# HG changeset patch
# User plus
# Date 1401345175 14400
# Node ID 3af9b7634b2d738e6324803a8d1d8d468a996d5b
# Parent  d5aed166429d6ec0317019a9cf85258e60dd7587
Uploaded

diff -r d5aed166429d -r 3af9b7634b2d archer.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/archer.pl	Thu May 29 02:32:55 2014 -0400
@@ -0,0 +1,1422 @@
+#!/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";
+}