmd);

for($i = 0; $i < $number_of_samples; $i++){

    # Define Tags
    &define_tags(\@samples, \@tags, \$reads, \$tag, \$fastq_file_1, \$fastq_file_2, \$parameters, \*LOG_FILE);

    # Define Summary File Names
    &define_summary_file_names(\$tag, \$parameters, \$files);

    if ( $proceed{$i} == 1 ){
	
	# Convert SAM -> BAM -> BED
	&define_alignments_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
	$cmd = &rename_sam_files(\$reads, \$files);
	$cmd .= &alignments(\$reads, \$fastq_file_1, \$fastq_file_2, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# De-duplicate the SAM File(s)
	&define_de_duplication_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
	$cmd = &de_duplication(\$reads, \$fastq_file_1, \$fastq_file_2, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);
	# What if only reverse read exists?  Don't want to de-duplicate?

	# Select On-/Off-Target Reads
	# Split marked files into two files
	&define_on_and_off_target_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
	$cmd = &select_on_and_off_target_reads(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Coverage and Start Sites
	&define_coverage_and_start_site_file_names(\$reads, \@tags, \$parameters, \$files);
	$cmd = &generate_coverage_and_start_sites(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Proceed through the rest of the pipeline using the on-target reads

	# Create Master Files - one line per read
	&define_master_files_file_names(\$reads, \@tags, \$parameters, \$files);
	$cmd = &generate_master_files(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Select Fusion Reads - do not count mapping to a 'novel', i.e., not in refseq, region as a fusion
	&define_fusion_reads_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
	$cmd = &select_fusion_reads(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Count Fusions
	&define_count_fusions_file_names(\$tag, \$parameters, \$files);
	$cmd = &count_fusions(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Flanking Sequences
	&define_flanking_sequences_file_names(\$tag, \$parameters, \$files);
	$cmd = &flanking_sequences(\$reads, \$fastq_file_1, \$fastq_file_2, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# BAM Dedup Files
	&define_bam_dedup_files_file_names(\$reads, \@tags, \$parameters, \$files);
	$cmd = &bam_dedup_files(\$reads, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Consensus Sequences - Fusion and Splice
	#&define_consensus_sequences_file_names(\$tag, \$parameters, \$files);
	#$cmd = &consensus_sequences(\$reads, \$fastq_file_1, \$fastq_file_2, \$tag, \$parameters, \$files);
	#print LOG_FILE $cmd;
	#system($cmd);

	# Sort SAM Files
	&define_sort_sam_files_file_names(\$reads, \@tags, \$parameters, \$files);
	$cmd = &sort_sam_files(\$reads, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# On-target Stats
	&define_on_target_stats_file_names(\$tag, \$parameters, \$files);
	$cmd = &on_target_stats(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Total Molecule Counts
	&define_total_molecule_counts_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
	$cmd = &total_molecule_counts(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# De-duplicated Molecule Counts
	&define_de_deduplicated_molecule_counts_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
	$cmd = &de_duplicated_molecule_counts(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# All Molecule Counts
	&define_all_molecule_counts_file_names(\$tag, \$parameters, \$files);
	$cmd = &all_molecule_counts(\$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# QC Check
	&define_qc_check_file_names(\$tag, \$parameters, \$files);
	$cmd = &qc_check(\$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Coverage Uniformity
	&define_coverage_uniformity_file_names(\$tag, \$parameters, \$files);
	$cmd = &coverage_uniformity(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Summary
	$cmd = &summary(\$tag, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);

	# Clean Up
	$cmd = &clean_up(\$reads, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);
    }
    else{
	# Summary for Unprocessed Sample
	$cmd = &summary_for_unprocessed_sample(\$reads, \$fastq_file_1, \$fastq_file_2, \$parameters, \$files);
	print LOG_FILE $cmd;
	system($cmd);
    }

    # Time Stamp
    $timestamp = localtime(time);
    print LOG_FILE $timestamp, "\n";
}

# Join Multiple Samples
#$cmd = &join_multiple_samples(\$parameters);
#print LOG_FILE $cmd;
#system($cmd);

close(LOG_FILE);

exit;

sub parse_command_line {
    my($parameters, @ARGV) = @_;
    my $next_arg;
    while(scalar @ARGV > 0){
	$next_arg = shift(@ARGV);
	if($next_arg eq "-config"){ $parameters->{config_file} = shift (@ARGV); }
    }
}


sub parse_config_file {
    my $samples_ref = shift;
    my $parameters_ref = shift;
    my @values = ();
    my $count = 0;
    open( FILE, "< $$parameters_ref->{config_file}" ) or die "Can't open $$parameters_ref->{config_file} : $!";
    while( <FILE> ) {
	chomp;
	if ( length($_) > 1 and $_ !~ /^\#/ ){
	    @values = ();
	    @values = split(/=/, $_);
	    if($values[0] eq 'sample'){
		@$samples_ref[$count] = $values[1];
		$count++;
	    }
	    else{
		$$parameters_ref->{$values[0]} = $values[1];
	    }
	}
    }
    my $num_samples = scalar @$samples_ref;
    print "number of samples = $num_samples\n";
    return $num_samples;
}


sub create_target_regions_file {
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $file_handle_ref = shift;
    my $cmd = '';

    if ( ($$parameters_ref->{control_regions_file} ne 'NULL') && ($$parameters_ref->{target_regions_file} ne 'NULL') ) {
	$cmd = "cat $$parameters_ref->{control_regions_file} $$parameters_ref->{target_regions_file} > $$files_ref->{target_regions_file}\n";
	print $file_handle_ref $cmd;
	system($cmd);
    }
    elsif ( $$parameters_ref->{target_regions_file} ne 'NULL' ) {
	$$files_ref->{target_regions_file} = $$parameters_ref->{target_regions_file};
    }
    elsif ( $$parameters_ref->{control_regions_file} ne 'NULL' ) {
	$$files_ref->{target_regions_file} = $$parameters_ref->{control_regions_file};
    }
    else { # Create Target Regions File
	my $label;
	my $target_file = $$parameters_ref->{directory} . "/target_file.dat";
	my $control_file = $$parameters_ref->{directory} . "/control_file.dat";
	my $target_temp_outputfile_1 = $$parameters_ref->{directory} . "/target_temp_1.dat";
	my $target_temp_outputfile_2 = $$parameters_ref->{directory} . "/target_temp_2.dat";
	my $control_temp_outputfile_1 = $$parameters_ref->{directory} . "/control_temp_1.dat";
	my $control_temp_outputfile_2 = $$parameters_ref->{directory} . "/control_temp_2.dat";
	my $path_to_annotation_script = $$parameters_ref->{path} . "/archer/annotation/";
	# Target Primers Fasta File
	if ( -e $$parameters_ref->{target_primers} ) {
	    if ( -s $$parameters_ref->{target_primers} ) {
		$label = 'fusion';
		$cmd = "$$parameters_ref->{path}/create_target_regions_file.pl -target $$parameters_ref->{target_primers} -label $label -refseq $$parameters_ref->{refseq_file} -gtf_file $$parameters_ref->{gtf_file} -path $path_to_annotation_script -t1 $target_temp_outputfile_1 -t2 $target_temp_outputfile_2 -o $target_file\n";
		print $file_handle_ref $cmd;
		system($cmd);
	    }
	}
	# Control Primers Fasta File
	if ( -e $$parameters_ref->{control_primers} ) {
	    if ( -s $$parameters_ref->{control_primers} ) {
		$label = 'housekeeping';
		$cmd = "$$parameters_ref->{path}/create_target_regions_file.pl -target $$parameters_ref->{control_primers} -label $label -refseq $$parameters_ref->{refseq_file} -gtf_file $$parameters_ref->{gtf_file} -path $path_to_annotation_script -t1 $control_temp_outputfile_1 -t2 $control_temp_outputfile_2 -o $control_file\n";
		print $file_handle_ref $cmd;
		system($cmd);
	    }
	}
	if ( -e $control_file ) {
	    if ( -s $control_file ) {
		$cmd = "cp $control_file $$files_ref->{target_regions_file}\n";
		if ( -e $target_file ) {
		    if ( -s $target_file ) {
			$cmd .= "cat $target_file >> $$files_ref->{target_regions_file}\n";
		    }
		}
		print $file_handle_ref $cmd;
		system($cmd);
	    }
	}
	elsif ( -e $target_file ) {
	    if ( -s $target_file ) {
		$cmd = "cp $target_file $$files_ref->{target_regions_file}\n";
		print $file_handle_ref $cmd;
		system($cmd);
	    }
	}
	$cmd = '';
	if ( -e $target_file ) {
	    $cmd .= "rm $target_temp_outputfile_1\n";
	    $cmd .= "rm $target_temp_outputfile_2\n";
	}
	if ( -e $control_file ) {
	    $cmd .= "rm $control_temp_outputfile_1\n";
	    $cmd .= "rm $control_temp_outputfile_2\n";
	}
	print $file_handle_ref $cmd;
	system($cmd);

	$cmd = '';
	if ( -e $target_file ) {
	    $cmd .= "rm $target_file\n";
	}
	if ( -e $control_file ) {
	    $cmd .= "rm $control_file\n";
	}
	print $file_handle_ref $cmd;
	system($cmd);

	print $file_handle_ref "\n";
    }
}


sub define_tags {
    my $samples_array_ref = shift;
    my $tags_array_ref = shift;
    my $reads_ref = shift;
    my $tag_ref = shift;
    my $fastq_file_1_ref = shift;
    my $fastq_file_2_ref = shift;
    my $parameters_ref = shift;
    my $file_handle_ref = shift;

    @$tags_array_ref = ();
    @$tags_array_ref = split(/\s+/, @$samples_array_ref[$i]); # Split samples on whitespace

    if( (scalar @$tags_array_ref) == 1 ){
	$$reads_ref = 'single';
	$$tag_ref = $tags[0];
	$$fastq_file_1_ref = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".fastq";
    }
    else{
	$$reads_ref = 'paired';
	$$tag_ref = @$tags_array_ref[0] . "_" . @$tags_array_ref[1];
	$$fastq_file_1_ref = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".fastq";
	$$fastq_file_2_ref = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".fastq";
    }

    print $$tag_ref, "\n";

    print $file_handle_ref $$tag_ref, "\n";
}


sub decide_to_proceed {
    my $reads_ref = shift;
    my $fastq_file_1_ref = shift;
    my $fastq_file_2_ref = shift;
    my $proceed = 0;

    if ( $$reads_ref eq 'single' ) {
	if ( -e $$fastq_file_1_ref ) {
	    if ( -s $$fastq_file_1_ref ) {
		$proceed = 1;
	    }
	}
	else{
	    $$fastq_file_1_ref .= ".gz"; # See if fastq_file_1 exists in gzipped form
	    if ( -e $$fastq_file_1_ref ) {
		if ( -s $$fastq_file_1_ref ) {
		    $proceed = 1;
		}
	    }
	}
    }
    if ( $$reads_ref eq 'paired' ) {
	if ( -e $$fastq_file_1_ref ) {
	    if ( -s $$fastq_file_1_ref ) {
		if ( -e $$fastq_file_2_ref ) {
		    if ( -s $$fastq_file_2_ref ) {
			$proceed = 1;
		    }
		}
		else{
		    $$fastq_file_2_ref .= ".gz"; # See if fastq_file_2 exists in gzipped form
		    if ( -e $$fastq_file_2_ref ) {
			if ( -s $$fastq_file_2_ref ) {
			    $proceed = 1;
			}
		    }
		}
	    }
	}
	else{
	    $$fastq_file_1_ref .= ".gz"; # See if fastq_file_1 exists in gzipped form
	    if ( -e $$fastq_file_1_ref ) {
		if ( -s $$fastq_file_1_ref ) {
		    if ( -e $$fastq_file_2_ref ) {
			if ( -s $$fastq_file_2_ref ) {
			    $proceed = 1;
			}
		    }
		    else{
			$$fastq_file_2_ref .= ".gz"; # See if fastq_file_2 exists in gzipped form
			if ( -e $$fastq_file_2_ref ) {
			    if ( -s $$fastq_file_2_ref ) {
				$proceed = 1;
			    }
			}
		    }
		}
	    }
	}
    }
    return $proceed;
}


sub create_alignment_string {
    my $proceed_value = shift;
    my $reads_ref = shift;
    my $number_of_alignment_files_ref = shift;
    my $alignment_string_ref = shift;
    my $fastq_file_1_ref = shift;
    my $fastq_file_2_ref = shift;

    if ( $proceed_value == 1 ) {
	if ( $$number_of_alignment_files_ref == 0 ){
	    $$alignment_string_ref = $$fastq_file_1_ref;
	}
	else {
	    $$alignment_string_ref .= " " . $$fastq_file_1_ref;
	}
	$$number_of_alignment_files_ref++;
	if ( $$reads_ref eq 'paired' ) {
	    $$alignment_string_ref .= " " . $$fastq_file_2_ref;
	    $$number_of_alignment_files_ref++;
	}
    }
}


sub align_reads {
    my $parameters_ref = shift;
    my $number_of_alignment_files_value = shift;
    my $alignment_string_value = shift;
    my $cmd_line = "echo Align Reads\n";
    if ( $number_of_alignment_files_value > 0 ) {
	$cmd_line .= "bwa_enz mem -Q 0 -m -D $$parameters_ref->{directory} $$parameters_ref->{reference_file} $alignment_string_value\n";	
    }
    return $cmd_line;
}


sub rename_sam_files {
    my $reads_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Rename SAM Files\n";
    $cmd_line .= "mv $$files_ref->{sam_file_1_orig} $$files_ref->{sam_file_1_full}\n";
    if ( $$reads_ref eq 'paired' ) {
	$cmd_line .= "mv $$files_ref->{sam_file_2_orig} $$files_ref->{sam_file_2_full}\n";
    }
    return $cmd_line;
}


sub alignments {
    my $reads_ref = shift;
    my $fastq_file_1_ref = shift;
    my $fastq_file_2_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Alignments\n";

    # -S input is SAM
    # -b output is BAM
    # -h print header for the SAM output

#    $cmd_line .= "bwa mem $$parameters_ref->{reference_file} $$fastq_file_1_ref > $$files_ref->{sam_file_1_full}\n";
    $cmd_line .= "samtools view -Shq 40 $$files_ref->{sam_file_1_full} > $$files_ref->{sam_file_1}\n";
    $cmd_line .= "samtools view -bS $$files_ref->{sam_file_1} > $$files_ref->{bam_file_1}\n";
    $cmd_line .= "bamToBed -i $$files_ref->{bam_file_1} > $$files_ref->{bed_file_1_orig}\n";
    if ( $$reads_ref eq 'single' ) {
	$cmd_line .= "mv $$files_ref->{bed_file_1_orig} $$files_ref->{bed_file_combined}\n";
    }
    elsif ( $$reads_ref eq 'paired' ) {
#	$cmd_line .= "bwa mem $$parameters_ref->{reference_file} $$fastq_file_2_ref > $$files_ref->{sam_file_2_full}\n";
	$cmd_line .= "samtools view -Shq 40 $$files_ref->{sam_file_2_full} > $$files_ref->{sam_file_2}\n";
	$cmd_line .= "samtools view -bS $$files_ref->{sam_file_2} > $$files_ref->{bam_file_2}\n";
	$cmd_line .= "bamToBed -i $$files_ref->{bam_file_2} > $$files_ref->{bed_file_2_orig}\n";
	$cmd_line .= "cat $$files_ref->{bed_file_1_orig} $$files_ref->{bed_file_2_orig} > $$files_ref->{bed_file_combined}\n";
	$cmd_line .= "rm $$files_ref->{bed_file_1_orig}\n";
	$cmd_line .= "rm $$files_ref->{bed_file_2_orig}\n";
    }
    return $cmd_line;
}


sub de_duplication {
    my $reads_ref = shift;
    my $fastq_file_1_ref = shift;
    my $fastq_file_2_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo De-duplication\n";

    if ( $$reads_ref eq 'single' ) {
	$cmd_line .= "sort -k4,4 $$files_ref->{bed_file_combined}|$$parameters_ref->{path}/dedup_pipeline.sh -p $$parameters_ref->{path} -b /dev/stdin -f $$fastq_file_1_ref > $$files_ref->{dedup_file}\n";
    }
    else{
	$cmd_line .= "sort -k4,4 $$files_ref->{bed_file_combined}|$$parameters_ref->{path}/dedup_pipeline.sh -p $$parameters_ref->{path} -b /dev/stdin -f $$fastq_file_1_ref -2 $$fastq_file_2_ref > $$files_ref->{dedup_file}\n";
    }
    $cmd_line .= "$$parameters_ref->{path}/de_dup_2_hash.pl -dedup $$files_ref->{dedup_file} -sam $$files_ref->{sam_file_1} -o $$files_ref->{sam_dedup_file_1}\n";
    $cmd_line .= "$$parameters_ref->{path}/de_dup_2_hash.pl -dedup $$files_ref->{dedup_file} -sam $$files_ref->{sam_file_1_full} -o $$files_ref->{sam_dedup_file_1_full}\n";
    if ( $$reads_ref eq 'paired' ) {
	$cmd_line .= "$$parameters_ref->{path}/de_dup_2_hash.pl -dedup $$files_ref->{dedup_file} -sam $$files_ref->{sam_file_2} -o $$files_ref->{sam_dedup_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/de_dup_2_hash.pl -dedup $$files_ref->{dedup_file} -sam $$files_ref->{sam_file_2_full} -o $$files_ref->{sam_dedup_file_2_full}\n";
    }
    return $cmd_line;
}


sub select_on_and_off_target_reads {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Select On- and Off-target Reads\n";

    # Create BED file of target regions
    $cmd_line .= "$$parameters_ref->{path}/convert_target_regions_to_bed.pl -t $$files_ref->{target_regions_file} -o $$files_ref->{target_regions_bed_file}\n";

    # All Reads
    # Create a master file from the SAM file
    # Join the master file
    # Select the appropriate segment for each read id and create a BED file - need to have only one entry for each read in the BED file
    # Convert BED files of reads to single points - do this so that only start of R2 and end of R1 are counted in overlapping with the target regions so that only the target region that overlaps with these end points will be counted as being hit - assumes that there are no overlapping regions in the target regions file
    # Get intersection of reads with target regions
    $cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_file_1} -o $$files_ref->{full_master_prejoin_file_1}\n";
    $cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{full_master_prejoin_file_1} -o $$files_ref->{full_master_file_1}\n";
    $cmd_line .= "$$parameters_ref->{path}/convert_master_file_to_bed.pl -master $$files_ref->{full_master_file_1} -read $$reads_ref -tag 1 -o $$files_ref->{bed_file_1}\n";
    $cmd_line .= "$$parameters_ref->{path}/convert_bed_to_single_points.pl -b $$files_ref->{bed_file_1} -read $$reads_ref -tag 1 -o $$files_ref->{bed_points_file_1}\n";
    $cmd_line .= "intersectBed -a $$files_ref->{target_regions_bed_file} -b $$files_ref->{bed_points_file_1} -wa -wb > $$files_ref->{intersect_file_1}\n";
    if ( $$reads_ref eq 'paired' ) {
	$cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_file_2} -o $$files_ref->{full_master_prejoin_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{full_master_prejoin_file_2} -o $$files_ref->{full_master_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/convert_master_file_to_bed.pl -master $$files_ref->{full_master_file_2} -read $$reads_ref -tag 2 -o $$files_ref->{bed_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/convert_bed_to_single_points.pl -b $$files_ref->{bed_file_2} -read $$reads_ref -tag 2 -o $$files_ref->{bed_points_file_2}\n";
	$cmd_line .= "intersectBed -a $$files_ref->{target_regions_bed_file} -b $$files_ref->{bed_points_file_2} -wa -wb > $$files_ref->{intersect_file_2}\n";
	$cmd_line .= "cat $$files_ref->{intersect_file_1} $$files_ref->{intersect_file_2} > $$files_ref->{intersect_file_combined}\n";
    }
    # Create SAM files of the on- and off-target reads.  On-target files contain all reads in which at least one of R1/R2 is on-target.  Off-target files contain the remaining reads.
    # On-/Off-target Alone Read 1
    $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_file_1} -i $$files_ref->{intersect_file_1} -on $$files_ref->{sam_on_target_alone_file_1}\n";
    $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_file_1} -on $$files_ref->{sam_on_target_alone_file_1} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_file_1_marked}\n";
    $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_file_1_marked} > $$files_ref->{sam_off_target_alone_file_1}\n";
    if ( $$reads_ref eq 'paired' ) {
	# On-/Off-target Alone Read 2
	$cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_file_2} -i $$files_ref->{intersect_file_2} -on $$files_ref->{sam_on_target_alone_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_file_2} -on $$files_ref->{sam_on_target_alone_file_2} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_file_2_marked}\n";
	$cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_file_2_marked} > $$files_ref->{sam_off_target_alone_file_2}\n";
	# On-/Off-target Either Read 1
	$cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_file_1} -i $$files_ref->{intersect_file_combined} -on $$files_ref->{sam_on_target_file_1}\n";
	$cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_file_1} -on $$files_ref->{sam_on_target_file_1} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_file_1_marked}\n";
	$cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_file_1_marked} > $$files_ref->{sam_off_target_file_1}\n";
	# On-/Off-target Either Read 2
	$cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_file_2} -i $$files_ref->{intersect_file_combined} -on $$files_ref->{sam_on_target_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_file_2} -on $$files_ref->{sam_on_target_file_2} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_file_2_marked}\n";
	$cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_file_2_marked} > $$files_ref->{sam_off_target_file_2}\n";
    }
    
    # De-duplicated Reads
    $cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_file_1} -o $$files_ref->{full_master_dedup_prejoin_file_1}\n";
    $cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{full_master_dedup_prejoin_file_1} -o $$files_ref->{full_master_dedup_file_1}\n";
    $cmd_line .= "$$parameters_ref->{path}/convert_master_file_to_bed.pl -master $$files_ref->{full_master_dedup_file_1} -read $$reads_ref -tag 1 -o $$files_ref->{bed_dedup_file_1}\n";
    $cmd_line .= "$$parameters_ref->{path}/convert_bed_to_single_points.pl -b $$files_ref->{bed_dedup_file_1} -read $$reads_ref -tag 1 -o $$files_ref->{bed_points_dedup_file_1}\n";
    $cmd_line .= "intersectBed -a $$files_ref->{target_regions_bed_file} -b $$files_ref->{bed_points_dedup_file_1} -wa -wb > $$files_ref->{intersect_dedup_file_1}\n";
    if ( $$reads_ref eq 'paired' ) {
	$cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_file_2} -o $$files_ref->{full_master_dedup_prejoin_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{full_master_dedup_prejoin_file_2} -o $$files_ref->{full_master_dedup_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/convert_master_file_to_bed.pl -master $$files_ref->{full_master_dedup_file_2} -read $$reads_ref -tag 2 -o $$files_ref->{bed_dedup_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/convert_bed_to_single_points.pl -b $$files_ref->{bed_dedup_file_2} -read $$reads_ref -tag 2 -o $$files_ref->{bed_points_dedup_file_2}\n";
	$cmd_line .= "intersectBed -a $$files_ref->{target_regions_bed_file} -b $$files_ref->{bed_points_dedup_file_2} -wa -wb > $$files_ref->{intersect_dedup_file_2}\n";
	$cmd_line .= "cat $$files_ref->{intersect_dedup_file_1} $$files_ref->{intersect_dedup_file_2} > $$files_ref->{intersect_dedup_file_combined}\n";
    }
    # Create SAM files of the on- and off-target reads.  On-target files contain all reads in which at least one of R1/R2 is on-target.  Off-target files contain the remaining reads.
    # On-/Off-target Alone Read 1
    $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_dedup_file_1} -i $$files_ref->{intersect_dedup_file_1} -on $$files_ref->{sam_dedup_on_target_alone_file_1}\n";
    $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_dedup_file_1} -on $$files_ref->{sam_dedup_on_target_alone_file_1} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_dedup_file_1_marked}\n";
    $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_dedup_file_1_marked} > $$files_ref->{sam_dedup_off_target_alone_file_1}\n";
    if ( $$reads_ref eq 'paired' ) {
	# On-/Off-target Alone Read 2
	$cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_dedup_file_2} -i $$files_ref->{intersect_dedup_file_2} -on $$files_ref->{sam_dedup_on_target_alone_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_dedup_file_2} -on $$files_ref->{sam_dedup_on_target_alone_file_2} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_dedup_file_2_marked}\n";
	$cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_dedup_file_2_marked} > $$files_ref->{sam_dedup_off_target_alone_file_2}\n";
	# On-/Off-target Either Read 1
	$cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_dedup_file_1} -i $$files_ref->{intersect_dedup_file_combined} -on $$files_ref->{sam_dedup_on_target_file_1}\n";
	$cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_dedup_file_1} -on $$files_ref->{sam_dedup_on_target_file_1} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_dedup_file_1_marked}\n";
	$cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_dedup_file_1_marked} > $$files_ref->{sam_dedup_off_target_file_1}\n";
        # On-/Off-target Either Read 2	
	$cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_dedup_file_2} -i $$files_ref->{intersect_dedup_file_combined} -on $$files_ref->{sam_dedup_on_target_file_2}\n";
	$cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_dedup_file_2} -on $$files_ref->{sam_dedup_on_target_file_2} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_dedup_file_2_marked}\n";
	$cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_dedup_file_2_marked} > $$files_ref->{sam_dedup_off_target_file_2}\n";
    }
    return $cmd_line;
}


sub generate_coverage_and_start_sites {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Generate Coverage and Start Sites\n";

    $cmd_line .= "bash $$parameters_ref->{path}/generateHistAndStartSiteInfo.sh $$files_ref->{sam_dedup_file_1} $$parameters_ref->{reference_file} $$parameters_ref->{reference_file_index} $$files_ref->{start_site_dedup_file_1} $$files_ref->{coverage_dedup_file_1} $$parameters_ref->{path}\n";

    if ( $$reads_ref eq 'paired' ) {
	$cmd_line .= "bash $$parameters_ref->{path}/generateHistAndStartSiteInfo.sh $$files_ref->{sam_dedup_file_2} $$parameters_ref->{reference_file} $$parameters_ref->{reference_file_index} $$files_ref->{start_site_dedup_file_2} $$files_ref->{coverage_dedup_file_2} $$parameters_ref->{path}\n";
    }

    return $cmd_line;
}


sub generate_master_files {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Generate Master Files\n";

    # Create a master file of all reads with one line per read
    if ( $$reads_ref eq 'single' ) {
	$cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_on_target_alone_file_1} -o $$files_ref->{master_dedup_no_annotation_file_1}\n";
    }
    else{
	$cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_on_target_file_1} -o $$files_ref->{master_dedup_no_annotation_file_1}\n";
    }

    $cmd_line .= "python $$parameters_ref->{path}/archer/annotation/annotate.py --gtf_file $$parameters_ref->{gtf_file} --coordinate_file $$files_ref->{master_dedup_no_annotation_file_1} --outfile $$files_ref->{master_dedup_prejoin_file_1} --chromosome_indices 1,1 --coordinate_indices 5,6\n";

    $cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{master_dedup_prejoin_file_1} -o $$files_ref->{master_dedup_file_1}\n";
    
    if ( $$reads_ref eq 'paired' ) {
	$cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_on_target_file_2} -o $$files_ref->{master_dedup_no_annotation_file_2}\n";

	$cmd_line .= "python $$parameters_ref->{path}/archer/annotation/annotate.py --gtf_file $$parameters_ref->{gtf_file} --coordinate_file $$files_ref->{master_dedup_no_annotation_file_2} --outfile $$files_ref->{master_dedup_prejoin_file_2} --chromosome_indices 1,1 --coordinate_indices 5,6\n";

	$cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{master_dedup_prejoin_file_2} -o $$files_ref->{master_dedup_file_2}\n";
    }
    
    return $cmd_line;
}

sub select_fusion_reads {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Select Fusion Reads\n";
 
    $cmd_line .= "$$parameters_ref->{path}/select_fusion_reads.pl -master $$files_ref->{master_dedup_file_1} -tag 1 -o1 $$files_ref->{one_segment_reads_file_1} -os $$files_ref->{splice_reads_file_1} -of $$files_ref->{fusion_reads_file_1} -omf $$files_ref->{multi_fusion_reads_file_1}\n";

    if ( $$reads_ref eq 'single' ) {
	$cmd_line .= "cp $$files_ref->{fusion_reads_file_1} $$files_ref->{fusion_reads_file}\n";
	$cmd_line .= "cp $$files_ref->{splice_reads_file_1} $$files_ref->{splice_reads_file}\n";
    }

    if ( $$reads_ref eq 'paired' ) {
	$cmd_line .= "$$parameters_ref->{path}/select_fusion_reads.pl -master $$files_ref->{master_dedup_file_2} -tag 2 -o1 $$files_ref->{one_segment_reads_file_2} -os $$files_ref->{splice_reads_file_2} -of $$files_ref->{fusion_reads_file_2} -omf $$files_ref->{multi_fusion_reads_file_2}\n";
	$cmd_line .= "cat $$files_ref->{fusion_reads_file_1} $$files_ref->{fusion_reads_file_2} > $$files_ref->{fusion_reads_file}\n";
	$cmd_line .= "cat $$files_ref->{splice_reads_file_1} $$files_ref->{splice_reads_file_2} > $$files_ref->{splice_reads_file}\n";
    }

    return $cmd_line;
}

sub count_fusions {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Count Fusions and Splice Events\n";

    # Count the number of each type of fusion pair, i.e., Gene A Exon X with Gene B Exon Y, get the median value of the coordinate of each breakpoint, sort and output each type
    $cmd_line .= "$$parameters_ref->{path}/count_fusions.pl -t $$files_ref->{target_regions_file} -fr $$files_ref->{fusion_reads_file} -min 30 -gtf $$parameters_ref->{gtf_file} -read $$reads_ref -limit 10 -min_occ 5 -ob $$files_ref->{fusion_counts_bare_file} -o $$files_ref->{fusion_counts_file}\n";

    # Count the number of each type of splice pair - Use default values for -limit and -min_occ so that all splices will be reported
    $cmd_line .= "$$parameters_ref->{path}/count_fusions.pl -t $$files_ref->{target_regions_file} -fr $$files_ref->{splice_reads_file} -min 30 -gtf $$parameters_ref->{gtf_file} -read $$reads_ref -ob $$files_ref->{splice_counts_bare_file} -o $$files_ref->{splice_counts_file}\n";

    # Add splice evidence to fusion counts
    $cmd_line .= "$$parameters_ref->{path}/add_splice_to_fusion_counts.pl -fcb $$files_ref->{fusion_counts_bare_file} -scb $$files_ref->{splice_counts_bare_file} -o $$files_ref->{fusion_counts_with_splice_bare_file} -om $$files_ref->{fusion_counts_with_splice_bare_file_machine}\n";

    return $cmd_line;
}


sub flanking_sequences {
    my $reads_ref = shift;
    my $fastq_file_1_ref = shift;
    my $fastq_file_2_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Flanking Sequences\n";
    
    if ( $$reads_ref eq 'single' ) {
	$cmd_line .= "$$parameters_ref->{path}/flanking_sequences.pl -fcb $$files_ref->{fusion_counts_bare_file} -fr $$files_ref->{fusion_reads_file} -read $$reads_ref -fastq_1 $$fastq_file_1_ref -o $$files_ref->{flanking_sequences_file}\n";
	$cmd_line .= "$$parameters_ref->{path}/flanking_sequences.pl -fcb $$files_ref->{splice_counts_bare_file} -fr $$files_ref->{splice_reads_file} -read $$reads_ref -fastq_1 $$fastq_file_1_ref -o $$files_ref->{flanking_splice_sequences_file}\n";
    }
    else{
	$cmd_line .= "$$parameters_ref->{path}/flanking_sequences.pl -fcb $$files_ref->{fusion_counts_bare_file} -fr $$files_ref->{fusion_reads_file} -read $$reads_ref -fastq_1 $$fastq_file_1_ref -fastq_2 $$fastq_file_2_ref -o $$files_ref->{flanking_sequences_file}\n";
	$cmd_line .= "$$parameters_ref->{path}/flanking_sequences.pl -fcb $$files_ref->{splice_counts_bare_file} -fr $$files_ref->{splice_reads_file} -read $$reads_ref -fastq_1 $$fastq_file_1_ref -fastq_2 $$fastq_file_2_ref -o $$files_ref->{flanking_splice_sequences_file}\n";
    }
    return $cmd_line;
}


sub bam_dedup_files {
    my $reads_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo BAM Dedup Files\n";
    # Make sorted de-dup BAM files
    $cmd_line .= "samtools view -bS $$files_ref->{sam_dedup_file_1} > $$files_ref->{bam_dedup_file_1}\n";
    $cmd_line .= "samtools sort $$files_ref->{bam_dedup_file_1} $$files_ref->{bam_dedup_sorted_file_1_name}\n";
    $cmd_line .= "samtools index $$files_ref->{bam_dedup_sorted_file_1}\n";
    if ( $$reads_ref eq 'paired' ) {
	$cmd_line .= "samtools view -bS $$files_ref->{sam_dedup_file_2} > $$files_ref->{bam_dedup_file_2}\n";
	$cmd_line .= "samtools sort $$files_ref->{bam_dedup_file_2} $$files_ref->{bam_dedup_sorted_file_2_name}\n";
	$cmd_line .= "samtools index $$files_ref->{bam_dedup_sorted_file_2}\n";
    }
    return $cmd_line;
}


sub consensus_sequences {
    my $reads_ref = shift;
    my $fastq_file_1_ref = shift;
    my $fastq_file_2_ref = shift;
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Consensus Sequences\n";

    # Fusion and Splice Consensus Sequences
    if ( $$reads_ref eq 'single' ) {
	$cmd_line .= "bash $$parameters_ref->{path}/consensus_pipeline/batch_pipeline.sh -1 $$files_ref->{bam_dedup_sorted_file_1} -a $$fastq_file_1_ref -f $$parameters_ref->{reference_file} -r $$files_ref->{flanking_sequences_file} -d $$parameters_ref->{path}/consensus_pipeline/ -s $$files_ref->{consensus_fusion_std_out_file} -e $$files_ref->{consensus_fusion_std_err_file}\n";
	$cmd_line .= "bash $$parameters_ref->{path}/consensus_pipeline/batch_pipeline.sh -1 $$files_ref->{bam_dedup_sorted_file_1} -a $$fastq_file_1_ref -f $$parameters_ref->{reference_file} -r $$files_ref->{flanking_splice_sequences_file} -d $$parameters_ref->{path}/consensus_pipeline/ -s $$files_ref->{consensus_splice_std_out_file} -e $$files_ref->{consensus_splice_std_err_file}\n";
    }
    else{
	$cmd_line .= "bash $$parameters_ref->{path}/consensus_pipeline/batch_pipeline.sh -1 $$files_ref->{bam_dedup_sorted_file_1} -2 $$files_ref->{bam_dedup_sorted_file_2} -a $$fastq_file_1_ref -b $$fastq_file_2_ref -f $$parameters_ref->{reference_file} -r $$files_ref->{flanking_sequences_file} -d $$parameters_ref->{path}/consensus_pipeline/ -s $$files_ref->{consensus_fusion_std_out_file} -e $$files_ref->{consensus_fusion_std_err_file}\n";
	$cmd_line .= "bash $$parameters_ref->{path}/consensus_pipeline/batch_pipeline.sh -1 $$files_ref->{bam_dedup_sorted_file_1} -2 $$files_ref->{bam_dedup_sorted_file_2} -a $$fastq_file_1_ref -b $$fastq_file_2_ref -f $$parameters_ref->{reference_file} -r $$files_ref->{flanking_splice_sequences_file} -d $$parameters_ref->{path}/consensus_pipeline/ -s $$files_ref->{consensus_splice_std_out_file} -e $$files_ref->{consensus_splice_std_err_file}\n";
    }
    
    # Pair Fusion Candidates with Splice Sequences
    $cmd_line .= "$$parameters_ref->{path}/pair_fusion_and_splice_sequences.pl -fc $$files_ref->{fusion_counts_bare_file} -sc $$files_ref->{splice_counts_bare_file} -tag $$tag_ref -o $$files_ref->{fusion_and_splice_consensus_file}\n";
    
    return $cmd_line;
}


sub sort_sam_files {
    my $reads_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Sort SAM Files\n";

    $cmd_line .= "sort -k1,1 $$files_ref->{sam_on_target_alone_file_1} > $$files_ref->{sam_on_target_alone_file_1_linux_sorted}\n";
    $cmd_line .= "sort -k1,1 $$files_ref->{sam_off_target_alone_file_1} > $$files_ref->{sam_off_target_alone_file_1_linux_sorted}\n";
    $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_on_target_alone_file_1} > $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted}\n";
    $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_off_target_alone_file_1} > $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted}\n";

    $cmd_line .= "samtools view -bS $$files_ref->{sam_file_1_full} > $$files_ref->{bam_file_1_full}\n";
    $cmd_line .= "samtools sort -n $$files_ref->{bam_file_1_full} $$files_ref->{bam_file_1_full_prefix}\n";
    $cmd_line .= "samtools view -h $$files_ref->{bam_file_1_full_sorted} > $$files_ref->{sam_file_1_full_sorted}\n";
    $cmd_line .= "samtools view -bS $$files_ref->{sam_dedup_file_1_full} > $$files_ref->{bam_dedup_file_1_full}\n";
    $cmd_line .= "samtools sort -n $$files_ref->{bam_dedup_file_1_full} $$files_ref->{bam_dedup_file_1_full_prefix}\n";
    $cmd_line .= "samtools view -h $$files_ref->{bam_dedup_file_1_full_sorted} > $$files_ref->{sam_dedup_file_1_full_sorted}\n";

    if ( $$reads_ref eq 'paired' ) { # Need to make this possible to be reverse only too

	$cmd_line .= "sort -k1,1 $$files_ref->{sam_on_target_file_1} > $$files_ref->{sam_on_target_file_1_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_off_target_file_1} > $$files_ref->{sam_off_target_file_1_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_on_target_file_1} > $$files_ref->{sam_dedup_on_target_file_1_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_off_target_file_1} > $$files_ref->{sam_dedup_off_target_file_1_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_on_target_alone_file_2} > $$files_ref->{sam_on_target_alone_file_2_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_off_target_alone_file_2} > $$files_ref->{sam_off_target_alone_file_2_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_on_target_alone_file_2} > $$files_ref->{sam_dedup_on_target_alone_file_2_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_off_target_alone_file_2} > $$files_ref->{sam_dedup_off_target_alone_file_2_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_on_target_file_2} > $$files_ref->{sam_on_target_file_2_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_off_target_file_2} > $$files_ref->{sam_off_target_file_2_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_on_target_file_2} > $$files_ref->{sam_dedup_on_target_file_2_linux_sorted}\n";
	$cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_off_target_file_2} > $$files_ref->{sam_dedup_off_target_file_2_linux_sorted}\n";

	$cmd_line .= "samtools view -bS $$files_ref->{sam_file_2_full} > $$files_ref->{bam_file_2_full}\n";
	$cmd_line .= "samtools sort -n $$files_ref->{bam_file_2_full} $$files_ref->{bam_file_2_full_prefix}\n";
	$cmd_line .= "samtools view -h $$files_ref->{bam_file_2_full_sorted} > $$files_ref->{sam_file_2_full_sorted}\n";
	$cmd_line .= "samtools view -bS $$files_ref->{sam_dedup_file_2_full} > $$files_ref->{bam_dedup_file_2_full}\n";
	$cmd_line .= "samtools sort -n $$files_ref->{bam_dedup_file_2_full} $$files_ref->{bam_dedup_file_2_full_prefix}\n";
	$cmd_line .= "samtools view -h $$files_ref->{bam_dedup_file_2_full_sorted} > $$files_ref->{sam_dedup_file_2_full_sorted}\n";
    }
    return $cmd_line;
}


sub on_target_stats {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo On-target Stats\n";

    if ( -e $$files_ref->{target_regions_file} ) {
	if ( -s $$files_ref->{target_regions_file} ) {

	    if ( $$reads_ref eq 'single' ) { # Need to make this possible to be reverse only too

		# Counts of on- and off-target reads
		$cmd_line .= "$$parameters_ref->{path}/on_target_counts.pl -on_alone_1 $$files_ref->{sam_on_target_alone_file_1_linux_sorted} -off_alone_1 $$files_ref->{sam_off_target_alone_file_1_linux_sorted} -o $$files_ref->{on_target_file}\n";
		$cmd_line .= "$$parameters_ref->{path}/on_target_counts.pl -on_alone_1 $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted} -off_alone_1 $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted} -o $$files_ref->{on_target_dedup_file}\n";

		# On-target Stats and Housekeeping Stats
		$cmd_line .= "$$parameters_ref->{path}/on_target_stats.pl -t $$files_ref->{target_regions_file} -i1 $$files_ref->{intersect_file_1} -o $$files_ref->{reads_per_exon_file} -oh $$files_ref->{housekeeping_file}\n";
		$cmd_line .= "$$parameters_ref->{path}/on_target_stats.pl -t $$files_ref->{target_regions_file} -i1 $$files_ref->{intersect_dedup_file_1} -o $$files_ref->{reads_per_exon_dedup_file} -oh $$files_ref->{housekeeping_dedup_file} -om $$files_ref->{reads_per_exon_dedup_file_machine}\n";
	    }
	    else{
		# Counts of on- and off-target reads
		$cmd_line .= "$$parameters_ref->{path}/on_target_counts.pl -on_alone_1 $$files_ref->{sam_on_target_alone_file_1_linux_sorted} -on_alone_2 $$files_ref->{sam_on_target_alone_file_2_linux_sorted} -off_alone_1 $$files_ref->{sam_off_target_alone_file_1_linux_sorted} -off_alone_2 $$files_ref->{sam_off_target_alone_file_2_linux_sorted} -on_1 $$files_ref->{sam_on_target_file_1_linux_sorted} -on_2 $$files_ref->{sam_on_target_file_2_linux_sorted} -off_1 $$files_ref->{sam_off_target_file_1_linux_sorted} -off_2 $$files_ref->{sam_off_target_file_2_linux_sorted} -o $$files_ref->{on_target_file}\n";
		$cmd_line .= "$$parameters_ref->{path}/on_target_counts.pl -on_alone_1 $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted} -on_alone_2 $$files_ref->{sam_dedup_on_target_alone_file_2_linux_sorted} -off_alone_1 $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted} -off_alone_2 $$files_ref->{sam_dedup_off_target_alone_file_2_linux_sorted} -on_1 $$files_ref->{sam_dedup_on_target_file_1_linux_sorted} -on_2 $$files_ref->{sam_dedup_on_target_file_2_linux_sorted} -off_1 $$files_ref->{sam_dedup_off_target_file_1_linux_sorted} -off_2 $$files_ref->{sam_dedup_off_target_file_2_linux_sorted} -o $$files_ref->{on_target_dedup_file}\n";
		
		# On-target Stats and Housekeeping Stats
		$cmd_line .= "$$parameters_ref->{path}/on_target_stats.pl -t $$files_ref->{target_regions_file} -i1 $$files_ref->{intersect_file_1} -i2 $$files_ref->{intersect_file_2} -o $$files_ref->{reads_per_exon_file} -oh $$files_ref->{housekeeping_file}\n";

		$cmd_line .= "$$parameters_ref->{path}/on_target_stats.pl -t $$files_ref->{target_regions_file} -i1 $$files_ref->{intersect_dedup_file_1} -i2 $$files_ref->{intersect_dedup_file_2} -o $$files_ref->{reads_per_exon_dedup_file} -oh $$files_ref->{housekeeping_dedup_file} -om $$files_ref->{reads_per_exon_dedup_file_machine}\n";
	    }
	}
    }
    return $cmd_line;
}

sub total_molecule_counts {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Total Molecule Counts\n";
    if ( $$reads_ref eq 'single' ) {
        $cmd_line .= "python $$parameters_ref->{path}/count_reads_and_alignments_v2.py -r1 $$files_ref->{sam_file_1_full_sorted} -o $$files_ref->{total_and_aligned_molecule_count_per_tag_file}\n";
    }
    else {
        $cmd_line .= "python $$parameters_ref->{path}/count_reads_and_alignments_v2.py -r1 $$files_ref->{sam_file_1_full_sorted} -r2 $$files_ref->{sam_file_2_full_sorted} -o $$files_ref->{total_and_aligned_molecule_count_per_tag_file}\n";
    }
    return $cmd_line;
}


sub de_duplicated_molecule_counts {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo De-duplicated Molecule Counts\n";
    if ( $$reads_ref eq 'single' ) {
        $cmd_line .= "python $$parameters_ref->{path}/count_reads_and_alignments_v2.py -r1 $$files_ref->{sam_dedup_file_1_full_sorted} -o $$files_ref->{unique_and_aligned_molecule_count_per_tag_file}\n";
    }
    else {
	$cmd_line .= "python $$parameters_ref->{path}/count_reads_and_alignments_v2.py -r1 $$files_ref->{sam_dedup_file_1_full_sorted} -r2 $$files_ref->{sam_dedup_file_2_full_sorted} -o $$files_ref->{unique_and_aligned_molecule_count_per_tag_file}\n";
    }
    return $cmd_line;
}


sub all_molecule_counts {
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo All Molecule Counts\n";
    $cmd_line .= "$$parameters_ref->{path}/counts_2.pl -tamc $$files_ref->{total_and_aligned_molecule_count_per_tag_file} -uamc $$files_ref->{unique_and_aligned_molecule_count_per_tag_file} -otd $$files_ref->{on_target_dedup_file} -ot $$files_ref->{on_target_file} -o $$files_ref->{counts_file} -om $$files_ref->{counts_file_machine}\n";
    return $cmd_line;
}

sub qc_check {
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo QC Check\n";
    $cmd_line .= "$$parameters_ref->{path}/qc_check.pl -hd $$files_ref->{housekeeping_dedup_file} -o $$files_ref->{qc_filter_file} -om $$files_ref->{qc_filter_file_machine}\n";
    return $cmd_line;
}

sub coverage_uniformity {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Coverage Uniformity\n";
    $cmd_line .= "$$parameters_ref->{path}/coverage_uniformity.pl -hd $$files_ref->{housekeeping_dedup_file} -r $$reads_ref -o $$files_ref->{coverage_uniformity_file} -om $$files_ref->{coverage_uniformity_file_machine}\n";
    return $cmd_line;
}


sub summary {
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Summary\n";

#    my $sample_name = "'" . @$samples_array_ref[$sample_element_number] . "'";
    
    $cmd_line .= "$$parameters_ref->{path}/summary.pl -s $$tag_ref -o $$files_ref->{summary_file} -om $$files_ref->{summary_file_machine}\n";
    $cmd_line .= "cat $$files_ref->{qc_filter_file} >> $$files_ref->{summary_file}\n";
#    $cmd_line .= "cat $$files_ref->{coverage_uniformity_file} >> $$files_ref->{summary_file}\n";
    $cmd_line .= "cat $$files_ref->{counts_file} >> $$files_ref->{summary_file}\n";
    if ( -e $$files_ref->{reads_per_exon_dedup_file} ) {
	if ( -s $$files_ref->{reads_per_exon_dedup_file} ) {
	    $cmd_line .= "cat $$files_ref->{reads_per_exon_dedup_file} >> $$files_ref->{summary_file}\n";
	}
    }
    $cmd_line .= "cat $$files_ref->{fusion_counts_with_splice_bare_file} >> $$files_ref->{summary_file}\n";
#    $cmd_line .= "enscript -f Courier8 -p $$files_ref->{summary_file_ps} $$files_ref->{summary_file}\n";
#    $cmd_line .= "ps2pdf $$files_ref->{summary_file_ps} $$files_ref->{summary_file_pdf}\n";

    # Machine Readable Summary File
    $cmd_line .= "cat $$files_ref->{qc_filter_file_machine} >> $$files_ref->{summary_file_machine}\n";
#    $cmd_line .= "cat $$files_ref->{coverage_uniformity_file_machine} >> $$files_ref->{summary_file_machine}\n";
    $cmd_line .= "cat $$files_ref->{counts_file_machine} >> $$files_ref->{summary_file_machine}\n";
    if ( -e $$files_ref->{reads_per_exon_dedup_file_machine} ) {
	if ( -s $$files_ref->{reads_per_exon_dedup_file_machine} ) {
	    $cmd_line .= "cat $$files_ref->{reads_per_exon_dedup_file_machine} >> $$files_ref->{summary_file_machine}\n";
	}
    }
    $cmd_line .= "cat $$files_ref->{fusion_counts_with_splice_bare_file_machine} >> $$files_ref->{summary_file_machine}\n";

    return $cmd_line;
}


sub clean_up {
    my $reads_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $file;
    my $cmd_line = "echo Clean Up\n";

    # Clean up Flanking Sequences Files
    $cmd_line .= "$$parameters_ref->{path}/clean_up_flanking_sequences.pl -f $$files_ref->{flanking_sequences_file}\n";

    # Clean up Flanking Splice Sequences Files
    $cmd_line .= "$$parameters_ref->{path}/clean_up_flanking_sequences.pl -f $$files_ref->{flanking_splice_sequences_file}\n";
    
    # Clean up
    $cmd_line .= "rm $$files_ref->{sam_file_1_full}\n";
    $cmd_line .= "rm $$files_ref->{bam_file_1}\n";
    $cmd_line .= "rm $$files_ref->{bed_file_1}\n";
    $cmd_line .= "rm $$files_ref->{bed_file_combined}\n";
    $cmd_line .= "rm $$files_ref->{sam_dedup_file_1}\n";
    $cmd_line .= "rm $$files_ref->{sam_dedup_file_1_full}\n";
    $cmd_line .= "rm $$files_ref->{bam_dedup_file_1}\n";
    $cmd_line .= "rm $$files_ref->{full_master_prejoin_file_1}\n";
    $cmd_line .= "rm $$files_ref->{full_master_file_1}\n";
    $cmd_line .= "rm $$files_ref->{full_master_dedup_prejoin_file_1}\n";
    $cmd_line .= "rm $$files_ref->{full_master_dedup_file_1}\n";
    $cmd_line .= "rm $$files_ref->{bed_points_file_1}\n";
    $cmd_line .= "rm $$files_ref->{bed_points_dedup_file_1}\n";
    $cmd_line .= "rm $$files_ref->{intersect_file_1}\n";
    $cmd_line .= "rm $$files_ref->{intersect_dedup_file_1}\n";
    $cmd_line .= "rm $$files_ref->{sam_on_target_alone_file_1}\n";
    $cmd_line .= "rm $$files_ref->{sam_off_target_alone_file_1}\n";
    $cmd_line .= "rm $$files_ref->{master_dedup_no_annotation_file_1}\n";
    $cmd_line .= "rm $$files_ref->{master_dedup_prejoin_file_1}\n";
    $cmd_line .= "rm $$files_ref->{master_dedup_file_1}\n";
    $cmd_line .= "rm $$files_ref->{fusion_reads_file}\n";
    $cmd_line .= "rm $$files_ref->{fusion_counts_file}\n";
    $cmd_line .= "rm $$files_ref->{fusion_counts_bare_file}\n";
#    $file = $$files_ref->{flanking_sequences_file} . ".tmp~";
#    $cmd_line .= "rm $file\n";
#    $file = $$files_ref->{flanking_splice_sequences_file} . ".tmp~";
#    $cmd_line .= "rm $file\n";
    $cmd_line .= "rm $$files_ref->{splice_counts_file}\n";
    $cmd_line .= "rm $$files_ref->{splice_counts_bare_file}\n";
    $cmd_line .= "rm $$files_ref->{fusion_counts_with_splice_bare_file}\n";
    $cmd_line .= "rm $$files_ref->{fusion_counts_with_splice_bare_file_machine}\n";
    $cmd_line .= "rm $$files_ref->{splice_reads_file}\n";
    $cmd_line .= "rm $$files_ref->{sam_on_target_alone_file_1_linux_sorted}\n";
    $cmd_line .= "rm $$files_ref->{sam_off_target_alone_file_1_linux_sorted}\n";
    $cmd_line .= "rm $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted}\n";
    $cmd_line .= "rm $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted}\n";
    $cmd_line .= "rm $$files_ref->{housekeeping_dedup_file}\n";
    $cmd_line .= "rm $$files_ref->{on_target_dedup_file}\n";
    $cmd_line .= "rm $$files_ref->{reads_per_exon_dedup_file}\n";
    $cmd_line .= "rm $$files_ref->{reads_per_exon_dedup_file_machine}\n";
    $cmd_line .= "rm $$files_ref->{housekeeping_file}\n";
    $cmd_line .= "rm $$files_ref->{on_target_file}\n";
    $cmd_line .= "rm $$files_ref->{reads_per_exon_file}\n";
    $cmd_line .= "rm $$files_ref->{sam_file_1_marked}\n";
    $cmd_line .= "rm $$files_ref->{sam_dedup_file_1_marked}\n";
    $cmd_line .= "rm $$files_ref->{bam_file_1_full}\n";
    $cmd_line .= "rm $$files_ref->{bam_file_1_full_sorted}\n";
    $cmd_line .= "rm $$files_ref->{sam_file_1_full_sorted}\n";
#    $cmd_line .= "rm $$files_ref->{total_and_aligned_molecule_count_file_1}\n";
    $cmd_line .= "rm $$files_ref->{total_and_aligned_molecule_count_per_tag_file}\n";
#    $cmd_line .= "rm $$files_ref->{unique_and_aligned_molecule_count_file_1}\n";
    $cmd_line .= "rm $$files_ref->{unique_and_aligned_molecule_count_per_tag_file}\n";
    $cmd_line .= "rm $$files_ref->{bam_dedup_file_1_full}\n";
    $cmd_line .= "rm $$files_ref->{bam_dedup_file_1_full_sorted}\n";
    $cmd_line .= "rm $$files_ref->{sam_dedup_file_1_full_sorted}\n";
    $cmd_line .= "rm $$files_ref->{qc_filter_file}\n";
    $cmd_line .= "rm $$files_ref->{qc_filter_file_machine}\n";
    $cmd_line .= "rm $$files_ref->{coverage_uniformity_file}\n";
    $cmd_line .= "rm $$files_ref->{coverage_uniformity_file_machine}\n";
    $cmd_line .= "rm $$files_ref->{counts_file}\n";
    $cmd_line .= "rm $$files_ref->{counts_file_machine}\n";
#    $cmd_line .= "rm $$files_ref->{summary_file_ps}\n";
    if ( $$reads_ref eq 'paired' ) {
	$cmd_line .= "rm $$files_ref->{sam_file_2_full}\n";
	$cmd_line .= "rm $$files_ref->{bam_file_2}\n";
	$cmd_line .= "rm $$files_ref->{bed_file_2}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_file_2}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_file_2_full}\n";
	$cmd_line .= "rm $$files_ref->{bam_dedup_file_2}\n";
	$cmd_line .= "rm $$files_ref->{full_master_prejoin_file_2}\n";
	$cmd_line .= "rm $$files_ref->{full_master_file_2}\n";
	$cmd_line .= "rm $$files_ref->{full_master_dedup_prejoin_file_2}\n";
	$cmd_line .= "rm $$files_ref->{full_master_dedup_file_2}\n";
	$cmd_line .= "rm $$files_ref->{bed_points_file_2}\n";
	$cmd_line .= "rm $$files_ref->{bed_points_dedup_file_2}\n";
	$cmd_line .= "rm $$files_ref->{intersect_file_2}\n";
	$cmd_line .= "rm $$files_ref->{intersect_dedup_file_2}\n";
	$cmd_line .= "rm $$files_ref->{intersect_file_combined}\n";
	$cmd_line .= "rm $$files_ref->{intersect_dedup_file_combined}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_on_target_alone_file_1}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_off_target_alone_file_1}\n";
	$cmd_line .= "rm $$files_ref->{sam_on_target_file_1}\n";
	$cmd_line .= "rm $$files_ref->{sam_off_target_file_1}\n";
	$cmd_line .= "rm $$files_ref->{sam_on_target_file_2}\n";
	$cmd_line .= "rm $$files_ref->{sam_off_target_file_2}\n";
	$cmd_line .= "rm $$files_ref->{sam_on_target_alone_file_2}\n";
	$cmd_line .= "rm $$files_ref->{sam_off_target_alone_file_2}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_on_target_alone_file_2}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_off_target_alone_file_2}\n";
	$cmd_line .= "rm $$files_ref->{master_dedup_no_annotation_file_2}\n";
	$cmd_line .= "rm $$files_ref->{master_dedup_prejoin_file_2}\n";
	$cmd_line .= "rm $$files_ref->{master_dedup_file_2}\n";
	$cmd_line .= "rm $$files_ref->{sam_on_target_file_1_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_off_target_file_1_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_on_target_file_1_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_off_target_file_1_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_on_target_alone_file_2_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_off_target_alone_file_2_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_on_target_alone_file_2_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_off_target_alone_file_2_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_on_target_file_2_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_off_target_file_2_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_on_target_file_2_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_off_target_file_2_linux_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_file_2_marked}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_file_2_marked}\n";
	$cmd_line .= "rm $$files_ref->{bam_file_2_full}\n";
	$cmd_line .= "rm $$files_ref->{bam_file_2_full_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_file_2_full_sorted}\n";
#	$cmd_line .= "rm $$files_ref->{total_and_aligned_molecule_count_file_2}\n";
#	$cmd_line .= "rm $$files_ref->{unique_and_aligned_molecule_count_file_2}\n";
	$cmd_line .= "rm $$files_ref->{bam_dedup_file_2_full}\n";
	$cmd_line .= "rm $$files_ref->{bam_dedup_file_2_full_sorted}\n";
	$cmd_line .= "rm $$files_ref->{sam_dedup_file_2_full_sorted}\n";
    }

    return $cmd_line;
}


sub summary_for_unprocessed_sample {
    my $reads_ref = shift;
    my $fastq_file_1_ref = shift;
    my $fastq_file_2_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    my $cmd_line = "echo Summary for Unprocessed Sample\n";
    $cmd_line .= "$$parameters_ref->{path}/summary_for_unprocessed_samples.pl -r $$reads_ref -f1 $$fastq_file_1_ref -f2 $$fastq_file_2_ref -o $$files_ref->{summary_file} -om $$files_ref->{summary_file_machine}\n";
#    $cmd_line .= "enscript -f Courier8 -p $$files_ref->{summary_file_ps} $$files_ref->{summary_file}\n";
#    $cmd_line .= "ps2pdf $$files_ref->{summary_file_ps} $$files_ref->{summary_file_pdf}\n";
    return $cmd_line;
}


sub join_multiple_samples {
    my $parameters_ref = shift;
    my $cmd_line = "echo Join Multiple Samples\n";
    $cmd_line = "$$parameters_ref->{path}/join_multisample_output.pl -config $$parameters_ref->{config_file} -o $$parameters_ref->{outputfile}\n";
    return $cmd_line;
}

#sub define_alignment_file_names {
#    my $reads_ref = shift;
#    my $tags_array_ref = shift;
#    my $parameters_ref = shift;
#    my $files_ref = shift;
#    $$files_ref->{sam_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam";
#    $$files_ref->{sam_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.full";
#    if ( $$reads_ref eq 'paired' ) {
#	$$files_ref->{sam_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam";
#	$$files_ref->{sam_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.full";
#    }
#}

sub define_alignments_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{sam_file_1_orig} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".fastq.sam";
    $$files_ref->{sam_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.full";
    $$files_ref->{sam_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam";
    $$files_ref->{bam_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bam";
    $$files_ref->{bed_file_1_orig} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bed.orig";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{sam_file_2_orig} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".fastq.sam";
	$$files_ref->{sam_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.full";
	$$files_ref->{sam_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam";
	$$files_ref->{bam_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bam";
	$$files_ref->{bed_file_2_orig} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bed.orig";
    }
    $$files_ref->{bed_file_combined} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".combined.bed";
}

sub define_de_duplication_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{dedup_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup_read_ids.dat";
    $$files_ref->{sam_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.dedup";
    $$files_ref->{sam_dedup_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.sam.full";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{sam_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.dedup";
	$$files_ref->{sam_dedup_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.sam.full";
    }
}

sub define_on_and_off_target_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    # File 1
    $$files_ref->{target_regions_bed_file} = $$parameters_ref->{directory} . "/target_regions.bed";
    $$files_ref->{full_master_prejoin_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".full.prejoin.master.dat";
    $$files_ref->{full_master_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".full.master.dat";
    $$files_ref->{bed_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bed";
    $$files_ref->{bed_points_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".points.bed";
    $$files_ref->{intersect_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".intersect.dat";
    $$files_ref->{sam_on_target_alone_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".on_target.alone.sam";
    $$files_ref->{sam_file_1_marked} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.marked";
    $$files_ref->{sam_off_target_alone_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".off_target.alone.sam";
    $$files_ref->{sam_on_target_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".on_target.sam";
    $$files_ref->{sam_off_target_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".off_target.sam";
    # File 1 Dedup
    $$files_ref->{full_master_dedup_prejoin_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".full.dedup.prejoin.master.dat";
    $$files_ref->{full_master_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".full.dedup.master.dat";
    $$files_ref->{bed_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.bed";
    $$files_ref->{bed_points_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.points.bed";
    $$files_ref->{intersect_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.intersect.dat";
    $$files_ref->{sam_dedup_on_target_alone_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.on_target.alone.sam";
    $$files_ref->{sam_dedup_file_1_marked} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.dedup.marked";
    $$files_ref->{sam_dedup_off_target_alone_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.off_target.alone.sam";
    $$files_ref->{sam_dedup_on_target_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.on_target.sam";
    $$files_ref->{sam_dedup_off_target_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.off_target.sam";
    # File 2
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{full_master_prejoin_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".full.prejoin.master.dat";
	$$files_ref->{full_master_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".full.master.dat";
	$$files_ref->{bed_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bed";
	$$files_ref->{bed_points_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".points.bed";
	$$files_ref->{intersect_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".intersect.dat";
	$$files_ref->{sam_on_target_alone_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".on_target.alone.sam";
	$$files_ref->{sam_file_2_marked} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.marked";
	$$files_ref->{sam_off_target_alone_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".off_target.alone.sam";
	$$files_ref->{sam_on_target_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".on_target.sam";
	$$files_ref->{sam_off_target_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".off_target.sam";
    }
    # File 2 Dedup
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{full_master_dedup_prejoin_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".full.dedup.prejoin.master.dat";
	$$files_ref->{full_master_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".full.dedup.master.dat";
	$$files_ref->{bed_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.bed";
	$$files_ref->{bed_points_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.points.bed";
	$$files_ref->{intersect_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.intersect.dat";
	$$files_ref->{sam_dedup_on_target_alone_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.on_target.alone.sam";
	$$files_ref->{sam_dedup_file_2_marked} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.dedup.marked";
	$$files_ref->{sam_dedup_off_target_alone_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.off_target.alone.sam";
	$$files_ref->{sam_dedup_on_target_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.on_target.sam";
	$$files_ref->{sam_dedup_off_target_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.off_target.sam";
    }
    $$files_ref->{intersect_file_combined} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".intersect_combined.dat";
    $$files_ref->{intersect_dedup_file_combined} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup.intersect_combined.dat";
}

sub define_coverage_and_start_site_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{start_site_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.start_site.bedgraph";
    $$files_ref->{coverage_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.coverage.bedgraph";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{start_site_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.start_site.bedgraph";
	$$files_ref->{coverage_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.coverage.bedgraph";
    }
}

sub define_master_files_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{master_dedup_no_annotation_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.no_annotation.master.dat";
    $$files_ref->{master_dedup_prejoin_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.prejoin.master.dat";
    $$files_ref->{master_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.master.dat";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{master_dedup_no_annotation_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.no_annotation.master.dat";
	$$files_ref->{master_dedup_prejoin_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.prejoin.master.dat";
	$$files_ref->{master_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.master.dat";
    }
}

sub define_fusion_reads_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{one_segment_reads_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".one_segment_reads.dat";
    $$files_ref->{splice_reads_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".splice_reads.dat";
    $$files_ref->{fusion_reads_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".fusion_reads.dat";
    $$files_ref->{multi_fusion_reads_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".multi_fusion_reads.dat";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{one_segment_reads_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".one_segment_reads.dat";
	$$files_ref->{splice_reads_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".splice_reads.dat";
	$$files_ref->{fusion_reads_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".fusion_reads.dat";
	$$files_ref->{multi_fusion_reads_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".multi_fusion_reads.dat";
    }
    $$files_ref->{fusion_reads_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_reads.combined.dat";
    $$files_ref->{splice_reads_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".splice_reads.combined.dat";
}

sub define_count_fusions_file_names {
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{fusion_counts_bare_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_counts_bare.dat";
    $$files_ref->{fusion_counts_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_counts.dat";
    $$files_ref->{splice_counts_bare_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".splice_counts_bare.dat";
    $$files_ref->{splice_counts_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".splice_counts.dat";
    $$files_ref->{fusion_counts_with_splice_bare_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_counts_with_splice_bare.dat";
    $$files_ref->{fusion_counts_with_splice_bare_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_counts_with_splice_bare.machine.dat";
}

sub define_flanking_sequences_file_names {
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{flanking_sequences_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".flanking_sequences.dat";
    $$files_ref->{flanking_splice_sequences_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".flanking_splice_sequences.dat";
}

sub define_consensus_sequences_file_names {
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{consensus_fusion_std_out_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".consensus_fusion_std_out.dat";
    $$files_ref->{consensus_fusion_std_err_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".consensus_fusion_std_err.dat";
    $$files_ref->{consensus_splice_std_out_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".consensus_splice_std_out.dat";
    $$files_ref->{consensus_splice_std_err_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".consensus_splice_std_err.dat";
    $$files_ref->{fusion_and_splice_consensus_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_and_splice_consensus_sequences.fasta";
}

sub define_bam_dedup_files_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{bam_dedup_file_1} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[0] . ".dedup.bam";
    $$files_ref->{bam_dedup_sorted_file_1_name} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[0] . ".dedup.sorted";
    $$files_ref->{bam_dedup_sorted_file_1} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[0] . ".dedup.sorted.bam";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{bam_dedup_file_2} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[1] . ".dedup.bam";
	$$files_ref->{bam_dedup_sorted_file_2_name} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[1] . ".dedup.sorted";
	$$files_ref->{bam_dedup_sorted_file_2} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[1] . ".dedup.sorted.bam";
    }
}

sub define_sort_sam_files_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{sam_on_target_alone_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".on_target.alone.linux_sorted.sam";
    $$files_ref->{sam_off_target_alone_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".off_target.alone.linux_sorted.sam";
    $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.on_target.alone.linux_sorted.sam";
    $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.off_target.alone.linux_sorted.sam";
    $$files_ref->{sam_on_target_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".on_target.linux_sorted.sam";
    $$files_ref->{sam_off_target_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".off_target.linux_sorted.sam";
    $$files_ref->{sam_dedup_on_target_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.on_target.linux_sorted.sam";
    $$files_ref->{sam_dedup_off_target_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.off_target.linux_sorted.sam";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{sam_on_target_alone_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".on_target.alone.linux_sorted.sam";
	$$files_ref->{sam_off_target_alone_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".off_target.alone.linux_sorted.sam";
	$$files_ref->{sam_dedup_on_target_alone_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.on_target.alone.linux_sorted.sam";
	$$files_ref->{sam_dedup_off_target_alone_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.off_target.alone.linux_sorted.sam";
	$$files_ref->{sam_on_target_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".on_target.linux_sorted.sam";
	$$files_ref->{sam_off_target_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".off_target.linux_sorted.sam";
	$$files_ref->{sam_dedup_on_target_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.on_target.linux_sorted.sam";
	$$files_ref->{sam_dedup_off_target_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.off_target.linux_sorted.sam";
    }

    $$files_ref->{bam_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bam.full";
    $$files_ref->{bam_file_1_full_prefix} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bam.full.prefix";
    $$files_ref->{bam_file_1_full_sorted} = $$files_ref->{bam_file_1_full_prefix} . ".bam";
    $$files_ref->{sam_file_1_full_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.full.sorted";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{bam_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bam.full";
	$$files_ref->{bam_file_2_full_prefix} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bam.full.prefix";
	$$files_ref->{bam_file_2_full_sorted} = $$files_ref->{bam_file_2_full_prefix} . ".bam";
	$$files_ref->{sam_file_2_full_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.full.sorted";
    }
    
    $$files_ref->{bam_dedup_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.bam.full";
    $$files_ref->{bam_dedup_file_1_full_prefix} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.bam.full.prefix";
    $$files_ref->{bam_dedup_file_1_full_sorted} = $$files_ref->{bam_dedup_file_1_full_prefix} . ".bam";
    $$files_ref->{sam_dedup_file_1_full_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.sam.full.sorted";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{bam_dedup_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.bam.full";
	$$files_ref->{bam_dedup_file_2_full_prefix} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.bam.full.prefix";
	$$files_ref->{bam_dedup_file_2_full_sorted} = $$files_ref->{bam_dedup_file_2_full_prefix} . ".bam";
	$$files_ref->{sam_dedup_file_2_full_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.sam.full.sorted";
    }
}

sub define_on_target_stats_file_names {
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{on_target_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".on_target.dat";
    $$files_ref->{on_target_dedup_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup.on_target.dat";
    $$files_ref->{reads_per_exon_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".reads_per_exon.dat";
    $$files_ref->{housekeeping_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".housekeeping.dat";
    $$files_ref->{reads_per_exon_dedup_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup.reads_per_exon.dat";
    $$files_ref->{housekeeping_dedup_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".housekeeping.dedup.dat";
    $$files_ref->{reads_per_exon_dedup_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup.reads_per_exon.machine.dat";
}

sub define_total_molecule_counts_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{total_and_aligned_molecule_count_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".total_and_aligned_molecule_count.dat";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{total_and_aligned_molecule_count_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".total_and_aligned_molecule_count.dat";
    }
    $$files_ref->{total_and_aligned_molecule_count_per_tag_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".per_tag.total_and_aligned_molecule_count.dat";
}

sub define_de_deduplicated_molecule_counts_file_names {
    my $reads_ref = shift;
    my $tags_array_ref = shift;
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{unique_and_aligned_molecule_count_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".unique_and_aligned_molecule_count.dat";
    if ( $$reads_ref eq 'paired' ) {
	$$files_ref->{unique_and_aligned_molecule_count_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".unique_and_aligned_molecule_count.dat";
    }
    $$files_ref->{unique_and_aligned_molecule_count_per_tag_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".per_tag.unique_and_aligned_molecule_count.dat";
}

sub define_all_molecule_counts_file_names {
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{counts_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".counts.dat";
    $$files_ref->{counts_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".counts.machine.dat";
}


sub define_qc_check_file_names {
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{qc_filter_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".qc_filter.dat";
    $$files_ref->{qc_filter_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".qc_filter.machine.dat";
}

sub define_coverage_uniformity_file_names {
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{coverage_uniformity_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".coverage_uniformity.dat";
    $$files_ref->{coverage_uniformity_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".coverage_uniformity.machine.dat";
}

sub define_summary_file_names {
    my $tag_ref = shift;
    my $parameters_ref = shift;
    my $files_ref = shift;
    $$files_ref->{summary_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".summary.dat";
    $$files_ref->{summary_file_ps} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".summary.ps";
    $$files_ref->{summary_file_pdf} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".summary.pdf";
    $$files_ref->{summary_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".summary.machine.dat";
}