changeset 1:183de9d00131 draft

add indices.loc files
author bjoern-gruening
date Tue, 25 Dec 2012 05:52:28 -0500
parents 36d124f44c0a
children 371bb57ac729
files README bismark bismark_bowtie2_wrapper.xml bismark_bowtie_wrapper.xml bismark_genome_preparation bismark_methylation_extractor bismark_methylation_extractor.py bismark_methylation_extractor.xml bismark_wrapper.py bismark_wrapper/README bismark_wrapper/bismark bismark_wrapper/bismark_bowtie2_wrapper.xml bismark_wrapper/bismark_bowtie_wrapper.xml bismark_wrapper/bismark_genome_preparation bismark_wrapper/bismark_methylation_extractor bismark_wrapper/bismark_methylation_extractor.py bismark_wrapper/bismark_methylation_extractor.xml bismark_wrapper/bismark_wrapper.py bismark_wrapper/tool-data/bowtie2_indices.loc.sample bismark_wrapper/tool-data/bowtie_indices.loc.sample bismark_wrapper/tool_data_table_conf.xml.sample bismark_wrapper/tool_dependencies.xml tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 24 files changed, 12810 insertions(+), 12736 deletions(-) [+]
line wrap: on
line diff
--- a/README	Tue Dec 25 05:45:46 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-Bismark uses Bowtie or Bowtie2 to map the reads.
-Create your reference index with bismark_genome_preparation in your
-normal Bowtie2/Botwie index directory. 
-bismark_genome_preparation will create a Bisulfite_Genome folder directly in
-your Bowtie2/Bowtie index directory. If you follow that approach you do not 
-need to specify or modify an extra *.loc file.
-That wrapper will extract the path to the Bisulfite_Genome folder from
-./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.
--- a/bismark	Tue Dec 25 05:45:46 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6615 +0,0 @@
-#!/usr/bin/perl --
-use strict;
-use warnings;
-use IO::Handle;
-use Cwd;
-$|++;
-use Getopt::Long;
-
-
-## This program is Copyright (C) 2010-12, Felix Krueger (felix.krueger@babraham.ac.uk)
-
-## This program is free software: you can redistribute it and/or modify
-## it under the terms of the GNU General Public License as published by
-## the Free Software Foundation, either version 3 of the License, or
-## (at your option) any later version.
-
-## This program is distributed in the hope that it will be useful,
-## but WITHOUT ANY WARRANTY; without even the implied warranty of
-## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-## GNU General Public License for more details.
-
-## You should have received a copy of the GNU General Public License
-## along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-
-my $parent_dir = getcwd;
-my $bismark_version = 'v0.7.7';
-my $command_line = join (" ",@ARGV);
-
-### before processing the command line we will replace --solexa1.3-quals with --phred64-quals as the '.' in the option name will cause Getopt::Long to fail
-foreach my $arg (@ARGV){
-  if ($arg eq '--solexa1.3-quals'){
-    $arg = '--phred64-quals';
-  }
-}
-my @filenames;   # will be populated by processing the command line
-
-my ($genome_folder,$CT_index_basename,$GA_index_basename,$path_to_bowtie,$sequence_file_format,$bowtie_options,$directional,$unmapped,$ambiguous,$phred64,$solexa,$output_dir,$bowtie2,$vanilla,$sam_no_hd,$skip,$upto,$temp_dir) = process_command_line();
-
-my @fhs;         # stores alignment process names, bisulfite index location, bowtie filehandles and the number of times sequences produced an alignment
-my %chromosomes; # stores the chromosome sequences of the mouse genome
-my %counting;    # counting various events
-
-my $seqID_contains_tabs;
-
-foreach my $filename (@filenames){
-
-  chdir $parent_dir or die "Unable to move to initial working directory $!\n";
-  ### resetting the counting hash and fhs
-  reset_counters_and_fhs($filename);
-  $seqID_contains_tabs = 0;
-
-  ### PAIRED-END ALIGNMENTS
-  if ($filename =~ ','){
-    my ($C_to_T_infile_1,$G_to_A_infile_1); # to be made from mate1 file
-
-    $fhs[0]->{name} = 'CTread1GAread2CTgenome';
-    $fhs[1]->{name} = 'GAread1CTread2GAgenome';
-    $fhs[2]->{name} = 'GAread1CTread2CTgenome';
-    $fhs[3]->{name} = 'CTread1GAread2GAgenome';
-
-    print "\nPaired-end alignments will be performed\n",'='x39,"\n\n";
-
-    my ($filename_1,$filename_2) = (split (/,/,$filename));
-    print "The provided filenames for paired-end alignments are $filename_1 and $filename_2\n";
-
-    ### additional variables only for paired-end alignments
-    my ($C_to_T_infile_2,$G_to_A_infile_2); # to be made from mate2 file
-
-    ### FastA format
-    if ($sequence_file_format eq 'FASTA'){
-      print "Input files are in FastA format\n";
-
-      if ($directional){
-	($C_to_T_infile_1) = biTransformFastAFiles_paired_end ($filename_1,1); # also passing the read number
-	($G_to_A_infile_2) = biTransformFastAFiles_paired_end ($filename_2,2);
-
-	$fhs[0]->{inputfile_1} = $C_to_T_infile_1;
-	$fhs[0]->{inputfile_2} = $G_to_A_infile_2;
-	$fhs[1]->{inputfile_1} = undef;
-	$fhs[1]->{inputfile_2} = undef;
-	$fhs[2]->{inputfile_1} = undef;
-	$fhs[2]->{inputfile_2} = undef;
-	$fhs[3]->{inputfile_1} = $C_to_T_infile_1;
-	$fhs[3]->{inputfile_2} = $G_to_A_infile_2;
-      }
-      else{
-	($C_to_T_infile_1,$G_to_A_infile_1) = biTransformFastAFiles_paired_end ($filename_1,1); # also passing the read number
-	($C_to_T_infile_2,$G_to_A_infile_2) = biTransformFastAFiles_paired_end ($filename_2,2);
-
-	$fhs[0]->{inputfile_1} = $C_to_T_infile_1;
-	$fhs[0]->{inputfile_2} = $G_to_A_infile_2;
-	$fhs[1]->{inputfile_1} = $G_to_A_infile_1;
-	$fhs[1]->{inputfile_2} = $C_to_T_infile_2;
-	$fhs[2]->{inputfile_1} = $G_to_A_infile_1;
-	$fhs[2]->{inputfile_2} = $C_to_T_infile_2;
-	$fhs[3]->{inputfile_1} = $C_to_T_infile_1;
-	$fhs[3]->{inputfile_2} = $G_to_A_infile_2;
-      }
-
-      if ($bowtie2){
-	paired_end_align_fragments_to_bisulfite_genome_fastA_bowtie2 ($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2);
-      }
-      else{
-	paired_end_align_fragments_to_bisulfite_genome_fastA ($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2);
-      }
-    }
-
-    ### FastQ format
-    else{
-      print "Input files are in FastQ format\n";
-      if ($directional){
-	($C_to_T_infile_1) = biTransformFastQFiles_paired_end ($filename_1,1); # also passing the read number
-	($G_to_A_infile_2) = biTransformFastQFiles_paired_end ($filename_2,2);
-	
-	$fhs[0]->{inputfile_1} = $C_to_T_infile_1;
-	$fhs[0]->{inputfile_2} = $G_to_A_infile_2;
-	$fhs[1]->{inputfile_1} = undef;
-	$fhs[1]->{inputfile_2} = undef;
-	$fhs[2]->{inputfile_1} = undef;
-	$fhs[2]->{inputfile_2} = undef;
-	$fhs[3]->{inputfile_1} = $C_to_T_infile_1;
-	$fhs[3]->{inputfile_2} = $G_to_A_infile_2;
-      }
-      else{
-	($C_to_T_infile_1,$G_to_A_infile_1) = biTransformFastQFiles_paired_end ($filename_1,1); # also passing the read number
-	($C_to_T_infile_2,$G_to_A_infile_2) = biTransformFastQFiles_paired_end ($filename_2,2);
-
-	$fhs[0]->{inputfile_1} = $C_to_T_infile_1;
-	$fhs[0]->{inputfile_2} = $G_to_A_infile_2;
-	$fhs[1]->{inputfile_1} = $G_to_A_infile_1;
-	$fhs[1]->{inputfile_2} = $C_to_T_infile_2;
-	$fhs[2]->{inputfile_1} = $G_to_A_infile_1;
-	$fhs[2]->{inputfile_2} = $C_to_T_infile_2;
-	$fhs[3]->{inputfile_1} = $C_to_T_infile_1;
-	$fhs[3]->{inputfile_2} = $G_to_A_infile_2;
-      }
-
-      if ($bowtie2){
-	paired_end_align_fragments_to_bisulfite_genome_fastQ_bowtie2 ($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2);
-      }
-      else{
-	paired_end_align_fragments_to_bisulfite_genome_fastQ ($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2);	
-      }
-    }
-    start_methylation_call_procedure_paired_ends($filename_1,$filename_2,$C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2);
-  }
-
-  ### Else we are performing SINGLE-END ALIGNMENTS
-  else{
-    print "\nSingle-end alignments will be performed\n",'='x39,"\n\n";
-    ### Initialising bisulfite conversion filenames
-    my ($C_to_T_infile,$G_to_A_infile);
-
-
-    ### FastA format
-    if ($sequence_file_format eq 'FASTA'){
-      print "Inut file is in FastA format\n";
-      if ($directional){
-	($C_to_T_infile) = biTransformFastAFiles ($filename);
-	$fhs[0]->{inputfile} = $fhs[1]->{inputfile} = $C_to_T_infile;
-      }
-      else{
-	($C_to_T_infile,$G_to_A_infile) = biTransformFastAFiles ($filename);
-	$fhs[0]->{inputfile} = $fhs[1]->{inputfile} = $C_to_T_infile;
-	$fhs[2]->{inputfile} = $fhs[3]->{inputfile} = $G_to_A_infile;
-      }
-
-      ### Creating 4 different bowtie filehandles and storing the first entry
-      if ($bowtie2){
-	single_end_align_fragments_to_bisulfite_genome_fastA_bowtie2 ($C_to_T_infile,$G_to_A_infile);
-      }
-      else{
-	single_end_align_fragments_to_bisulfite_genome_fastA ($C_to_T_infile,$G_to_A_infile);
-      }
-    }
-
-    ## FastQ format
-    else{
-      print "Input file is in FastQ format\n";
-      if ($directional){
-	($C_to_T_infile) = biTransformFastQFiles ($filename);
-	$fhs[0]->{inputfile} = $fhs[1]->{inputfile} = $C_to_T_infile;
-      }
-      else{
-	($C_to_T_infile,$G_to_A_infile) = biTransformFastQFiles ($filename);
-	$fhs[0]->{inputfile} = $fhs[1]->{inputfile} = $C_to_T_infile;
-	$fhs[2]->{inputfile} = $fhs[3]->{inputfile} = $G_to_A_infile;
-      }
-
-      ### Creating 4 different bowtie filehandles and storing the first entry
-      if ($bowtie2){
-	single_end_align_fragments_to_bisulfite_genome_fastQ_bowtie2 ($C_to_T_infile,$G_to_A_infile);
-      }
-      else{
-	single_end_align_fragments_to_bisulfite_genome_fastQ ($C_to_T_infile,$G_to_A_infile);
-      }
-    }
-
-    start_methylation_call_procedure_single_ends($filename,$C_to_T_infile,$G_to_A_infile);
-
-  }
-}
-
-sub start_methylation_call_procedure_single_ends {
-  my ($sequence_file,$C_to_T_infile,$G_to_A_infile) = @_;
-  my ($dir,$filename);
-
-  if ($sequence_file =~ /\//){
-    ($dir,$filename) = $sequence_file =~ m/(.*\/)(.*)$/;
-  }
-  else{
-    $filename = $sequence_file;
-  }
-
-  ### printing all alignments to a results file
-  my $outfile = $filename;
-
-  if ($bowtie2){ # SAM format is the default for Bowtie 2
-    $outfile =~ s/$/_bt2_bismark.sam/;
-  }
-  elsif ($vanilla){ # vanilla custom Bismark output single-end output (like Bismark versions 0.5.X)
-    $outfile =~ s/$/_bismark.txt/;
-  }
-  else{ # SAM is the default output
-    $outfile =~ s/$/_bismark.sam/;
-  }
-  print "Writing bisulfite mapping results to $output_dir$outfile\n\n";
-  open (OUT,'>',"$output_dir$outfile") or die "Failed to write to $outfile: $!\n";
-  if ($vanilla){
-    print OUT "Bismark version: $bismark_version\n";
-  }
-
-  ### printing alignment and methylation call summary to a report file
-  my $reportfile = $filename;
-  if ($bowtie2){
-    $reportfile =~ s/$/_bt2_Bismark_mapping_report.txt/;
-  }
-  else{
-    $reportfile =~ s/$/_Bismark_mapping_report.txt/;
-  }
-
-  open (REPORT,'>',"$output_dir$reportfile") or die "Failed to write to $reportfile: $!\n";
-  print REPORT "Bismark report for: $sequence_file (version: $bismark_version)\n";
-
-  if ($unmapped){
-    my $unmapped_file = $filename;
-    $unmapped_file =~ s/$/_unmapped_reads.txt/;
-    open (UNMAPPED,'>',"$output_dir$unmapped_file") or die "Failed to write to $unmapped_file: $!\n";
-    print "Unmapped sequences will be written to $output_dir$unmapped_file\n";
-  }
-  if ($ambiguous){
-    my $ambiguous_file = $filename;
-    $ambiguous_file =~ s/$/_ambiguous_reads.txt/;
-    open (AMBIG,'>',"$output_dir$ambiguous_file") or die "Failed to write to $ambiguous_file: $!\n";
-    print "Ambiguously mapping sequences will be written to $output_dir$ambiguous_file\n";
-  }
-
-  if ($directional){
-    print REPORT "Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!)\n";
-  }
-  print REPORT "Bowtie was run against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-
-
-  ### if 2 or more files are provided we can hold the genome in memory and don't need to read it in a second time
-  unless (%chromosomes){
-    my $cwd = getcwd; # storing the path of the current working directory
-    print "Current working directory is: $cwd\n\n";
-    read_genome_into_memory($cwd);
-  }
-
-  unless ($vanilla or $sam_no_hd){
-    generate_SAM_header();
-  }
-
-  ### Input file is in FastA format
-  if ($sequence_file_format eq 'FASTA'){
-    process_single_end_fastA_file_for_methylation_call($sequence_file,$C_to_T_infile,$G_to_A_infile);
-  }
-  ### Input file is in FastQ format
-  else{
-    process_single_end_fastQ_file_for_methylation_call($sequence_file,$C_to_T_infile,$G_to_A_infile);
-  }
-}
-
-sub start_methylation_call_procedure_paired_ends {
-  my ($sequence_file_1,$sequence_file_2,$C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2) = @_;
-
-  my ($dir_1,$filename_1);
-
-  if ($sequence_file_1 =~ /\//){
-    ($dir_1,$filename_1) = $sequence_file_1 =~ m/(.*\/)(.*)$/;
-  }
-  else{
-    $filename_1 = $sequence_file_1;
-  }
-
-  my ($dir_2,$filename_2);
-
-  if  ($sequence_file_2 =~ /\//){
-    ($dir_2,$filename_2) = $sequence_file_2 =~ m/(.*\/)(.*)$/;
-  }
-  else{
-    $filename_2 = $sequence_file_2;
-  }
-
-  ### printing all alignments to a results file
-  my $outfile = $filename_1;
-  if ($bowtie2){ # SAM format is the default Bowtie 2 output
-    $outfile =~ s/$/_bismark_bt2_pe.sam/;
-  }
-  elsif ($vanilla){ # vanilla custom Bismark paired-end output (like Bismark versions 0.5.X)
-    $outfile =~ s/$/_bismark_pe.txt/;
-  }
-  else{ # SAM format is the default Bowtie 1 output
-    $outfile =~ s/$/_bismark_pe.sam/;
-  }
-
-  print "Writing bisulfite mapping results to $outfile\n\n";
-  open (OUT,'>',"$output_dir$outfile") or die "Failed to write to $outfile: $!";
-  if ($vanilla){
-    print OUT "Bismark version: $bismark_version\n";
-  }
-
-  ### printing alignment and methylation call summary to a report file
-  my $reportfile = $filename_1;
-  if ($bowtie2){
-    $reportfile =~ s/$/_Bismark_bt2_paired-end_mapping_report.txt/;
-  }
-  else{
-    $reportfile =~ s/$/_Bismark_paired-end_mapping_report.txt/;
-  }
-
-  open (REPORT,'>',"$output_dir$reportfile") or die "Failed to write to $reportfile: $!\n";
-  print REPORT "Bismark report for: $sequence_file_1 and $sequence_file_2 (version: $bismark_version)\n";
-  print REPORT "Bowtie was run against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-
-
-  ### Unmapped read output
-  if ($unmapped){
-    my $unmapped_1 = $filename_1;
-    my $unmapped_2 = $filename_2;
-    $unmapped_1 =~ s/$/_unmapped_reads_1.txt/;
-    $unmapped_2 =~ s/$/_unmapped_reads_2.txt/;
-    open (UNMAPPED_1,'>',"$output_dir$unmapped_1") or die "Failed to write to $unmapped_1: $!\n";
-    open (UNMAPPED_2,'>',"$output_dir$unmapped_2") or die "Failed to write to $unmapped_2: $!\n";
-    print "Unmapped sequences will be written to $unmapped_1 and $unmapped_2\n";
-  }
-
-  if ($ambiguous){
-    my $amb_1 = $filename_1;
-    my $amb_2 = $filename_2;
-    $amb_1 =~ s/$/_ambiguous_reads_1.txt/;
-    $amb_2 =~ s/$/_ambiguous_reads_2.txt/;
-    open (AMBIG_1,'>',"$output_dir$amb_1") or die "Failed to write to $amb_1: $!\n";
-    open (AMBIG_2,'>',"$output_dir$amb_2") or die "Failed to write to $amb_2: $!\n";
-    print "Ambiguously mapping sequences will be written to $amb_1 and $amb_2\n";
-  }
-
-  if ($directional){
-    print REPORT "Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed)\n";
-  }
-
-  ### if 2 or more files are provided we might still hold the genome in memory and don't need to read it in a second time
-  unless (%chromosomes){
-    my $cwd = getcwd; # storing the path of the current working directory
-    print "Current working directory is: $cwd\n\n";
-    read_genome_into_memory($cwd);
-  }
-
-  unless ($vanilla or $sam_no_hd){
-    generate_SAM_header();
-  }
-
-  ### Input files are in FastA format
-  if ($sequence_file_format eq 'FASTA'){
-    process_fastA_files_for_paired_end_methylation_calls($sequence_file_1,$sequence_file_2,$C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2);
-  }
-  ### Input files are in FastQ format
-  else{
-    process_fastQ_files_for_paired_end_methylation_calls($sequence_file_1,$sequence_file_2,$C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2);
-  }
-}
-
-sub print_final_analysis_report_single_end{
-  my ($C_to_T_infile,$G_to_A_infile) = @_;
-  ### All sequences from the original sequence file have been analysed now
-  ### deleting temporary C->T or G->A infiles
-
-  if ($directional){
-    my $deletion_successful =  unlink "$temp_dir$C_to_T_infile";
-    if ($deletion_successful == 1){
-      warn "\nSuccessfully deleted the temporary file $temp_dir$C_to_T_infile\n\n";
-    }
-    else{
-      warn "Could not delete temporary file $C_to_T_infile properly $!\n";
-    }
-  }
-
-  else{
-    my $deletion_successful =  unlink "$temp_dir$C_to_T_infile","$temp_dir$G_to_A_infile";
-    if ($deletion_successful == 2){
-      warn "\nSuccessfully deleted the temporary files $temp_dir$C_to_T_infile and $temp_dir$G_to_A_infile\n\n";
-    }
-    else{
-      warn "Could not delete temporary files properly $!\n";
-    }
-  }
-
-  ### printing a final report for the alignment procedure
-  print REPORT "Final Alignment report\n",'='x22,"\n";
-  print "Final Alignment report\n",'='x22,"\n";
-  #  foreach my $index (0..$#fhs){
-  #    print "$fhs[$index]->{name}\n";
-  #    print "$fhs[$index]->{seen}\talignments on the correct strand in total\n";
-  #    print "$fhs[$index]->{wrong_strand}\talignments were discarded (nonsensical alignments)\n\n";
-  #  }
-
-  ### printing a final report for the methylation call procedure
-  warn "Sequences analysed in total:\t$counting{sequences_count}\n";
-  print REPORT "Sequences analysed in total:\t$counting{sequences_count}\n";
-  my $percent_alignable_sequences;
-
-  if ($counting{sequences_count} == 0){
-    $percent_alignable_sequences = 0;
-  }
-  else{
-    $percent_alignable_sequences = sprintf ("%.1f",$counting{unique_best_alignment_count}*100/$counting{sequences_count});
-  }
-
-  warn "Number of alignments with a unique best hit from the different alignments:\t$counting{unique_best_alignment_count}\nMapping efficiency:\t${percent_alignable_sequences}%\n\n";
-  print REPORT "Number of alignments with a unique best hit from the different alignments:\t$counting{unique_best_alignment_count}\nMapping efficiency:\t${percent_alignable_sequences}%\n";
-
-  ### percentage of low complexity reads overruled because of low complexity (thereby creating a bias for highly methylated reads),
-  ### only calculating the percentage if there were any overruled alignments
-  if ($counting{low_complexity_alignments_overruled_count}){
-    my $percent_overruled_low_complexity_alignments = sprintf ("%.1f",$counting{low_complexity_alignments_overruled_count}*100/$counting{sequences_count});
-    #   print REPORT "Number of low complexity alignments which were overruled to have a unique best hit rather than discarding them:\t$counting{low_complexity_alignments_overruled_count}\t(${percent_overruled_low_complexity_alignments}%)\n";
-  }
-
-  print "Sequences with no alignments under any condition:\t$counting{no_single_alignment_found}\n";
-  print "Sequences did not map uniquely:\t$counting{unsuitable_sequence_count}\n";
-  print "Sequences which were discarded because genomic sequence could not be extracted:\t$counting{genomic_sequence_could_not_be_extracted_count}\n\n";
-  print "Number of sequences with unique best (first) alignment came from the bowtie output:\n";
-  print join ("\n","CT/CT:\t$counting{CT_CT_count}\t((converted) top strand)","CT/GA:\t$counting{CT_GA_count}\t((converted) bottom strand)","GA/CT:\t$counting{GA_CT_count}\t(complementary to (converted) top strand)","GA/GA:\t$counting{GA_GA_count}\t(complementary to (converted) bottom strand)"),"\n\n";
-
-  print REPORT "Sequences with no alignments under any condition:\t$counting{no_single_alignment_found}\n";
-  print REPORT "Sequences did not map uniquely:\t$counting{unsuitable_sequence_count}\n";
-  print REPORT "Sequences which were discarded because genomic sequence could not be extracted:\t$counting{genomic_sequence_could_not_be_extracted_count}\n\n";
-  print REPORT "Number of sequences with unique best (first) alignment came from the bowtie output:\n";
-  print REPORT join ("\n","CT/CT:\t$counting{CT_CT_count}\t((converted) top strand)","CT/GA:\t$counting{CT_GA_count}\t((converted) bottom strand)","GA/CT:\t$counting{GA_CT_count}\t(complementary to (converted) top strand)","GA/GA:\t$counting{GA_GA_count}\t(complementary to (converted) bottom strand)"),"\n\n";
-
-  if ($directional){
-    print "Number of alignments to (merely theoretical) complementary strands being rejected in total:\t$counting{alignments_rejected_count}\n\n";
-    print REPORT "Number of alignments to (merely theoretical) complementary strands being rejected in total:\t$counting{alignments_rejected_count}\n\n";
-  }
-
-  ### detailed information about Cs analysed
-  warn "Final Cytosine Methylation Report\n",'='x33,"\n";
-  my $total_number_of_C = $counting{total_meCHH_count}+$counting{total_meCHG_count}+$counting{total_meCpG_count}+$counting{total_unmethylated_CHH_count}+$counting{total_unmethylated_CHG_count}+$counting{total_unmethylated_CpG_count};
-  warn "Total number of C's analysed:\t$total_number_of_C\n\n";
-  warn "Total methylated C's in CpG context:\t$counting{total_meCpG_count}\n";
-  warn "Total methylated C's in CHG context:\t$counting{total_meCHG_count}\n";
-  warn "Total methylated C's in CHH context:\t$counting{total_meCHH_count}\n\n";
-  warn "Total C to T conversions in CpG context:\t$counting{total_unmethylated_CpG_count}\n";
-  warn "Total C to T conversions in CHG context:\t$counting{total_unmethylated_CHG_count}\n";
-  warn "Total C to T conversions in CHH context:\t$counting{total_unmethylated_CHH_count}\n\n";
-
-  print REPORT "Final Cytosine Methylation Report\n",'='x33,"\n";
-  print REPORT "Total number of C's analysed:\t$total_number_of_C\n\n";
-  print REPORT "Total methylated C's in CpG context:\t $counting{total_meCpG_count}\n";
-  print REPORT "Total methylated C's in CHG context:\t$counting{total_meCHG_count}\n";
-  print REPORT "Total methylated C's in CHH context:\t$counting{total_meCHH_count}\n\n";
-  print REPORT "Total C to T conversions in CpG context:\t$counting{total_unmethylated_CpG_count}\n";
-  print REPORT "Total C to T conversions in CHG context:\t$counting{total_unmethylated_CHG_count}\n";
-  print REPORT "Total C to T conversions in CHH context:\t$counting{total_unmethylated_CHH_count}\n\n";
-
-  my $percent_meCHG;
-  if (($counting{total_meCHG_count}+$counting{total_unmethylated_CHG_count}) > 0){
-    $percent_meCHG = sprintf("%.1f",100*$counting{total_meCHG_count}/($counting{total_meCHG_count}+$counting{total_unmethylated_CHG_count}));
-  }
-
-  my $percent_meCHH;
-  if (($counting{total_meCHH_count}+$counting{total_unmethylated_CHH_count}) > 0){
-    $percent_meCHH = sprintf("%.1f",100*$counting{total_meCHH_count}/($counting{total_meCHH_count}+$counting{total_unmethylated_CHH_count}));
-  }
-
-  my $percent_meCpG;
-  if (($counting{total_meCpG_count}+$counting{total_unmethylated_CpG_count}) > 0){
-    $percent_meCpG = sprintf("%.1f",100*$counting{total_meCpG_count}/($counting{total_meCpG_count}+$counting{total_unmethylated_CpG_count}));
-  }
-
-  ### printing methylated CpG percentage if applicable
-  if ($percent_meCpG){
-    warn "C methylated in CpG context:\t${percent_meCpG}%\n";
-    print REPORT "C methylated in CpG context:\t${percent_meCpG}%\n";
-  }
-  else{
-    warn "Can't determine percentage of methylated Cs in CpG context if value was 0\n";
-    print REPORT "Can't determine percentage of methylated Cs in CpG context if value was 0\n";
-  }
-
-  ### printing methylated C percentage (CHG context) if applicable
-  if ($percent_meCHG){
-    warn "C methylated in CHG context:\t${percent_meCHG}%\n";
-    print REPORT "C methylated in CHG context:\t${percent_meCHG}%\n";
-  }
-  else{
-    warn "Can't determine percentage of methylated Cs in CHG context if value was 0\n";
-    print REPORT "Can't determine percentage of methylated Cs in CHG context if value was 0\n";
-  }
-
-  ### printing methylated C percentage (CHH context) if applicable
-  if ($percent_meCHH){
-    warn "C methylated in CHH context:\t${percent_meCHH}%\n\n\n";
-    print REPORT "C methylated in CHH context:\t${percent_meCHH}%\n\n\n";
-  }
-  else{
-    warn "Can't determine percentage of methylated Cs in CHH context if value was 0\n\n\n";
-    print REPORT "Can't determine percentage of methylated Cs in CHH context if value was 0\n\n\n";
-  }
-
-  if ($seqID_contains_tabs){
-    warn "The sequence IDs in the provided file contain tab-stops which might prevent sequence alignments. If this happened, please replace all tab characters within the seqID field with spaces before running Bismark.\n\n";
-    print REPORT "The sequence IDs in the provided file contain tab-stops which might prevent sequence alignments. If this happened, please replace all tab characters within the seqID field with spaces before running Bismark.\n\n";
-  }
-}
-
-sub print_final_analysis_report_paired_ends{
-  my ($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2) = @_;
-  ### All sequences from the original sequence file have been analysed now, therefore deleting temporary C->T or G->A infiles
-  if ($directional){
-    my $deletion_successful =  unlink "$temp_dir$C_to_T_infile_1","$temp_dir$G_to_A_infile_2";
-    if ($deletion_successful == 2){
-      warn "\nSuccessfully deleted the temporary files $temp_dir$C_to_T_infile_1 and $temp_dir$G_to_A_infile_2\n\n";
-    }
-    else{
-      warn "Could not delete temporary files $temp_dir$C_to_T_infile_1 and $temp_dir$G_to_A_infile_2 properly: $!\n";
-    }
-  }
-  else{
-    my $deletion_successful =  unlink "$temp_dir$C_to_T_infile_1","$temp_dir$G_to_A_infile_1","$temp_dir$C_to_T_infile_2","$temp_dir$G_to_A_infile_2";
-    if ($deletion_successful == 4){
-      warn "\nSuccessfully deleted the temporary files $temp_dir$C_to_T_infile_1, $temp_dir$G_to_A_infile_1, $temp_dir$C_to_T_infile_2 and $temp_dir$G_to_A_infile_2\n\n";
-    }
-    else{
-      warn "Could not delete temporary files properly: $!\n";
-    }
-  }
-
-  ### printing a final report for the alignment procedure
-  warn "Final Alignment report\n",'='x22,"\n";
-  print REPORT "Final Alignment report\n",'='x22,"\n";
-  #  foreach my $index (0..$#fhs){
-  #    print "$fhs[$index]->{name}\n";
-  #    print "$fhs[$index]->{seen}\talignments on the correct strand in total\n";
-  #    print "$fhs[$index]->{wrong_strand}\talignments were discarded (nonsensical alignments)\n\n";
-  #  }
-
-  ### printing a final report for the methylation call procedure
-  warn "Sequence pairs analysed in total:\t$counting{sequences_count}\n";
-  print REPORT "Sequence pairs analysed in total:\t$counting{sequences_count}\n";
-
-  my $percent_alignable_sequence_pairs;
-  if ($counting{sequences_count} == 0){
-    $percent_alignable_sequence_pairs = 0;
-  }
-  else{
-    $percent_alignable_sequence_pairs = sprintf ("%.1f",$counting{unique_best_alignment_count}*100/$counting{sequences_count});
-  }
-  print "Number of paired-end alignments with a unique best hit:\t$counting{unique_best_alignment_count}\nMapping efficiency:\t${percent_alignable_sequence_pairs}%\n\n";
-  print REPORT "Number of paired-end alignments with a unique best hit:\t$counting{unique_best_alignment_count}\nMapping efficiency:\t${percent_alignable_sequence_pairs}% \n";
-
-  print "Sequence pairs with no alignments under any condition:\t$counting{no_single_alignment_found}\n";
-  print "Sequence pairs did not map uniquely:\t$counting{unsuitable_sequence_count}\n";
-  print "Sequence pairs which were discarded because genomic sequence could not be extracted:\t$counting{genomic_sequence_could_not_be_extracted_count}\n\n";
-  print "Number of sequence pairs with unique best (first) alignment came from the bowtie output:\n";
-  print join ("\n","CT/GA/CT:\t$counting{CT_GA_CT_count}\t((converted) top strand)","GA/CT/CT:\t$counting{GA_CT_CT_count}\t(complementary to (converted) top strand)","GA/CT/GA:\t$counting{GA_CT_GA_count}\t(complementary to (converted) bottom strand)","CT/GA/GA:\t$counting{CT_GA_GA_count}\t((converted) bottom strand)"),"\n\n";
-
-
-  print REPORT "Sequence pairs with no alignments under any condition:\t$counting{no_single_alignment_found}\n";
-  print REPORT "Sequence pairs did not map uniquely:\t$counting{unsuitable_sequence_count}\n";
-  print REPORT "Sequence pairs which were discarded because genomic sequence could not be extracted:\t$counting{genomic_sequence_could_not_be_extracted_count}\n\n";
-  print REPORT "Number of sequence pairs with unique best (first) alignment came from the bowtie output:\n";
-  print REPORT join ("\n","CT/GA/CT:\t$counting{CT_GA_CT_count}\t((converted) top strand)","GA/CT/CT:\t$counting{GA_CT_CT_count}\t(complementary to (converted) top strand)","GA/CT/GA:\t$counting{GA_CT_GA_count}\t(complementary to (converted) bottom strand)","CT/GA/GA:\t$counting{CT_GA_GA_count}\t((converted) bottom strand)"),"\n\n";
-  ### detailed information about Cs analysed
-
-  if ($directional){
-    print "Number of alignments to (merely theoretical) complementary strands being rejected in total:\t$counting{alignments_rejected_count}\n\n";
-    print REPORT "Number of alignments to (merely theoretical) complementary strands being rejected in total:\t$counting{alignments_rejected_count}\n\n";
-  }
-
-  warn "Final Cytosine Methylation Report\n",'='x33,"\n";
-  print REPORT "Final Cytosine Methylation Report\n",'='x33,"\n";
-
-  my $total_number_of_C = $counting{total_meCHG_count}+ $counting{total_meCHH_count}+$counting{total_meCpG_count}+$counting{total_unmethylated_CHG_count}+$counting{total_unmethylated_CHH_count}+$counting{total_unmethylated_CpG_count};
-  warn "Total number of C's analysed:\t$total_number_of_C\n\n";
-  warn "Total methylated C's in CpG context:\t$counting{total_meCpG_count}\n";
-  warn "Total methylated C's in CHG context:\t$counting{total_meCHG_count}\n";
-  warn "Total methylated C's in CHH context:\t$counting{total_meCHH_count}\n\n";
-  warn "Total C to T conversions in CpG context:\t$counting{total_unmethylated_CpG_count}\n";
-  warn "Total C to T conversions in CHG context:\t$counting{total_unmethylated_CHG_count}\n";
-  warn "Total C to T conversions in CHH context:\t$counting{total_unmethylated_CHH_count}\n\n";
-
-  print REPORT "Total number of C's analysed:\t$total_number_of_C\n\n";
-  print REPORT "Total methylated C's in CpG context:\t$counting{total_meCpG_count}\n";
-  print REPORT "Total methylated C's in CHG context:\t$counting{total_meCHG_count}\n";
-  print REPORT "Total methylated C's in CHH context:\t$counting{total_meCHH_count}\n\n";
-  print REPORT "Total C to T conversions in CpG context:\t$counting{total_unmethylated_CpG_count}\n";
-  print REPORT "Total C to T conversions in CHG context:\t$counting{total_unmethylated_CHG_count}\n";
-  print REPORT "Total C to T conversions in CHH context:\t$counting{total_unmethylated_CHH_count}\n\n";
-
-  my $percent_meCHG;
-  if (($counting{total_meCHG_count}+$counting{total_unmethylated_CHG_count}) > 0){
-    $percent_meCHG = sprintf("%.1f",100*$counting{total_meCHG_count}/($counting{total_meCHG_count}+$counting{total_unmethylated_CHG_count}));
-  }
-
-  my $percent_meCHH;
-  if (($counting{total_meCHH_count}+$counting{total_unmethylated_CHH_count}) > 0){
-    $percent_meCHH = sprintf("%.1f",100*$counting{total_meCHH_count}/($counting{total_meCHH_count}+$counting{total_unmethylated_CHH_count}));
-  }
-
-  my $percent_meCpG;
-  if (($counting{total_meCpG_count}+$counting{total_unmethylated_CpG_count}) > 0){
-    $percent_meCpG = sprintf("%.1f",100*$counting{total_meCpG_count}/($counting{total_meCpG_count}+$counting{total_unmethylated_CpG_count}));
-  }
-
-  ### printing methylated CpG percentage if applicable
-  if ($percent_meCpG){
-    warn "C methylated in CpG context:\t${percent_meCpG}%\n";
-    print REPORT "C methylated in CpG context:\t${percent_meCpG}%\n";
-  }
-  else{
-    warn "Can't determine percentage of methylated Cs in CpG context if value was 0\n";
-    print REPORT "Can't determine percentage of methylated Cs in CpG context if value was 0\n";
-  }
-
-  ### printing methylated C percentage in CHG context if applicable
-  if ($percent_meCHG){
-    warn "C methylated in CHG context:\t${percent_meCHG}%\n";
-    print REPORT "C methylated in CHG context:\t${percent_meCHG}%\n";
-  }
-  else{
-    warn "Can't determine percentage of methylated Cs in CHG context if value was 0\n";
-    print REPORT "Can't determine percentage of methylated Cs in CHG context if value was 0\n";
-  }
-
-  ### printing methylated C percentage in CHH context if applicable
-  if ($percent_meCHH){
-    warn "C methylated in CHH context:\t${percent_meCHH}%\n\n\n";
-    print REPORT "C methylated in CHH context:\t${percent_meCHH}%\n\n\n";
-  }
-  else{
-    warn "Can't determine percentage of methylated Cs in CHH context if value was 0\n\n\n";
-    print REPORT "Can't determine percentage of methylated Cs in CHH context if value was 0\n\n\n";
-  }
-
-}
-
-sub process_single_end_fastA_file_for_methylation_call{
-  my ($sequence_file,$C_to_T_infile,$G_to_A_infile) = @_;
-  ### this is a FastA sequence file; we need the actual sequence to compare it against the genomic sequence in order to make a methylation call.
-  ### Now reading in the sequence file sequence by sequence and see if the current sequence was mapped to one (or both) of the converted genomes in either
-  ### the C->T or G->A version
-
-  ### gzipped version of the infile
-  if ($sequence_file =~ /\.gz$/){
-    open (IN,"zcat $sequence_file |") or die $!;
-  }
-  else{
-    open (IN,$sequence_file) or die $!;
-  }
-
-  my $count = 0;
-
-  warn "\nReading in the sequence file $sequence_file\n";
-  while (1) {
-    # last if ($counting{sequences_count} > 100);
-    my $identifier = <IN>;
-    my $sequence = <IN>;
-    last unless ($identifier and $sequence);
-
-    $identifier = fix_IDs($identifier); # this is to avoid problems with truncated read ID when they contain white spaces
-
-    ++$count;
-
-    if ($skip){
-      next unless ($count > $skip);
-    }
-    if ($upto){
-      last if ($count > $upto);
-    }
-
-    $counting{sequences_count}++;
-    if ($counting{sequences_count}%100000==0) {
-      warn "Processed $counting{sequences_count} sequences so far\n";
-    }
-    chomp $sequence;
-    chomp $identifier;
-
-    $identifier =~ s/^>//; # deletes the > at the beginning of FastA headers
-
-    my $return;
-    if ($bowtie2){
-      $return = check_bowtie_results_single_end_bowtie2 (uc$sequence,$identifier);
-    }
-    else{
-      $return = check_bowtie_results_single_end(uc$sequence,$identifier); # default Bowtie 1
-    }
-
-    unless ($return){
-      $return = 0;
-    }
-
-    # print the sequence to ambiguous.out if --ambiguous was specified
-    if ($ambiguous and $return == 2){
-      print AMBIG ">$identifier\n";	
-      print AMBIG "$sequence\n";
-    }
-
-    # print the sequence to <unmapped.out> file if --un was specified
-    elsif ($unmapped and $return == 1){
-      print UNMAPPED ">$identifier\n";	
-      print UNMAPPED "$sequence\n";
-    }
-  }
-  print "Processed $counting{sequences_count} sequences in total\n\n";
-
-  print_final_analysis_report_single_end($C_to_T_infile,$G_to_A_infile);
-
-}
-
-sub process_single_end_fastQ_file_for_methylation_call{
-  my ($sequence_file,$C_to_T_infile,$G_to_A_infile) = @_;
-  ### this is the Illumina sequence file; we need the actual sequence to compare it against the genomic sequence in order to make a methylation call.
-  ### Now reading in the sequence file sequence by sequence and see if the current sequence was mapped to one (or both) of the converted genomes in either
-  ### the C->T or G->A version
-
-  ### gzipped version of the infile
-  if ($sequence_file =~ /\.gz$/){
-    open (IN,"zcat $sequence_file |") or die $!;
-  }
-  else{
-    open (IN,$sequence_file) or die $!;
-  }
-
-  my $count = 0;
-
-  warn "\nReading in the sequence file $sequence_file\n";
-  while (1) {
-    my $identifier = <IN>;
-    my $sequence = <IN>;
-    my $identifier_2 = <IN>;
-    my $quality_value = <IN>;
-    last unless ($identifier and $sequence and $identifier_2 and $quality_value);
-
-    $identifier = fix_IDs($identifier); # this is to avoid problems with truncated read ID when they contain white spaces
-
-    ++$count;
-
-    if ($skip){
-      next unless ($count > $skip);
-    }
-    if ($upto){
-      last if ($count > $upto);
-    }
-
-    $counting{sequences_count}++;
-
-    if ($counting{sequences_count}%1000000==0) {
-      warn "Processed $counting{sequences_count} sequences so far\n";
-    }
-    chomp $sequence;
-    chomp $identifier;
-    chomp $quality_value;
-
-    $identifier =~ s/^\@//;  # deletes the @ at the beginning of Illumin FastQ headers
-
-    my $return;
-    if ($bowtie2){
-      $return = check_bowtie_results_single_end_bowtie2 (uc$sequence,$identifier,$quality_value);
-    }
-    else{
-      $return = check_bowtie_results_single_end(uc$sequence,$identifier,$quality_value); # default Bowtie 1
-    }
-
-    unless ($return){
-      $return = 0;
-    }
-
-    # print the sequence to ambiguous.out if --ambiguous was specified
-    if ($ambiguous and $return == 2){
-      print AMBIG "\@$identifier\n";	
-      print AMBIG "$sequence\n";
-      print AMBIG $identifier_2;	
-      print AMBIG "$quality_value\n";
-    }
-
-    # print the sequence to <unmapped.out> file if --un was specified
-    elsif ($unmapped and $return == 1){
-      print UNMAPPED "\@$identifier\n";	
-      print UNMAPPED "$sequence\n";
-      print UNMAPPED $identifier_2;	
-      print UNMAPPED "$quality_value\n";
-    }
-  }
-  print "Processed $counting{sequences_count} sequences in total\n\n";
-
-  print_final_analysis_report_single_end($C_to_T_infile,$G_to_A_infile);
-
-}
-
-sub process_fastA_files_for_paired_end_methylation_calls{
-  my ($sequence_file_1,$sequence_file_2,$C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2) = @_;
-  ### Processing the two FastA sequence files; we need the actual sequences of both reads to compare them against the genomic sequence in order to
-  ### make a methylation call. The sequence idetifier per definition needs to be the same for a sequence pair used for paired-end mapping.
-  ### Now reading in the sequence files sequence by sequence and see if the current sequences produced an alignment to one (or both) of the
-  ### converted genomes (either the C->T or G->A version)
-
-  ### gzipped version of the infiles
-  if ($sequence_file_1 =~ /\.gz$/ and $sequence_file_2 =~ /\.gz$/){
-    open (IN1,"zcat $sequence_file_1 |") or die "Failed to open zcat pipe to $sequence_file_1 $!\n";
-    open (IN2,"zcat $sequence_file_2 |") or die "Failed to open zcat pipe to $sequence_file_2 $!\n";
-  }
-  else{
-    open (IN1,$sequence_file_1) or die $!;
-    open (IN2,$sequence_file_2) or die $!;
-  }
-
-  warn "\nReading in the sequence files $sequence_file_1 and $sequence_file_2\n";
-  ### Both files are required to have the exact same number of sequences, therefore we can process the sequences jointly one by one
-
-  my $count = 0;
-
-  while (1) {
-    # reading from the first input file
-    my $identifier_1 = <IN1>;
-    my $sequence_1 = <IN1>;
-    # reading from the second input file
-    my $identifier_2 = <IN2>;
-    my $sequence_2 = <IN2>;
-    last unless ($identifier_1 and $sequence_1 and $identifier_2 and $sequence_2);
-
-    $identifier_1 = fix_IDs($identifier_1); # this is to avoid problems with truncated read ID when they contain white spaces
-    $identifier_2 = fix_IDs($identifier_2);
-
-    ++$count;
-
-    if ($skip){
-      next unless ($count > $skip);
-    }
-    if ($upto){
-      last if ($count > $upto);
-    }
-
-    $counting{sequences_count}++;
-    if ($counting{sequences_count}%100000==0) {
-      warn "Processed $counting{sequences_count} sequences so far\n";
-    }
-    my $orig_identifier_1 = $identifier_1;
-    my $orig_identifier_2 = $identifier_2;
-
-    chomp $sequence_1;
-    chomp $identifier_1;
-    chomp $sequence_2;
-    chomp $identifier_2;
-
-    $identifier_1 =~ s/^>//; # deletes the > at the beginning of FastA headers
-
-    my $return;
-    if ($bowtie2){
-      $return = check_bowtie_results_paired_ends_bowtie2 (uc$sequence_1,uc$sequence_2,$identifier_1);
-    }
-    else{
-      $return = check_bowtie_results_paired_ends (uc$sequence_1,uc$sequence_2,$identifier_1);
-    }
-
-    unless ($return){
-      $return = 0;
-    }
-
-    # print the sequences to ambiguous_1 and _2 if --ambiguous was specified
-    if ($ambiguous and $return == 2){
-      print AMBIG_1 $orig_identifier_1;	
-      print AMBIG_1 "$sequence_1\n";
-      print AMBIG_2 $orig_identifier_2;	
-      print AMBIG_2 "$sequence_2\n";
-    }
-
-    # print the sequences to unmapped_1.out and unmapped_2.out if --un was specified
-    elsif ($unmapped and $return == 1){
-      print UNMAPPED_1 $orig_identifier_1;	
-      print UNMAPPED_1 "$sequence_1\n";
-      print UNMAPPED_2 $orig_identifier_2;	
-      print UNMAPPED_2 "$sequence_2\n";
-    }
-  }
-
-  print "Processed $counting{sequences_count} sequences in total\n\n";
-
-  print_final_analysis_report_paired_ends($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2);
-
-}
-
-sub process_fastQ_files_for_paired_end_methylation_calls{
-  my ($sequence_file_1,$sequence_file_2,$C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2) = @_;
-  ### Processing the two Illumina sequence files; we need the actual sequence of both reads to compare them against the genomic sequence in order to
-  ### make a methylation call. The sequence identifier per definition needs to be same for a sequence pair used for paired-end alignments.
-  ### Now reading in the sequence files sequence by sequence and see if the current sequences produced a paired-end alignment to one (or both)
-  ### of the converted genomes (either C->T or G->A version)
-
-  ### gzipped version of the infiles
-  if ($sequence_file_1 =~ /\.gz$/ and $sequence_file_2 =~ /\.gz$/){
-    open (IN1,"zcat $sequence_file_1 |") or die "Failed to open zcat pipe to $sequence_file_1 $!\n";
-    open (IN2,"zcat $sequence_file_2 |") or die "Failed to open zcat pipe to $sequence_file_2 $!\n";
-  }
-  else{
-    open (IN1,$sequence_file_1) or die $!;
-    open (IN2,$sequence_file_2) or die $!;
-  }
-
-  my $count = 0;
-
-  warn "\nReading in the sequence files $sequence_file_1 and $sequence_file_2\n";
-  ### Both files are required to have the exact same number of sequences, therefore we can process the sequences jointly one by one
-  while (1) {
-    # reading from the first input file
-    my $identifier_1 = <IN1>;
-    my $sequence_1 = <IN1>;
-    my $ident_1 = <IN1>;         # not needed
-    my $quality_value_1 = <IN1>; # not needed
-    # reading from the second input file
-    my $identifier_2 = <IN2>;
-    my $sequence_2 = <IN2>;
-    my $ident_2 = <IN2>;         # not needed
-    my $quality_value_2 = <IN2>; # not needed
-    last unless ($identifier_1 and $sequence_1 and $quality_value_1 and $identifier_2 and $sequence_2 and $quality_value_2);
-
-    $identifier_1 = fix_IDs($identifier_1); # this is to avoid problems with truncated read ID when they contain white spaces
-    $identifier_2 = fix_IDs($identifier_2);
-
-    ++$count;
-
-    if ($skip){
-      next unless ($count > $skip);
-    }
-    if ($upto){
-      last if ($count > $upto);
-    }
-
-    $counting{sequences_count}++;
-    if ($counting{sequences_count}%100000==0) {
-      warn "Processed $counting{sequences_count} sequences so far\n";
-    }
-
-    my $orig_identifier_1 = $identifier_1;
-    my $orig_identifier_2 = $identifier_2;
-
-    chomp $sequence_1;
-    chomp $identifier_1;
-    chomp $sequence_2;
-    chomp $identifier_2;
-    chomp $quality_value_1;
-    chomp $quality_value_2;
-
-    $identifier_1 =~ s/^\@//;  # deletes the @ at the beginning of the FastQ ID
-
-    my $return;
-    if ($bowtie2){
-      $return = check_bowtie_results_paired_ends_bowtie2 (uc$sequence_1,uc$sequence_2,$identifier_1,$quality_value_1,$quality_value_2);
-    }
-    else{
-      $return = check_bowtie_results_paired_ends (uc$sequence_1,uc$sequence_2,$identifier_1,$quality_value_1,$quality_value_2);
-    }
-
-    unless ($return){
-      $return = 0;
-    }
-
-    # print the sequences to ambiguous_1 and _2 if --ambiguous was specified
-    if ($ambiguous and $return == 2){
-      # seq_1
-      print AMBIG_1 $orig_identifier_1;	
-      print AMBIG_1 "$sequence_1\n";
-      print AMBIG_1 $ident_1;	
-      print AMBIG_1 "$quality_value_1\n";
-	# seq_2
-      print AMBIG_2 $orig_identifier_2;	
-      print AMBIG_2 "$sequence_2\n";
-      print AMBIG_2 $ident_2;	
-      print AMBIG_2 "$quality_value_2\n";
-    }
-
-    # print the sequences to unmapped_1.out and unmapped_2.out if --un was specified
-    elsif ($unmapped and $return == 1){
-      # seq_1
-      print UNMAPPED_1 $orig_identifier_1;	
-      print UNMAPPED_1 "$sequence_1\n";
-      print UNMAPPED_1 $ident_1;	
-      print UNMAPPED_1 "$quality_value_1\n";
-      # seq_2
-      print UNMAPPED_2 $orig_identifier_2;	
-      print UNMAPPED_2 "$sequence_2\n";
-      print UNMAPPED_2 $ident_2;	
-      print UNMAPPED_2 "$quality_value_2\n";
-    }
-  }
-
-  print "Processed $counting{sequences_count} sequences in total\n\n";
-
-  print_final_analysis_report_paired_ends($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2);
-
-}
-
-sub check_bowtie_results_single_end{
-  my ($sequence,$identifier,$quality_value) = @_;
-
-  unless ($quality_value){ # FastA sequences get assigned a quality value of Phred 40 throughout
-    $quality_value = 'I'x(length$sequence);
-  }
-
-  my %mismatches = ();
-  ### reading from the bowtie output files to see if this sequence aligned to a bisulfite converted genome
-  foreach my $index (0..$#fhs){
-
-    ### skipping this index if the last alignment has been set to undefined already (i.e. end of bowtie output)
-    next unless ($fhs[$index]->{last_line} and defined $fhs[$index]->{last_seq_id});
-    ### if the sequence we are currently looking at produced an alignment we are doing various things with it
-    if ($fhs[$index]->{last_seq_id} eq $identifier) {
-      ###############################################################
-      ### STEP I Now processing the alignment stored in last_line ###
-      ###############################################################
-      my $valid_alignment_found_1 = decide_whether_single_end_alignment_is_valid($index,$identifier);
-      ### sequences can fail at this point if there was only 1 seq in the wrong orientation, or if there were 2 seqs, both in the wrong orientation
-      ### we only continue to extract useful information about this alignment if 1 was returned
-      if ($valid_alignment_found_1 == 1){
-	### Bowtie outputs which made it this far are in the correct orientation, so we can continue to analyse the alignment itself
-	### need to extract the chromosome number from the bowtie output (which is either XY_cf (complete forward) or XY_cr (complete reverse)
-	my ($id,$strand,$mapped_chromosome,$position,$bowtie_sequence,$mismatch_info) = (split (/\t/,$fhs[$index]->{last_line},-1))[0,1,2,3,4,7];
-
-	unless($mismatch_info){
-	  $mismatch_info = '';
-	}
-
-	chomp $mismatch_info;
-	my $chromosome;
-	if ($mapped_chromosome =~ s/_(CT|GA)_converted$//){
-	  $chromosome = $mapped_chromosome;
-	}
-	else{
-	  die "Chromosome number extraction failed for $mapped_chromosome\n";
-	}
-	### Now extracting the number of mismatches to the converted genome
-	my $number_of_mismatches;
-	if ($mismatch_info eq ''){
-	  $number_of_mismatches = 0;
-	}
-	elsif ($mismatch_info =~ /^\d/){
-	  my @mismatches = split (/,/,$mismatch_info);
-	  $number_of_mismatches = scalar @mismatches;
-	}
-	else{
-	  die "Something weird is going on with the mismatch field:\t>>> $mismatch_info <<<\n";
-	}
-	### creating a composite location variable from $chromosome and $position and storing the alignment information in a temporary hash table
-	my $alignment_location = join (":",$chromosome,$position);
-	### If a sequence aligns to exactly the same location twice the sequence does either not contain any C or G, or all the Cs (or Gs on the reverse
-	### strand) were methylated and therefore protected. It is not needed to overwrite the same positional entry with a second entry for the same
-	### location (the genomic sequence extraction and methylation would not be affected by this, only the thing which would change is the index
-	### number for the found alignment)
-	unless (exists $mismatches{$number_of_mismatches}->{$alignment_location}){
-	  $mismatches{$number_of_mismatches}->{$alignment_location}->{seq_id}=$id;
-	  $mismatches{$number_of_mismatches}->{$alignment_location}->{bowtie_sequence}=$bowtie_sequence;
-	  $mismatches{$number_of_mismatches}->{$alignment_location}->{index}=$index;
-	  $mismatches{$number_of_mismatches}->{$alignment_location}->{chromosome}=$chromosome;
-	  $mismatches{$number_of_mismatches}->{$alignment_location}->{position}=$position;
-	}
-	$number_of_mismatches = undef;
-	##################################################################################################################################################
-	### STEP II Now reading in the next line from the bowtie filehandle. The next alignment can either be a second alignment of the same sequence or a
-	### a new sequence. In either case we will store the next line in @fhs ->{last_line}. In case the alignment is already the next entry, a 0 will
-	### be returned as $valid_alignment_found and it will then be processed in the next round only.
-	##################################################################################################################################################
-	my $newline = $fhs[$index]->{fh}-> getline();
-	if ($newline){
-	  my ($seq_id) = split (/\t/,$newline);
-	  $fhs[$index]->{last_seq_id} = $seq_id;
-	  $fhs[$index]->{last_line} = $newline;
-	}
-	else {
-	  # assigning undef to last_seq_id and last_line and jumping to the next index (end of bowtie output)
-	  $fhs[$index]->{last_seq_id} = undef;
-	  $fhs[$index]->{last_line} = undef;
-	  next;
-	}	
-	my $valid_alignment_found_2 = decide_whether_single_end_alignment_is_valid($index,$identifier);
-	### we only continue to extract useful information about this second alignment if 1 was returned
-	if ($valid_alignment_found_2 == 1){
-	  ### If the second Bowtie output made it this far it is in the correct orientation, so we can continue to analyse the alignment itself
-	  ### need to extract the chromosome number from the bowtie output (which is either XY_cf (complete forward) or XY_cr (complete reverse)
-	  my ($id,$strand,$mapped_chromosome,$position,$bowtie_sequence,$mismatch_info) = (split (/\t/,$fhs[$index]->{last_line},-1))[0,1,2,3,4,7];
-	  unless($mismatch_info){
-	    $mismatch_info = '';
-	  }	
-	  chomp $mismatch_info;
-
-	  my $chromosome;	
-	  if ($mapped_chromosome =~ s/_(CT|GA)_converted$//){
-	    $chromosome = $mapped_chromosome;
-	  }
-	  else{
-	    die "Chromosome number extraction failed for $mapped_chromosome\n";
-	  }
-
-	  ### Now extracting the number of mismatches to the converted genome
-	  my $number_of_mismatches;
-	  if ($mismatch_info eq ''){
-	    $number_of_mismatches = 0;
-	  }
-	  elsif ($mismatch_info =~ /^\d/){
-	    my @mismatches = split (/,/,$mismatch_info);
-	    $number_of_mismatches = scalar @mismatches;
-	  }
-	  else{
-	    die "Something weird is going on with the mismatch field\n";
-	  }
-	  ### creating a composite location variable from $chromosome and $position and storing the alignment information in a temporary hash table
-	  ### extracting the chromosome number from the bowtie output (see above)
-	  my $alignment_location = join (":",$chromosome,$position);
-	  ### In the special case that two differently converted sequences align against differently converted genomes, but to the same position
-	  ### with the same number of mismatches (or perfect matches), the chromosome, position and number of mismatches are the same. In this
-	  ### case we are not writing the same entry out a second time.
-	  unless (exists $mismatches{$number_of_mismatches}->{$alignment_location}){
-	    $mismatches{$number_of_mismatches}->{$alignment_location}->{seq_id}=$id;
-	    $mismatches{$number_of_mismatches}->{$alignment_location}->{bowtie_sequence}=$bowtie_sequence;
-	    $mismatches{$number_of_mismatches}->{$alignment_location}->{index}=$index;
-	    $mismatches{$number_of_mismatches}->{$alignment_location}->{chromosome}=$chromosome;
-	    $mismatches{$number_of_mismatches}->{$alignment_location}->{position}=$position;
-	  }
-	  ####################################################################################################################################
-	  #### STEP III Now reading in one more line which has to be the next alignment to be analysed. Adding it to @fhs ->{last_line}    ###
-	  ####################################################################################################################################
-	  $newline = $fhs[$index]->{fh}-> getline();
-	  if ($newline){
-	    my ($seq_id) = split (/\t/,$newline);
-	    die "The same seq ID occurred more than twice in a row\n" if ($seq_id eq $identifier);
-	    $fhs[$index]->{last_seq_id} = $seq_id;
-	    $fhs[$index]->{last_line} = $newline;
-	    next;
-	  }	
-	  else {
-	    # assigning undef to last_seq_id and last_line and jumping to the next index (end of bowtie output)
-	    $fhs[$index]->{last_seq_id} = undef;
-	    $fhs[$index]->{last_line} = undef;
-	    next;
-	  }
-	  ### still within the 2nd sequence in correct orientation found	
-	}
-	### still withing the 1st sequence in correct orientation found
-      }
-      ### still within the if (last_seq_id eq identifier) condition
-    }
-    ### still within foreach index loop
-  }
-  ### if there was not a single alignment found for a certain sequence we will continue with the next sequence in the sequence file
-  unless(%mismatches){
-    $counting{no_single_alignment_found}++;
-    if ($unmapped){
-      return 1; ### We will print this sequence out as unmapped sequence if --un unmapped.out has been specified
-    }
-    else{
-      return;
-    }
-  }
-  #######################################################################################################################################################
-  #######################################################################################################################################################
-  ### We are now looking if there is a unique best alignment for a certain sequence. This means we are sorting in ascending order and look at the     ###
-  ### sequence with the lowest amount of mismatches. If there is only one single best position we are going to store the alignment information in the ###
-  ### meth_call variables, if there are multiple hits with the same amount of (lowest) mismatches we are discarding the sequence altogether           ###
-  #######################################################################################################################################################
-  #######################################################################################################################################################
-  ### Going to use the variable $sequence_fails as a 'memory' if a sequence could not be aligned uniquely (set to 1 then)
-  my $sequence_fails = 0;
-  ### Declaring an empty hash reference which will store all information we need for the methylation call
-  my $methylation_call_params; # hash reference!
-  ### sorting in ascending order
-  foreach my $mismatch_number (sort {$a<=>$b} keys %mismatches){
-
-    ### if there is only 1 entry in the hash with the lowest number of mismatches we accept it as the best alignment
-    if (scalar keys %{$mismatches{$mismatch_number}} == 1){
-      for my $unique_best_alignment (keys %{$mismatches{$mismatch_number}}){
-	$methylation_call_params->{$identifier}->{bowtie_sequence} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{bowtie_sequence};
-	$methylation_call_params->{$identifier}->{chromosome} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{chromosome};
-	$methylation_call_params->{$identifier}->{position} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{position};
-	$methylation_call_params->{$identifier}->{index} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{index};
-    	$methylation_call_params->{$identifier}->{number_of_mismatches} = $mismatch_number;
-      }
-    }
-    elsif (scalar keys %{$mismatches{$mismatch_number}} == 3){
-      ### If there are 3 sequences with the same number of lowest mismatches we can discriminate 2 cases: (i) all 3 alignments are unique best hits and
-      ### come from different alignments processes (== indices) or (ii) one sequence alignment (== index) will give a unique best alignment, whereas a
-      ### second one will produce 2 (or potentially many) alignments for the same sequence but in a different conversion state or against a different genome
-      ### version (or both). This becomes especially relevant for highly converted sequences in which all Cs have been converted to Ts in the bisulfite
-      ### reaction. E.g.
-      ### CAGTCACGCGCGCGCG will become
-      ### TAGTTATGTGTGTGTG in the CT transformed version, which will ideally still give the correct alignment in the CT->CT alignment condition.
-      ### If the same read will then become G->A transformed as well however, the resulting sequence will look differently and potentially behave
-      ### differently in a GA->GA alignment and this depends on the methylation state of the original sequence!:
-      ### G->A conversion:
-      ### highly methylated: CAATCACACACACACA
-      ### highly converted : TAATTATATATATATA <== this sequence has a reduced complexity (only 2 bases left and not 3), and it is more likely to produce
-      ### an alignment with a low complexity genomic region than the one above. This would normally lead to the entire sequence being kicked out as the
-      ### there will be 3 alignments with the same number of lowest mismatches!! This in turn means that highly methylated and thereby not converted
-      ### sequences are more likely to pass the alignment step, thereby creating a bias for methylated reads compared to their non-methylated counterparts.
-      ### We do not want any bias, whatsover. Therefore if we have 1 sequence producing a unique best alignment and the second and third conditions
-      ### producing alignments only after performing an additional (theoretical) conversion we want to keep the best alignment with the lowest number of
-      ### additional transliterations performed. Thus we want to have a look at the level of complexity of the sequences producing the alignment.
-      ### In the above example the number of transliterations required to transform the actual sequence
-      ### to the C->T version would be TAGTTATGTGTGTGTG -> TAGTTATGTGTGTGTG = 0; (assuming this gives the correct alignment)
-      ### in the G->A case it would be TAGTTATGTGTGTGTG -> TAATTATATATATATA = 6; (assuming this gives multiple wrong alignments)
-      ### if the sequence giving a unique best alignment required a lower number of transliterations than the second best sequence yielding alignments
-      ### while requiring a much higher number of transliterations, we are going to accept the unique best alignment with the lowest number of performed
-      ### transliterations. As a threshold which does scale we will start with the number of tranliterations of the lowest best match x 2 must still be
-      ### smaller than the number of tranliterations of the second best sequence. Everything will be flagged with $sequence_fails = 1 and discarded.
-      my @three_candidate_seqs;
-      foreach my $composite_location (keys (%{$mismatches{$mismatch_number}}) ){
-	my $transliterations_performed;
-	if ($mismatches{$mismatch_number}->{$composite_location}->{index} == 0 or $mismatches{$mismatch_number}->{$composite_location}->{index} == 1){
-	  $transliterations_performed = determine_number_of_transliterations_performed($sequence,'CT');
-	}
-	elsif ($mismatches{$mismatch_number}->{$composite_location}->{index} == 2 or $mismatches{$mismatch_number}->{$composite_location}->{index} == 3){
-	  $transliterations_performed = determine_number_of_transliterations_performed($sequence,'GA');
-	}
-	else{
-	  die "unexpected index number range $!\n";
-	}
-	push @three_candidate_seqs,{
-				    index =>$mismatches{$mismatch_number}->{$composite_location}->{index},
-				    bowtie_sequence => $mismatches{$mismatch_number}->{$composite_location}->{bowtie_sequence},
-				    mismatch_number => $mismatch_number,
-				    chromosome => $mismatches{$mismatch_number}->{$composite_location}->{chromosome},
-				    position => $mismatches{$mismatch_number}->{$composite_location}->{position},
-				    seq_id => $mismatches{$mismatch_number}->{$composite_location}->{seq_id},
-				    transliterations_performed => $transliterations_performed,
-				   };
-      }
-      ### sorting in ascending order for the lowest number of transliterations performed
-      @three_candidate_seqs = sort {$a->{transliterations_performed} <=> $b->{transliterations_performed}} @three_candidate_seqs;
-      my $first_array_element = $three_candidate_seqs[0]->{transliterations_performed};
-      my $second_array_element = $three_candidate_seqs[1]->{transliterations_performed};
-      my $third_array_element = $three_candidate_seqs[2]->{transliterations_performed};
-      # print "$first_array_element\t$second_array_element\t$third_array_element\n";
-      if (($first_array_element*2) < $second_array_element){
-	$counting{low_complexity_alignments_overruled_count}++;
-	### taking the index with the unique best hit and over ruling low complexity alignments with 2 hits
-	$methylation_call_params->{$identifier}->{bowtie_sequence} = $three_candidate_seqs[0]->{bowtie_sequence};
-	$methylation_call_params->{$identifier}->{chromosome} = $three_candidate_seqs[0]->{chromosome};
-	$methylation_call_params->{$identifier}->{position} = $three_candidate_seqs[0]->{position};
-	$methylation_call_params->{$identifier}->{index} = $three_candidate_seqs[0]->{index};
-	$methylation_call_params->{$identifier}->{number_of_mismatches} = $mismatch_number;
-	# print "Overruled low complexity alignments! Using $first_array_element and disregarding $second_array_element and $third_array_element\n";
-      }
-      else{
-	$sequence_fails = 1;
-      }
-    }
-    else{
-      $sequence_fails = 1;
-    }
-    ### after processing the alignment with the lowest number of mismatches we exit
-    last;
-  }
-  ### skipping the sequence completely if there were multiple alignments with the same amount of lowest mismatches found at different positions
-  if ($sequence_fails == 1){
-    $counting{unsuitable_sequence_count}++;
-    if ($ambiguous){
-      return 2; # => exits to next sequence, and prints it out to multiple_alignments.out if --ambiguous has been specified
-    }
-    if ($unmapped){
-      return 1; # => exits to next sequence, and prints it out to unmapped.out if --un has been specified
-    }
-    else{
-      return 0; # => exits to next sequence (default)
-    }
-  }
-
-  ### --DIRECTIONAL
-  ### If the option --directional has been specified the user wants to consider only alignments to the original top strand or the original bottom strand. We will therefore
-  ### discard all alignments to strands complementary to the original strands, as they should not exist in reality due to the library preparation protocol
-  if ($directional){
-    if ( ($methylation_call_params->{$identifier}->{index} == 2) or ($methylation_call_params->{$identifier}->{index} == 3) ){
-      #    warn "Alignment rejected! (index was: $methylation_call_params->{$identifier}->{index})\n";
-      $counting{alignments_rejected_count}++;
-      return 0;
-    }
-  }
-
-  ### If the sequence has not been rejected so far it will have a unique best alignment
-  $counting{unique_best_alignment_count}++;
-  extract_corresponding_genomic_sequence_single_end($identifier,$methylation_call_params);
-  ### check test to see if the genomic sequence we extracted has the same length as the observed sequence+2, and only then we perform the methylation call
-  if (length($methylation_call_params->{$identifier}->{unmodified_genomic_sequence}) != length($sequence)+2){
-    warn "Chromosomal sequence could not be extracted for\t$identifier\t$methylation_call_params->{$identifier}->{chromosome}\t$methylation_call_params->{$identifier}->{position}\n";
-    $counting{genomic_sequence_could_not_be_extracted_count}++;
-    return 0;
-  }
-
-  ### otherwise we are set to perform the actual methylation call
-  $methylation_call_params->{$identifier}->{methylation_call} = methylation_call($identifier,$sequence,$methylation_call_params->{$identifier}->{unmodified_genomic_sequence},$methylation_call_params->{$identifier}->{read_conversion});
-
-  print_bisulfite_mapping_result_single_end($identifier,$sequence,$methylation_call_params,$quality_value);
-  return 0; ## otherwise 1 will be returned by default, which would print the sequence to unmapped.out
-}
-
-sub check_bowtie_results_single_end_bowtie2{
-  my ($sequence,$identifier,$quality_value) = @_;
-
-  unless ($quality_value){ # FastA sequences get assigned a quality value of Phred 40 throughout
-    $quality_value = 'I'x(length$sequence);
-  }
-
-  # as of version Bowtie 2 2.0.0 beta7, when input reads are unpaired, Bowtie 2 no longer removes the trailing /1 or /2 from the read name.
-  # $identifier =~ s/\/[1234567890]+$//; # some sequencers don't just have /1 or /2 at the end of read IDs
-
-  my $alignment_ambiguous = 0;
-
-  my %alignments = ();
-
-  ### reading from the Bowtie 2 output filehandles
-  foreach my $index (0..$#fhs){
-    # print "Index: $index\n";
-    # print "$fhs[$index]->{last_line}\n";
-    # print "$fhs[$index]->{last_seq_id}\n\n";
-
-    ### skipping this index if the last alignment has been set to undefined already (i.e. end of bowtie output)
-    next unless ($fhs[$index]->{last_line} and defined $fhs[$index]->{last_seq_id});
-
-    ### if the sequence we are currently looking at produced an alignment we are doing various things with it
-    # print "last seq id: $fhs[$index]->{last_seq_id} and identifier: $identifier\n";
-
-   if ($fhs[$index]->{last_seq_id} eq $identifier) {
-
-      #  SAM format specifications for Bowtie 2
-      #  (1) Name of read that aligned
-      #  (2) Sum of all applicable flags. Flags relevant to Bowtie are:
-      #        1 The read is one of a pair
-      #        2 The alignment is one end of a proper paired-end alignment
-      #        4 The read has no reported alignments
-      #        8 The read is one of a pair and has no reported alignments
-      #       16 The alignment is to the reverse reference strand
-      #       32 The other mate in the paired-end alignment is aligned to the reverse reference strand
-      #       64 The read is mate 1 in a pair
-      #      128 The read is mate 2 in a pair
-      #      256 The read has multiple mapping states
-      #  (3) Name of reference sequence where alignment occurs (unmapped reads have a *)
-      #  (4) 1-based offset into the forward reference strand where leftmost character of the alignment occurs (0 for unmapped reads)
-      #  (5) Mapping quality (255 means MAPQ is not available)
-      #  (6) CIGAR string representation of alignment (* if unavailable)
-      #  (7) Name of reference sequence where mate's alignment occurs. Set to = if the mate's reference sequence is the same as this alignment's, or * if there is no mate.
-      #  (8) 1-based offset into the forward reference strand where leftmost character of the mate's alignment occurs. Offset is 0 if there is no mate.
-      #  (9) Inferred fragment size. Size is negative if the mate's alignment occurs upstream of this alignment. Size is 0 if there is no mate.
-      # (10) Read sequence (reverse-complemented if aligned to the reverse strand)
-      # (11) ASCII-encoded read qualities (reverse-complemented if the read aligned to the reverse strand). The encoded quality values are on the Phred quality scale and the encoding is ASCII-offset by 33 (ASCII char !), similarly to a FASTQ file.
-      # (12) Optional fields. Fields are tab-separated. bowtie2 outputs zero or more of these optional fields for each alignment, depending on the type of the alignment:
-      # AS:i:<N> Alignment score. Can be negative. Can be greater than 0 in --local mode (but not in --end-to-end mode). Only present if SAM record is for an aligned read.
-      # XS:i:<N> Alignment score for second-best alignment. Can be negative. Can be greater than 0 in --local mode (but not in --end-to-end mode). Only present if the SAM record is for an aligned read and more than one alignment was found for the read.
-      # YS:i:<N> Alignment score for opposite mate in the paired-end alignment. Only present if the SAM record is for a read that aligned as part of a paired-end alignment.
-      # XN:i:<N> The number of ambiguous bases in the reference covering this alignment. Only present if SAM record is for an aligned read.
-      # XM:i:<N> The number of mismatches in the alignment. Only present if SAM record is for an aligned read.
-      # XO:i:<N> The number of gap opens, for both read and reference gaps, in the alignment. Only present if SAM record is for an aligned read.
-      # XG:i:<N> The number of gap extensions, for both read and reference gaps, in the alignment. Only present if SAM record is for an aligned read.
-      # NM:i:<N> The edit distance; that is, the minimal number of one-nucleotide edits (substitutions, insertions and deletions) needed to transform the read string into the reference string. Only present if SAM record is for an aligned read.
-      # YF:Z:<N> String indicating reason why the read was filtered out. See also: Filtering. Only appears for reads that were filtered out.
-      # MD:Z:<S> A string representation of the mismatched reference bases in the alignment. See SAM format specification for details. Only present if SAM record is for an aligned read.
-
-      my ($id,$flag,$mapped_chromosome,$position,$mapping_quality,$cigar,$bowtie_sequence,$qual) = (split (/\t/,$fhs[$index]->{last_line}))[0,1,2,3,4,5,9,10];
-
-      ### If a sequence has no reported alignments there will be a single output line with a bit-wise flag value of 4. We can store the next alignment and move on to the next Bowtie 2 instance
-      if ($flag == 4){
-	## reading in the next alignment, which must be the next sequence
-	my $newline = $fhs[$index]->{fh}-> getline();
-	if ($newline){
-	  chomp $newline;
-	  my ($seq_id) = split (/\t/,$newline);
-	  $fhs[$index]->{last_seq_id} = $seq_id;
-	  $fhs[$index]->{last_line} = $newline;
-	  if ($seq_id eq $identifier){
-	    die "Sequence with ID $identifier did not produce any alignment, but next seq-ID was also $fhs[$index]->{last_seq_id}!\n";
-	  }
-	  next; # next instance
-	}
-	else{
-	  # assigning undef to last_seq_id and last_line and jumping to the next index (end of Bowtie 2 output)
-	  $fhs[$index]->{last_seq_id} = undef;
-	  $fhs[$index]->{last_line} = undef;
-	  next;
-	}
-      }
-
-      # if there are one or more proper alignments we can extract the chromosome number
-      my $chromosome;
-      if ($mapped_chromosome =~ s/_(CT|GA)_converted$//){
-	$chromosome = $mapped_chromosome;
-      }
-      else{
-	die "Chromosome number extraction failed for $mapped_chromosome\n";
-      }
-	  
-      ### We will use the optional field to determine the best alignment. Later on we extract the number of mismatches and/or indels from the CIGAR string
-      my ($alignment_score,$second_best,$MD_tag);
-      my @fields = split (/\t/,$fhs[$index]->{last_line});
-
-      foreach (11..$#fields){
-	if ($fields[$_] =~ /AS:i:(.*)/){
-	  $alignment_score = $1;
-	}
-	elsif ($fields[$_] =~ /XS:i:(.*)/){
-	  $second_best = $1;
-	}
-	elsif ($fields[$_] =~ /MD:Z:(.*)/){
-	  $MD_tag = $1;
-	}
-      }
-
-      # warn "First  best alignment_score is: '$alignment_score'\n";
-      # warn "MD tag is: '$MD_tag'\n";
-      die "Failed to extract alignment score ($alignment_score) and MD tag ($MD_tag)!\n" unless (defined $alignment_score and defined $MD_tag);
-
-      if (defined $second_best){
-	# warn "second best alignment_score is: '$second_best'\n";
-
-	# If the first alignment score is the same as the alignment score of the second best hit we are going to boot this sequence altogether
-	if ($alignment_score == $second_best){
-	  $alignment_ambiguous = 1;
-	  ## need to read and discard all additional ambiguous reads until we reach the next sequence
-	  until ($fhs[$index]->{last_seq_id} ne $identifier){
-	    my $newline = $fhs[$index]->{fh}-> getline();
-	    if ($newline){
-	      chomp $newline;
-	      my ($seq_id) = split (/\t/,$newline);
-	      $fhs[$index]->{last_seq_id} = $seq_id;
-	      $fhs[$index]->{last_line} = $newline;
-	    }
-	    else{
-	      # assigning undef to last_seq_id and last_line and jumping to the next index (end of Bowtie 2 output)
-	      $fhs[$index]->{last_seq_id} = undef;
-	      $fhs[$index]->{last_line} = undef;
-	      last; # break free in case we have reached the end of the alignment output
-	    }
-	  }
-	  #  warn "Index: $index\tThe current Seq-ID is $identifier, skipped all ambiguous sequences until the next ID which is: $fhs[$index]->{last_seq_id}\n";
-	}
-	else{ # the next best alignment has a lower alignment score than the current read, so we can safely store the current alignment
-
-	  my $alignment_location = join (":",$chromosome,$position);
-	
-	  ### If a sequence aligns to exactly the same location with a perfect match twice the sequence does either not contain any C or G, or all the Cs (or Gs on the reverse
-	  ### strand) were methylated and therefore protected. Alternatively it will align better in one condition than in the other. In any case, it is not needed to overwrite
-	  ### the same positional entry with a second entry for the same location, as the genomic sequence extraction and methylation call would not be affected by this. The only
-	  ### thing which would change is the index number for the found alignment). We will continue to assign these alignments to the first indexes 0 and 1, i.e. OT and OB 
-	
-	  unless (exists $alignments{$alignment_location}){
-	    $alignments{$alignment_location}->{seq_id} = $id; 
-	    $alignments{$alignment_location}->{alignment_score} = $alignment_score;
-	    $alignments{$alignment_location}->{bowtie_sequence} = $bowtie_sequence;
-	    $alignments{$alignment_location}->{index} = $index;
-	    $alignments{$alignment_location}->{chromosome} = $chromosome;
-	    $alignments{$alignment_location}->{position} = $position;
-	    $alignments{$alignment_location}->{CIGAR} = $cigar;
-	    $alignments{$alignment_location}->{MD_tag} = $MD_tag;
-	  }
-	
-	  ### now reading and discarding all (inferior) alignments of this sequencing read until we hit the next sequence
-	  until ($fhs[$index]->{last_seq_id} ne $identifier){
-	    my $newline = $fhs[$index]->{fh}-> getline();
-	    if ($newline){
-	      chomp $newline;
-	      my ($seq_id) = split (/\t/,$newline);
-	      $fhs[$index]->{last_seq_id} = $seq_id;
-	      $fhs[$index]->{last_line} = $newline;
-	    }
-	    else{
-	      # assigning undef to last_seq_id and last_line and jumping to the next index (end of Bowtie 2 output)
-	      $fhs[$index]->{last_seq_id} = undef;
-	      $fhs[$index]->{last_line} = undef;
-	      last; # break free in case we have reached the end of the alignment output
-	    }
-	  }
-	  #  warn "Index: $index\tThe current Seq-ID is $identifier, skipped all ambiguous sequences until the next ID which is: $fhs[$index]->{last_seq_id}\n";
-	}
-      }
-      else{ # there is no second best hit, so we can just store this one and read in the next sequence
-	
-	my $alignment_location = join (":",$chromosome,$position);
-	
-	### If a sequence aligns to exactly the same location with a perfect match twice the sequence does either not contain any C or G, or all the Cs (or Gs on the reverse
-	### strand) were methylated and therefore protected. Alternatively it will align better in one condition than in the other. In any case, it is not needed to overwrite
-	### the same positional entry with a second entry for the same location, as the genomic sequence extraction and methylation call would not be affected by this. The only
-	### thing which would change is the index number for the found alignment). We will continue to assign these alignments to the first indexes 0 and 1, i.e. OT and OB 
-
-	unless (exists $alignments{$alignment_location}){
-	  $alignments{$alignment_location}->{seq_id} = $id; 
-	  $alignments{$alignment_location}->{alignment_score} = $alignment_score;
-	  $alignments{$alignment_location}->{bowtie_sequence} = $bowtie_sequence;
-	  $alignments{$alignment_location}->{index} = $index;
-	  $alignments{$alignment_location}->{chromosome} = $chromosome;
-	  $alignments{$alignment_location}->{position} = $position;
-	  $alignments{$alignment_location}->{MD_tag} = $MD_tag;
-	  $alignments{$alignment_location}->{CIGAR} = $cigar;
-	}
-	
-	my $newline = $fhs[$index]->{fh}-> getline();
-	if ($newline){
-	  chomp $newline;
-	  my ($seq_id) = split (/\t/,$newline);
-	  $fhs[$index]->{last_seq_id} = $seq_id;
-	  $fhs[$index]->{last_line} = $newline;
-	  if ($seq_id eq $identifier){
-	    die "Sequence with ID $identifier did not have a second best alignment, but next seq-ID was also $fhs[$index]->{last_seq_id}!\n";
-	  }
-	}
-	else{
-	  # assigning undef to last_seq_id and last_line and jumping to the next index (end of Bowtie 2 output)
-	  $fhs[$index]->{last_seq_id} = undef;
-	  $fhs[$index]->{last_line} = undef;
-	}
-      }
-    }
-  }
-
-  ### if the read produced several ambiguous alignments already now can returning already now. If --ambiguous or --unmapped was specified the read sequence will be printed out.
-  if ($alignment_ambiguous == 1){
-    $counting{unsuitable_sequence_count}++;
-    ### report that the sequence has multiple hits with bitwise flag 256. We can print the sequence to the result file straight away and skip everything else
-    # my $ambiguous_read_output = join("\t",$identifier,'256','*','0','0','*','*','0','0',$sequence,$quality_value);
-    # print "$ambiguous_read_output\n";
-
-    if ($ambiguous){
-      return 2; # => exits to next sequence, and prints it out to _ambiguous_reads.txt if '--ambiguous' was specified
-    }
-    elsif ($unmapped){
-      return 1; # => exits to next sequence, and prints it out to _unmapped_reads.txt if '--unmapped' but not '--ambiguous' was specified
-    }
-    else{
-      return 0;
-    }
-  }
-
-  ### if there was no alignment found for a certain sequence at all we continue with the next sequence in the sequence file
-  unless(%alignments){
-    $counting{no_single_alignment_found}++;
-    # my $unmapped_read_output = join("\t",$identifier,'4','*','0','0','*','*','0','0',$sequence,$quality_value);
-    # print  "$unmapped_read_output\n";
-    if ($unmapped){
-      return 1; # => exits to next sequence, and prints it out to _unmapped_reads.txt if '--unmapped' was specified
-    }
-    else{
-      return 0; # default
-    }
-  }
-
-  #######################################################################################################################################################
-
-  ### If the sequence was not rejected so far we are now looking if there is a unique best alignment among all alignment instances. If there is only one
-  ### single best position we are going to store the alignment information in the $meth_call variable. If there are multiple hits with the same (highest)
-  ### alignment score we are discarding the sequence altogether.
-  ### For end-to-end alignments the maximum alignment score can be 0, each mismatch can receive penalties up to 6, and each gap receives penalties for
-  ### opening (5) and extending (3 per bp) the gap.
-
-  #######################################################################################################################################################
-
-  my $methylation_call_params; # hash reference which will store all information we need for the methylation call
-  my $sequence_fails = 0; # Going to use $sequence_fails as a 'memory' if a sequence could not be aligned uniquely (set to 1 then)
-
-  ### print contents of %alignments for debugging
-  #   if (scalar keys %alignments > 1){
-  #     print "\n******\n";
-  #     foreach my $alignment_location (sort {$a cmp $b} keys %alignments){
-  #       print "Loc:  $alignment_location\n";
-  #       print "ID:   $alignments{$alignment_location}->{seq_id}\n";
-  #       print "AS:   $alignments{$alignment_location}->{alignment_score}\n";
-  #       print "Seq:  $alignments{$alignment_location}->{bowtie_sequence}\n";
-  #       print "Index $alignments{$alignment_location}->{index}\n";
-  #       print "Chr:  $alignments{$alignment_location}->{chromosome}\n";
-  #       print "pos:  $alignments{$alignment_location}->{position}\n";
-  #       print "MD:   $alignments{$alignment_location}->{MD_tag}\n\n";
-  #     }
-  #     print "\n******\n";
-  #   }
-
-  ### if there is only 1 entry in the hash with we accept it as the best alignment
-  if (scalar keys %alignments == 1){
-    for my $unique_best_alignment (keys %alignments){
-      $methylation_call_params->{$identifier}->{bowtie_sequence} = $alignments{$unique_best_alignment}->{bowtie_sequence};
-      $methylation_call_params->{$identifier}->{chromosome}      = $alignments{$unique_best_alignment}->{chromosome};
-      $methylation_call_params->{$identifier}->{position}        = $alignments{$unique_best_alignment}->{position};
-      $methylation_call_params->{$identifier}->{index}           = $alignments{$unique_best_alignment}->{index};
-      $methylation_call_params->{$identifier}->{alignment_score} = $alignments{$unique_best_alignment}->{alignment_score};
-      $methylation_call_params->{$identifier}->{MD_tag}          = $alignments{$unique_best_alignment}->{MD_tag};
-      $methylation_call_params->{$identifier}->{CIGAR}           = $alignments{$unique_best_alignment}->{CIGAR};
-    }
-  }
-
-  ### otherwise we are going to find out if there is a best match among the multiple alignments, or whether there are 2 or more equally good alignments (in which case
-  ### we boot the sequence altogether
-  elsif (scalar keys %alignments >= 2  and scalar keys %alignments <= 4){
-    my $best_alignment_score;
-    my $best_alignment_location;
-    foreach my $alignment_location (sort {$alignments{$b}->{alignment_score} <=> $alignments{$a}->{alignment_score}} keys %alignments){
-      # print "$alignments{$alignment_location}->{alignment_score}\n";
-      unless (defined $best_alignment_score){
-	$best_alignment_score = $alignments{$alignment_location}->{alignment_score};
-	$best_alignment_location = $alignment_location;
-	# print "setting best alignment score: $best_alignment_score\n";
-      }
-      else{
-	### if the second best alignment has the same alignment score as the first one, the sequence will get booted
-	if ($alignments{$alignment_location}->{alignment_score} == $best_alignment_score){
-	  # warn "Same alignment score, the sequence will get booted!\n";
-	  $sequence_fails = 1;
-	  last; # exiting after the second alignment since we know that the sequence has ambiguous alignments
-	}
-	### else we are going to store the best alignment for further processing
-	else{
-	  $methylation_call_params->{$identifier}->{bowtie_sequence} = $alignments{$best_alignment_location}->{bowtie_sequence};
-	  $methylation_call_params->{$identifier}->{chromosome}      = $alignments{$best_alignment_location}->{chromosome};
-	  $methylation_call_params->{$identifier}->{position}        = $alignments{$best_alignment_location}->{position};
-	  $methylation_call_params->{$identifier}->{index}           = $alignments{$best_alignment_location}->{index};
-	  $methylation_call_params->{$identifier}->{alignment_score} = $alignments{$best_alignment_location}->{alignment_score};
-	  $methylation_call_params->{$identifier}->{MD_tag}          = $alignments{$best_alignment_location}->{MD_tag};
-	  $methylation_call_params->{$identifier}->{CIGAR}           = $alignments{$best_alignment_location}->{CIGAR};
-	  last; # exiting after processing the second alignment since the sequence produced a unique best alignment
-	}
-      }
-    }
-  }
-  else{
-    die "There are too many potential hits for this sequence (1-4 expected, but found: ",scalar keys %alignments,")\n";;
-  }
-
-  ### skipping the sequence completely if there were multiple alignments with the same best alignment score at different positions
-  if ($sequence_fails == 1){
-    $counting{unsuitable_sequence_count}++;
-
-    ### report that the sequence has multiple hits with bitwise flag 256. We can print the sequence to the result file straight away and skip everything else
-    # my $ambiguous_read_output = join("\t",$identifier,'256','*','0','0','*','*','0','0',$sequence,$quality_value);
-    # print OUT "$ambiguous_read_output\n";
-
-    if ($ambiguous){
-      return 2; # => exits to next sequence, and prints it out (in FastQ format) to _ambiguous_reads.txt if '--ambiguous' was specified
-    }
-    elsif ($unmapped){
-      return 1; # => exits to next sequence, and prints it out (in FastQ format) to _unmapped_reads.txt if '--unmapped' but not '--ambiguous' was specified
-    }
-    else{
-      return 0; # => exits to next sequence (default)
-    }
-  }
-
-  ### --DIRECTIONAL
-  ### If the option --directional has been specified the user wants to consider only alignments to the original top strand or the original bottom strand. We will therefore
-  ### discard all alignments to strands complementary to the original strands, as they should not exist in reality due to the library preparation protocol
-  if ($directional){
-    if ( ($methylation_call_params->{$identifier}->{index} == 2) or ($methylation_call_params->{$identifier}->{index} == 3) ){
-      # warn "Alignment rejected! (index was: $methylation_call_params->{$identifier}->{index})\n";
-      $counting{alignments_rejected_count}++;
-      return 0;
-    }
-  }
-
-  ### If the sequence has not been rejected so far it has a unique best alignment
-  $counting{unique_best_alignment_count}++;
-
-  ### Now we need to extract a genomic sequence that exactly corresponds to the reported alignment. This potentially means that we need to deal with insertions or deletions as well
-  extract_corresponding_genomic_sequence_single_end_bowtie2 ($identifier,$methylation_call_params);
-
-  ### check test to see if the genomic sequence we extracted has the same length as the observed sequence+2, and only then we perform the methylation call
-  if (length($methylation_call_params->{$identifier}->{unmodified_genomic_sequence}) != length($sequence)+2){
-    warn "Chromosomal sequence could not be extracted for\t$identifier\t$methylation_call_params->{$identifier}->{chromosome}\t$methylation_call_params->{$identifier}->{position}\n";
-    $counting{genomic_sequence_could_not_be_extracted_count}++;
-    return 0;
-  }
-
-
-  ### otherwise we are set to perform the actual methylation call
-  $methylation_call_params->{$identifier}->{methylation_call} = methylation_call($identifier,$sequence,$methylation_call_params->{$identifier}->{unmodified_genomic_sequence},$methylation_call_params->{$identifier}->{read_conversion});
-  print_bisulfite_mapping_result_single_end_bowtie2 ($identifier,$sequence,$methylation_call_params,$quality_value);
-  return 0; ## if a sequence got this far we do not want to print it to unmapped or ambiguous.out
-}
-
-
-sub determine_number_of_transliterations_performed{
-  my ($sequence,$read_conversion) = @_;
-  my $number_of_transliterations;
-  if ($read_conversion eq 'CT'){
-    $number_of_transliterations = $sequence =~ tr/C/T/;
-  }
-  elsif ($read_conversion eq 'GA'){
-    $number_of_transliterations = $sequence =~ tr/G/A/;
-  }
-  else{
-    die "Read conversion mode of the read was not specified $!\n";
-  }
-  return $number_of_transliterations;
-}
-
-sub decide_whether_single_end_alignment_is_valid{
-  my ($index,$identifier) = @_;
-
-  # extracting from Bowtie 1 format
-  my ($id,$strand) = (split (/\t/,$fhs[$index]->{last_line}))[0,1];
-
-  ### ensuring that the entry is the correct sequence
-  if (($id eq $fhs[$index]->{last_seq_id}) and ($id eq $identifier)){
-    ### checking the orientation of the alignment. We need to discriminate between 8 different conditions, however only 4 of them are theoretically
-    ### sensible alignments
-    my $orientation = ensure_sensical_alignment_orientation_single_end ($index,$strand);
-    ### If the orientation was correct can we move on
-    if ($orientation == 1){
-      return 1; ### 1st possibility for a sequence to pass
-    }
-    ### If the alignment was in the wrong orientation we need to read in a new line
-    elsif($orientation == 0){
-      my $newline = $fhs[$index]->{fh}->getline();
-      if ($newline){
-		($id,$strand) = (split (/\t/,$newline))[0,1];
-		
-	### ensuring that the next entry is still the correct sequence
-	if ($id eq $identifier){
-	  ### checking orientation again
-	  $orientation = ensure_sensical_alignment_orientation_single_end ($index,$strand);
-	  ### If the orientation was correct can we move on
-	  if ($orientation == 1){
-	    $fhs[$index]->{last_seq_id} = $id;
-	    $fhs[$index]->{last_line} = $newline;
-	    return 1; ### 2nd possibility for a sequence to pass
-	  }
-	  ### If the alignment was in the wrong orientation again we need to read in yet another new line and store it in @fhs
-	  elsif ($orientation == 0){
-	    $newline = $fhs[$index]->{fh}->getline();
-	    if ($newline){
-	      my ($seq_id) = split (/\t/,$newline);
-	      ### check if the next line still has the same seq ID (must not happen), and if not overwrite the current seq-ID and bowtie output with
-	      ### the same fields of the just read next entry
-	      die "Same seq ID 3 or more times in a row!(should be 2 max) $!" if ($seq_id eq $identifier);
-	      $fhs[$index]->{last_seq_id} = $seq_id;
-	      $fhs[$index]->{last_line} = $newline;
-	      return 0; # not processing anything this round as the alignment currently stored in last_line was in the wrong orientation
-	    }
-	    else{
-	      # assigning undef to last_seq_id and last_line (end of bowtie output)
-	      $fhs[$index]->{last_seq_id} = undef;
-	      $fhs[$index]->{last_line} = undef;
-	      return 0; # not processing anything as the alignment currently stored in last_line was in the wrong orientation
-	    }
-	  }
-	  else{
-	    die "The orientation of the alignment must be either correct or incorrect\n";
-	  }
-	}
-	### the sequence we just read in is already the next sequence to be analysed -> store it in @fhs
-	else{
-	  $fhs[$index]->{last_seq_id} = $id;
-	  $fhs[$index]->{last_line} = $newline;
-	  return 0; # processing the new alignment result only in the next round
-	}
-      }
-      else {
-	# assigning undef to last_seq_id and last_line (end of bowtie output)
-	$fhs[$index]->{last_seq_id} = undef;
-	$fhs[$index]->{last_line} = undef;
-	return 0; # not processing anything as the alignment currently stored in last_line was in the wrong orientation
-      }
-    }
-    else{
-      die "The orientation of the alignment must be either correct or incorrect\n";
-    }
-  }
-  ### the sequence stored in @fhs as last_line is already the next sequence to be analysed -> analyse next round
-  else{
-    return 0;
-  }
-}
-#########################
-### BOWTIE 1 | PAIRED-END
-#########################
-
-sub check_bowtie_results_paired_ends{
-  my ($sequence_1,$sequence_2,$identifier,$quality_value_1,$quality_value_2) = @_;
-
-  ### quality values are not given for FastA files, so they are initialised with a Phred quality of 40
-  unless ($quality_value_1){
-    $quality_value_1 = 'I'x(length$sequence_1);
-  }
-  unless ($quality_value_2){
-    $quality_value_2 = 'I'x(length$sequence_2);
-  }
-
-  #  print "$identifier\n$fhs[0]->{last_seq_id}\n$fhs[1]->{last_seq_id}\n$fhs[2]->{last_seq_id}\n$fhs[3]->{last_seq_id}\n\n";
-
-  my %mismatches = ();
-  ### reading from the bowtie output files to see if this sequence pair aligned to a bisulfite converted genome
-
-
-  ### for paired end reads we are reporting alignments to the OT strand first (index 0), then the OB strand (index 3!!), similiar to the single end way.
-  ### alignments to the complementary strands are reported afterwards (CTOT got index 1, and CTOB got index 2).
-  ### This is needed so that alignments which either contain no single C or G or reads which contain only protected Cs are reported to the original strands (OT and OB)
-  ### Before the complementary strands. Remember that it does not make any difference for the methylation calls, but it will matter if alignment to the complementary
-  ### strands are not being reported by specifying --directional
-
-  foreach my $index (0,3,1,2){
-    ### skipping this index if the last alignment has been set to undefined already (i.e. end of bowtie output)
-    next unless ($fhs[$index]->{last_line_1} and $fhs[$index]->{last_line_2} and defined $fhs[$index]->{last_seq_id});
-    ### if the sequence pair we are currently looking at produced an alignment we are doing various things with it
-    if ($fhs[$index]->{last_seq_id} eq $identifier) {
-      # print "$identifier\n$fhs[$index]->{last_seq_id}\n\n";
-
-      ##################################################################################
-      ### STEP I Processing the entry which is stored in last_line_1 and last_line_2 ###
-      ##################################################################################
-      my $valid_alignment_found = decide_whether_paired_end_alignment_is_valid($index,$identifier);
-      ### sequences can fail at this point if there was only 1 alignment in the wrong orientation, or if there were 2 aligments both in the wrong
-      ### orientation. We only continue to extract useful information about this alignment if 1 was returned
-      if ($valid_alignment_found == 1){
-	### Bowtie outputs which made it this far are in the correct orientation, so we can continue to analyse the alignment itself.
-	### we store the useful information in %mismatches
-	my ($id_1,$strand_1,$mapped_chromosome_1,$position_1,$bowtie_sequence_1,$mismatch_info_1) = (split (/\t/,$fhs[$index]->{last_line_1},-1))[0,1,2,3,4,7];
-	my ($id_2,$strand_2,$mapped_chromosome_2,$position_2,$bowtie_sequence_2,$mismatch_info_2) = (split (/\t/,$fhs[$index]->{last_line_2},-1))[0,1,2,3,4,7];
-	chomp $mismatch_info_1;
-	chomp $mismatch_info_2;
-	
-	### need to extract the chromosome number from the bowtie output (which is either XY_CT_converted or XY_GA_converted
-	my ($chromosome_1,$chromosome_2);
-	if ($mapped_chromosome_1 =~ s/_(CT|GA)_converted$//){
-	  $chromosome_1 = $mapped_chromosome_1;
-	}	
-	else{
-	  die "Chromosome number extraction failed for $mapped_chromosome_1\n";
-	}
-	if ($mapped_chromosome_2 =~ s/_(CT|GA)_converted$//){
-	  $chromosome_2 = $mapped_chromosome_2;
-	}
-	else{
-	  die "Chromosome number extraction failed for $mapped_chromosome_2\n";
-	}
-	
-	### Now extracting the number of mismatches to the converted genome
-	my $number_of_mismatches_1;
-	my $number_of_mismatches_2;
-	if ($mismatch_info_1 eq ''){
-	  $number_of_mismatches_1 = 0;
-	}
-	elsif ($mismatch_info_1 =~ /^\d/){
-	  my @mismatches = split (/,/,$mismatch_info_1);
-	  $number_of_mismatches_1 = scalar @mismatches;
-	}
-	else{
-	  die "Something weird is going on with the mismatch field\n";
-	}
-	if ($mismatch_info_2 eq ''){
-	  $number_of_mismatches_2 = 0;
-	}
-	elsif ($mismatch_info_2 =~ /^\d/){
-	  my @mismatches = split (/,/,$mismatch_info_2);
-	  $number_of_mismatches_2 = scalar @mismatches;
-	}
-	else{
-	  die "Something weird is going on with the mismatch field\n";
-	}
-	### To decide whether a sequence pair has a unique best alignment we will look at the lowest sum of mismatches from both alignments
-	my $sum_of_mismatches = $number_of_mismatches_1+$number_of_mismatches_2;
-	### creating a composite location variable from $chromosome and $position and storing the alignment information in a temporary hash table
-	die "Position 1 is higher than position 2" if ($position_1 > $position_2);
-	die "Paired-end alignments need to be on the same chromosome\n" unless ($chromosome_1 eq $chromosome_2);
-	my $alignment_location = join(":",$chromosome_1,$position_1,$position_2);
-	### If a sequence aligns to exactly the same location twice the sequence does either not contain any C or G, or all the Cs (or Gs on the reverse
-	### strand) were methylated and therefore protected. It is not needed to overwrite the same positional entry with a second entry for the same
-	### location (the genomic sequence extraction and methylation would not be affected by this, only the thing which would change is the index
-	### number for the found alignment)
-	unless (exists $mismatches{$sum_of_mismatches}->{$alignment_location}){
-	  $mismatches{$sum_of_mismatches}->{$alignment_location}->{seq_id}=$id_1; # either is fine
-	  $mismatches{$sum_of_mismatches}->{$alignment_location}->{bowtie_sequence_1}=$bowtie_sequence_1;
-	  $mismatches{$sum_of_mismatches}->{$alignment_location}->{bowtie_sequence_2}=$bowtie_sequence_2;
-	  $mismatches{$sum_of_mismatches}->{$alignment_location}->{index}=$index;
-	  $mismatches{$sum_of_mismatches}->{$alignment_location}->{chromosome}=$chromosome_1; # either is fine
-	  $mismatches{$sum_of_mismatches}->{$alignment_location}->{start_seq_1}=$position_1;
-	  $mismatches{$sum_of_mismatches}->{$alignment_location}->{start_seq_2}=$position_2;
-	  $mismatches{$sum_of_mismatches}->{$alignment_location}->{number_of_mismatches_1} = $number_of_mismatches_1;
-	  $mismatches{$sum_of_mismatches}->{$alignment_location}->{number_of_mismatches_2} = $number_of_mismatches_2;
-	}
-	###################################################################################################################################################
-	### STEP II Now reading in the next 2 lines from the bowtie filehandle. If there are 2 next lines in the alignments filehandle it can either    ###
-	### be a second alignment of the same sequence pair or a new sequence pair. In any case we will just add it to last_line_1 and last_line _2.    ###
-	### If it is the alignment of the next sequence pair, 0 will be returned as $valid_alignment_found, so it will not be processed any further in  ###
-	### this round                                                                                                                                  ###
-	###################################################################################################################################################
-	my $newline_1 = $fhs[$index]->{fh}-> getline();
-	my $newline_2 = $fhs[$index]->{fh}-> getline();
-
-	if ($newline_1 and $newline_2){
-	  my ($seq_id_1) = split (/\t/,$newline_1);
-	  my ($seq_id_2) = split (/\t/,$newline_2);
-	
-	  if ($seq_id_1 =~ s/\/1$//){ # removing the read /1 tag
-	    $fhs[$index]->{last_seq_id} = $seq_id_1;
-	  }
-	  elsif ($seq_id_2 =~ s/\/1$//){ # removing the read /1 tag
-	    $fhs[$index]->{last_seq_id} = $seq_id_2;
-	  }
-	  else{
-	    die "Either read 1 or read 2 needs to end on '/1'\n";
-	  }
-	
-	  $fhs[$index]->{last_line_1} = $newline_1;
-	  $fhs[$index]->{last_line_2} = $newline_2;
-	}
-	else {
-	  # assigning undef to last_seq_id and both last_lines and jumping to the next index (end of bowtie output)
-	  $fhs[$index]->{last_seq_id} = undef;
-	  $fhs[$index]->{last_line_1} = undef;
-	  $fhs[$index]->{last_line_2} = undef;
-	  next; # jumping to the next index
-	}
-	### Now processing the entry we just stored in last_line_1 and last_line_2
-	$valid_alignment_found = decide_whether_paired_end_alignment_is_valid($index,$identifier);
-	### only processing the alignment further if 1 was returned. 0 will be returned either if the alignment is already the next sequence pair to
-	### be analysed or if it was a second alignment of the current sequence pair but in the wrong orientation
-	if ($valid_alignment_found == 1){
-	  ### we store the useful information in %mismatches
-	  ($id_1,$strand_1,$mapped_chromosome_1,$position_1,$bowtie_sequence_1,$mismatch_info_1) = (split (/\t/,$fhs[$index]->{last_line_1}))[0,1,2,3,4,7];
-	  ($id_2,$strand_2,$mapped_chromosome_2,$position_2,$bowtie_sequence_2,$mismatch_info_2) = (split (/\t/,$fhs[$index]->{last_line_2}))[0,1,2,3,4,7];
-	  chomp $mismatch_info_1;
-	  chomp $mismatch_info_2;
-	  ### need to extract the chromosome number from the bowtie output (which is either _CT_converted or _GA_converted)
-	  if ($mapped_chromosome_1 =~ s/_(CT|GA)_converted$//){
-	    $chromosome_1 = $mapped_chromosome_1;
-	  }	
-	  else{
-	    die "Chromosome number extraction failed for $mapped_chromosome_1\n";
-	  }
-	  if ($mapped_chromosome_2 =~ s/_(CT|GA)_converted$//){
-	    $chromosome_2 = $mapped_chromosome_2;
-	  }
-	  else{
-	    die "Chromosome number extraction failed for $mapped_chromosome_2\n";
-	  }
-	
-	  $number_of_mismatches_1='';
-	  $number_of_mismatches_2='';
-	  ### Now extracting the number of mismatches to the converted genome
-	  if ($mismatch_info_1 eq ''){
-	    $number_of_mismatches_1 = 0;
-	  }
-	  elsif ($mismatch_info_1 =~ /^\d/){
-	    my @mismatches = split (/,/,$mismatch_info_1);
-	    $number_of_mismatches_1 = scalar @mismatches;
-	  }
-	  else{
-	    die "Something weird is going on with the mismatch field\n";
-	  }
-	  if ($mismatch_info_2 eq ''){
-	    $number_of_mismatches_2 = 0;
-	  }
-	  elsif ($mismatch_info_2 =~ /^\d/){
-	    my @mismatches = split (/,/,$mismatch_info_2);
-	    $number_of_mismatches_2 = scalar @mismatches;
-	  }
-	  else{
-	    die "Something weird is going on with the mismatch field\n";
-	  }
-	  ### To decide whether a sequence pair has a unique best alignment we will look at the lowest sum of mismatches from both alignments
-	  $sum_of_mismatches = $number_of_mismatches_1+$number_of_mismatches_2;
-	  ### creating a composite location variable from $chromosome and $position and storing the alignment information in a temporary hash table
-	  die "position 1 is greater than position 2" if ($position_1 > $position_2);
-	  die "Paired-end alignments need to be on the same chromosome\n" unless ($chromosome_1 eq $chromosome_2);
-	  $alignment_location = join(":",$chromosome_1,$position_1,$position_2);
-	  ### If a sequence aligns to exactly the same location twice the sequence does either not contain any C or G, or all the Cs (or Gs on the reverse
-	  ### strand) were methylated and therefore protected. It is not needed to overwrite the same positional entry with a second entry for the same
-	  ### location (the genomic sequence extraction and methylation would not be affected by this, only the thing which would change is the index
-	  ### number for the found alignment)
-	  unless (exists $mismatches{$sum_of_mismatches}->{$alignment_location}){
-	    $mismatches{$sum_of_mismatches}->{$alignment_location}->{seq_id}=$id_1; # either is fine
-	    $mismatches{$sum_of_mismatches}->{$alignment_location}->{bowtie_sequence_1}=$bowtie_sequence_1;
-	    $mismatches{$sum_of_mismatches}->{$alignment_location}->{bowtie_sequence_2}=$bowtie_sequence_2;
-	    $mismatches{$sum_of_mismatches}->{$alignment_location}->{index}=$index;
-	    $mismatches{$sum_of_mismatches}->{$alignment_location}->{chromosome}=$chromosome_1; # either is fine
-	    $mismatches{$sum_of_mismatches}->{$alignment_location}->{start_seq_1}=$position_1;
-	    $mismatches{$sum_of_mismatches}->{$alignment_location}->{start_seq_2}=$position_2;
-	    $mismatches{$sum_of_mismatches}->{$alignment_location}->{number_of_mismatches_1} = $number_of_mismatches_1;
-	    $mismatches{$sum_of_mismatches}->{$alignment_location}->{number_of_mismatches_2} = $number_of_mismatches_2;
-	  }
-	  ###############################################################################################################################################
-	  ### STEP III Now reading in two more lines. These have to be the next entry and we will just add assign them to last_line_1 and last_line_2 ###
-	  ###############################################################################################################################################
-	  $newline_1 = $fhs[$index]->{fh}-> getline();
-	  $newline_2 = $fhs[$index]->{fh}-> getline();
-
-	  if ($newline_1 and $newline_2){
-	    my ($seq_id_1) = split (/\t/,$newline_1);
-	    my ($seq_id_2) = split (/\t/,$newline_2);
-
-	    if ($seq_id_1 =~ s/\/1$//){ # removing the read /1 tag
-	      $fhs[$index]->{last_seq_id} = $seq_id_1;
-	    }
-	    if ($seq_id_2 =~ s/\/1$//){ # removing the read /1 tag
-	      $fhs[$index]->{last_seq_id} = $seq_id_2;
-	    }
-	    $fhs[$index]->{last_line_1} = $newline_1;
-	    $fhs[$index]->{last_line_2} = $newline_2;
-	  }
-	  else {
-	    # assigning undef to last_seq_id and both last_lines and jumping to the next index (end of bowtie output)
-	    $fhs[$index]->{last_seq_id} = undef;
-	    $fhs[$index]->{last_line_1} = undef;
-	    $fhs[$index]->{last_line_2} = undef;
-	    next; # jumping to the next index
-	  }
-	  ### within the 2nd sequence pair alignment in correct orientation found
-	}
-	### within the 1st sequence pair alignment in correct orientation found
-      }
-      ### still within the (last_seq_id eq identifier) condition
-    }
-    ### still within foreach index loop
-  }
-  ### if there was no single alignment found for a certain sequence we will continue with the next sequence in the sequence file
-  unless(%mismatches){
-    $counting{no_single_alignment_found}++;
-    return 1; ### We will print this sequence out as unmapped sequence if --un unmapped.out has been specified
-  }
-  ### Going to use the variable $sequence_pair_fails as a 'memory' if a sequence could not be aligned uniquely (set to 1 then)
-  my $sequence_pair_fails = 0;
-  ### Declaring an empty hash reference which will store all information we need for the methylation call
-  my $methylation_call_params; # hash reference!
-  ### We are now looking if there is a unique best alignment for a certain sequence. This means we are sorting in ascending order and look at the
-  ### sequence with the lowest amount of mismatches. If there is only one single best position we are going to store the alignment information in the
-  ### meth_call variables, if there are multiple hits with the same amount of (lowest) mismatches we are discarding the sequence altogether
-  foreach my $mismatch_number (sort {$a<=>$b} keys %mismatches){
-    #dev print "Number of mismatches: $mismatch_number\t$identifier\t$sequence_1\t$sequence_2\n";
-    foreach my $entry (keys (%{$mismatches{$mismatch_number}}) ){
-      #dev print "$mismatch_number\t$entry\t$mismatches{$mismatch_number}->{$entry}->{index}\n";
-      # print join("\t",$mismatch_number,$mismatches{$mismatch_number}->{$entry}->{seq_id},$sequence,$mismatches{$mismatch_number}->{$entry}->{bowtie_sequence},$mismatches{$mismatch_number}->{$entry}->{chromosome},$mismatches{$mismatch_number}->{$entry}->{position},$mismatches{$mismatch_number}->{$entry}->{index}),"\n";
-    }
-    if (scalar keys %{$mismatches{$mismatch_number}} == 1){
-      #  print "Unique best alignment for sequence pair $sequence_1\t$sequence_1\n";
-      for my $unique_best_alignment (keys %{$mismatches{$mismatch_number}}){
-	$methylation_call_params->{$identifier}->{seq_id} = $identifier;
- 	$methylation_call_params->{$identifier}->{bowtie_sequence_1} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{bowtie_sequence_1};
-	$methylation_call_params->{$identifier}->{bowtie_sequence_2} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{bowtie_sequence_2};
-       	$methylation_call_params->{$identifier}->{chromosome} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{chromosome};
-      	$methylation_call_params->{$identifier}->{start_seq_1} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{start_seq_1};
-	$methylation_call_params->{$identifier}->{start_seq_2} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{start_seq_2};
-	$methylation_call_params->{$identifier}->{alignment_end} = ($mismatches{$mismatch_number}->{$unique_best_alignment}->{start_seq_2}+length($mismatches{$mismatch_number}->{$unique_best_alignment}->{bowtie_sequence_2}));
-	$methylation_call_params->{$identifier}->{index} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{index};
-     	$methylation_call_params->{$identifier}->{number_of_mismatches_1} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{number_of_mismatches_1};
-	$methylation_call_params->{$identifier}->{number_of_mismatches_2} = $mismatches{$mismatch_number}->{$unique_best_alignment}->{number_of_mismatches_2};
-      }
-    }
-    else{
-      $sequence_pair_fails = 1;
-    }
-    ### after processing the alignment with the lowest number of mismatches we exit
-    last;
-  }
-  ### skipping the sequence completely if there were multiple alignments with the same amount of lowest mismatches found at different positions
-  if ($sequence_pair_fails == 1){
-    $counting{unsuitable_sequence_count}++;
-    if ($ambiguous){
-      return 2; # => exits to next sequence pair, and prints both seqs out to multiple_alignments_1 and -2 if --ambiguous has been specified
-    }
-    if ($unmapped){
-      return 1; # => exits to next sequence pair, and prints both seqs out to unmapped_1 and _2  if --un has been specified
-    }
-    else{
-      return 0; # => exits to next sequence (default)
-    }
-  }
-
-  ### --DIRECTIONAL
-  ### If the option --directional has been specified the user wants to consider only alignments to the original top strand or the original bottom strand. We will therefore
-  ### discard all alignments to strands complementary to the original strands, as they should not exist in reality due to the library preparation protocol
-  if ($directional){
-    if ( ($methylation_call_params->{$identifier}->{index} == 1) or ($methylation_call_params->{$identifier}->{index} == 2) ){
-      #    warn "Alignment rejected! (index was: $methylation_call_params->{$identifier}->{index})\n";
-      $counting{alignments_rejected_count}++;
-      return 0;
-    }
-  }
-
-  ### If the sequence has not been rejected so far it does have a unique best alignment
-  $counting{unique_best_alignment_count}++;
-  extract_corresponding_genomic_sequence_paired_ends($identifier,$methylation_call_params);
-
-  ### check test to see if the genomic sequences we extracted has the same length as the observed sequences +2, and only then we perform the methylation call
-  if (length($methylation_call_params->{$identifier}->{unmodified_genomic_sequence_1}) != length($sequence_1)+2){
-    warn "Chromosomal sequence could not be extracted for\t$identifier\t$methylation_call_params->{$identifier}->{chromosome}\t$methylation_call_params->{$identifier}->{start_seq_1}\n";
-    $counting{genomic_sequence_could_not_be_extracted_count}++;
-    return 0;
-  }
-  if (length($methylation_call_params->{$identifier}->{unmodified_genomic_sequence_2}) != length($sequence_2)+2){
-    warn "Chromosomal sequence could not be extracted for\t$identifier\t$methylation_call_params->{$identifier}->{chromosome}\t$methylation_call_params->{$identifier}->{start_seq_2}\n";
-    $counting{genomic_sequence_could_not_be_extracted_count}++;
-    return 0;
-  }
-
-  ### otherwise we are set to perform the actual methylation call
-  $methylation_call_params->{$identifier}->{methylation_call_1} = methylation_call($identifier,$sequence_1,$methylation_call_params->{$identifier}->{unmodified_genomic_sequence_1},$methylation_call_params->{$identifier}->{read_conversion_1});
-  $methylation_call_params->{$identifier}->{methylation_call_2} = methylation_call($identifier,$sequence_2,$methylation_call_params->{$identifier}->{unmodified_genomic_sequence_2},$methylation_call_params->{$identifier}->{read_conversion_2});
-
-  print_bisulfite_mapping_results_paired_ends($identifier,$sequence_1,$sequence_2,$methylation_call_params,$quality_value_1,$quality_value_2);
-  return 0; ## otherwise 1 will be returned by default, which would print the sequence pair to unmapped_1 and _2
-}
-
-#########################
-### BOWTIE 2 | PAIRED-END
-#########################
-
-sub check_bowtie_results_paired_ends_bowtie2{
-  my ($sequence_1,$sequence_2,$identifier,$quality_value_1,$quality_value_2) = @_;
-
-  ### quality values are not given for FastA files, so they are initialised with a Phred quality of 40
-  unless ($quality_value_1){
-    $quality_value_1 = 'I'x(length$sequence_1);
-  }
-
-  unless ($quality_value_2){
-    $quality_value_2 = 'I'x(length$sequence_2);
-  }
-
-
-  # print "$identifier\n$fhs[0]->{last_seq_id}\n$fhs[1]->{last_seq_id}\n$fhs[2]->{last_seq_id}\n$fhs[3]->{last_seq_id}\n\n";
-
-
-  my %alignments;
-  my $alignment_ambiguous = 0;
-
-  ### reading from the Bowtie 2 output filehandles
-
-  ### for paired end reads we are reporting alignments to the OT strand first (index 0), then the OB strand (index 3!!), similiar to the single end way.
-  ### alignments to the complementary strands are reported afterwards (CTOT got index 1, and CTOB got index 2).
-  ### This is needed so that alignments which either contain no single C or G or reads which contain only protected Cs are reported to the original strands (OT and OB)
-  ### Before the complementary strands. Remember that it does not make any difference for the methylation calls, but it will matter if alignments to the complementary
-  ### strands are not being reported when '--directional' is specified
-
-  foreach my $index (0,3,1,2){
-    ### skipping this index if the last alignment has been set to undefined already (i.e. end of bowtie output)
-    next unless ($fhs[$index]->{last_line_1} and $fhs[$index]->{last_line_2} and defined $fhs[$index]->{last_seq_id});
-
-    ### if the sequence pair we are currently looking at produced an alignment we are doing various things with it
-    if ($fhs[$index]->{last_seq_id} eq $identifier) {
-
-      my ($id_1,$flag_1,$mapped_chromosome_1,$position_1,$mapping_quality_1,$cigar_1,$bowtie_sequence_1,$qual_1) = (split (/\t/,$fhs[$index]->{last_line_1}))[0,1,2,3,4,5,9,10];
-      my ($id_2,$flag_2,$mapped_chromosome_2,$position_2,$mapping_quality_2,$cigar_2,$bowtie_sequence_2,$qual_2) = (split (/\t/,$fhs[$index]->{last_line_2}))[0,1,2,3,4,5,9,10];
-      #  print "Index: $index\t$fhs[$index]->{last_line_1}\n";
-      #  print "Index: $index\t$fhs[$index]->{last_line_2}\n";	
-      #  print join ("\t",$id_1,$flag_1,$mapped_chromosome_1,$position_1,$mapping_quality_1,$cigar_1,$bowtie_sequence_1,$qual_1),"\n";
-      #  print join ("\t",$id_2,$flag_2,$mapped_chromosome_2,$position_2,$mapping_quality_2,$cigar_2,$bowtie_sequence_2,$qual_2),"\n";
-      $id_1 =~ s/\/1$//;
-      $id_2 =~ s/\/2$//;
-
-      #  SAM format specifications for Bowtie 2
-      #  (1) Name of read that aligned
-      #  (2) Sum of all applicable flags. Flags relevant to Bowtie are:
-      #        1 The read is one of a pair
-      #        2 The alignment is one end of a proper paired-end alignment
-      #        4 The read has no reported alignments
-      #        8 The read is one of a pair and has no reported alignments
-      #       16 The alignment is to the reverse reference strand
-      #       32 The other mate in the paired-end alignment is aligned to the reverse reference strand
-      #       64 The read is mate 1 in a pair
-      #      128 The read is mate 2 in a pair
-      #      256 The read has multiple mapping states
-      #  (3) Name of reference sequence where alignment occurs (unmapped reads have a *)
-      #  (4) 1-based offset into the forward reference strand where leftmost character of the alignment occurs (0 for unmapped reads)
-      #  (5) Mapping quality (255 means MAPQ is not available)
-      #  (6) CIGAR string representation of alignment (* if unavailable)
-      #  (7) Name of reference sequence where mate's alignment occurs. Set to = if the mate's reference sequence is the same as this alignment's, or * if there is no mate.
-      #  (8) 1-based offset into the forward reference strand where leftmost character of the mate's alignment occurs. Offset is 0 if there is no mate.
-      #  (9) Inferred fragment size. Size is negative if the mate's alignment occurs upstream of this alignment. Size is 0 if there is no mate.
-      # (10) Read sequence (reverse-complemented if aligned to the reverse strand)
-      # (11) ASCII-encoded read qualities (reverse-complemented if the read aligned to the reverse strand). The encoded quality values are on the Phred quality scale and the encoding is ASCII-offset by 33 (ASCII char !), similarly to a FASTQ file.
-      # (12) Optional fields. Fields are tab-separated. bowtie2 outputs zero or more of these optional fields for each alignment, depending on the type of the alignment:
-      # AS:i:<N> Alignment score. Can be negative. Can be greater than 0 in --local mode (but not in --end-to-end mode). Only present if SAM record is for an aligned read.
-      # XS:i:<N> Alignment score for second-best alignment. Can be negative. Can be greater than 0 in --local mode (but not in --end-to-end mode). Only present if the SAM record is for an aligned read and more than one alignment was found for the read.
-      # YS:i:<N> Alignment score for opposite mate in the paired-end alignment. Only present if the SAM record is for a read that aligned as part of a paired-end alignment.
-      # XN:i:<N> The number of ambiguous bases in the reference covering this alignment. Only present if SAM record is for an aligned read.
-      # XM:i:<N> The number of mismatches in the alignment. Only present if SAM record is for an aligned read.
-      # XO:i:<N> The number of gap opens, for both read and reference gaps, in the alignment. Only present if SAM record is for an aligned read.
-      # XG:i:<N> The number of gap extensions, for both read and reference gaps, in the alignment. Only present if SAM record is for an aligned read.
-      # NM:i:<N> The edit distance; that is, the minimal number of one-nucleotide edits (substitutions, insertions and deletions) needed to transform the read string into the reference string. Only present if SAM record is for an aligned read.
-      # YF:Z:<N> String indicating reason why the read was filtered out. See also: Filtering. Only appears for reads that were filtered out.
-      # MD:Z:<S> A string representation of the mismatched reference bases in the alignment. See SAM format specification for details. Only present if SAM record is for an aligned read.
-
-      ### If a sequence has no reported alignments there will be a single output line per sequence with a bit-wise flag value of 77 for read 1 (1+4+8+64), or 141 for read 2 (1+4+8+128).
-      ### We can store the next alignment and move on to the next Bowtie 2 instance
-      if ($flag_1 == 77 and $flag_2 == 141){
-	## reading in the next alignment, which must be the next sequence
-	my $newline_1 = $fhs[$index]->{fh}-> getline();
-	my $newline_2 = $fhs[$index]->{fh}-> getline();
-	
-	if ($newline_1 and $newline_2){
-	  chomp $newline_1;
-	  chomp $newline_2;
-	  my ($seq_id_1) = split (/\t/,$newline_1);
-	  my ($seq_id_2) = split (/\t/,$newline_2);
-	  $seq_id_1 =~ s/\/1$//;
-	  $seq_id_2 =~ s/\/2$//;
-	  $fhs[$index]->{last_seq_id} = $seq_id_1;
-	  $fhs[$index]->{last_line_1} = $newline_1;
-	  $fhs[$index]->{last_line_2} = $newline_2;
-
-	  #  print "current sequence ($identifier) did not map, reading in next sequence\n";
-	  #  print "$index\t$fhs[$index]->{last_seq_id}\n";
-	  #  print "$index\t$fhs[$index]->{last_line_1}\n";
-	  #  print "$index\t$fhs[$index]->{last_line_2}\n";
-	  next; # next instance
-	}
-	else{
-	  # assigning undef to last_seq_id and last_line and jumping to the next index (end of Bowtie 2 output)
-	  $fhs[$index]->{last_seq_id} = undef;
-	  $fhs[$index]->{last_line_1} = undef;
-	  $fhs[$index]->{last_line_2} = undef;
-	  next;
-	}
-      }
-
-      ### If there are one or more proper alignments we can extract the chromosome number
-      my ($chromosome_1,$chromosome_2);
-      if ($mapped_chromosome_1 =~ s/_(CT|GA)_converted$//){
-	$chromosome_1 = $mapped_chromosome_1;
-      }	
-      else{
-	die "Chromosome number extraction failed for $mapped_chromosome_1\n";
-      }
-      if ($mapped_chromosome_2 =~ s/_(CT|GA)_converted$//){
-	$chromosome_2 = $mapped_chromosome_2;
-      }
-      else{
-	die "Chromosome number extraction failed for $mapped_chromosome_2\n";
-      }
-
-      die "Paired-end alignments need to be on the same chromosome\n" unless ($chromosome_1 eq $chromosome_2);
-
-      ### We will use the optional fields to determine the best alignments. Later on we extract the number of mismatches and/or indels from the CIGAR string
-      my ($alignment_score_1,$alignment_score_2,$second_best_1,$second_best_2,$MD_tag_1,$MD_tag_2);
-
-      my @fields_1 = split (/\t/,$fhs[$index]->{last_line_1});
-      my @fields_2 = split (/\t/,$fhs[$index]->{last_line_2});
-
-      foreach (11..$#fields_1){
-	if ($fields_1[$_] =~ /AS:i:(.*)/){
-	  $alignment_score_1 = $1;
-	}
-	elsif ($fields_1[$_] =~ /XS:i:(.*)/){
-	  $second_best_1 = $1;
-	}
-	elsif ($fields_1[$_] =~ /MD:Z:(.*)/){
-	  $MD_tag_1 = $1;
-	}
-      }
-
-      foreach (11..$#fields_2){
-	if ($fields_2[$_] =~ /AS:i:(.*)/){
-	  $alignment_score_2 = $1;
-	}
-	elsif ($fields_2[$_] =~ /XS:i:(.*)/){
-	  $second_best_2 = $1;
-	}
-	elsif ($fields_2[$_] =~ /MD:Z:(.*)/){
-	  $MD_tag_2 = $1;
-	}
-      }
-
-      die "Failed to extract alignment score 1 ($alignment_score_1) and MD tag ($MD_tag_1)!\nlast alignment 1: $fhs[$index]->{last_line_1}\nlast alignment 2: $fhs[$index]->{last_line_2}\n" unless (defined $alignment_score_1 and defined $MD_tag_1);
-      die "Failed to extract alignment score 2 ($alignment_score_2) and MD tag ($MD_tag_2)!\nlast alignment 1: $fhs[$index]->{last_line_1}\nlast alignment 2: $fhs[$index]->{last_line_2}\n" unless (defined $alignment_score_2 and defined $MD_tag_2);
-
-      # warn "First read 1 alignment score is: '$alignment_score_1'\n";
-      # warn "First read 2 alignment score is: '$alignment_score_2'\n";
-      # warn "MD tag 1 is: '$MD_tag_1'\n";
-      # warn "MD tag 2 is: '$MD_tag_2'\n";
-
-      ### To decide whether a sequence pair has a unique best alignment we will look at the highest sum of alignment scores from both alignments
-      my $sum_of_alignment_scores_1 = $alignment_score_1 + $alignment_score_2 ;
-      # print "sum of alignment scores: $sum_of_alignment_scores_1\n\n";
-
-      if (defined $second_best_1 and defined $second_best_2){
-	my $sum_of_alignment_scores_second_best = $second_best_1 + $second_best_2;
-	# warn "Second best alignment_score_1 is: '$second_best_1'\n";
-	# warn "Second best alignment_score_2 is: '$second_best_2'\n";
-	# warn "Second best alignment sum of alignment scores is: '$sum_of_alignment_scores_second_best'\n";
-
-	# If the first alignment score for the first read pair is the same as the alignment score of the second best hit we are going to boot this sequence pair altogether
-	if ($sum_of_alignment_scores_1 == $sum_of_alignment_scores_second_best){
-	  $alignment_ambiguous = 1;
-	  # print "This read will be chucked (AS==XS detected)!\n";
-
- 	  ## need to read and discard all additional ambiguous reads until we reach the next sequence
- 	  until ($fhs[$index]->{last_seq_id} ne $identifier){
- 	    my $newline_1 = $fhs[$index]->{fh}-> getline();
-	    my $newline_2 = $fhs[$index]->{fh}-> getline();
-	    if ($newline_1 and $newline_2){
-	      chomp $newline_1;
-	      chomp $newline_2;
-	      my ($seq_id_1) = split (/\t/,$newline_1);
-	      my ($seq_id_2) = split (/\t/,$newline_2);
-	      $seq_id_1 =~ s/\/1$//;
-	      $seq_id_2 =~ s/\/2$//;
-	      # print "New Seq IDs:\t$seq_id_1\t$seq_id_2\n";
-
-	      $fhs[$index]->{last_seq_id} = $seq_id_1;
-	      $fhs[$index]->{last_line_1} = $newline_1;
-	      $fhs[$index]->{last_line_2} = $newline_2;
-		}
- 	    else{
- 	      # assigning undef to last_seq_id and last_line and jumping to the next index (end of Bowtie 2 output)
- 	      $fhs[$index]->{last_seq_id} = undef;
- 	      $fhs[$index]->{last_line_1} = undef;
-	      $fhs[$index]->{last_line_2} = undef;
-	      last; # break free if the end of the alignment output was reached
- 	    }
- 	  }
-	  #  if ($fhs[$index]->{last_seq_id}){
-	  #    warn "Index: $index\tThis Seq-ID is $identifier, skipped all ambiguous sequences until the next ID which is: $fhs[$index]->{last_seq_id}\n";
-	  #  }
-	}
- 	else{ # the next best alignment has a lower alignment score than the current read, so we can safely store the current alignment
-	
-	  my $alignment_location;
-	  if ($position_1 <= $position_2){
-	    $alignment_location = join(":",$chromosome_1,$position_1,$position_2);
-	  }
-	  elsif($position_2 < $position_1){	
-	    $alignment_location = join(":",$chromosome_1,$position_2,$position_1);
-	  }
-	
- 	  ### If a sequence aligns to exactly the same location twice the sequence does either not contain any C or G, or all the Cs (or Gs on the reverse
- 	  ### strand) were methylated and therefore protected. Alternatively it will align better in one condition than in the other. In any case, it is not needed to overwrite
- 	  ### the same positional entry with a second entry for the same location, as the genomic sequence extraction and methylation call would not be affected by this. The only
- 	  ### thing which would change is the index number for the found alignment). We will continue to assign these alignments to the first indexes 0 and 3, i.e. OT and OB 
-	
-	  unless (exists $alignments{$alignment_location}){
-	    $alignments{$alignment_location}->{seq_id} = $id_1;
- 	    $alignments{$alignment_location}->{alignment_score_1} = $alignment_score_1;
-	    $alignments{$alignment_location}->{alignment_score_2} = $alignment_score_2;
-	    $alignments{$alignment_location}->{sum_of_alignment_scores} = $sum_of_alignment_scores_1;
-	    $alignments{$alignment_location}->{bowtie_sequence_1} = $bowtie_sequence_1;
-	    $alignments{$alignment_location}->{bowtie_sequence_2} = $bowtie_sequence_2;
-	    $alignments{$alignment_location}->{index} = $index;
- 	    $alignments{$alignment_location}->{chromosome} = $chromosome_1; # either is fine
- 	    $alignments{$alignment_location}->{position_1} = $position_1;
-	    $alignments{$alignment_location}->{position_2} = $position_2;
- 	    $alignments{$alignment_location}->{mismatch_info_1} = $MD_tag_1;
- 	    $alignments{$alignment_location}->{mismatch_info_2} = $MD_tag_2;
-	    $alignments{$alignment_location}->{CIGAR_1} = $cigar_1;
-	    $alignments{$alignment_location}->{CIGAR_2} = $cigar_2;
-	    $alignments{$alignment_location}->{flag_1} = $flag_1;
-	    $alignments{$alignment_location}->{flag_2} = $flag_2;
- 	  }
-	  # warn "added best of several alignments to \%alignments hash\n";
-	
- 	  ### now reading and discarding all (inferior) alignments of this read pair until we hit the next sequence
-	  until ($fhs[$index]->{last_seq_id} ne $identifier){
- 	    my $newline_1 = $fhs[$index]->{fh}-> getline();
-	    my $newline_2 = $fhs[$index]->{fh}-> getline();
-	    if ($newline_1 and $newline_2){
-	      chomp $newline_1;
-	      chomp $newline_2;
-	      my ($seq_id_1) = split (/\t/,$newline_1);
-	      my ($seq_id_2) = split (/\t/,$newline_2);
-	      $seq_id_1 =~ s/\/1$//;
-	      $seq_id_2 =~ s/\/2$//;
-	      # print "New Seq IDs:\t$seq_id_1\t$seq_id_2\n";
-
-	      $fhs[$index]->{last_seq_id} = $seq_id_1;
-	      $fhs[$index]->{last_line_1} = $newline_1;
-	      $fhs[$index]->{last_line_2} = $newline_2;
-	    }
- 	    else{
- 	      # assigning undef to last_seq_id and last_line_1 and _2 and jumping to the next index (end of Bowtie 2 output)
- 	      $fhs[$index]->{last_seq_id} = undef;
- 	      $fhs[$index]->{last_line_1} = undef;
-	      $fhs[$index]->{last_line_2} = undef;
-	      last; # break free if the end of the alignment output was reached
- 	    }
-	  }
-	  # if($fhs[$index]->{last_seq_id}){
-	  #   warn "Index: $index\tThis Seq-ID is $identifier, skipped all other alignments until the next ID was reached which is: $fhs[$index]->{last_seq_id}\n";
-	  # }
-	}	
-      }
-      else{ # there is no second best hit, so we can just store this one and read in the next sequence
-	
-	my $alignment_location = join(":",$chromosome_1,$position_1,$position_2);
-	# print "$alignment_location\n";
-	### If a sequence aligns to exactly the same location with a perfect match twice the sequence does either not contain any C or G, or all the Cs (or Gs on the reverse
- 	### strand) were methylated and therefore protected. Alternatively it will align better in one condition than in the other. In any case, it is not needed to overwrite
- 	### the same positional entry with a second entry for the same location, as the genomic sequence extraction and methylation call would not be affected by this. The only
- 	### thing which would change is the index number for the found alignment). We will continue to assign these alignments to the first indexes 0 and 3, i.e. OT and OB 
-
-	unless (exists $alignments{$alignment_location}){
-	  $alignments{$alignment_location}->{seq_id} = $id_1;
-	  $alignments{$alignment_location}->{alignment_score_1} = $alignment_score_1;
-	  $alignments{$alignment_location}->{alignment_score_2} = $alignment_score_2;
-	  $alignments{$alignment_location}->{sum_of_alignment_scores} = $sum_of_alignment_scores_1;
-	  $alignments{$alignment_location}->{bowtie_sequence_1} = $bowtie_sequence_1;
-	  $alignments{$alignment_location}->{bowtie_sequence_2} = $bowtie_sequence_2;
-	  $alignments{$alignment_location}->{index} = $index;
-	  $alignments{$alignment_location}->{chromosome} = $chromosome_1; # either is fine
-	  $alignments{$alignment_location}->{position_1} = $position_1;
-	  $alignments{$alignment_location}->{position_2} = $position_2;
-	  $alignments{$alignment_location}->{mismatch_info_1} = $MD_tag_1;
-	  $alignments{$alignment_location}->{mismatch_info_2} = $MD_tag_2;
-	  $alignments{$alignment_location}->{CIGAR_1} = $cigar_1;
-	  $alignments{$alignment_location}->{CIGAR_2} = $cigar_2;
-	  $alignments{$alignment_location}->{flag_1} = $flag_1;
-	  $alignments{$alignment_location}->{flag_2} = $flag_2;
-	}
-	
-	# warn "added unique alignment to \%alignments hash\n";
-
-	# Now reading and storing the next read pair
-	my $newline_1 = $fhs[$index]->{fh}-> getline();
-	my $newline_2 = $fhs[$index]->{fh}-> getline();
-	if ($newline_1 and $newline_2){
-	  chomp $newline_1;
-	  chomp $newline_2;
-	  # print "$newline_1\n";
-	  # print "$newline_2\n";
-	  my ($seq_id_1) = split (/\t/,$newline_1);
-	  my ($seq_id_2) = split (/\t/,$newline_2);
-	  $seq_id_1 =~ s/\/1$//;
-	  $seq_id_2 =~ s/\/2$//;
-	  # print "New Seq IDs:\t$seq_id_1\t$seq_id_2\n";
-
-	  $fhs[$index]->{last_seq_id} = $seq_id_1;
-	  $fhs[$index]->{last_line_1} = $newline_1;
-	  $fhs[$index]->{last_line_2} = $newline_2;
-
-	  if ($seq_id_1 eq $identifier){
- 	    die "Sequence with ID $identifier did not have a second best alignment, but next seq-ID was also $fhs[$index]->{last_seq_id}!\n";
- 	  }
-  	}
-	else{
-	  # assigning undef to last_seq_id and last_line_1 and _2 and jumping to the next index (end of Bowtie 2 output)
-	  $fhs[$index]->{last_seq_id} = undef;
-	  $fhs[$index]->{last_line_1} = undef;
-	  $fhs[$index]->{last_line_2} = undef;
-	}
-      }
-    }
-  }
-
-  ### if the read produced several ambiguous alignments for a single instance of Bowtie 2 we can return already now. If --ambiguous was specified the read sequence will be printed out in FastQ format
-  if ($alignment_ambiguous == 1){
-    $counting{unsuitable_sequence_count}++;
-    ### report that the sequence pair has multiple hits with bitwise flag 256. We can print the sequence to the result file straight away and skip everything else
-    #  my $ambiguous_read_1 = join("\t",$identifier.'/1','256','*','0','0','*','*','0','0',$sequence_1,$quality_value_1);
-    #  my $ambiguous_read_2 = join("\t",$identifier.'/2','256','*','0','0','*','*','0','0',$sequence_2,$quality_value_2);
-    #  print "$ambiguous_read_1\n";
-    #  print "$ambiguous_read_2\n";
-
-    if ($ambiguous){
-      return 2; # => exits to next sequence pair, and prints it out to _ambiguous_reads_1.txt and _ambiguous_reads_2.txt if '--ambiguous' was specified
-    }
-    elsif ($unmapped){
-      return 1; # => exits to next sequence pair, and prints it out to _unmapped_reads_1.txt and _unmapped_reads_2.txt if '--unmapped' but not '--ambiguous' was specified
-    }
-    else{
-      return 0;
-    }
-  }
-
-  ### if no alignment was found for a certain sequence at all we continue with the next sequence in the sequence file
-  unless (%alignments){
-    $counting{no_single_alignment_found}++;
-
-    # my $unmapped_read_1 = join("\t",$identifier.'/1','77','*','0','0','*','*','0','0',$sequence_1,$quality_value_1);
-    # my $unmapped_read_2 = join("\t",$identifier.'/2','141','*','0','0','*','*','0','0',$sequence_2,$quality_value_2);
-    # print "$unmapped_read_1\n";
-    # print "$unmapped_read_2\n";
-    if ($unmapped){
-      return 1; # => exits to next sequence pair, and prints it out to _unmapped_reads_1.txt and _unmapped_read_2.txt if '--unmapped' was specified
-    }
-    else{
-      return 0;
-    }
-  }
-
-  #######################################################################################################################################################
-
-  ### If the sequence pair was not rejected so far we are now looking if there is a unique best alignment among all alignment instances. If there is only one
-  ### single best position we are going to store the alignment information in the $meth_call variable. If there are multiple hits with the same (highest)
-  ### alignment score we are discarding the sequence pair altogether.
-  ### For end-to-end alignments the maximum alignment score is 0, each mismatch receives a penalty of 6, and each gap receives penalties for opening (5)
-  ### and extending (3 per bp) the gap.
-
-  #######################################################################################################################################################
-
-  ### Declaring an empty hash reference which will store all information we need for the methylation call
-  my $methylation_call_params; # hash reference
-  my $sequence_pair_fails = 0; # using $sequence_pair_fails as a 'memory' if a sequence could not be aligned uniquely (set to 1 then)
-
-  ### print contents of %alignments for debugging
-  ##  if (scalar keys %alignments >= 1){
-  #     print "\n******\n";
-  #     foreach my $alignment_location (sort {$a cmp $b} keys %alignments){
-  #       print "Loc:  $alignment_location\n";
-  #       print "ID:      $alignments{$alignment_location}->{seq_id}\n";
-  #       print "AS_1:    $alignments{$alignment_location}->{alignment_score_1}\n";
-  #       print "AS_2:    $alignments{$alignment_location}->{alignment_score_2}\n";
-  #       print "Seq_1:   $alignments{$alignment_location}->{bowtie_sequence_1}\n";
-  #       print "Seq_2:   $alignments{$alignment_location}->{bowtie_sequence_2}\n";
-  #       print "Index    $alignments{$alignment_location}->{index}\n";
-  #       print "Chr:     $alignments{$alignment_location}->{chromosome}\n";
-  #       print "Pos_1:   $alignments{$alignment_location}->{position_1}\n";
-  #       print "Pos_2:   $alignments{$alignment_location}->{position_2}\n";
-  #       print "CIGAR_1: $alignments{$alignment_location}->{CIGAR_1}\n";
-  #       print "CIGAR_2: $alignments{$alignment_location}->{CIGAR_2}\n";
-  #       print "MD_1:    $alignments{$alignment_location}->{mismatch_info_1}\n";
-  #       print "MD_2:    $alignments{$alignment_location}->{mismatch_info_2}\n";
-  #       print "Flag 1:  $alignments{$alignment_location}->{flag_1}\n";
-  #       print "Flag 2:  $alignments{$alignment_location}->{flag_2}\n";
-  #    }
-  #    print "\n******\n";
-  #  }
-
-  ### if there is only 1 entry in the %alignments hash we accept it as the best alignment
-  if (scalar keys %alignments == 1){
-    for my $unique_best_alignment (keys %alignments){
-      $methylation_call_params->{$identifier}->{bowtie_sequence_1} = $alignments{$unique_best_alignment}->{bowtie_sequence_1};
-      $methylation_call_params->{$identifier}->{bowtie_sequence_2} = $alignments{$unique_best_alignment}->{bowtie_sequence_2};
-      $methylation_call_params->{$identifier}->{chromosome}        = $alignments{$unique_best_alignment}->{chromosome};
-      $methylation_call_params->{$identifier}->{position_1}        = $alignments{$unique_best_alignment}->{position_1};
-      $methylation_call_params->{$identifier}->{position_2}        = $alignments{$unique_best_alignment}->{position_2};
-      $methylation_call_params->{$identifier}->{index}             = $alignments{$unique_best_alignment}->{index};
-      $methylation_call_params->{$identifier}->{alignment_score_1} = $alignments{$unique_best_alignment}->{alignment_score_1};
-      $methylation_call_params->{$identifier}->{alignment_score_2} = $alignments{$unique_best_alignment}->{alignment_score_2};
-      $methylation_call_params->{$identifier}->{sum_of_alignment_scores} = $alignments{$unique_best_alignment}->{sum_of_alignment_scores};
-      $methylation_call_params->{$identifier}->{mismatch_info_1}   = $alignments{$unique_best_alignment}->{mismatch_info_1};
-      $methylation_call_params->{$identifier}->{mismatch_info_2}   = $alignments{$unique_best_alignment}->{mismatch_info_2};
-      $methylation_call_params->{$identifier}->{CIGAR_1}           = $alignments{$unique_best_alignment}->{CIGAR_1};
-      $methylation_call_params->{$identifier}->{CIGAR_2}           = $alignments{$unique_best_alignment}->{CIGAR_2};
-      $methylation_call_params->{$identifier}->{flag_1}            = $alignments{$unique_best_alignment}->{flag_1};
-      $methylation_call_params->{$identifier}->{flag_2}            = $alignments{$unique_best_alignment}->{flag_2};
-    }
-  }
-
-  ### otherwise we are going to find out if there is a best match among the multiple alignments, or whether there are 2 or more equally good alignments (in which case
-  ### we boot the sequence pair altogether)
-  elsif (scalar keys %alignments >= 2  and scalar keys %alignments <= 4){
-    my $best_sum_of_alignment_scores;
-    my $best_alignment_location;
-    foreach my $alignment_location (sort {$alignments{$b}->{sum_of_alignment_scores} <=> $alignments{$a}->{sum_of_alignment_scores}} keys %alignments){
-      # print "$alignments{$alignment_location}->{sum_of_alignment_scores}\n";
-      unless (defined $best_sum_of_alignment_scores){
-	$best_sum_of_alignment_scores = $alignments{$alignment_location}->{sum_of_alignment_scores};
-	$best_alignment_location = $alignment_location;
-	# print "setting best alignment score to: $best_sum_of_alignment_scores\n";
-      }
-      else{
-	### if the second best alignment has the same sum of alignment scores as the first one, the sequence pair will get booted
-	if ($alignments{$alignment_location}->{sum_of_alignment_scores} == $best_sum_of_alignment_scores){
-	  # warn "Same sum of alignment scores for 2 different alignments, the sequence pair will get booted!\n";
-	  $sequence_pair_fails = 1;
-	  last; # exiting since we know that the sequence has ambiguous alignments
-	}
-	### else we are going to store the best alignment for further processing
-	else{
-	  $methylation_call_params->{$identifier}->{bowtie_sequence_1} = $alignments{$best_alignment_location}->{bowtie_sequence_1};
-	  $methylation_call_params->{$identifier}->{bowtie_sequence_2} = $alignments{$best_alignment_location}->{bowtie_sequence_2};
-	  $methylation_call_params->{$identifier}->{chromosome}        = $alignments{$best_alignment_location}->{chromosome};
-	  $methylation_call_params->{$identifier}->{position_1}        = $alignments{$best_alignment_location}->{position_1};
-	  $methylation_call_params->{$identifier}->{position_2}        = $alignments{$best_alignment_location}->{position_2};
-	  $methylation_call_params->{$identifier}->{index}             = $alignments{$best_alignment_location}->{index};
-	  $methylation_call_params->{$identifier}->{alignment_score_1} = $alignments{$best_alignment_location}->{alignment_score_1};
-	  $methylation_call_params->{$identifier}->{alignment_score_2} = $alignments{$best_alignment_location}->{alignment_score_2};
-	  $methylation_call_params->{$identifier}->{sum_of_alignment_scores} = $alignments{$best_alignment_location}->{sum_of_alignment_scores};
-	  $methylation_call_params->{$identifier}->{mismatch_info_1}   = $alignments{$best_alignment_location}->{mismatch_info_1};
-	  $methylation_call_params->{$identifier}->{mismatch_info_2}   = $alignments{$best_alignment_location}->{mismatch_info_2};
-	  $methylation_call_params->{$identifier}->{CIGAR_1}           = $alignments{$best_alignment_location}->{CIGAR_1};
-	  $methylation_call_params->{$identifier}->{CIGAR_2}           = $alignments{$best_alignment_location}->{CIGAR_2};
-	  $methylation_call_params->{$identifier}->{flag_1}            = $alignments{$best_alignment_location}->{flag_1};
-	  $methylation_call_params->{$identifier}->{flag_2}            = $alignments{$best_alignment_location}->{flag_2};
-	  last; # exiting since the sequence produced a unique best alignment
-	}
-      }
-    }
-  }
-  else{
-    die "There are too many potential hits for this sequence pair (1-4 expected, but found: '",scalar keys %alignments,"')\n";;
-  }
-
-  ### skipping the sequence completely if there were multiple alignments with the same best sum of alignment scores at different positions
-  if ($sequence_pair_fails == 1){
-    $counting{unsuitable_sequence_count}++;
-
-    ### report that the sequence has multiple hits with bitwise flag 256. We can print the sequence to the result file straight away and skip everything else
-    # my $ambiguous_read_1 = join("\t",$identifier.'/1','256','*','0','0','*','*','0','0',$sequence_1,$quality_value_1);
-    # my $ambiguous_read_2 = join("\t",$identifier.'/2','256','*','0','0','*','*','0','0',$sequence_2,$quality_value_2);
-    # print "$ambiguous_read_1\n";
-    # print "$ambiguous_read_2\n";
-
-    if ($ambiguous){
-      return 2; # => exits to next sequence pair, and prints it out (in FastQ format) to _ambiguous_reads_1.txt and _ambiguous_reads_2.txt if '--ambiguous' was specified
-      }
-    elsif ($unmapped){
-      return 1; # => exits to next sequence pair, and prints it out (in FastQ format) to _unmapped_reads_1.txt and _unmapped_reads_2.txt if '--unmapped' but not '--ambiguous' was specified
-    }
-    else{
-      return 0; # => exits to next sequence pair (default)
-    }
-  }
-
-  ### --DIRECTIONAL
-  ### If the option --directional has been specified the user wants to consider only alignments to the original top strand or the original bottom strand. We will therefore
-  ### discard all alignments to strands complementary to the original strands, as they should not exist in reality due to the library preparation protocol
-  if ($directional){
-    if ( ($methylation_call_params->{$identifier}->{index} == 1) or ($methylation_call_params->{$identifier}->{index} == 2) ){
-      #    warn "Alignment rejected! (index was: $methylation_call_params->{$identifier}->{index})\n";
-      $counting{alignments_rejected_count}++;
-      return 0;
-    }
-  }
-
-  ### If the sequence pair has not been rejected so far it does have a unique best alignment
-  $counting{unique_best_alignment_count}++;
-  extract_corresponding_genomic_sequence_paired_ends_bowtie2($identifier,$methylation_call_params);
-
-  ### check to see if the genomic sequences we extracted has the same length as the observed sequences +2, and only then we perform the methylation call
-  if (length($methylation_call_params->{$identifier}->{unmodified_genomic_sequence_1}) != length($sequence_1)+2){
-    warn "Chromosomal sequence could not be extracted for\t$identifier\t$methylation_call_params->{$identifier}->{chromosome}\t$methylation_call_params->{$identifier}->{start_seq_1}\n";
-    $counting{genomic_sequence_could_not_be_extracted_count}++;
-    return 0;
-  }
-  if (length($methylation_call_params->{$identifier}->{unmodified_genomic_sequence_2}) != length($sequence_2)+2){
-    warn "Chromosomal sequence could not be extracted for\t$identifier\t$methylation_call_params->{$identifier}->{chromosome}\t$methylation_call_params->{$identifier}->{start_seq_2}\n";
-    $counting{genomic_sequence_could_not_be_extracted_count}++;
-    return 0;
-  }
-
-  ### now we are set to perform the actual methylation call
-  $methylation_call_params->{$identifier}->{methylation_call_1} = methylation_call($identifier,$sequence_1,$methylation_call_params->{$identifier}->{unmodified_genomic_sequence_1},$methylation_call_params->{$identifier}->{read_conversion_1});
-  $methylation_call_params->{$identifier}->{methylation_call_2} = methylation_call($identifier,$sequence_2,$methylation_call_params->{$identifier}->{unmodified_genomic_sequence_2},$methylation_call_params->{$identifier}->{read_conversion_2});
-  # print "$methylation_call_params->{$identifier}->{read_conversion_2}\n";
-  # print "  $sequence_2\n";
-  # print "$methylation_call_params->{$identifier}->{unmodified_genomic_sequence_2}\n";
-  # print "  $methylation_call_params->{$identifier}->{methylation_call_2}\n";
-
-  print_bisulfite_mapping_results_paired_ends_bowtie2($identifier,$sequence_1,$sequence_2,$methylation_call_params,$quality_value_1,$quality_value_2);
-  return 0; ## otherwise 1 will be returned by default, which would print the sequence pair to unmapped_1 and _2
-}
-
-###
-
-sub decide_whether_paired_end_alignment_is_valid{
-  my ($index,$identifier) = @_;
-  my ($id_1,$strand_1,$mapped_chromosome_1,$position_1,$bowtie_sequence_1,$mismatch_info_1) = (split (/\t/,$fhs[$index]->{last_line_1},-1))[0,1,2,3,4,7];
-  my ($id_2,$strand_2,$mapped_chromosome_2,$position_2,$bowtie_sequence_2,$mismatch_info_2) = (split (/\t/,$fhs[$index]->{last_line_2},-1))[0,1,2,3,4,7];
-  chomp $mismatch_info_1;
-  chomp $mismatch_info_2;
-  my $seq_id_1 = $id_1;
-  my $seq_id_2 = $id_2;
-  $seq_id_1 =~ s/\/1$//; # removing the read /1
-  $seq_id_2 =~ s/\/1$//; # removing the read /1
-
-  ### ensuring that the current entry is the correct sequence
-  if ($seq_id_1 eq $identifier or $seq_id_2 eq $identifier){
-    ### checking the orientation of the alignment. We need to discriminate between 8 different conditions, however only 4 of them are theoretically
-    ### sensible alignments
-    my $orientation = ensure_sensical_alignment_orientation_paired_ends ($index,$id_1,$strand_1,$id_2,$strand_2);
-    ### If the orientation was correct can we move on
-    if ($orientation == 1){
-      return 1; ### 1st possibility for A SEQUENCE-PAIR TO PASS
-    }
-    ### If the alignment was in the wrong orientation we need to read in two new lines
-    elsif($orientation == 0){
-      my $newline_1 = $fhs[$index]->{fh}->getline();
-      my $newline_2 = $fhs[$index]->{fh}->getline();
-      if ($newline_1 and $newline_2){
-	### extract detailed information about the alignment again (from $newline_1 and $newline_2 this time)
-	($id_1,$strand_1) = (split (/\t/,$newline_1))[0,1];
-	($id_2,$strand_2) = (split (/\t/,$newline_2))[0,1];
-
-	my $seqid;
-	$seq_id_1 = $id_1;
-	$seq_id_2 = $id_2;
-	# we need to capture the first read (ending on /1)
-	if ($seq_id_1 =~ s/\/1$//){ # removing the read /1 tag
-	  $seqid = $seq_id_1;
-	}
-	elsif ($seq_id_2 =~ s/\/1$//){ # removing the read /1 tag
-	  $seqid = $seq_id_2;
-	}
-	else{
-	  die "One of the two reads needs to end on /1!!";
-	}
-	
-	### ensuring that the next entry is still the correct sequence
-	if ($seq_id_1 eq $identifier or  $seq_id_2 eq $identifier){
-	  ### checking orientation again
-	  $orientation = ensure_sensical_alignment_orientation_paired_ends ($index,$id_1,$strand_1,$id_2,$strand_2);
-	  ### If the orientation was correct can we move on
-	  if ($orientation == 1){
-	    ### Writing the current sequence to last_line_1 and last_line_2
-	    $fhs[$index]->{last_seq_id} = $seqid;
-	    $fhs[$index]->{last_line_1} = $newline_1;
-	    $fhs[$index]->{last_line_2} = $newline_2;
-	    return 1; ### 2nd possibility for a SEQUENCE-PAIR TO PASS
-	  }
-	  ### If the alignment was in the wrong orientation again we need to read in yet another 2 new lines and store them in @fhs (this must be
-	  ### the next entry)
-	  elsif ($orientation == 0){
-	    $newline_1 = $fhs[$index]->{fh}->getline();
-	    $newline_2 = $fhs[$index]->{fh}->getline();
-	    if ($newline_1 and $newline_2){
-	      ($seq_id_1) = split (/\t/,$newline_1);
-	      ($seq_id_2) = split (/\t/,$newline_2);
-	
-	      $seqid = '';
-	      if ($seq_id_1 =~ s/\/1$//){ # removing the read /1 tag
-		$seqid = $seq_id_1;
-	      }
-	      elsif ($seq_id_2 =~ s/\/1$//){ # removing the read /1 tag
-		$seqid = $seq_id_2;
-	      }
-	      else{
-		die "One of the two reads needs to end on /1!!";
-	      }
-	
-	      ### check if the next 2 lines still have the same seq ID (must not happen), and if not overwrite the current seq-ID and bowtie output with
-	      ### the same fields of the just read next entry
-	      die "Same seq ID 3 or more times in a row!(should be 2 max)" if ($seqid eq $identifier);
-	      $fhs[$index]->{last_seq_id} = $seqid;
-	      $fhs[$index]->{last_line_1} = $newline_1;
-	      $fhs[$index]->{last_line_2} = $newline_2;
-	      return 0; # not processing anything this round as the alignment currently stored in last_line_1 and _2 was in the wrong orientation
-	    }
-	    else {
-	      ### assigning undef to last_seq_id and last_line (end of bowtie output)
-	      $fhs[$index]->{last_seq_id} = undef;
-	      $fhs[$index]->{last_line_1} = undef;
-	      $fhs[$index]->{last_line_2} = undef;
-	      return 0; # not processing anything as the alignment currently stored in last_line_1 and _2 was in the wrong orientation
-	    }
-	  }
-	  else{
-	    die "The orientation of the alignment must be either correct or incorrect\n";
-	  }
-	}
-	### the sequence pair we just read in is already the next sequence pair to be analysed -> store it in @fhs
-	else{
-	  $fhs[$index]->{last_seq_id} = $seqid;
-	  $fhs[$index]->{last_line_1} = $newline_1;
-	  $fhs[$index]->{last_line_2} = $newline_2;
-	  return 0; # processing the new alignment result only in the next round
-	}
-      }
-      else {
-	# assigning undef to last_seq_id and both last_lines (end of bowtie output)
-	$fhs[$index]->{last_seq_id} = undef;
-	$fhs[$index]->{last_line_1} = undef;
-	$fhs[$index]->{last_line_2} = undef;
-	return 0; # not processing anything as the alignment currently stored in last_line_1 and _2 was in the wrong orientation
-      }
-    }
-    else{
-      die "The orientation of the alignment must be either correct or incorrect\n";
-    }
-  }
-  ### the sequence pair stored in @fhs as last_line_1 and last_line_2 is already the next sequence pair to be analysed -> analyse next round
-  else{
-    return 0;
-  }
-}
-
-### EXTRACT GENOMIC SEQUENCE | BOWTIE 1 | PAIRED-END
-
-sub extract_corresponding_genomic_sequence_paired_ends {
-  my ($sequence_identifier,$methylation_call_params) = @_;
-  ### A bisulfite sequence pair for 1 location in the genome can theoretically be on any of the 4 possible converted strands. We are also giving the
-  ### sequence a 'memory' of the conversion we are expecting which we will need later for the methylation call
-  my $alignment_read_1;
-  my $alignment_read_2;
-  my $read_conversion_info_1;
-  my $read_conversion_info_2;
-  my $genome_conversion;
-
-  ### Now extracting the same sequence from the mouse genomic sequence, +2 extra bases at oone of the ends so that we can also make a CpG, CHG or CHH methylation call
-  ### if the C happens to be at the first or last position of the actually observed sequence
-  my $non_bisulfite_sequence_1;
-  my $non_bisulfite_sequence_2;
-
-  ### all alignments reported by bowtie have the + alignment first and the - alignment as the second one irrespective of whether read 1 or read 2 was
-  ### the + alignment. We however always read in sequences read 1 then read 2, so if read 2 is the + alignment we need to swap the extracted genomic
-  ### sequences around!
-  ### results from CT converted read 1 plus GA converted read 2 vs. CT converted genome (+/- orientation alignments are reported only)
-  if ($methylation_call_params->{$sequence_identifier}->{index} == 0){
-    ### [Index 0, sequence originated from (converted) forward strand]
-    $counting{CT_GA_CT_count}++;
-    $alignment_read_1 = '+';
-    $alignment_read_2 = '-';
-    $read_conversion_info_1 = 'CT';
-    $read_conversion_info_2 = 'GA';
-    $genome_conversion = 'CT';
-    ### SEQUENCE 1 (this is always the forward hit, in this case it is read 1)
-    ### for hits on the forward strand we need to capture 2 extra bases at the 3' end
-
-    $non_bisulfite_sequence_1 = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$methylation_call_params->{$sequence_identifier}->{start_seq_1},length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_1})+2); ##CHH change
-
-    ### SEQUENCE 2 (this will always be on the reverse strand, in this case it is read 2)
-    ### As the second conversion is GA we need to capture 1 base 3', so that it is a 5' base after reverse complementation
-    if (length($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}}) > $methylation_call_params->{$sequence_identifier}->{start_seq_2}+length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_2})+1){ ## CHH change to +1
-
-      $non_bisulfite_sequence_2 = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},($methylation_call_params->{$sequence_identifier}->{start_seq_2}),length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_2})+2);
-      ### the reverse strand sequence needs to be reverse complemented
-      $non_bisulfite_sequence_2 = reverse_complement($non_bisulfite_sequence_2);
-    }
-    else{
-       $non_bisulfite_sequence_2 = '';
-     }
-   }
-
-   ### results from GA converted read 1 plus CT converted read 2 vs. GA converted genome (+/- orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 1){
-    ### [Index 1, sequence originated from complementary to (converted) reverse strand]
-    $counting{GA_CT_GA_count}++;
-    $alignment_read_1 = '+';
-    $alignment_read_2 = '-';
-    $read_conversion_info_1 = 'GA';
-    $read_conversion_info_2 = 'CT';
-    $genome_conversion = 'GA';
-
-    ### SEQUENCE 1 (this is always the forward hit, in this case it is read 1)
-    ### as we need to make the methylation call for the base 5' of the first base (GA conversion!) we need to capture 2 extra bases at the 5' end
-    if ($methylation_call_params->{$sequence_identifier}->{start_seq_1}-1 > 0){ ## CHH change to -1
-      $non_bisulfite_sequence_1 = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$methylation_call_params->{$sequence_identifier}->{start_seq_1}-2,length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_1})+2); ### CHH change to -2/+2
-    }
-    else{
-      $non_bisulfite_sequence_1 = '';
-    }
-
-    ### SEQUENCE 2 (this will always be on the reverse strand, in this case it is read 2)
-    ### As we are doing a CT comparison for the reverse strand we are taking 2 bases extra at the 5' end, so it is a 3' base after reverse complementation
-    $non_bisulfite_sequence_2 = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},($methylation_call_params->{$sequence_identifier}->{start_seq_2})-2,length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_2})+2); ### CHH change to -2/+2
-    ### the reverse strand sequence needs to be reverse complemented
-    $non_bisulfite_sequence_2 = reverse_complement($non_bisulfite_sequence_2);
-  }
-
-  ### results from GA converted read 1 plus CT converted read 2 vs. CT converted genome (-/+ orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 2){
-    ### [Index 2, sequence originated from the complementary to (converted) forward strand]
-    $counting{GA_CT_CT_count}++;
-    $alignment_read_1 = '-';
-    $alignment_read_2 = '+';
-    $read_conversion_info_1 = 'GA';
-    $read_conversion_info_2 = 'CT';
-    $genome_conversion = 'CT';
-
-    ### Here we switch the sequence information round!!  non_bisulfite_sequence_1 will later correspond to the read 1!!!!
-    ### SEQUENCE 1 (this is always the forward hit, in this case it is READ 2), read 1 is in - orientation on the reverse strand
-    ### As read 1 is GA converted we need to capture 2 extra 3' bases which will be 2 extra 5' base after reverse complementation
-    $non_bisulfite_sequence_1 = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},($methylation_call_params->{$sequence_identifier}->{start_seq_2}),length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_2})+2); ### CHH change to +2
-    ### the reverse strand sequence needs to be reverse complemented
-    $non_bisulfite_sequence_1 = reverse_complement($non_bisulfite_sequence_1);
-
-    ### SEQUENCE 2 (this will always be on the reverse strand, in this case it is READ 1)
-    ### non_bisulfite_sequence_2 will later correspond to the read 2!!!!
-    ### Read 2 is CT converted so we need to capture 2 extra 3' bases
-    if (length($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}}) > ($methylation_call_params->{$sequence_identifier}->{start_seq_1})+length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_1})+1){ ## CHH change to +1
-      $non_bisulfite_sequence_2 = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},($methylation_call_params->{$sequence_identifier}->{start_seq_1}),length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_1})+2); ## CHH changed from +1 to +2
-    }
-    else{
-      $non_bisulfite_sequence_2 = '';
-    }
-  }
-
-  ### results from CT converted read 1 plus GA converted read 2 vs. GA converted genome (-/+ orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 3){
-    ### [Index 3, sequence originated from the (converted) reverse strand]
-    $counting{CT_GA_GA_count}++;
-    $alignment_read_1 = '-';
-    $alignment_read_2 = '+';
-    $read_conversion_info_1 = 'CT';
-    $read_conversion_info_2 = 'GA';
-    $genome_conversion = 'GA';
-
-    ### Here we switch the sequence information round!!  non_bisulfite_sequence_1 will later correspond to the read 1!!!!
-    ### SEQUENCE 1 (this is always the forward hit, in this case it is READ 2), read 1 is in - orientation on the reverse strand
-    ### As read 1 is CT converted we need to capture 2 extra 5' bases which will be 2 extra 3' base after reverse complementation
-    if ( ($methylation_call_params->{$sequence_identifier}->{start_seq_2}-1) > 0){ ## CHH changed to -1
-      $non_bisulfite_sequence_1 = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},($methylation_call_params->{$sequence_identifier}->{start_seq_2})-2,length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_2})+2); ### CHH changed to -2/+2
-      ### the reverse strand sequence needs to be reverse complemented
-      $non_bisulfite_sequence_1 = reverse_complement($non_bisulfite_sequence_1);
-    }
-    else{
-      $non_bisulfite_sequence_1 = '';
-    }
-
-    ### SEQUENCE 2 (this will always be on the reverse strand, in this case it is READ 1)
-    ### non_bisulfite_sequence_2 will later correspond to the read 2!!!!
-    ### Read 2 is GA converted so we need to capture 2 extra 5' bases
-    $non_bisulfite_sequence_2 = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},($methylation_call_params->{$sequence_identifier}->{start_seq_1})-2,length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence_1})+2); ### CHH changed to -2/+2
-  }
-  else{
-    die "Too many bowtie result filehandles\n";
-  }
-  ### the alignment_strand information is needed to determine which strand of the genomic sequence we are comparing the read against,
-  ### the read_conversion information is needed to know whether we are looking for C->T or G->A substitutions
-
-  $methylation_call_params->{$sequence_identifier}->{alignment_read_1} = $alignment_read_1;
-  $methylation_call_params->{$sequence_identifier}->{alignment_read_2} = $alignment_read_2;
-  $methylation_call_params->{$sequence_identifier}->{genome_conversion} = $genome_conversion;
-  $methylation_call_params->{$sequence_identifier}->{read_conversion_1} = $read_conversion_info_1;
-  $methylation_call_params->{$sequence_identifier}->{read_conversion_2} = $read_conversion_info_2;
-  $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence_1} = $non_bisulfite_sequence_1;
-  $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence_2} = $non_bisulfite_sequence_2;
-}
-
-### EXTRACT GENOMIC SEQUENCE BOWTIE 2 | PAIRED-END
-
-sub extract_corresponding_genomic_sequence_paired_ends_bowtie2{
-  my ($sequence_identifier,$methylation_call_params) = @_;
-  ### A bisulfite sequence pair for 1 location in the genome can theoretically be on any of the 4 possible converted strands. We are also giving the
-  ### sequence a 'memory' of the conversion we are expecting which we will need later for the methylation call
-
-  my $cigar_1 = $methylation_call_params->{$sequence_identifier}->{CIGAR_1};
-  my $cigar_2 = $methylation_call_params->{$sequence_identifier}->{CIGAR_2};
-  my $flag_1 =  $methylation_call_params->{$sequence_identifier}->{flag_1};
-  my $flag_2 =  $methylation_call_params->{$sequence_identifier}->{flag_2};
-#  print "$cigar_1\t$cigar_2\t$flag_1\t$flag_2\n";
-  ### We are now extracting the corresponding genomic sequence, +2 extra bases at the end (or start) so that we can also make a CpG methylation call and
-  ### in addition make differential calls for Cs in CHG or CHH context if the C happens to be at the last (or first)  position of the actually observed sequence
-
-  ### the alignment_strand information is needed to determine which strand of the genomic sequence we are comparing the read against,
-  ### the read_conversion information is needed to know whether we are looking for C->T or G->A substitutions
-  my $alignment_read_1;
-  my $alignment_read_2;
-  my $read_conversion_info_1;
-  my $read_conversion_info_2;
-  my $genome_conversion;
-
-  ### Now extracting the same sequence from the mouse genomic sequence, +2 extra bases at one of the ends so that we can also make a CpG, CHG or CHH methylation call
-  ### if the C happens to be at the last position of the actually observed sequence
-  my $non_bisulfite_sequence_1 = '';
-  my $non_bisulfite_sequence_2 = '';
-
-  ### Positions in SAM format are 1 based, so we need to subract 1 when getting substrings
-  my $pos_1 = $methylation_call_params->{$sequence_identifier}->{position_1}-1;
-  my $pos_2 = $methylation_call_params->{$sequence_identifier}->{position_2}-1;
-
-  # parsing CIGAR 1 string
-  my @len_1 = split (/\D+/,$cigar_1); # storing the length per operation
-  my @ops_1 = split (/\d+/,$cigar_1); # storing the operation
-  shift @ops_1; # remove the empty first element
-  die "CIGAR 1 string contained a non-matching number of lengths and operations\n" unless (scalar @len_1 == scalar @ops_1);
-  # parsing CIGAR 2 string
-  my @len_2 = split (/\D+/,$cigar_2); # storing the length per operation
-  my @ops_2 = split (/\d+/,$cigar_2); # storing the operation
-  shift @ops_2; # remove the empty first element
-  die "CIGAR 2 string contained a non-matching number of lengths and operations\n" unless (scalar @len_2 == scalar @ops_2);
-
-  my $indels_1 = 0; # addiong these to the hemming distance value (needed for the NM field in the final SAM output
-  my $indels_2 = 0;
-  
-  ### Extracting read 1 genomic sequence ###
-
-  # extracting 2 additional bp at the 5' end (read 1)
-  if ( ($methylation_call_params->{$sequence_identifier}->{index} == 1) or ($methylation_call_params->{$sequence_identifier}->{index} == 3) ){
-    # checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    unless ( ($pos_1-2) > 0){# exiting with en empty genomic sequence otherwise
-      $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence_1} = $non_bisulfite_sequence_1;
-      return;
-    }
-    $non_bisulfite_sequence_1 .= substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$pos_1-2,2);
-  }
-
-  foreach (0..$#len_1){
-    if ($ops_1[$_] eq 'M'){
-      # extracting genomic sequence
-      $non_bisulfite_sequence_1 .= substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$pos_1,$len_1[$_]);
-      #   warn "$non_bisulfite_sequence_1\n";
-      # adjusting position
-      $pos_1 += $len_1[$_];
-    }
-    elsif ($ops_1[$_] eq 'I'){ # insertion in the read sequence
-      # we simply add padding Ns instead of finding genomic sequence. This will not be used to infer methylation calls
-      $non_bisulfite_sequence_1 .= 'N' x $len_1[$_];
-      #    warn "$non_bisulfite_sequence_1\n";
-      # position doesn't need adjusting
-	  $indels_1 += $len_1[$_]; # adding to $indels_1 to determine the hemming distance (= single base mismatches, insertions or deletions) for the SAM output
-    }
-    elsif ($ops_1[$_] eq 'D'){ # deletion in the read sequence
-      # we do not add any genomic sequence but only adjust the position
-      #     warn "Just adjusting the position by: ",$len_1[$_],"bp\n";
-      $pos_1 += $len_1[$_];
-	  $indels_1 += $len_1[$_]; # adding to $indels_1 to determine the hemming distance (= single base mismatches, insertions or deletions) for the SAM output
-    }
-    elsif($cigar_1 =~ tr/[NSHPX=]//){ # if these (for standard mapping) illegal characters exist we die
-      die "The CIGAR 1 string contained illegal CIGAR operations in addition to 'M', 'I' and 'D': $cigar_1\n";
-    }
-    else{
-      die "The CIGAR 1 string contained undefined CIGAR operations in addition to 'M', 'I' and 'D': $cigar_1\n";
-    }
-  }
-
-  ### 3' end of read 1
-  if ( ($methylation_call_params->{$sequence_identifier}->{index} == 0) or ($methylation_call_params->{$sequence_identifier}->{index} == 2) ){
-    ## checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    unless (length($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}}) >= $pos_1+2){# exiting with en empty genomic sequence otherwise
-      $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence_1} = $non_bisulfite_sequence_1;
-      return;
-    }
-    $non_bisulfite_sequence_1 .= substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$pos_1,2);
-  }
-
-
-  ### Extracting read 2 genomic sequence ###
-
-  ### 5' end of read 2
-  if ( ($methylation_call_params->{$sequence_identifier}->{index} == 1) or ($methylation_call_params->{$sequence_identifier}->{index} == 3) ){
-    ## checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    unless ( ($pos_2-2) >= 0){# exiting with en empty genomic sequence otherwise
-      $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence_2} = $non_bisulfite_sequence_2;
-      return;
-    }
-    $non_bisulfite_sequence_2 .= substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$pos_2-2,2);
-  }
-
-  foreach (0..$#len_2){
-    if ($ops_2[$_] eq 'M'){
-      # extracting genomic sequence
-      $non_bisulfite_sequence_2 .= substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$pos_2,$len_2[$_]);
-      # warn "$non_bisulfite_sequence_2\n";
-      # adjusting position
-      $pos_2 += $len_2[$_];
-    }
-    elsif ($ops_2[$_] eq 'I'){ # insertion in the read sequence
-      # we simply add padding Ns instead of finding genomic sequence. This will not be used to infer methylation calls
-      $non_bisulfite_sequence_2 .= 'N' x $len_2[$_];
-      # warn "$non_bisulfite_sequence_2\n";
-      # position doesn't need adjusting
-	  $indels_2 += $len_2[$_]; # adding to $indels_1 to determine the hemming distance (= single base mismatches, insertions or deletions) for the SAM output
-    }
-    elsif ($ops_2[$_] eq 'D'){ # deletion in the read sequence
-      # we do not add any genomic sequence but only adjust the position
-      # warn "Just adjusting the position by: ",$len_2[$_],"bp\n";
-      $pos_2 += $len_2[$_];
-	  $indels_2 += $len_2[$_]; # adding to $indels_1 to determine the hemming distance (= single base mismatches, insertions or deletions) for the SAM output
-    }
-    elsif($cigar_2 =~ tr/[NSHPX=]//){ # if these (for standard mapping) illegal characters exist we die
-      die "The CIGAR 2 string contained illegal CIGAR operations in addition to 'M', 'I' and 'D': $cigar_2\n";
-    }
-    else{
-      die "The CIGAR 2 string contained undefined CIGAR operations in addition to 'M', 'I' and 'D': $cigar_2\n";
-    }
-  }
-
-  ### 3' end of read 2
-  if ( ($methylation_call_params->{$sequence_identifier}->{index} == 0) or ($methylation_call_params->{$sequence_identifier}->{index} == 2) ){
-    ## checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    unless (length($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}}) >= $pos_2+2){# exiting with en empty genomic sequence otherwise
-      $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence_2} = $non_bisulfite_sequence_2;
-      return;
-    }
-    $non_bisulfite_sequence_2 .= substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$pos_2,2);
-  }
-
-  ### all paired-end alignments reported by Bowtie 2 have the Read 1 alignment first and the Read 2 alignment as the second one irrespective of whether read 1 or read 2 was
-  ### the + alignment. We also read in sequences read 1 then read 2 so they should correspond perfectly
-
-  ### results from CT converted read 1 plus GA converted read 2 vs. CT converted genome (+/- orientation alignments are reported only)
-  if ($methylation_call_params->{$sequence_identifier}->{index} == 0){
-    ### [Index 0, sequence originated from (converted) forward strand]
-    $counting{CT_GA_CT_count}++;
-    $alignment_read_1 = '+';
-    $alignment_read_2 = '-';
-    $read_conversion_info_1 = 'CT';
-    $read_conversion_info_2 = 'GA';
-    $genome_conversion = 'CT';
-    ### Read 1 is always the forward hit
-    ### Read 2 is will always on the reverse strand, so it needs to be reverse complemented
-    $non_bisulfite_sequence_2 = reverse_complement($non_bisulfite_sequence_2);
-  }
-
-  ### results from GA converted read 1 plus CT converted read 2 vs. GA converted genome (+/- orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 1){
-    ### [Index 1, sequence originated from complementary to (converted) bottom strand]
-    $counting{GA_CT_GA_count}++;
-    $alignment_read_1 = '+';
-    $alignment_read_2 = '-';
-    $read_conversion_info_1 = 'GA';
-    $read_conversion_info_2 = 'CT';
-    $genome_conversion = 'GA';
-    ### Read 1 is always the forward hit
-    ### Read 2 is will always on the reverse strand, so it needs to be reverse complemented
-    $non_bisulfite_sequence_2 = reverse_complement($non_bisulfite_sequence_2);
-  }
-
-  ### results from GA converted read 1 plus CT converted read 2 vs. CT converted genome (-/+ orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 2){
-    ### [Index 2, sequence originated from the complementary to (converted) top strand]
-    $counting{GA_CT_CT_count}++;
-    $alignment_read_1 = '-';
-    $alignment_read_2 = '+';
-    $read_conversion_info_1 = 'GA';
-    $read_conversion_info_2 = 'CT';
-    $genome_conversion = 'CT';
-
-    ### Read 1 (the reverse strand) genomic sequence needs to be reverse complemented
-    $non_bisulfite_sequence_1 = reverse_complement($non_bisulfite_sequence_1);
-  }
-
-  ### results from CT converted read 1 plus GA converted read 2 vs. GA converted genome (-/+ orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 3){
-    ### [Index 3, sequence originated from the (converted) reverse strand]
-    $counting{CT_GA_GA_count}++;
-    $alignment_read_1 = '-';
-    $alignment_read_2 = '+';
-    $read_conversion_info_1 = 'CT';
-    $read_conversion_info_2 = 'GA';
-    $genome_conversion = 'GA';
-    ### Read 1 (the reverse strand) genomic sequence needs to be reverse complemented
-    $non_bisulfite_sequence_1 = reverse_complement($non_bisulfite_sequence_1);
-  }
-  else{
-    die "Too many bowtie result filehandles\n";
-  }
-  ### the alignment_strand information is needed to determine which strand of the genomic sequence we are comparing the read against,
-  ### the read_conversion information is needed to know whether we are looking for C->T or G->A substitutions
-
-  $methylation_call_params->{$sequence_identifier}->{alignment_read_1} = $alignment_read_1;
-  $methylation_call_params->{$sequence_identifier}->{alignment_read_2} = $alignment_read_2;
-  $methylation_call_params->{$sequence_identifier}->{genome_conversion} = $genome_conversion;
-  $methylation_call_params->{$sequence_identifier}->{read_conversion_1} = $read_conversion_info_1;
-  $methylation_call_params->{$sequence_identifier}->{read_conversion_2} = $read_conversion_info_2;
-  $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence_1} = $non_bisulfite_sequence_1;
-  $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence_2} = $non_bisulfite_sequence_2;
-  ## the end position of a read is stored in $pos
-  $methylation_call_params->{$sequence_identifier}->{end_position_1} = $pos_1;
-  $methylation_call_params->{$sequence_identifier}->{end_position_2} = $pos_2;
-  $methylation_call_params->{$sequence_identifier}->{indels_1} = $indels_1;
-  $methylation_call_params->{$sequence_identifier}->{indels_2} = $indels_2;
-}
-
-##########################################
-### PRINT SINGLE END RESULTS: Bowtie 1 ###
-##########################################
-
-sub print_bisulfite_mapping_result_single_end{
-  my ($identifier,$sequence,$methylation_call_params,$quality_value)= @_;
-
-  ### we will output the FastQ quality in Sanger encoding (Phred 33 scale)
-  if ($phred64){
-    $quality_value = convert_phred64_quals_to_phred33($quality_value);
-  }
-  elsif ($solexa){
-    $quality_value = convert_solexa_quals_to_phred33($quality_value);
-  }
-
-  ### We will add +1 bp to the starting position of single-end reads, as Bowtie 1 reports the index and not the bp position. 
-  $methylation_call_params->{$identifier}->{position} += 1;
-	
-  ### writing every uniquely mapped read and its methylation call to the output file
-  if ($vanilla){
-    my $bowtie1_output = join("\t",$identifier,$methylation_call_params->{$identifier}->{alignment_strand},$methylation_call_params->{$identifier}->{chromosome},$methylation_call_params->{$identifier}->{position},$methylation_call_params->{$identifier}->{end_position},$sequence,$methylation_call_params->{$identifier}->{unmodified_genomic_sequence},$methylation_call_params->{$identifier}->{methylation_call},$methylation_call_params->{$identifier}->{read_conversion},$methylation_call_params->{$identifier}->{genome_conversion},$quality_value);
-    print OUT "$bowtie1_output\n";
-  }
-  else{ # SAM output, default since Bismark v1.0.0
-    single_end_SAM_output($identifier,$sequence,$methylation_call_params,$quality_value); # at the end of the script
-  }
-}
-
-##########################################
-### PRINT SINGLE END RESULTS: Bowtie 2 ###
-##########################################
-
-sub print_bisulfite_mapping_result_single_end_bowtie2{
-  my ($identifier,$sequence,$methylation_call_params,$quality_value)= @_;
-
-  ### we will output the FastQ quality in Sanger encoding (Phred 33 scale)
-  if ($phred64){
-    $quality_value = convert_phred64_quals_to_phred33($quality_value);
-  }
-  elsif ($solexa){
-    $quality_value = convert_solexa_quals_to_phred33($quality_value);
-  }
-
-  ### writing every mapped read and its methylation call to the SAM output file (unmapped and ambiguous reads were already printed)
-	single_end_SAM_output($identifier,$sequence,$methylation_call_params,$quality_value); # at the end of the script
-}
-
-##########################################
-### PRINT PAIRED END ESULTS: Bowtie 1  ###
-##########################################
-
-sub print_bisulfite_mapping_results_paired_ends{
-  my ($identifier,$sequence_1,$sequence_2,$methylation_call_params,$quality_value_1,$quality_value_2)= @_;
-
-  ### we will output the FastQ quality in Sanger encoding (Phred 33 scale)
-  if ($phred64){
-    $quality_value_1 = convert_phred64_quals_to_phred33($quality_value_1);
-    $quality_value_2 = convert_phred64_quals_to_phred33($quality_value_2);
-  }
-  elsif ($solexa){
-    $quality_value_1 = convert_solexa_quals_to_phred33($quality_value_1);
-    $quality_value_2 = convert_solexa_quals_to_phred33($quality_value_2);
-  }
-
-  ### We will add +1 bp to the start position of paired-end reads, as Bowtie 1 reports the index and not the bp position. (End position is already 1-based)
-  $methylation_call_params->{$identifier}->{start_seq_1} += 1;
-
-  ### writing every single aligned read and its methylation call to the output file
-  if ($vanilla){	
-    my $bowtie1_output_paired_end = join("\t",$identifier,$methylation_call_params->{$identifier}->{alignment_read_1},$methylation_call_params->{$identifier}->{chromosome},$methylation_call_params->{$identifier}->{start_seq_1},$methylation_call_params->{$identifier}->{alignment_end},$sequence_1,$methylation_call_params->{$identifier}->{unmodified_genomic_sequence_1},$methylation_call_params->{$identifier}->{methylation_call_1},$sequence_2,$methylation_call_params->{$identifier}->{unmodified_genomic_sequence_2},$methylation_call_params->{$identifier}->{methylation_call_2},$methylation_call_params->{$identifier}->{read_conversion_1},$methylation_call_params->{$identifier}->{genome_conversion},$quality_value_1,$quality_value_2);
-    print OUT "$bowtie1_output_paired_end\n";
-  }
-  else{ # SAM output, default since Bismark v1.0.0
-    paired_end_SAM_output($identifier,$sequence_1,$sequence_2,$methylation_call_params,$quality_value_1,$quality_value_2); # at the end of the script
-  }
-
-}
-
-##########################################
-### PRINT PAIRED END ESULTS: Bowtie 2  ###
-##########################################
-
-sub print_bisulfite_mapping_results_paired_ends_bowtie2{
-  my ($identifier,$sequence_1,$sequence_2,$methylation_call_params,$quality_value_1,$quality_value_2)= @_;
-
-  ### we will output the FastQ quality in Sanger encoding (Phred 33 scale)
-  if ($phred64){
-    $quality_value_1 = convert_phred64_quals_to_phred33($quality_value_1);
-    $quality_value_2 = convert_phred64_quals_to_phred33($quality_value_2);
-  }
-  elsif ($solexa){
-    $quality_value_1 = convert_solexa_quals_to_phred33($quality_value_1);
-    $quality_value_2 = convert_solexa_quals_to_phred33($quality_value_2);
-  }
-
-  ### writing every single aligned read and its methylation call to the output file  (unmapped and ambiguous reads were already printed)
-  paired_end_SAM_output($identifier,$sequence_1,$sequence_2,$methylation_call_params,$quality_value_1,$quality_value_2); # at the end of the script
-
-}
-	
-	
-sub convert_phred64_quals_to_phred33{
-
-  my $qual = shift;
-  my @quals = split (//,$qual);
-  my @new_quals;
-
-  foreach my $index (0..$#quals){
-    my $phred_score = convert_phred64_quality_string_into_phred_score ($quals[$index]);
-    my $phred33_quality_string = convert_phred_score_into_phred33_quality_string ($phred_score);
-    $new_quals[$index] = $phred33_quality_string;
-  }
-
-  my $phred33_quality = join ("",@new_quals);
-  return $phred33_quality;
-}
-
-sub convert_solexa_quals_to_phred33{
-
-  my $qual = shift;
-  my @quals = split (//,$qual);
-  my @new_quals;
-
-  foreach my $index (0..$#quals){
-    my $phred_score = convert_solexa_pre1_3_quality_string_into_phred_score ($quals[$index]);
-    my $phred33_quality_string = convert_phred_score_into_phred33_quality_string ($phred_score);
-    $new_quals[$index] = $phred33_quality_string;
-  }
-
-  my $phred33_quality = join ("",@new_quals);
-  return $phred33_quality;
-}
-
-sub convert_phred_score_into_phred33_quality_string{
-  my $qual = shift;
-  $qual = chr($qual+33);
-  return $qual;
-}
-
-sub convert_phred64_quality_string_into_phred_score{
-  my $string = shift;
-  my $qual = ord($string)-64;
-  return $qual;
-}
-
-sub convert_solexa_pre1_3_quality_string_into_phred_score{
-  ### We will just use 59 as the offset here as all Phred Scores between 10 and 40 look exactly the same, there is only a minute difference for values between 0 and 10
-  my $string = shift;
-  my $qual = ord($string)-59;
-  return $qual;
-}
-
-
-sub extract_corresponding_genomic_sequence_single_end {
-  my ($sequence_identifier,$methylation_call_params) = @_;
-  ### A bisulfite sequence for 1 location in the genome can theoretically be any of the 4 possible converted strands. We are also giving the
-  ### sequence a 'memory' of the conversion we are expecting which we will need later for the methylation call
-
-  ### the alignment_strand information is needed to determine which strand of the genomic sequence we are comparing the read against,
-  ### the read_conversion information is needed to know whether we are looking for C->T or G->A substitutions
-  my $alignment_strand;
-  my $read_conversion_info;
-  my $genome_conversion;
-  ### Also extracting the corresponding genomic sequence, +2 extra bases at the end so that we can also make a CpG methylation call and
-  ### in addition make differential calls for Cs non-CpG context, which will now be divided into CHG and CHH methylation,
-  ### if the C happens to be at the last position of the actually observed sequence
-  my $non_bisulfite_sequence;
-  ### depending on the conversion we want to make need to capture 1 extra base at the 3' end
-
-  ### results from CT converted read vs. CT converted genome (+ orientation alignments are reported only)
-  if ($methylation_call_params->{$sequence_identifier}->{index} == 0){
-    ### [Index 0, sequence originated from (converted) forward strand]
-    $counting{CT_CT_count}++;
-    $alignment_strand = '+';
-    $read_conversion_info = 'CT';
-    $genome_conversion = 'CT';
-
-    ## checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    if (length($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}}) > $methylation_call_params->{$sequence_identifier}->{position}+length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence})+1){ ## CHH changed to +1
-      ### + 2 extra base at the 3' end
-      $non_bisulfite_sequence = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$methylation_call_params->{$sequence_identifier}->{position},length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence})+2); ## CHH changed to +2
-    }
-    else{
-      $non_bisulfite_sequence = '';
-    }
-  }
-
-  ### results from CT converted reads vs. GA converted genome (- orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 1){
-    ### [Index 1, sequence originated from (converted) reverse strand]
-    $counting{CT_GA_count}++;
-    $alignment_strand = '-';
-    $read_conversion_info = 'CT';
-    $genome_conversion = 'GA';
-
-    ## checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    if ($methylation_call_params->{$sequence_identifier}->{position}-2 >= 0){ ## CHH changed to -2 # 02 02 2012 Changed this to >= from >
-      ### Extracting 2 extra 5' bases on forward strand which will become 2 extra 3' bases after reverse complementation
-      $non_bisulfite_sequence = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$methylation_call_params->{$sequence_identifier}->{position}-2,length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence})+2); ## CHH changed to -2/+2
-      ## reverse complement!
-      $non_bisulfite_sequence = reverse_complement($non_bisulfite_sequence);
-    }
-    else{
-      $non_bisulfite_sequence = '';
-    }
-  }
-
-  ### results from GA converted reads vs. CT converted genome (- orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 2){
-    ### [Index 2, sequence originated from complementary to (converted) forward strand]
-    $counting{GA_CT_count}++;
-    $alignment_strand = '-';
-    $read_conversion_info = 'GA';
-    $genome_conversion = 'CT';
-
-    ### +2 extra bases on the forward strand 3', which will become 2 extra 5' bases after reverse complementation
-    ## checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    if (length($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}}) > $methylation_call_params->{$sequence_identifier}->{position}+length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence})+1){ ## changed to +1 on 02 02 2012
-      $non_bisulfite_sequence = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$methylation_call_params->{$sequence_identifier}->{position},length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence})+2); ## CHH changed to +2
-      ## reverse complement!
-      $non_bisulfite_sequence = reverse_complement($non_bisulfite_sequence);
-    }
-    else{
-      $non_bisulfite_sequence = '';
-    }
-  }
-
-  ### results from GA converted reads vs. GA converted genome (+ orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 3){
-    ### [Index 3, sequence originated from complementary to (converted) reverse strand]
-    $counting{GA_GA_count}++;
-    $alignment_strand = '+';
-    $read_conversion_info = 'GA';
-    $genome_conversion = 'GA';
-
-    ## checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    if ($methylation_call_params->{$sequence_identifier}->{position}-2 >= 0){ ## CHH changed to +2 # 02 02 2012 Changed this to >= from >
-      ### +2 extra base at the 5' end as we are nominally checking the converted reverse strand
-      $non_bisulfite_sequence = substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$methylation_call_params->{$sequence_identifier}->{position}-2,length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence})+2); ## CHH changed to -2/+2
-    }
-    else{
-      $non_bisulfite_sequence = '';
-    }
-  }
-  else{
-    die "Too many bowtie result filehandles\n";
-  }
-
-  $methylation_call_params->{$sequence_identifier}->{alignment_strand} = $alignment_strand;
-  $methylation_call_params->{$sequence_identifier}->{read_conversion} = $read_conversion_info;
-  $methylation_call_params->{$sequence_identifier}->{genome_conversion} = $genome_conversion;
-  $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence} = $non_bisulfite_sequence;
-
-  ### at this point we can also determine the end position of a read
-  $methylation_call_params->{$sequence_identifier}->{end_position} = $methylation_call_params->{$sequence_identifier}->{position}+length($methylation_call_params->{$sequence_identifier}->{bowtie_sequence});
-}
-
-
-sub extract_corresponding_genomic_sequence_single_end_bowtie2{
-  my ($sequence_identifier,$methylation_call_params) = @_;
-
-  my $MD_tag = $methylation_call_params->{$sequence_identifier}->{mismatch_info};
-  my $cigar = $methylation_call_params->{$sequence_identifier}->{CIGAR};
-
-  ### A bisulfite sequence for 1 location in the genome can theoretically be any of the 4 possible converted strands. We are also giving the
-  ### sequence a 'memory' of the conversion we are expecting which we will need later for the methylation call
-
-  ### the alignment_strand information is needed to determine which strand of the genomic sequence we are comparing the read against,
-  ### the read_conversion information is needed to know whether we are looking for C->T or G->A substitutions
-  my $alignment_strand;
-  my $read_conversion_info;
-  my $genome_conversion;
-  ### We are now extracting the corresponding genomic sequence, +2 extra bases at the end (or start) so that we can also make a CpG methylation call and
-  ### in addition make differential calls for Cs in CHG or CHH context if the C happens to be at the last (or first)  position of the actually observed sequence
-  my $non_bisulfite_sequence = '';
-
-  ### Positions in SAM format are 1 based, so we need to subract 1 when getting substrings
-  my $pos = $methylation_call_params->{$sequence_identifier}->{position}-1;
-
-  # parsing CIGAR string
-  my @len = split (/\D+/,$cigar); # storing the length per operation
-  my @ops = split (/\d+/,$cigar); # storing the operation
-  shift @ops; # remove the empty first element
-  die "CIGAR string contained a non-matching number of lengths and operations\n" unless (scalar @len == scalar @ops);
-
-  ### If the sequence aligns best as CT converted reads vs. GA converted genome (OB, index 1) or GA converted reads vs. GA converted genome (CTOB, index 3)
-  if ( ($methylation_call_params->{$sequence_identifier}->{index} == 1) or ($methylation_call_params->{$sequence_identifier}->{index} == 3) ){
-    ## checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    unless ( ($pos-2) >= 0){ # exiting with en empty genomic sequence otherwise
-      $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence} = $non_bisulfite_sequence;
-      return;
-    }
-    $non_bisulfite_sequence .= substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$pos-2,2);
-  }
-  my $indels = 0;	
-
-  foreach (0..$#len){
-    if ($ops[$_] eq 'M'){
-      #extracting genomic sequence
-      $non_bisulfite_sequence .= substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$pos,$len[$_]);
-      # adjusting position
-      $pos += $len[$_];
-    }
-    elsif ($ops[$_] eq 'I'){ # insertion in the read sequence
-      # we simply add padding Ns instead of finding genomic sequence. This will not be used to infer methylation calls
-      $non_bisulfite_sequence .= 'N' x $len[$_];
-      # warn "$non_bisulfite_sequence\n";
-      # position doesn't need to be adjusting
-      $indels += $len[$_]; # adding this to $indels so we can determine the hemming distance for the SAM output (= single-base substitutions (mismatches, insertions, deletions)
-    }
-    elsif ($ops[$_] eq 'D'){ # deletion in the read sequence
-      # we do not add any genomic sequence but only adjust the position
-      $pos += $len[$_];
-      $indels += $len[$_]; # adding this to $indels so we can determine the hemming distance for the SAM output (= single-base substitutions (mismatches, insertions, deletions)
-    }
-    elsif($cigar =~ tr/[NSHPX=]//){ # if these (for standard mapping) illegal characters exist we die
-      die "The CIGAR string contained illegal CIGAR operations in addition to 'M', 'I' and 'D': $cigar\n";
-    }
-    else{
-      die "The CIGAR string contained undefined CIGAR operations in addition to 'M', 'I' and 'D': $cigar\n";
-    }
-  }
-
-  ### If the sequence aligns best as CT converted reads vs. CT converted genome (OT, index 0) or GA converted reads vs. CT converted genome (CTOT, index 2)
-  if ( ($methylation_call_params->{$sequence_identifier}->{index} == 0) or ($methylation_call_params->{$sequence_identifier}->{index} == 2) ){
-    ## checking if the substring will be valid or if we can't extract the sequence because we are right at the edge of a chromosome
-    unless (length($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}}) >= $pos+2){ # exiting with en empty genomic sequence otherwise
-      $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence} = $non_bisulfite_sequence;
-      return;
-    }
-    $non_bisulfite_sequence .= substr ($chromosomes{$methylation_call_params->{$sequence_identifier}->{chromosome}},$pos,2);
-    # print "$methylation_call_params->{$sequence_identifier}->{bowtie_sequence}\n$non_bisulfite_sequence\n";
-  }
-
-
-
-  ### results from CT converted read vs. CT converted genome (+ orientation alignments are reported only)
-  if ($methylation_call_params->{$sequence_identifier}->{index} == 0){
-    ### [Index 0, sequence originated from (converted) forward strand]
-    $counting{CT_CT_count}++;
-    $alignment_strand = '+';
-    $read_conversion_info = 'CT';
-    $genome_conversion = 'CT';
-  }
-
-  ### results from CT converted reads vs. GA converted genome (- orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 1){
-    ### [Index 1, sequence originated from (converted) reverse strand]
-    $counting{CT_GA_count}++;
-    $alignment_strand = '-';
-    $read_conversion_info = 'CT';
-    $genome_conversion = 'GA';
-
-    ### reverse complement!
-    $non_bisulfite_sequence = reverse_complement($non_bisulfite_sequence);
-  }
-
-  ### results from GA converted reads vs. CT converted genome (- orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 2){
-    ### [Index 2, sequence originated from complementary to (converted) forward strand]
-    $counting{GA_CT_count}++;
-    $alignment_strand = '-';
-    $read_conversion_info = 'GA';
-    $genome_conversion = 'CT';
-
-    ### reverse complement!
-    $non_bisulfite_sequence = reverse_complement($non_bisulfite_sequence);
-  }
-
-  ### results from GA converted reads vs. GA converted genome (+ orientation alignments are reported only)
-  elsif ($methylation_call_params->{$sequence_identifier}->{index} == 3){
-    ### [Index 3, sequence originated from complementary to (converted) reverse strand]
-    $counting{GA_GA_count}++;
-    $alignment_strand = '+';
-    $read_conversion_info = 'GA';
-    $genome_conversion = 'GA';
-
-  }
-  else{
-    die "Too many Bowtie 2 result filehandles\n";
-  }
-
-  $methylation_call_params->{$sequence_identifier}->{alignment_strand} = $alignment_strand;
-  $methylation_call_params->{$sequence_identifier}->{read_conversion} = $read_conversion_info;
-  $methylation_call_params->{$sequence_identifier}->{genome_conversion} = $genome_conversion;
-  $methylation_call_params->{$sequence_identifier}->{unmodified_genomic_sequence} = $non_bisulfite_sequence;
-
-  ### the end position of a read is stored in $pos
-  $methylation_call_params->{$sequence_identifier}->{end_position} = $pos;
-  $methylation_call_params->{$sequence_identifier}->{indels} = $indels;
-}
-
-### METHYLATION CALL
-
-sub methylation_call{
-  my ($identifier,$sequence_actually_observed,$genomic_sequence,$read_conversion) = @_;
-  ### splitting both the actually observed sequence and the genomic sequence up into single bases so we can compare them one by one
-  my @seq = split(//,$sequence_actually_observed);
-  my @genomic = split(//,$genomic_sequence);
-  #  print join ("\n",$identifier,$sequence_actually_observed,$genomic_sequence,$read_conversion),"\n";
-  ### Creating a match-string with different characters for non-cytosine bases (disregarding mismatches here), methyl-Cs or non-methyl Cs in either
-  ### CpG, CHH or CHG context
-
-  #################################################################
-  ### . for bases not involving cytosines                       ###
-  ### X for methylated C in CHG context (was protected)         ###
-  ### x for not methylated C in CHG context (was converted)     ###
-  ### H for methylated C in CHH context (was protected)         ###
-  ### h for not methylated C in CHH context (was converted)     ###
-  ### Z for methylated C in CpG context (was protected)         ###
-  ### z for not methylated C in CpG context (was converted)     ###
-  #################################################################
-
-  my @match =();
-  warn "length of \@seq: ",scalar @seq,"\tlength of \@genomic: ",scalar @genomic,"\n" unless (scalar @seq eq (scalar@genomic-2)); ## CHH changed to -2
-  my $methyl_CHH_count = 0;
-  my $methyl_CHG_count = 0;
-  my $methyl_CpG_count = 0;
-  my $unmethylated_CHH_count = 0;
-  my $unmethylated_CHG_count = 0;
-  my $unmethylated_CpG_count = 0;
-
-  if ($read_conversion eq 'CT'){
-    for my $index (0..$#seq) {
-      if ($seq[$index] eq $genomic[$index]) {
-	### The residue can only be a C if it was not converted to T, i.e. protected my methylation
-	if ($genomic[$index] eq 'C') {
-	  ### If the residue is a C we want to know if it was in CpG context or in any other context
-	  my $downstream_base = $genomic[$index+1];
-	
-	  if ($downstream_base eq 'G'){
-	    ++$methyl_CpG_count;
-	    push @match,'Z'; # protected C, methylated, in CpG context
-	  }
-	
-	  else {
-	    ### C in not in CpG-context, determining the second downstream base context
-	    my $second_downstream_base = $genomic[$index+2];
-	
-	    if ($second_downstream_base eq 'G'){
-	      ++$methyl_CHG_count;
-	      push @match,'X'; # protected C, methylated, in CHG context
-	    }
-	    else{
-	      ++$methyl_CHH_count;
-	      push @match,'H'; # protected C, methylated, in CHH context
-	    }
-	  }
-	}
-	else {
-	  push @match, '.';
-	}
-      }
-      elsif ($seq[$index] ne $genomic[$index]) {
-	### for the methylation call we are only interested in mismatches involving cytosines (in the genomic sequence) which were converted into Ts
-	### in the actually observed sequence
-	if ($genomic[$index] eq 'C' and $seq[$index] eq 'T') {
-	  ### If the residue was converted to T we want to know if it was in CpG, CHG or CHH  context
-	  my $downstream_base = $genomic[$index+1];
-	
-	  if ($downstream_base eq 'G'){
-	    ++$unmethylated_CpG_count;
-	    push @match,'z'; # converted C, not methylated, in CpG context
-	  }
-
-	  else{
-	    ### C in not in CpG-context, determining the second downstream base context
-	    my $second_downstream_base = $genomic[$index+2];
-	
-	    if ($second_downstream_base eq 'G'){
-	      ++$unmethylated_CHG_count;
-	      push @match,'x'; # converted C, not methylated, in CHG context
-	    }
-	    else{
-	      ++$unmethylated_CHH_count;
-	      push @match,'h'; # converted C, not methylated, in CHH context
-	    }
-	  }
-	}
-	### all other mismatches are not of interest for a methylation call
-	else {
-	  push @match,'.';
-	}
-      }
-      else{
-	die "There can be only 2 possibilities\n";
-      }
-    }
-  }
-  elsif ($read_conversion eq 'GA'){
-    # print join ("\n",'***',$identifier,$sequence_actually_observed,$genomic_sequence,$read_conversion,'***'),"\n";
-
-    for my $index (0..$#seq) {
-      if ($seq[$index] eq $genomic[$index+2]) {
-	### The residue can only be a G if the C on the other strand was not converted to T, i.e. protected my methylation
-	if ($genomic[$index+2] eq 'G') {
-	  ### If the residue is a G we want to know if the C on the other strand was in CpG, CHG or CHH context, therefore we need
-	  ### to look if the base upstream is a C
-
-	  my $upstream_base = $genomic[$index+1];
-	
-	  if ($upstream_base eq 'C'){
-	    ++$methyl_CpG_count;
-	    push @match,'Z'; # protected C on opposing strand, methylated, in CpG context
-	  }
-
-	  else{
-	    ### C in not in CpG-context, determining the second upstream base context
-	    my $second_upstream_base = $genomic[$index];
-	
-	    if ($second_upstream_base eq 'C'){
-	      ++$methyl_CHG_count;
-	      push @match,'X'; # protected C on opposing strand, methylated, in CHG context
-	    }
-	    else{
-	      ++$methyl_CHH_count;
-	      push @match,'H'; # protected C on opposing strand, methylated, in CHH context
-	    }
-	  }
-	}
-	else{
-	  push @match, '.';
-	}
-      }
-      elsif ($seq[$index] ne $genomic[$index+2]) {
-	### for the methylation call we are only interested in mismatches involving cytosines (in the genomic sequence) which were converted to Ts
-	### on the opposing strand, so G to A conversions in the actually observed sequence
-	if ($genomic[$index+2] eq 'G' and $seq[$index] eq 'A') {
-	  ### If the C residue on the opposing strand was converted to T then we will see an A in the currently observed sequence. We want to know if
-	  ### the C on the opposing strand was it was in CpG, CHG or CHH context, therefore we need to look one (or two) bases upstream!
-
-	  my $upstream_base = $genomic[$index+1];
-
-	  if ($upstream_base eq 'C'){
-	    ++$unmethylated_CpG_count;
-	    push @match,'z'; # converted C on opposing strand, not methylated, in CpG context
-	  }
-
-	  else{
-	    ### C in not in CpG-context, determining the second upstream base context
-	    my $second_upstream_base = $genomic[$index];
-	
-	    if ($second_upstream_base eq 'C'){
-	      ++$unmethylated_CHG_count;
-	      push @match,'x'; # converted C on opposing strand, not methylated, in CHG context
-	    }
-	    else{
-	      ++$unmethylated_CHH_count;
-	      push @match,'h'; # converted C on opposing strand, not methylated, in CHH context
-	    }
-	  }
-	}
-	### all other mismatches are not of interest for a methylation call
-	else {
-	  push @match,'.';
-	}
-      }
-      else{
-	die "There can be only 2 possibilities\n";
-      }
-    }
-  }
-  else{
-    die "Strand conversion info is required to perform a methylation call\n";
-  }
-
-  my $methylation_call = join ("",@match);
-
-  $counting{total_meCHH_count} += $methyl_CHH_count;
-  $counting{total_meCHG_count} += $methyl_CHG_count;
-  $counting{total_meCpG_count} += $methyl_CpG_count;
-  $counting{total_unmethylated_CHH_count} += $unmethylated_CHH_count;
-  $counting{total_unmethylated_CHG_count} += $unmethylated_CHG_count;
-  $counting{total_unmethylated_CpG_count} += $unmethylated_CpG_count;
-
-  # print "\n$sequence_actually_observed\n$genomic_sequence\n",@match,"\n$read_conversion\n\n";
-  return $methylation_call;
-}
-
-sub read_genome_into_memory{
-    ## working directoy
-    my $cwd = shift;
-    ## reading in and storing the specified genome in the %chromosomes hash
-    chdir ($genome_folder) or die "Can't move to $genome_folder: $!";
-    print "Now reading in and storing sequence information of the genome specified in: $genome_folder\n\n";
-
-    my @chromosome_filenames =  <*.fa>;
-
-    ### if there aren't any genomic files with the extension .fa we will look for files with the extension .fasta
-    unless (@chromosome_filenames){
-      @chromosome_filenames =  <*.fasta>;
-    }
-
-    unless (@chromosome_filenames){
-      die "The specified genome folder $genome_folder does not contain any sequence files in FastA format (with .fa or .fasta file extensions)\n";
-    }
-
-    foreach my $chromosome_filename (@chromosome_filenames){
-
-	open (CHR_IN,$chromosome_filename) or die "Failed to read from sequence file $chromosome_filename $!\n";
-	### first line needs to be a fastA header
-	my $first_line = <CHR_IN>;
-	chomp $first_line;
-	$first_line =~ s/\r//;
-	
-	### Extracting chromosome name from the FastA header
-	my $chromosome_name = extract_chromosome_name($first_line);
-	
-	my $sequence;
-	while (<CHR_IN>){
-	    chomp;
-	    $_ =~ s/\r//;
-	    if ($_ =~ /^>/){
-		### storing the previous chromosome in the %chromosomes hash, only relevant for Multi-Fasta-Files (MFA)
-		if (exists $chromosomes{$chromosome_name}){
-		    print "chr $chromosome_name (",length $sequence ," bp)\n";
-		    die "Exiting because chromosome name already exists. Please make sure all chromosomes have a unique name!\n";
-		}
-		else {
-		    if (length($sequence) == 0){
-			warn "Chromosome $chromosome_name in the multi-fasta file $chromosome_filename did not contain any sequence information!\n";
-		    }
-		    print "chr $chromosome_name (",length $sequence ," bp)\n";
-		    $chromosomes{$chromosome_name} = $sequence;
-		}
-		### resetting the sequence variable
-		$sequence = '';
-		### setting new chromosome name
-		$chromosome_name = extract_chromosome_name($_);
-	    }
-	    else{
-		$sequence .= uc$_;
-	    }
-	}
-	
-	if (exists $chromosomes{$chromosome_name}){
-	    print "chr $chromosome_name (",length $sequence ," bp)\t";
-	    die "Exiting because chromosome name already exists. Please make sure all chromosomes have a unique name.\n";
-	}
-	else{
-	    if (length($sequence) == 0){
-		warn "Chromosome $chromosome_name in the file $chromosome_filename did not contain any sequence information!\n";
-	    }
-	    print "chr $chromosome_name (",length $sequence ," bp)\n";
-	    $chromosomes{$chromosome_name} = $sequence;
-	}
-    }
-    print "\n";
-    chdir $cwd or die "Failed to move to directory $cwd\n";
-}
-
-sub extract_chromosome_name {
-    ## Bowtie seems to extract the first string after the inition > in the FASTA file, so we are doing this as well
-    my $fasta_header = shift;
-    if ($fasta_header =~ s/^>//){
-	my ($chromosome_name) = split (/\s+/,$fasta_header);
-	return $chromosome_name;
-    }
-    else{
-	die "The specified chromosome ($fasta_header) file doesn't seem to be in FASTA format as required!\n";
-    }
-}
-
-sub reverse_complement{
-  my $sequence = shift;
-  $sequence =~ tr/CATG/GTAC/;
-  $sequence = reverse($sequence);
-  return $sequence;
-}
-
-sub biTransformFastAFiles {
-  my $file = shift;
-  my ($dir,$filename);
-  if ($file =~ /\//){
-    ($dir,$filename) = $file =~ m/(.*\/)(.*)$/;
-  }
-  else{
-    $filename = $file;
-  }
-
-  ### gzipped version of the infile
-  if ($file =~ /\.gz$/){
-    open (IN,"zcat $file |") or die "Couldn't read from file $file: $!\n";
-  }
-  else{
-    open (IN,$file) or die "Couldn't read from file $file: $!\n";
-  }
-
-  if ($skip){
-    warn "Skipping the first $skip reads from $file\n";
-    sleep (1);
-  }
-  if ($upto){
-    warn "Processing reads up to sequence no. $upto from $file\n";
-    sleep (1);
-  }
-
-  my $C_to_T_infile = my $G_to_A_infile = $filename;
-  $C_to_T_infile =~ s/$/_C_to_T.fa/;
-  $G_to_A_infile =~ s/$/_G_to_A.fa/;
-  print "Writing a C -> T converted version of the input file $filename to $temp_dir$C_to_T_infile\n";
-  open (CTOT,'>',"$temp_dir$C_to_T_infile") or die "Couldn't write to file $!\n";
-
-  unless ($directional){
-    print "Writing a G -> A converted version of the input file $filename to $temp_dir$G_to_A_infile\n";
-    open (GTOA,'>',"$temp_dir$G_to_A_infile") or die "Couldn't write to file $!\n";
-  }
-
-  my $count = 0;
-  while (1){
-    my $header = <IN>;
-    my $sequence= <IN>;
-    last unless ($header and $sequence);
-
-    $header = fix_IDs($header); # this is to avoid problems with truncated read ID when they contain white spaces
-
-    ++$count;
-
-    if ($skip){
-      next unless ($count > $skip);
-    }
-    if ($upto){
-      last if ($count > $upto);
-    }
-
-    $sequence = uc$sequence; # make input file case insensitive
-
-    # detecting if the input file contains tab stops, as this is likely to result in no alignments
-    if (index($header,"\t") != -1){
-      $seqID_contains_tabs++;
-    }
-
-    ### small check if the sequence seems to be in FastA format
-    die "Input file doesn't seem to be in FastA format at sequence $count: $!\n" unless ($header =~ /^>.*/);
-
-    my $sequence_C_to_T = $sequence;
-    $sequence_C_to_T =~ tr/C/T/;
-    print CTOT "$header$sequence_C_to_T";
-
-    unless ($directional){
-      my $sequence_G_to_A = $sequence;
-      $sequence_G_to_A =~ tr/G/A/;
-      print GTOA "$header$sequence_G_to_A";
-    }
-  }
-  if ($directional){
-    print "\nCreated C -> T converted versions of the FastA file $filename ($count sequences in total)\n\n";
-  }
-  else{
-    print "\nCreated C -> T as well as G -> A converted versions of the FastA file $filename ($count sequences in total)\n\n";
-  }
-  return ($C_to_T_infile,$G_to_A_infile);
-}
-
-sub biTransformFastAFiles_paired_end {
-  my ($file,$read_number) = @_;
-
-  my ($dir,$filename);
-  if ($file =~ /\//){
-    ($dir,$filename) = $file =~ m/(.*\/)(.*)$/;
-  }
-  else{
-    $filename = $file;
-  }
-
-  ### gzipped version of the infile
-  if ($file =~ /\.gz$/){
-    open (IN,"zcat $file |") or die "Couldn't read from file $file: $!\n";
-  }
-  else{
-    open (IN,$file) or die "Couldn't read from file $file: $!\n";
-  }
-
-  if ($skip){
-    warn "Skipping the first $skip reads from $file\n";
-    sleep (1);
-  }
-  if ($upto){
-    warn "Processing reads up to sequence no. $upto from $file\n";
-    sleep (1);
-  }
-
-  my $C_to_T_infile = my $G_to_A_infile = $filename;
-  $C_to_T_infile =~ s/$/_C_to_T.fa/;
-  $G_to_A_infile =~ s/$/_G_to_A.fa/;
-
-  if ($directional){
-    if ($read_number == 1){
-      print "Writing a C -> T converted version of the input file $filename to $temp_dir$C_to_T_infile\n";
-      open (CTOT,'>',"$temp_dir$C_to_T_infile") or die "Couldn't write to file $!\n";
-    }
-    elsif ($read_number == 2){
-      print "Writing a G -> A converted version of the input file $filename to $temp_dir$G_to_A_infile\n";
-      open (GTOA,'>',"$temp_dir$G_to_A_infile") or die "Couldn't write to file $!\n";
-    }
-    else{
-      die "Read number needs to be 1 or 2, but was: $read_number\n\n";
-    }
-  }
-  else{ # all four strand output
-    print "Writing a C -> T converted version of the input file $filename to $temp_dir$C_to_T_infile\n";
-    print "Writing a G -> A converted version of the input file $filename to $temp_dir$G_to_A_infile\n";
-    open (CTOT,'>',"$temp_dir$C_to_T_infile") or die "Couldn't write to file $!\n";
-    open (GTOA,'>',"$temp_dir$G_to_A_infile") or die "Couldn't write to file $!\n";
-  }
-
-  my $count = 0;
-
-  while (1){
-    my $header = <IN>;
-    my $sequence= <IN>;
-    last unless ($header and $sequence);
-
-    $header = fix_IDs($header); # this is to avoid problems with truncated read ID when they contain white spaces
-
-    ++$count;
-
-    if ($skip){
-      next unless ($count > $skip);
-    }
-    if ($upto){
-      last if ($count > $upto);
-    }
-
-    $sequence = uc$sequence; # make input file case insensitive
-
-    # detecting if the input file contains tab stops, as this is likely to result in no alignments
-    if (index($header,"\t") != -1){
-      $seqID_contains_tabs++;
-    }
-
-    ## small check if the sequence seems to be in FastA format
-    die "Input file doesn't seem to be in FastA format at sequence $count: $!\n" unless ($header =~ /^>.*/);
-
-    if ($read_number == 1){
-      if ($bowtie2){
-	$header =~ s/$/\/1\/1/;
-      }
-      else{	
-	$header =~ s/$/\/1/;
-      }
-    }
-    elsif ($read_number == 2){
-      if ($bowtie2){
-	$header =~ s/$/\/2\/2/;
-      }
-      else{
-	$header =~ s/$/\/2/;
-      }
-    }
-    else{
-      die "Read number needs to be 1 or 2, but was: $read_number\n\n";
-    }
-    my $sequence_C_to_T = my $sequence_G_to_A = $sequence;
-
-    $sequence_C_to_T =~ tr/C/T/;
-    $sequence_G_to_A =~ tr/G/A/;
-
-    if ($directional){
-
-      if ($read_number == 1){
-	print CTOT "$header$sequence_C_to_T";
-      }
-      elsif ($read_number == 2){
-	print GTOA "$header$sequence_G_to_A";
-      }
-    }
-    else{
-      print CTOT "$header$sequence_C_to_T";
-      print GTOA "$header$sequence_G_to_A";
-    }
-  }
-
-  if ($directional){
-    if ($read_number == 1){
-      print "\nCreated C -> T converted version of the FastA file $filename ($count sequences in total)\n\n";
-    }
-    else{
-      print "\nCreated G -> A converted version of the FastA file $filename ($count sequences in total)\n\n";
-    }
-  }
-  else{
-    print "\nCreated C -> T as well as G -> A converted versions of the FastA file $filename ($count sequences in total)\n\n";
-  }
-
-  if ($directional){
-    if ($read_number == 1){
-      return ($C_to_T_infile);
-    }
-    else{
-      return ($G_to_A_infile);
-    }
-  }
-  else{
-    return ($C_to_T_infile,$G_to_A_infile);
-  }
-}
-
-
-sub biTransformFastQFiles {
-  my $file = shift;
-  my ($dir,$filename);
-  if ($file =~ /\//){
-    ($dir,$filename) = $file =~ m/(.*\/)(.*)$/;
-  }
-  else{
-    $filename = $file;
-  }
-
-  ### gzipped version of the infile
-  if ($file =~ /\.gz$/){
-    open (IN,"zcat $file |") or die "Couldn't read from file $file: $!\n";
-  }
-  else{
-    open (IN,$file) or die "Couldn't read from file $file: $!\n";
-  }
-
-  if ($skip){
-    warn "Skipping the first $skip reads from $file\n";
-    sleep (1);
-  }
-  if ($upto){
-    warn "Processing reads up to sequence no. $upto from $file\n";
-    sleep (1);
-  }
-
-  my $C_to_T_infile = my $G_to_A_infile = $filename;
-
-  $C_to_T_infile =~ s/$/_C_to_T.fastq/;
-  print "Writing a C -> T converted version of the input file $filename to $temp_dir$C_to_T_infile\n";
-  open (CTOT,'>',"$temp_dir$C_to_T_infile") or die "Couldn't write to file $!\n";
-
-  unless ($directional){
-    $G_to_A_infile =~ s/$/_G_to_A.fastq/;
-    print "Writing a G -> A converted version of the input file $filename to $temp_dir$G_to_A_infile\n";
-    open (GTOA,'>',"$temp_dir$G_to_A_infile") or die "Couldn't write to file $!\n";
-  }
-
-  my $count = 0;
-  while (1){
-    my $identifier = <IN>;
-    my $sequence = <IN>;
-    my $identifier2 = <IN>;
-    my $quality_score = <IN>;
-    last unless ($identifier and $sequence and $identifier2 and $quality_score);
-
-    $identifier = fix_IDs($identifier); # this is to avoid problems with truncated read ID when they contain white spaces
-
-    ++$count;
-
-    if ($skip){
-      next unless ($count > $skip);
-    }
-    if ($upto){
-      last if ($count > $upto);
-    }
-
-    $sequence = uc$sequence; # make input file case insensitive
-
-    # detecting if the input file contains tab stops, as this is likely to result in no alignments
-    if (index($identifier,"\t") != -1){
-      $seqID_contains_tabs++;
-    }
-
-    ## small check if the sequence file appears to be a FastQ file
-    if ($identifier !~ /^\@/ or $identifier2 !~ /^\+/){
-      die "Input file doesn't seem to be in FastQ format at sequence $count: $!\n";
-    }
-
-    my $sequence_C_to_T = $sequence;
-    $sequence_C_to_T =~ tr/C/T/;
-    print CTOT join ('',$identifier,$sequence_C_to_T,$identifier2,$quality_score);
-
-    unless ($directional){
-      my $sequence_G_to_A = $sequence;
-      $sequence_G_to_A =~ tr/G/A/;
-      print GTOA join ('',$identifier,$sequence_G_to_A,$identifier2,$quality_score);
-    }
-  }
-
-  if ($directional){
-    print "\nCreated C -> T converted versions of the FastQ file $filename ($count sequences in total)\n\n";
-  }
-  else{
-    print "\nCreated C -> T as well as G -> A converted versions of the FastQ file $filename ($count sequences in total)\n\n";
-  }
-
-  return ($C_to_T_infile,$G_to_A_infile);
-}
-
-sub biTransformFastQFiles_paired_end {
-  my ($file,$read_number) = @_;
-  my ($dir,$filename);
-
-  if ($file =~ /\//){
-    ($dir,$filename) = $file =~ m/(.*\/)(.*)$/;
-  }
-  else{
-    $filename = $file;
-  }
-
-  ### gzipped version of the infile
-  if ($file =~ /\.gz$/){
-    open (IN,"zcat $file |") or die "Couldn't read from file $file: $!\n";
-  }
-  else{
-    open (IN,$file) or die "Couldn't read from file $file: $!\n";
-  }
-
-  if ($skip){
-    warn "Skipping the first $skip reads from $file\n";
-    sleep (1);
-  }
-  if ($upto){
-    warn "Processing reads up to sequence no. $upto from $file\n";
-    sleep (1);
-  }
-
-  my $C_to_T_infile = my $G_to_A_infile = $filename;
-  $C_to_T_infile =~ s/$/_C_to_T.fastq/;
-  $G_to_A_infile =~ s/$/_G_to_A.fastq/;
-
-  if ($directional){
-    if ($read_number == 1){
-      print "Writing a C -> T converted version of the input file $filename to $temp_dir$C_to_T_infile\n";
-      open (CTOT,'>',"$temp_dir$C_to_T_infile") or die "Couldn't write to file $!\n";
-    }
-    elsif ($read_number == 2){
-      print "Writing a G -> A converted version of the input file $filename to $temp_dir$G_to_A_infile\n";
-      open (GTOA,'>',"$temp_dir$G_to_A_infile") or die "Couldn't write to file $!\n";
-    }
-    else{
-      die "Read number needs to be 1 or 2, but was $read_number!\n\n";
-    }
-  }
-  else{
-    print "Writing a C -> T converted version of the input file $filename to $temp_dir$C_to_T_infile\n";
-    print "Writing a G -> A converted version of the input file $filename to $temp_dir$G_to_A_infile\n";
-    open (CTOT,'>',"$temp_dir$C_to_T_infile") or die "Couldn't write to file $!\n";
-    open (GTOA,'>',"$temp_dir$G_to_A_infile") or die "Couldn't write to file $!\n";
-  }
-
-  my $count = 0;
-
-  while (1){
-    my $identifier = <IN>;
-    my $sequence = <IN>;
-    my $identifier2 = <IN>;
-    my $quality_score = <IN>;
-    last unless ($identifier and $sequence and $identifier2 and $quality_score);
-    ++$count;
-
-    $identifier = fix_IDs($identifier); # this is to avoid problems with truncated read ID when they contain white spaces
-
-    if ($skip){
-      next unless ($count > $skip);
-    }
-    if ($upto){
-      last if ($count > $upto);
-    }
-
-    $sequence= uc$sequence; # make input file case insensitive
-
-    ## small check if the sequence file appears to be a FastQ file
-    if ($identifier !~ /^\@/ or $identifier2 !~ /^\+/){
-      die "Input file doesn't seem to be in FastQ format at sequence $count: $!\n";
-    }
-    my $sequence_C_to_T = my $sequence_G_to_A = $sequence;
-
-    if ($read_number == 1){
-      if ($bowtie2){
-	$identifier =~ s/$/\/1\/1/;
-      }
-      else{
-	$identifier =~ s/$/\/1/;
-      }
-    }
-    elsif ($read_number == 2){
-      if ($bowtie2){
-	$identifier =~ s/$/\/2\/2/;
-       }
-      else{
-	$identifier =~ s/$/\/2/;
-      }
-    }
-    else{
-      die "Read number needs to be 1 or 2\n";
-    }
-
-    $sequence_C_to_T =~ tr/C/T/;
-    $sequence_G_to_A =~ tr/G/A/;
-
-    if ($directional){
-      if ($read_number == 1){
-	print CTOT join ('',$identifier,$sequence_C_to_T,$identifier2,$quality_score);
-      }
-      else{
-	print GTOA join ('',$identifier,$sequence_G_to_A,$identifier2,$quality_score);
-      }
-    }
-    else{
-      print CTOT join ('',$identifier,$sequence_C_to_T,$identifier2,$quality_score);
-      print GTOA join ('',$identifier,$sequence_G_to_A,$identifier2,$quality_score);
-    }
-  }
-
-  if ($directional){
-    if ($read_number == 1){
-      print "\nCreated C -> T converted version of the FastQ file $filename ($count sequences in total)\n\n";
-    }
-    else{
-      print "\nCreated G -> A converted version of the FastQ file $filename ($count sequences in total)\n\n";
-    }
-  }
-  else{
-    print "\nCreated C -> T as well as G -> A converted versions of the FastQ file $filename ($count sequences in total)\n\n";
-  }
-  if ($directional){
-    if ($read_number == 1){
-      return ($C_to_T_infile);
-    }
-    else{
-      return ($G_to_A_infile);
-    }
-  }
-  else{
-    return ($C_to_T_infile,$G_to_A_infile);
-  }
-}
-
-sub fix_IDs{
-  my $id = shift;
-  $id =~ s/[ \t]+/_/g; # replace spaces or tabs with underscores
-  return $id;
-}
-
-sub ensure_sensical_alignment_orientation_single_end{
-  my $index = shift; # index number if the sequence produced an alignment
-  my $strand = shift;
-  ###  setting $orientation to 1 if it is in the correct orientation, and leave it 0 if it is the nonsensical wrong one
-  my $orientation = 0;
-  ##############################################################################################################
-  ## FORWARD converted read against FORWARD converted genome (read: C->T.....C->T..      genome:C->T.......C->T)
-  ## here we only want reads in the forward (+) orientation
-  if ($fhs[$index]->{name} eq 'CTreadCTgenome') {
-    ### if the alignment is (+) we count it, and return 1 for a correct orientation
-    if ($strand eq '+') {
-      $fhs[$index]->{seen}++;
-      $orientation = 1;
-      return $orientation;
-    }
-    ### if the orientation equals (-) the alignment is nonsensical
-    elsif ($strand eq '-') {
-      $fhs[$index]->{wrong_strand}++;
-      return $orientation;
-    }
-  }
-  ###############################################################################################################
-  ## FORWARD converted read against reverse converted genome (read: C->T.....C->T..      genome: G->A.......G->A)
-  ## here we only want reads in the forward (-) orientation
-  elsif ($fhs[$index]->{name} eq 'CTreadGAgenome') {
-    ### if the alignment is (-) we count it and return 1 for a correct orientation
-    if ($strand eq '-') {
-      $fhs[$index]->{seen}++;
-      $orientation = 1;
-      return $orientation;
-    }
-    ### if the orientation equals (+) the alignment is nonsensical
-    elsif ($strand eq '+') {
-      $fhs[$index]->{wrong_strand}++;
-      return $orientation;
-    }
-  }
-  ###############################################################################################################
-  ## Reverse converted read against FORWARD converted genome (read: G->A.....G->A..      genome: C->T.......C->T)
-  ## here we only want reads in the forward (-) orientation
-  elsif ($fhs[$index]->{name} eq 'GAreadCTgenome') {
-    ### if the alignment is (-) we count it and return 1 for a correct orientation
-    if ($strand eq '-') {
-      $fhs[$index]->{seen}++;
-      $orientation = 1;
-      return $orientation;
-    }
-    ### if the orientation equals (+) the alignment is nonsensical
-    elsif ($strand eq '+') {
-      $fhs[$index]->{wrong_strand}++;
-      return $orientation;
-    }
-  }
-  ###############################################################################################################
-  ## Reverse converted read against reverse converted genome (read: G->A.....G->A..      genome: G->A.......G->A)
-  ## here we only want reads in the forward (+) orientation
-  elsif ($fhs[$index]->{name} eq 'GAreadGAgenome') {
-    ### if the alignment is (+) we count it and return 1 for a correct orientation
-    if ($strand eq '+') {
-      $fhs[$index]->{seen}++;
-      $orientation = 1;
-      return $orientation;
-    }
-    ### if the orientation equals (-) the alignment is nonsensical
-    elsif ($strand eq '-') {
-      $fhs[$index]->{wrong_strand}++;
-      return $orientation;
-    }
-  } else{
-    die "One of the above conditions must be true\n";
-  }
-}
-
-sub ensure_sensical_alignment_orientation_paired_ends{
-  my ($index,$id_1,$strand_1,$id_2,$strand_2) = @_; # index number if the sequence produced an alignment
-  ###  setting $orientation to 1 if it is in the correct orientation, and leave it 0 if it is the nonsensical wrong one
-  my $orientation = 0;
-  ##############################################################################################################
-  ## [Index 0, sequence originated from (converted) forward strand]
-  ## CT converted read 1
-  ## GA converted read 2
-  ## CT converted genome
-  ## here we only want read 1 in (+) orientation and read 2 in (-) orientation
-  if ($fhs[$index]->{name} eq 'CTread1GAread2CTgenome') {
-    ### if the paired-end alignment is read1 (+) and read2 (-) we count it, and return 1 for a correct orientation
-    if ($id_1 =~ /1$/ and $strand_1 eq '+' and $id_2 =~ /2$/ and $strand_2 eq '-') {
-      $fhs[$index]->{seen}++;
-      $orientation = 1;
-      return $orientation;
-    }
-    ### if the read 2 is in (+) orientation and read 1 in (-) the alignment is nonsensical
-    elsif ($id_1 =~ /2$/ and $strand_1 eq '+' and $id_2 =~ /1$/ and $strand_2 eq '-') {
-      $fhs[$index]->{wrong_strand}++;
-      return $orientation;
-    }
-    else{
-      die "id1: $id_1\tid2: $id_2\tThis should be impossible\n";
-    }
-  }
-  ###############################################################################################################
-  ## [Index 1, sequence originated from (converted) reverse strand]
-  ## GA converted read 1
-  ## CT converted read 2
-  ## GA converted genome
-  ## here we only want read 1 in (+) orientation and read 2 in (-) orientation
-  elsif ($fhs[$index]->{name} eq 'GAread1CTread2GAgenome') {
-    ### if the paired-end alignment is read1 (+) and read2 (-) we count it, and return 1 for a correct orientation
-    if ($id_1 =~ /1$/ and $strand_1 eq '+' and $id_2 =~ /2$/ and $strand_2 eq '-') {
-      $fhs[$index]->{seen}++;
-      $orientation = 1;
-      return $orientation;
-    }
-    ### if the read 2 is in (+) orientation and read 1 in (-) the alignment is nonsensical
-    elsif ($id_1 =~ /2$/ and $strand_1 eq '+' and $id_2 =~ /1$/ and $strand_2 eq '-') {
-      $fhs[$index]->{wrong_strand}++;
-      return $orientation;
-    }
-    else{
-      die "id1: $id_1\tid2: $id_2\tThis should be impossible\n";
-    }
-  }
-  ###############################################################################################################
-  ## [Index 2, sequence originated from complementary to (converted) forward strand]
-  ## GA converted read 1
-  ## CT converted read 2
-  ## CT converted genome
-  ## here we only want read 1 in (-) orientation and read 2 in (+) orientation
-  elsif ($fhs[$index]->{name} eq 'GAread1CTread2CTgenome') {
-    ### if the paired-end alignment is read1 (-) and read2 (+) we count it, and return 1 for a correct orientation
-    if ($id_1 =~ /2$/ and $strand_1 eq '+' and $id_2 =~ /1$/ and $strand_2 eq '-') {
-      $fhs[$index]->{seen}++;
-      $orientation = 1;
-      return $orientation;
-    }
-    ### if the read 2 is in (+) orientation and read 1 in (-) the alignment is nonsensical
-    elsif ($id_1 =~ /1$/ and $strand_1 eq '+' and $id_2 =~ /2$/ and $strand_2 eq '-') {
-      $fhs[$index]->{wrong_strand}++;
-      return $orientation;
-    }
-    else{
-      die "id1: $id_1\tid2: $id_2\tThis should be impossible\n";
-    }
-  }
-  ###############################################################################################################
-  ## [Index 3, sequence originated from complementary to (converted) reverse strand]
-  ## CT converted read 1
-  ## GA converted read 2
-  ## GA converted genome
-  ## here we only want read 1 in (+) orientation and read 2 in (-) orientation
-  elsif ($fhs[$index]->{name} eq 'CTread1GAread2GAgenome') {
-    ### if the paired-end alignment is read1 (-) and read2 (+) we count it, and return 1 for a correct orientation
-    if ($id_1 =~ /2$/ and $strand_1 eq '+' and $id_2 =~ /1$/ and $strand_2 eq '-') {
-      $fhs[$index]->{seen}++;
-      $orientation = 1;
-      return $orientation;
-    }
-    ### if the read 2 is in (+) orientation and read 1 in (-) the alignment is nonsensical
-    elsif ($id_1 =~ /1$/ and $strand_1 eq '+' and $id_2 =~ /2$/ and $strand_2 eq '-') {
-      $fhs[$index]->{wrong_strand}++;
-      return $orientation;
-    }
-    else{
-      die "id1: $id_1\tid2: $id_2\tThis should be impossible\n";
-    }
-  }
-  else{
-    die "One of the above conditions must be true\n";
-  }
-}
-
-#####################################################################################################################################################
-
-### Bowtie 1 (default) | PAIRED-END | FASTA
-
-sub paired_end_align_fragments_to_bisulfite_genome_fastA {
-
-  my ($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2) = @_;
-
-  if ($directional){
-    print "Input files are $C_to_T_infile_1 and $G_to_A_infile_2 (FastA)\n";
-  }
-  else{
-    print "Input files are $C_to_T_infile_1 and $G_to_A_infile_1 and $C_to_T_infile_2 and $G_to_A_infile_2 (FastA)\n";
-  }
-
-  ## Now starting up to 4 instances of Bowtie feeding in the converted sequence files and reading in the first line of the bowtie output, and storing it in the
-  ## data structure above
-  if ($directional){
-    warn "Now running 2 instances of Bowtie against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-  else{
-    warn "Now running 4 individual instances of Bowtie against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-
-  foreach my $fh (@fhs) {
-
-    if ($directional){
-      unless ($fh->{inputfile_1}){
-	$fh->{last_seq_id} = undef;
-	$fh->{last_line_1} = undef;
-	$fh->{last_line_2} = undef;
-	next;
-      }
-    }
-
-    my $bt_options = $bowtie_options;
-    if ($fh->{name} eq 'CTread1GAread2CTgenome' or $fh->{name} eq 'GAread1CTread2GAgenome'){
-      $bt_options .= ' --norc'; ### ensuring the alignments are only reported in a sensible manner
-    }
-    else {
-      $bt_options .= ' --nofw';
-    }
-
-    warn "Now starting a Bowtie paired-end alignment for $fh->{name} (reading in sequences from $temp_dir$fh->{inputfile_1} and $temp_dir$fh->{inputfile_2}, with the options: $bt_options)\n";
-    open ($fh->{fh},"$path_to_bowtie $bt_options $fh->{bisulfiteIndex} -1 $temp_dir$fh->{inputfile_1} -2 $temp_dir$fh->{inputfile_2} |") or die "Can't open pipe to bowtie: $!";
-
-    my $line_1 = $fh->{fh}->getline();
-    my $line_2 = $fh->{fh}->getline();
-
-    # if Bowtie produces an alignment we store the first line of the output
-    if ($line_1 and $line_2) {
-      chomp $line_1;
-      chomp $line_2;
-      my $id_1 = (split(/\t/,$line_1))[0]; # this is the first element of the first bowtie output line (= the sequence identifier)
-      my $id_2 = (split(/\t/,$line_2))[0]; # this is the first element of the second bowtie output line
-
-      ### Bowtie always reports the alignment with the smaller chromosomal position first. This can be either sequence 1 or sequence 2.
-      ### We will thus identify which sequence was read 1 and store this ID as last_seq_id
-
-      if ($id_1 =~ s/\/1$//){ # removing the read 1 tag if present
-	$fh->{last_seq_id} = $id_1;
-      }
-      elsif ($id_2 =~ s/\/1$//){ # removing the read 1 tag if present
-	$fh->{last_seq_id} = $id_2;
-      }
-      else{
-	die "Either the first or the second id need to be read 1! ID1 was: $id_1; ID2 was: $id_2\n";
-      }
-
-      $fh->{last_line_1} = $line_1; # this contains either read 1 or read 2
-      $fh->{last_line_2} = $line_2; # this contains either read 1 or read 2
-      warn "Found first alignment:\n$fh->{last_line_1}\n$fh->{last_line_2}\n";
-    }
-    # otherwise we just initialise last_seq_id and last_lines as undefined
-    else {
-      print "Found no alignment, assigning undef to last_seq_id and last_lines\n";
-      $fh->{last_seq_id} = undef;
-      $fh->{last_line_1} = undef;
-      $fh->{last_line_2} = undef;
-    }
-  }
-}
-
-### Bowtie 2 | PAIRED-END | FASTA
-
-sub paired_end_align_fragments_to_bisulfite_genome_fastA_bowtie2 {
-  my ($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2) = @_;
-  if ($directional){
-    print "Input files are $C_to_T_infile_1 and $G_to_A_infile_2 (FastA)\n";
-  }
-  else{
-    print "Input files are $C_to_T_infile_1 and $G_to_A_infile_1 and $C_to_T_infile_2 and $G_to_A_infile_2 (FastA)\n";
-  }
-
-  ## Now starting up to 4 instances of Bowtie feeding in the converted sequence files and reading in the first line of the bowtie output, and storing it in the
-  ## data structure above
-  if ($directional){
-    warn "Now running 2 instances of Bowtie 2 against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-  else{
-    warn "Now running 4 individual instances of Bowtie 2 against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-
-  foreach my $fh (@fhs) {
-
-    if ($directional){
-      unless ($fh->{inputfile_1}){
-	$fh->{last_seq_id} = undef;
-	$fh->{last_line_1} = undef;
-	$fh->{last_line_2} = undef;
-	next;
-      }
-    }
-
-    my $bt2_options = $bowtie_options;
-    if ($fh->{name} eq 'CTread1GAread2CTgenome' or $fh->{name} eq 'GAread1CTread2GAgenome'){
-      $bt2_options .= ' --norc'; ### ensuring the alignments are only reported in a sensible manner
-    }
-    else {
-      $bt2_options .= ' --nofw';
-    }
-
-    warn "Now starting a Bowtie 2 paired-end alignment for $fh->{name} (reading in sequences from $temp_dir$fh->{inputfile_1} and $temp_dir$fh->{inputfile_2}, with the options: $bt2_options))\n";
-    open ($fh->{fh},"$path_to_bowtie $bt2_options $fh->{bisulfiteIndex} -1 $temp_dir$fh->{inputfile_1} -2 $temp_dir$fh->{inputfile_2} |") or die "Can't open pipe to bowtie: $!";
-
-    ### Bowtie 2 outputs out SAM format, so we need to skip everything until the first sequence
-    while (1){
-      $_ = $fh->{fh}->getline();
-      if ($_) {
-	last unless ($_ =~ /^\@/); # SAM headers start with @
-      }
-      else{
-	last; # no alignment output
-      }
-    }
-
-    my $line_1 = $_;
-    my $line_2 = $fh->{fh}->getline();
-
-    # if Bowtie produces an alignment we store the first line of the output
-    if ($line_1 and $line_2) {
-      chomp $line_1;
-      chomp $line_2;
-      my $id_1 = (split(/\t/,$line_1))[0]; # this is the first element of the first bowtie output line (= the sequence identifier)
-      my $id_2 = (split(/\t/,$line_2))[0]; # this is the first element of the second bowtie output line
-
-      ### Bowtie always reports the alignment with the smaller chromosomal position first. This can be either sequence 1 or sequence 2.
-      ### We will thus identify which sequence was read 1 and store this ID as last_seq_id
-
-      if ($id_1 =~ s/\/1$//){ # removing the read 1 /1 tag if present (remember that Bowtie2 clips off /1 or /2 line endings itself, so we added /1/1 or /2/2 to start with
-	$fh->{last_seq_id} = $id_1;
-      }
-      elsif ($id_2 =~ s/\/1$//){ # removing the read 1 /2 tag if present
-	$fh->{last_seq_id} = $id_2;
-      }
-      else{
-	warn "Either the first or the second id need to be read 1! ID1 was: $id_1; ID2 was: $id_2\n";
-      }
-
-      $fh->{last_line_1} = $line_1; # this contains either read 1 or read 2
-      $fh->{last_line_2} = $line_2; # this contains either read 1 or read 2
-      warn "Found first alignment:\n$fh->{last_line_1}\n$fh->{last_line_2}\n";
-    }
-    # otherwise we just initialise last_seq_id and last_lines as undefined
-    else {
-      print "Found no alignment, assigning undef to last_seq_id and last_lines\n";
-      $fh->{last_seq_id} = undef;
-      $fh->{last_line_1} = undef;
-      $fh->{last_line_2} = undef;
-    }
-  }
-}
-
-### Bowtie 1 (default) | PAIRED-END | FASTQ
-
-sub paired_end_align_fragments_to_bisulfite_genome_fastQ {
-  my ($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2) = @_;
-  if ($directional){
-    print "Input files are $C_to_T_infile_1 $G_to_A_infile_2 (FastQ)\n";
-  }
-  else{
-    print "Input files are $C_to_T_infile_1 and $G_to_A_infile_1 and $C_to_T_infile_2 and $G_to_A_infile_2 (FastQ)\n";
-  }
-
-  ## Now starting up to 4 instances of Bowtie feeding in the converted sequence files and reading in the first line of the bowtie output, and storing it in the
-  ## data structure above
-  if ($directional){
-    warn "Now running 2 instances of Bowtie against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-  else{
-    warn "Now running 4 individual instances of Bowtie against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-
-  foreach my $fh (@fhs) {
-
-    if ($directional){
-      unless ($fh->{inputfile_1}){
-	$fh->{last_seq_id} = undef;
-	$fh->{last_line_1} = undef;
-	$fh->{last_line_2} = undef;
-	next;
-      }
-    }
-
-    my $bt_options = $bowtie_options;
-    if ($fh->{name} eq 'CTread1GAread2CTgenome' or $fh->{name} eq 'GAread1CTread2GAgenome'){
-      $bt_options .= ' --norc'; ### ensuring the alignments are only reported in a sensible manner
-    }
-    else {
-      $bt_options .= ' --nofw';
-    }
-
-    warn "Now starting a Bowtie paired-end alignment for $fh->{name} (reading in sequences from $temp_dir$fh->{inputfile_1} and $temp_dir$fh->{inputfile_2}, with the options: $bt_options))\n";
-    open ($fh->{fh},"$path_to_bowtie $bt_options $fh->{bisulfiteIndex} -1 $temp_dir$fh->{inputfile_1} -2 $temp_dir$fh->{inputfile_2} |") or die "Can't open pipe to bowtie: $!";
-
-    my $line_1 = $fh->{fh}->getline();
-    my $line_2 = $fh->{fh}->getline();
-
-    # if Bowtie produces an alignment we store the first line of the output
-    if ($line_1 and $line_2) {
-      chomp $line_1;
-      chomp $line_2;
-      ### Bowtie always reports the alignment with the smaller chromosomal position first. This can be either sequence 1 or sequence 2.
-      ### We will thus identify which sequence was read 1 and store this ID as last_seq_id
-
-      my $id_1 = (split(/\t/,$line_1))[0]; # this is the first element of the first bowtie output line (= the sequence identifier)
-      my $id_2 = (split(/\t/,$line_2))[0]; # this is the first element of the second bowtie output line
-
-      if ($id_1 =~ s/\/1$//){ # removing the read 1 tag if present
-	$fh->{last_seq_id} = $id_1;
-      }
-      elsif ($id_2 =~ s/\/1$//){ # removing the read 1 tag if present
-	$fh->{last_seq_id} = $id_2;
-      }
-      else{
-	die "Either the first or the second id need to be read 1! ID1 was: $id_1; ID2 was: $id_2\n";
-      }
-
-      $fh->{last_line_1} = $line_1; # this contains read 1 or read 2
-      $fh->{last_line_2} = $line_2; # this contains read 1 or read 2
-      warn "Found first alignment:\n$fh->{last_line_1}\n$fh->{last_line_2}\n";
-    }
-
-    # otherwise we just initialise last_seq_id and last_lines as undefined
-    else {
-      print "Found no alignment, assigning undef to last_seq_id and last_lines\n";
-      $fh->{last_seq_id} = undef;
-      $fh->{last_line_1} = undef;
-      $fh->{last_line_2} = undef;
-    }
-  }
-}
-
-### Bowtie 2 | PAIRED-END | FASTQ
-
-sub paired_end_align_fragments_to_bisulfite_genome_fastQ_bowtie2 {
-  my ($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2) = @_;
-  if ($directional){
-    print "Input files are $C_to_T_infile_1 and $G_to_A_infile_2 (FastQ)\n";
-  }
-  else{
-    print "Input files are $C_to_T_infile_1 and $G_to_A_infile_1 and $C_to_T_infile_2 and $G_to_A_infile_2 (FastQ)\n";
-  }
-
-  ## Now starting up 4 instances of Bowtie 2 feeding in the converted sequence files and reading in the first line of the bowtie output, and storing it in the
-  ## data structure above
-  if ($directional){
-    warn "Now running 2 instances of Bowtie 2 against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-  else{
-    warn "Now running 4 individual instances of Bowtie 2 against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-
-  foreach my $fh (@fhs) {
-
-    if ($directional){
-      unless ($fh->{inputfile_1}){
-	$fh->{last_seq_id} = undef;
-	$fh->{last_line_1} = undef;
-	$fh->{last_line_2} = undef;
-	next;
-      }
-    }
-
-    my $bt2_options = $bowtie_options;
-    if ($fh->{name} eq 'CTread1GAread2CTgenome' or $fh->{name} eq 'GAread1CTread2GAgenome'){
-      $bt2_options .= ' --norc'; ### ensuring the alignments are only reported in a sensible manner
-    }
-    else {
-      $bt2_options .= ' --nofw';
-    }
-
-    warn "Now starting a Bowtie 2 paired-end alignment for $fh->{name} (reading in sequences from $temp_dir$fh->{inputfile_1} and $temp_dir$fh->{inputfile_2}, with the options: $bt2_options))\n";
-    open ($fh->{fh},"$path_to_bowtie $bt2_options $fh->{bisulfiteIndex} -1 $temp_dir$fh->{inputfile_1} -2 $temp_dir$fh->{inputfile_2} |") or die "Can't open pipe to bowtie: $!";
-
-    ### Bowtie 2 outputs out SAM format, so we need to skip everything until the first sequence
-    while (1){
-      $_ = $fh->{fh}->getline();
-      if ($_) {
-	last unless ($_ =~ /^\@/); # SAM headers start with @
-      }
-      else{
-	last; # no alignment output
-      }
-    }
-
-    my $line_1 = $_;
-    my $line_2 = $fh->{fh}->getline();
-
-    # if Bowtie produces an alignment we store the first line of the output
-    if ($line_1 and $line_2) {
-      chomp $line_1;
-      chomp $line_2;
-      ### Bowtie always reports the alignment with the smaller chromosomal position first. This can be either sequence 1 or sequence 2.
-      ### We will thus identify which sequence was read 1 and store this ID as last_seq_id
-
-      my $id_1 = (split(/\t/,$line_1))[0]; # this is the first element of the first bowtie output line (= the sequence identifier)
-      my $id_2 = (split(/\t/,$line_2))[0]; # this is the first element of the second bowtie output line
-
-      if ($id_1 =~ s/\/1$//){ # removing the read 1 tag if present (remember that Bowtie2 clips off /1 or /2 line endings itself, so we added /1/1 or /2/2 to start with
-	$fh->{last_seq_id} = $id_1;
-      }
-      elsif ($id_2 =~ s/\/1$//){ # removing the read 1 tag if present
-	$fh->{last_seq_id} = $id_2;
-      }
-      else{
-	die "Either the first or the second id need to be read 1! ID1 was: $id_1; ID2 was: $id_2\n";
-      }
-
-      $fh->{last_line_1} = $line_1; # this contains read 1 or read 2
-      $fh->{last_line_2} = $line_2; # this contains read 1 or read 2
-      warn "Found first alignment:\n$fh->{last_line_1}\n$fh->{last_line_2}\n";
-    }
-
-    # otherwise we just initialise last_seq_id and last_lines as undefined
-    else {
-      print "Found no alignment, assigning undef to last_seq_id and last_lines\n";
-      $fh->{last_seq_id} = undef;
-      $fh->{last_line_1} = undef;
-      $fh->{last_line_2} = undef;
-    }
-  }
-}
-
-#####################################################################################################################################################
-
-### Bowtie 1 (default) | SINGLE-END | FASTA
-sub single_end_align_fragments_to_bisulfite_genome_fastA {
-  my ($C_to_T_infile,$G_to_A_infile) = @_;
-  if ($directional){
-    print "Input file is $C_to_T_infile (FastA)\n";
-  }
-  else{
-    print "Input files are $C_to_T_infile and $G_to_A_infile (FastA)\n";
-  }
-
-  ## Now starting up to 4 instances of Bowtie feeding in the converted sequence files and reading in the first line of the bowtie output, and storing it in
-  ## data structure above
-  if ($directional){
-    warn "Now running 2 instances of Bowtie against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-  else{
-    warn "Now running 4 individual instances of Bowtie against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-
-  foreach my $fh (@fhs) {
-
-    my $bt_options = $bowtie_options;
-    if ($fh->{name} eq 'CTreadCTgenome' or $fh->{name} eq 'GAreadGAgenome'){
-      $bt_options .= ' --norc'; ### ensuring the alignments are only reported in a sensible manner
-    }
-    else {
-      $bt_options .= ' --nofw';
-    }
-
-    warn "Now starting the Bowtie aligner for $fh->{name} (reading in sequences from $temp_dir$fh->{inputfile} with options: $bt_options)\n";
-    open ($fh->{fh},"$path_to_bowtie $bt_options $fh->{bisulfiteIndex} $temp_dir$fh->{inputfile} |") or die "Can't open pipe to bowtie: $!";
-
-    # if Bowtie produces an alignment we store the first line of the output
-    $_ = $fh->{fh}->getline();
-    if ($_) {
-      chomp;
-      my $id = (split(/\t/))[0]; # this is the first element of the bowtie output (= the sequence identifier)
-      $fh->{last_seq_id} = $id;
-      $fh->{last_line} = $_;
-      warn "Found first alignment:\t$fh->{last_line}\n";
-    }
-    # otherwise we just initialise last_seq_id and last_line as undefined
-    else {
-      print "Found no alignment, assigning undef to last_seq_id and last_line\n";
-      $fh->{last_seq_id} = undef;
-      $fh->{last_line} = undef;
-    }
-  }
-}
-
-### Bowtie 2 | SINGLE-END | FASTA
-sub single_end_align_fragments_to_bisulfite_genome_fastA_bowtie2 {
-  my ($C_to_T_infile,$G_to_A_infile) = @_;
-  if ($directional){
-    print "Input file is $C_to_T_infile (FastA)\n";
-  }
-  else{
-    print "Input files are $C_to_T_infile and $G_to_A_infile (FastA)\n";
-  }
-
-  ## Now starting up to 4 instances of Bowtie feeding in the converted sequence files and reading in the first line of the bowtie output, and storing it in
-  ## data structure above
-  if ($directional){
-    warn "Now running 2 instances of Bowtie 2 against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-  else{
-    warn "Now running 4 individual instances of Bowtie 2 against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-
-  foreach my $fh (@fhs) {
-
-    my $bt2_options = $bowtie_options;
-    if ($fh->{name} eq 'CTreadCTgenome' or $fh->{name} eq 'GAreadGAgenome'){
-      $bt2_options .= ' --norc'; ### ensuring the alignments are only reported in a sensible manner
-    }
-    else {
-      $bt2_options .= ' --nofw';
-    }
-
-    warn "Now starting the Bowtie 2 aligner for $fh->{name} (reading in sequences from $temp_dir$fh->{inputfile} with options: $bt2_options)\n";
-    open ($fh->{fh},"$path_to_bowtie $bt2_options $fh->{bisulfiteIndex} -U $temp_dir$fh->{inputfile} |") or die "Can't open pipe to bowtie: $!";
-
-    ### Bowtie 2 outputs out SAM format, so we need to skip everything until the first sequence
-    while (1){
-      $_ = $fh->{fh}->getline();
-      if ($_) {
-	last unless ($_ =~ /^\@/); # SAM headers start with @
-      }
-      else{
-	last; # no alignment output
-      }
-    }
-
-    # Bowtie 2 outputs a result line even for sequences without any alignments. We thus store the first line of the output
-    if ($_) {
-      chomp;
-      my $id = (split(/\t/))[0]; # this is the first element of the Bowtie output (= the sequence identifier)
-      $fh->{last_seq_id} = $id;
-      $fh->{last_line} = $_;
-      warn "Found first alignment:\t$fh->{last_line}\n";
-    }
-    # otherwise we just initialise last_seq_id and last_line as undefinded. This should only happen at the end of a file for Bowtie 2 output
-    else {
-      print "Found no alignment, assigning undef to last_seq_id and last_line\n";
-      $fh->{last_seq_id} = undef;
-      $fh->{last_line} = undef;
-    }
-  }
-}
-
-
-### Bowtie 1 (default) | SINGLE-END | FASTQ
-sub single_end_align_fragments_to_bisulfite_genome_fastQ {
-  my ($C_to_T_infile,$G_to_A_infile) = @_;
-  if ($directional){
-    print "Input file is $C_to_T_infile (FastQ)\n";
-  }
-  else{
-    print "Input files are $C_to_T_infile and $G_to_A_infile (FastQ)\n";
-  }
-
-  ## Now starting up to 4 instances of Bowtie feeding in the converted sequence files and reading in the first line of the bowtie output, and storing it in
-  ## the data structure above
-  if ($directional){
-    warn "Now running 2 instances of Bowtie against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-  else{
-    warn "Now running 4 individual instances of Bowtie against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-
-  foreach my $fh (@fhs) {
-    my $bt_options = $bowtie_options;
-    if ($fh->{name} eq 'CTreadCTgenome' or $fh->{name} eq 'GAreadGAgenome'){
-      $bt_options .= ' --norc'; ### ensuring the alignments are only reported in a sensible manner
-    }
-    else {
-      $bt_options .= ' --nofw';
-    }
-
-    warn "Now starting the Bowtie aligner for $fh->{name} (reading in sequences from $temp_dir$fh->{inputfile} with options: $bt_options)\n";
-    open ($fh->{fh},"$path_to_bowtie $bowtie_options $fh->{bisulfiteIndex} $temp_dir$fh->{inputfile} |") or die "Can't open pipe to bowtie: $!";
-
-    # if Bowtie produces an alignment we store the first line of the output
-    $_ = $fh->{fh}->getline();
-    if ($_) {
-      chomp;
-      my $id = (split(/\t/))[0]; # this is the first element of the Bowtie output (= the sequence identifier)
-      $fh->{last_seq_id} = $id;
-      $fh->{last_line} = $_;
-      warn "Found first alignment:\t$fh->{last_line}\n";
-    }
-    # otherwise we just initialise last_seq_id and last_line as undefined
-    else {
-      print "Found no alignment, assigning undef to last_seq_id and last_line\n";
-      $fh->{last_seq_id} = undef;
-      $fh->{last_line} = undef;
-    }
-  }
-}
-
-### Bowtie 2 | SINGLE-END | FASTQ
-sub single_end_align_fragments_to_bisulfite_genome_fastQ_bowtie2 {
-  my ($C_to_T_infile,$G_to_A_infile) = @_;
-  if ($directional){
-    print "Input file is $C_to_T_infile (FastQ)\n\n";
-  }
-  else{
-    print "Input files are $C_to_T_infile and $G_to_A_infile (FastQ)\n\n";
-  }
-
-  ## Now starting up to 4 instances of Bowtie 2 feeding in the converted sequence files and reading in the first line of the bowtie output, and storing it in
-  ## the data structure above
-  if ($directional){
-    warn "Now running 2 instances of Bowtie 2 against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-  else{
-    warn "Now running 4 individual instances of Bowtie 2 against the bisulfite genome of $genome_folder with the specified options: $bowtie_options\n\n";
-  }
-
-  foreach my $fh (@fhs) {
-    my $bt2_options = $bowtie_options;
-    if ($fh->{name} eq 'CTreadCTgenome' or $fh->{name} eq 'GAreadGAgenome'){
-      $bt2_options .= ' --norc'; ### ensuring the alignments are only reported in a sensible manner
-    }
-    else {
-      $bt2_options .= ' --nofw';
-    }
-    warn "Now starting the Bowtie 2 aligner for $fh->{name} (reading in sequences from $temp_dir$fh->{inputfile} with options $bt2_options)\n";
-    warn "Using Bowtie 2 index: $fh->{bisulfiteIndex}\n\n";
-
-    open ($fh->{fh},"$path_to_bowtie $bt2_options $fh->{bisulfiteIndex} -U $temp_dir$fh->{inputfile} |") or die "Can't open pipe to bowtie: $!";
-    ### Bowtie 2 outputs out SAM format, so we need to skip everything until the first sequence
-    while (1){
-      $_ = $fh->{fh}->getline();
-      if ($_) {
-	last unless ($_ =~ /^\@/); # SAM headers start with @
-      }
-      else {
-	last;
-      }
-    }
-
-    # Bowtie 2 outputs a result line even for sequences without any alignments. We thus store the first line of the output
-    if ($_) {
-      chomp;
-      my $id = (split(/\t/))[0]; # this is the first element of the Bowtie 2 output (= the sequence identifier)
-      $fh->{last_seq_id} = $id;
-      $fh->{last_line} = $_;
-      warn "Found first alignment:\t$fh->{last_line}\n";
-    }
-    # otherwise we just initialise last_seq_id and last_line as undefined. This should only happen at the end of a file for Bowtie 2 output
-    else {
-      print "Found no alignment, assigning undef to last_seq_id and last_line\n";
-      $fh->{last_seq_id} = undef;
-      $fh->{last_line} = undef;
-    }
-  }
-}
-
-###########################################################################################################################################
-
-sub reset_counters_and_fhs{
-  my $filename = shift;
-  %counting=(
-	     total_meCHH_count => 0,
-	     total_meCHG_count => 0,
-	     total_meCpG_count => 0,
-	     total_unmethylated_CHH_count => 0,
-	     total_unmethylated_CHG_count => 0,
-	     total_unmethylated_CpG_count => 0,
-	     sequences_count => 0,
-	     no_single_alignment_found => 0,
-	     unsuitable_sequence_count => 0,
-	     genomic_sequence_could_not_be_extracted_count => 0,
-	     unique_best_alignment_count => 0,
-	     low_complexity_alignments_overruled_count => 0,
-	     CT_CT_count => 0, #(CT read/CT genome, original top strand)
-	     CT_GA_count => 0, #(CT read/GA genome, original bottom strand)
-	     GA_CT_count => 0, #(GA read/CT genome, complementary to original top strand)
-	     GA_GA_count => 0, #(GA read/GA genome, complementary to original bottom strand)
-	     CT_GA_CT_count => 0, #(CT read1/GA read2/CT genome, original top strand)
-	     GA_CT_GA_count => 0, #(GA read1/CT read2/GA genome, complementary to original bottom strand)
-	     GA_CT_CT_count => 0, #(GA read1/CT read2/CT genome, complementary to original top strand)
-	     CT_GA_GA_count => 0, #(CT read1/GA read2/GA genome, original bottom strand)
-	     alignments_rejected_count => 0, # only relevant if --directional was specified
-	    );
-
-  if ($directional){
-    if ($filename =~ ','){ # paired-end files
-      @fhs=(
-	    { name => 'CTreadCTgenome',
-	      strand_identity => 'con ori forward',
-	      bisulfiteIndex => $CT_index_basename,
-	      seen => 0,
-	      wrong_strand => 0,
-	    },
-	    { name => 'CTreadGAgenome',
-	      strand_identity => 'con ori reverse',
-	      bisulfiteIndex => $GA_index_basename,
-	      seen => 0,
-	      wrong_strand => 0,
-	    },
-	    { name => 'GAreadCTgenome',
-	      strand_identity => 'compl ori con forward',
-	      bisulfiteIndex => $CT_index_basename,
-	      seen => 0,
-	      wrong_strand => 0,
-	    },
-	    { name => 'GAreadGAgenome',
-	    strand_identity => 'compl ori con reverse',
-	      bisulfiteIndex => $GA_index_basename,
-	      seen => 0,
-	      wrong_strand => 0,
-	    },
-	   );
-    }
-    else{ # single-end files
-      @fhs=(
-	    { name => 'CTreadCTgenome',
-	      strand_identity => 'con ori forward',
-	      bisulfiteIndex => $CT_index_basename,
-	      seen => 0,
-	      wrong_strand => 0,
-	    },
-	    { name => 'CTreadGAgenome',
-	      strand_identity => 'con ori reverse',
-	      bisulfiteIndex => $GA_index_basename,
-	      seen => 0,
-	      wrong_strand => 0,
-	    },
-	   );
-    }
-  }
-  else{
-    @fhs=(
-	  { name => 'CTreadCTgenome',
-	    strand_identity => 'con ori forward',
-	    bisulfiteIndex => $CT_index_basename,
-	    seen => 0,
-	    wrong_strand => 0,
-	  },
-	  { name => 'CTreadGAgenome',
-	    strand_identity => 'con ori reverse',
-	    bisulfiteIndex => $GA_index_basename,
-	    seen => 0,
-	    wrong_strand => 0,
-	  },
-	  { name => 'GAreadCTgenome',
-	    strand_identity => 'compl ori con forward',
-	    bisulfiteIndex => $CT_index_basename,
-	    seen => 0,
-	    wrong_strand => 0,
-	  },
-	  { name => 'GAreadGAgenome',
-	    strand_identity => 'compl ori con reverse',
-	    bisulfiteIndex => $GA_index_basename,
-	    seen => 0,
-	    wrong_strand => 0,
-	  },
-	 );
-  }
-}
-
-
-sub process_command_line{
-  my @bowtie_options;
-  my $help;
-  my $mates1;
-  my $mates2;
-  my $path_to_bowtie;
-  my $fastq;
-  my $fasta;
-  my $skip;
-  my $qupto;
-  my $phred64;
-  my $phred33;
-  my $solexa;
-  my $mismatches;
-  my $seed_length;
-  my $best;
-  my $sequence_format;
-  my $version;
-  my $quiet;
-  my $chunk;
-  my $non_directional;
-  my $ceiling;
-  my $maxins;
-  my $minins;
-  my $unmapped;
-  my $multi_map;
-  my $output_dir;
-  my $bowtie2;
-  my $vanilla;
-  my $sam_no_hd;
-  my $seed_extension_fails;
-  my $reseed_repetitive_seeds;
-  my $most_valid_alignments;
-  my $score_min;
-  my $parallel;
-  my $temp_dir;
-  my $rdg;
-  my $rfg;
-
-  my $command_line = GetOptions ('help|man' => \$help,
-				 '1=s' => \$mates1,
-				 '2=s' => \$mates2,
-				 'path_to_bowtie=s' => \$path_to_bowtie,
-				 'f|fasta' => \$fasta,
-				 'q|fastq' => \$fastq,
-				 's|skip=i' => \$skip,
-				 'u|upto=i' => \$qupto,
-				 'phred33-quals' => \$phred33,
-				 'phred64-quals|solexa1' => \$phred64,
-				 'solexa-quals' => \$solexa,
-				 'n|seedmms=i' => \$mismatches,
-				 'l|seedlen=i' => \$seed_length,
-				 'no_best' => \$best,
-				 'version' => \$version,
-				 'quiet' => \$quiet,
-				 'chunkmbs=i' => \$chunk,
-				 'non_directional' => \$non_directional,
-				 'I|minins=i' => \$minins,
-				 'X|maxins=i' => \$maxins,
-				 'e|maqerr=i' => \$ceiling,
-				 'un|unmapped' => \$unmapped,
-				 'ambiguous' => \$multi_map,
-				 'o|output_dir=s' => \$output_dir,
-				 'bowtie2' => \$bowtie2,
-				 'vanilla' => \$vanilla,
-				 'sam-no-hd' => \$sam_no_hd,
-				 'D=i' => \$seed_extension_fails,
-				 'R=i' => \$reseed_repetitive_seeds,
-				 'score_min=s' => \$score_min,
-				 'most_valid_alignments=i' => \$most_valid_alignments,
-				 'p=i' => \$parallel,
-				 'temp_dir=s' => \$temp_dir,
-				 'rdg=s' => \$rdg,
-				 'rfg=s' => \$rfg,
-				);
-
-
-  ### EXIT ON ERROR if there were errors with any of the supplied options
-  unless ($command_line){
-    die "Please respecify command line options\n";
-  }
-  ### HELPFILE
-  if ($help){
-    print_helpfile();
-    exit;
-  }
-  if ($version){
-    print << "VERSION";
-
-
-          Bismark - Bisulfite Mapper and Methylation Caller.
-
-   Bismark Version: $bismark_version Copyright 2010-12 Felix Krueger, Babraham Bioinformatics
-              www.bioinformatics.babraham.ac.uk/projects/
-
-
-VERSION
-    exit;
-  }
-
-
-  ##########################
-  ### PROCESSING OPTIONS ###
-  ##########################
-
-  unless ($bowtie2){
-    $bowtie2 = 0;
-  }
-  unless ($sam_no_hd){
-    $sam_no_hd =0;
-  }
-
-  ### PATH TO BOWTIE
-  ### if a special path to Bowtie 1/2 was specified we will use that one, otherwise it is assumed that Bowtie 1/2 is in the PATH
-  if ($path_to_bowtie){
-    unless ($path_to_bowtie =~ /\/$/){
-      $path_to_bowtie =~ s/$/\//;
-    }
-    if (-d $path_to_bowtie){
-      if ($bowtie2){
-	$path_to_bowtie = "${path_to_bowtie}bowtie2";
-      }
-      else{
-	$path_to_bowtie = "${path_to_bowtie}bowtie";
-      }
-    }
-    else{
-      die "The path to bowtie provided ($path_to_bowtie) is invalid (not a directory)!\n";
-    }
-  }
-  else{
-    if ($bowtie2){
-      $path_to_bowtie = 'bowtie2';
-      warn "Path to Bowtie 2 specified as: $path_to_bowtie\n";  }
-    else{
-      $path_to_bowtie = 'bowtie';
-      warn "Path to Bowtie specified as: $path_to_bowtie\n";
-    }
-  }
-
-  ####################################
-  ### PROCESSING ARGUMENTS
-
-  ### GENOME FOLDER
-  my $genome_folder = shift @ARGV; # mandatory
-  unless ($genome_folder){
-    warn "Genome folder was not specified!\n";
-    print_helpfile();
-    exit;
-  }
-
-  ### checking that the genome folder, all subfolders and the required bowtie index files exist
-  unless ($genome_folder =~/\/$/){
-    $genome_folder =~ s/$/\//;
-  }
-
-  if (chdir $genome_folder){
-    my $absolute_genome_folder = getcwd; ## making the genome folder path absolute
-    unless ($absolute_genome_folder =~/\/$/){
-      $absolute_genome_folder =~ s/$/\//;
-    }
-    warn "Reference genome folder provided is $genome_folder\t(absolute path is '$absolute_genome_folder)'\n";
-    $genome_folder = $absolute_genome_folder;
-  }
-  else{
-    die "Failed to move to $genome_folder: $!\nUSAGE: Bismark.pl [options] <genome_folder> {-1 <mates1> -2 <mates2> | <singles>} [<hits>]    (--help for more details)\n";
-  }
-
-  my $CT_dir = "${genome_folder}Bisulfite_Genome/CT_conversion/";
-  my $GA_dir = "${genome_folder}Bisulfite_Genome/GA_conversion/";
-
-  if ($bowtie2){ ### Bowtie 2 (new)
-    ### checking the integrity of $CT_dir
-    chdir $CT_dir or die "Failed to move to directory $CT_dir: $!\n";
-    my @CT_bowtie_index = ('BS_CT.1.bt2','BS_CT.2.bt2','BS_CT.3.bt2','BS_CT.4.bt2','BS_CT.rev.1.bt2','BS_CT.rev.2.bt2');
-    foreach my $file(@CT_bowtie_index){
-      unless (-f $file){
-	die "The Bowtie 2 index of the C->T converted genome seems to be faulty ($file). Please run the bismark_genome_preparation before running Bismark.\n";
-      }
-    }
-    ### checking the integrity of $GA_dir
-    chdir $GA_dir or die "Failed to move to directory $GA_dir: $!\n";
-    my @GA_bowtie_index = ('BS_GA.1.bt2','BS_GA.2.bt2','BS_GA.3.bt2','BS_GA.4.bt2','BS_GA.rev.1.bt2','BS_GA.rev.2.bt2');
-    foreach my $file(@GA_bowtie_index){
-      unless (-f $file){
-	die "The Bowtie 2 index of the G->A converted genome seems to be faulty ($file). Please run bismark_genome_preparation before running Bismark.\n";
-      }
-    }
-  }
-
-  else{ ### Bowtie 1 (default)
-    ### checking the integrity of $CT_dir
-    chdir $CT_dir or die "Failed to move to directory $CT_dir: $!\n";
-    my @CT_bowtie_index = ('BS_CT.1.ebwt','BS_CT.2.ebwt','BS_CT.3.ebwt','BS_CT.4.ebwt','BS_CT.rev.1.ebwt','BS_CT.rev.2.ebwt');
-    foreach my $file(@CT_bowtie_index){
-      unless (-f $file){
-	die "The Bowtie index of the C->T converted genome seems to be faulty ($file). Please run bismark_genome_preparation before running Bismark.\n";
-      }
-    }
-    ### checking the integrity of $GA_dir
-    chdir $GA_dir or die "Failed to move to directory $GA_dir: $!\n";
-    my @GA_bowtie_index = ('BS_GA.1.ebwt','BS_GA.2.ebwt','BS_GA.3.ebwt','BS_GA.4.ebwt','BS_GA.rev.1.ebwt','BS_GA.rev.2.ebwt');
-    foreach my $file(@GA_bowtie_index){
-      unless (-f $file){
-	die "The Bowtie index of the G->A converted genome seems to be faulty ($file). Please run bismark_genome_preparation before running Bismark.\n";
-      }
-    }
-  }
-
-  my $CT_index_basename = "${CT_dir}BS_CT";
-  my $GA_index_basename = "${GA_dir}BS_GA";
-
-  ### INPUT OPTIONS
-
-  ### SEQUENCE FILE FORMAT
-  ### exits if both fastA and FastQ were specified
-  if ($fasta and $fastq){
-    die "Only one sequence filetype can be specified (fastA or fastQ)\n";
-  }
-
-  ### unless fastA is specified explicitely, fastQ sequence format is expected by default
-  if ($fasta){
-    print "FastA format specified\n";
-    $sequence_format = 'FASTA';
-    push @bowtie_options, '-f';
-  }
-  elsif ($fastq){
-    print "FastQ format specified\n";
-    $sequence_format = 'FASTQ';
-    push @bowtie_options, '-q';
-  }
-  else{
-    $fastq = 1;
-    print "FastQ format assumed (by default)\n";
-    $sequence_format = 'FASTQ';
-    push @bowtie_options, '-q';
-  }
-
-  ### SKIP
-  if ($skip){
-    warn "Skipping the first $skip reads from the input file\n";
-    # push @bowtie_options,"-s $skip";
-  }
-
-  ### UPTO
-  if ($qupto){
-    warn "Processing sequences up to read no. $qupto from the input file\n";
-    if ($bowtie2){
-      #      push @bowtie_options,"--upto $qupto"; ## slightly changed for Bowtie 2
-    }
-    else{
-      #     push @bowtie_options,"--qupto $qupto";
-    }
-  }
-
-  ### QUALITY VALUES
-  if (($phred33 and $phred64) or ($phred33 and $solexa) or ($phred64 and $solexa)){
-    die "You can only specify one type of quality value at a time! (--phred33-quals or --phred64-quals or --solexa-quals)";
-  }
-  if ($phred33){ ## if nothing else is specified $phred33 will be used as default by both Bowtie 1 and 2.
-    # Phred quality values work only when -q is specified
-    unless ($fastq){
-      die "Phred quality values works only when -q (FASTQ) is specified\n";
-    }
-    if ($bowtie2){
-      push @bowtie_options,"--phred33";
-    }
-    else{
-      push @bowtie_options,"--phred33-quals";
-    }
-  }
-  if ($phred64){
-    # Phred quality values work only when -q is specified
-    unless ($fastq){
-      die "Phred quality values work only when -q (FASTQ) is specified\n";
-    }
-    if ($bowtie2){
-      push @bowtie_options,"--phred64";
-    }
-    else{
-      push @bowtie_options,"--phred64-quals";
-    }
-  }
-  else{
-    $phred64 = 0;
-  }
-
-  if ($solexa){
-    if ($bowtie2){
-      die "The option '--solexa-quals' is not compatible with Bowtie 2. Please respecify!\n";
-    }
-    # Solexa to Phred value conversion works only when -q is specified
-    unless ($fastq){
-      die "Conversion from Solexa to Phred quality values works only when -q (FASTQ) is specified\n";
-    }
-    push @bowtie_options,"--solexa-quals";
-  }
-  else{
-    $solexa = 0;
-  }
-
-  ### ALIGNMENT OPTIONS
-
-  ### MISMATCHES
-  if (defined $mismatches){
-    if ($bowtie2){
-      if ($mismatches == 0 or $mismatches == 1){
-	push @bowtie_options,"-N $mismatches";
-      }
-      else{
-	die "Please set the number of multiseed mismatches for Bowtie 2 with '-N <int>' (where <int> can be 0 or 1)\n";
-      }
-    }
-    else{
-      if ($mismatches >= 0 and $mismatches <= 3){
-	push @bowtie_options,"-n $mismatches";
-      }
-      else{
-	die "Please set the number of seed mismatches for Bowtie 1 with '-n <int>' (where <int> can be 0,1,2 or 3)\n";
-      }
-    }
-  }
-  else{
-    unless ($bowtie2){
-      push @bowtie_options,"-n 1"; # setting -n to 1 by default (for use with Bowtie only) because it is much quicker than the default mode of -n 2
-    }
-  }
-
-  ### SEED LENGTH
-  if (defined $seed_length){
-    if ($bowtie2){
-      push @bowtie_options,"-L $seed_length";
-    }
-    else{
-      push @bowtie_options,"-l $seed_length";
-    }
-  }
-
-  ### MISMATCH CEILING
-  if (defined $ceiling){
-    die "The option '-e' is not compatible with Bowtie 2. Please respecify options\n" if ($bowtie2);
-    push @bowtie_options,"-e $ceiling";
-  }
-
-
-  ### BOWTIE 2 EFFORT OPTIONS
-
-  ### CONSECUTIVE SEED EXTENSION FAILS
-  if (defined $seed_extension_fails){
-    die "The option '-D <int>' is only available when using Bowtie 2\n\n" unless ($bowtie2);
-    push @bowtie_options,"-D $seed_extension_fails";
-  }
-
-  ### RE-SEEDING REPETITIVE SEEDS
-  if (defined $reseed_repetitive_seeds){
-    die "The option '-R <int>' is only available when using Bowtie 2\n\n" unless ($bowtie2);
-    push @bowtie_options,"-R $reseed_repetitive_seeds";
-  }
-
-
-  ### BOWTIE 2 SCORING OPTIONS
-  if ($score_min){
-    die "The option '--score_min <func>' is only available when using Bowtie 2\n\n" unless ($bowtie2);
-    unless ($score_min =~ /^L,.+,.+$/){
-      die "The option '--score_min <func>' needs to be in the format <L,value,value> . Please consult \"setting up functions\" in the Bowtie 2 manual for further information\n\n";
-    }
-    push @bowtie_options,"--score-min $score_min";
-  }
-  else{
-    if ($bowtie2){
-      push @bowtie_options,"--score-min L,0,-0.2"; # default setting, more stringent than normal Bowtie2
-    }
-  }
-
-  ### BOWTIE 2 READ GAP OPTIONS
-  if ($rdg){
-    die "The option '--rdg <int1>,<int2>' is only available when using Bowtie 2\n\n" unless ($bowtie2);
-    unless ($rdg =~ /^.+,.+$/){
-      die "The option '--rdg <int1>,<int2>' needs to be in the format <integer,integer> . Please consult \"setting up functions\" in the Bowtie 2 manual for further information\n\n";
-    }
-    push @bowtie_options,"--rdg $rdg";
-  }
-
-  ### BOWTIE 2 REFERENCE GAP OPTIONS
-  if ($rfg){
-    die "The option '--rfg <int1>,<int2>' is only available when using Bowtie 2\n\n" unless ($bowtie2);
-    unless ($rfg =~ /^.+,.+$/){
-      die "The option '--rfg <int1>,<int2>' needs to be in the format <integer,integer> . Please consult \"setting up functions\" in the Bowtie 2 manual for further information\n\n";
-    }
-    push @bowtie_options,"--rfg $rfg";
-  }
-
-
-
-  ### BOWTIE 2 PARALLELIZATION OPTIONS
-  if (defined $parallel){
-    die "The parallelization switch '-p' only works for Bowtie 2. Please respecify!" unless ($bowtie2);
-  }
-  if ($bowtie2){
-    if ($parallel){
-      die "Please select a value for -p of 2 or more!\n" unless ($parallel > 1);
-      push @bowtie_options,"-p $parallel";
-      push @bowtie_options,'--reorder'; ## re-orders the bowtie 2 output so that it does match the input files. This is abolutely required for parallelization to work.
-      print "Each Bowtie 2 instance is going to be run with $parallel threads. Please monitor performance closely and tune down if needed!\n";
-      sleep (2);
-    }
-  }
-
-  ### REPORTING OPTIONS
-
-  if ($bowtie2){
-    push @bowtie_options,'--ignore-quals'; ## All mismatches will receive penalty for mismatches as if they were of high quality, which is 6 by default
-
-    ### Option -M is deprecated since Bowtie 2 version 2.0.0 beta7. I'll leave this option commented out for a while
-    if(defined $most_valid_alignments){
-
-      warn "\nThe option -M is now deprecated (as of Bowtie 2 version 2.0.0 beta7). What used to be called -M mode is still the default mode. Use the -D and -R options to adjust the effort expended to find valid alignments.\n\n";
-      #      push @bowtie_options,"-M $most_valid_alignments";sleep (5);
-    }
-    #  else{
-    #    push @bowtie_options,'-M 10';    # the default behavior for Bowtie 2 is to report (and sort) up to 500 alignments for a given sequence
-    #  }
-  }
-  else{ # Because of the way Bismark works we will always use the reporting option -k 2 (report up to 2 valid alignments) for Bowtie 1
-    push @bowtie_options,'-k 2';
-  }
-
-  ### --BEST
-  if ($bowtie2){
-    if ($best){    # Bowtie 2 does away with the concept of --best, so one can also not select --no-best when Bowtie 2 is to be used
-      die "The option '--no-best' is not compatible with Bowtie 2. Please respecify options\n";
-    }
-  }
-  else{
-    # --best is the default option for Bowtie 1, specifying --no-best can turn it off (e.g. to speed up alignment process)
-    unless ($best){
-      push @bowtie_options,'--best';
-    }
-  }
-
-  ### VANILLA BISMARK (BOWTIE 1) OUTPUT
-  if ($vanilla){
-    if ($bowtie2){
-      die "The options --bowtie2 and the --vanilla are not compatible. Please respecify!\n\n";
-    }
-  }
-  else{
-    $vanilla = 0;
-  }
-
-  ### PAIRED-END MAPPING
-  if ($mates1){
-    my @mates1 = (split (/,/,$mates1));
-    die "Paired-end mapping requires the format: -1 <mates1> -2 <mates2>, please respecify!\n" unless ($mates2);
-    my @mates2 = (split(/,/,$mates2));
-    unless (scalar @mates1 == scalar @mates2){
-      die "Paired-end mapping requires the same amounnt of mate1 and mate2 files, please respecify! (format: -1 <mates1> -2 <mates2>)\n";
-    }
-    while (1){
-      my $mate1 = shift @mates1;
-      my $mate2 = shift @mates2;
-      last unless ($mate1 and $mate2);
-      push @filenames,"$mate1,$mate2";
-    }
-    if ($bowtie2){
-      push @bowtie_options,'--no-mixed';     ## By default Bowtie 2 is not looking for single-end alignments if it can't find concordant or discordant alignments
-      push @bowtie_options,'--no-discordant';## By default Bowtie 2 is not looking for discordant alignments if it can't find concordant ones
-    }
-  }
-  elsif ($mates2){
-    die "Paired-end mapping requires the format: -1 <mates1> -2 <mates2>, please respecify!\n";
-  }
-
-  ### SINGLE-END MAPPING
-  # Single-end mapping will be performed if no mate pairs for paired-end mapping have been specified
-  my $singles;
-  unless ($mates1 and $mates2){
-    $singles = join (',',@ARGV);
-    unless ($singles){
-      die "\nNo filename supplied! Please specify one or more files for single-end Bismark mapping!\n";
-    }
-    $singles =~ s/\s/,/g;
-    @filenames = (split(/,/,$singles));
-    warn "\nFiles to be analysed:\n";
-    warn "@filenames\n\n";
-    sleep (3);
-  }
-
-  ### MININUM INSERT SIZE (PAIRED-END ONLY)
-  if (defined $minins){
-    die "-I/--minins can only be used for paired-end mapping!\n\n" if ($singles);
-    push @bowtie_options,"--minins $minins";
-  }
-
-  ### MAXIMUM INSERT SIZE (PAIRED-END ONLY)
-  if (defined $maxins){
-    die "-X/--maxins can only be used for paired-end mapping!\n\n" if ($singles);
-    push @bowtie_options,"--maxins $maxins";
-  }
-  else{
-    unless ($singles){
-      push @bowtie_options,'--maxins 500';
-    }
-  }
-
-  ### QUIET prints nothing  besides alignments (suppresses warnings)
-  if ($quiet){
-    push @bowtie_options,'--quiet';
-  }
-
-  ### CHUNKMBS needed to be increased to avoid memory exhaustion warnings for Bowtie 1, particularly for --best (and paired-end) alignments
-  unless ($bowtie2){ # Bowtie 2 does not have a chunkmbs option
-    if (defined $chunk){
-      push @bowtie_options,"--chunkmbs $chunk";
-    }
-    else{
-      push @bowtie_options,'--chunkmbs 512'; ## setting the default to 512MB (up from 64 default)
-    }
-  }
-
-
-  ### SUMMARY OF ALL BOWTIE OPTIONS
-  my $bowtie_options = join (' ',@bowtie_options);
-
-
-  ### STRAND-SPECIFIC LIBRARIES
-  my $directional;
-  if ($non_directional){
-    print "Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported.\n";
-    sleep (3);
-    $directional = 0;
-  }
-  else{
-    print "Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!).\n";
-    sleep (3);
-    $directional = 1; # Changed this to being the default behaviour
-  }
-
-  ### UNMAPPED SEQUENCE OUTPUT
-  $unmapped = 0 unless ($unmapped);
-
-  ### AMBIGUOUS ALIGNMENT SEQUENCE OUTPUT
-  $multi_map = 0 unless ($multi_map);
-
-
-  ### OUTPUT DIRECTORY
-
-  chdir $parent_dir or die "Failed to move back to current working directory\n";
-  if ($output_dir){
-    unless ($output_dir =~ /\/$/){
-      $output_dir =~ s/$/\//;
-    }
-
-    if (chdir $output_dir){
-      $output_dir = getcwd; #  making the path absolute
-      unless ($output_dir =~ /\/$/){
-	$output_dir =~ s/$/\//;
-      }
-    }
-    else{
-      mkdir $output_dir or die "Unable to create directory $output_dir $!\n";
-      warn "Created output directory $output_dir!\n\n";
-      chdir $output_dir or die "Failed to move to $output_dir\n";
-      $output_dir = getcwd; #  making the path absolute
-      unless ($output_dir =~ /\/$/){
-	$output_dir =~ s/$/\//;
-      }
-    }
-    warn "Output will be written into the directory: $output_dir\n";
-  }
-  else{
-    $output_dir = '';
-  }
-
-  ### TEMPORARY DIRECTORY for C->T and G->A transcribed files
-
-  chdir $parent_dir or die "Failed to move back to current working directory\n";
-  if ($temp_dir){
-    warn "\nUsing temp directory: $temp_dir\n";
-    unless ($temp_dir =~ /\/$/){
-      $temp_dir =~ s/$/\//;
-    }
-
-    if (chdir $temp_dir){
-      $temp_dir = getcwd; #  making the path absolute
-      unless ($temp_dir =~ /\/$/){
-	$temp_dir =~ s/$/\//;
-      }
-    }
-    else{
-      mkdir $temp_dir or die "Unable to create directory $temp_dir $!\n";
-      warn "Created temporary directory $temp_dir!\n\n";
-      chdir $temp_dir or die "Failed to move to $temp_dir\n";
-      $temp_dir = getcwd; #  making the path absolute
-      unless ($temp_dir =~ /\/$/){
-	$temp_dir =~ s/$/\//;
-      }
-    }
-    warn "Temporary files will be written into the directory: $temp_dir\n";
-  }
-  else{
-    $temp_dir = '';
-  }
-
-
-  return ($genome_folder,$CT_index_basename,$GA_index_basename,$path_to_bowtie,$sequence_format,$bowtie_options,$directional,$unmapped,$multi_map,$phred64,$solexa,$output_dir,$bowtie2,$vanilla,$sam_no_hd,$skip,$qupto,$temp_dir);
-}
-
-
-
-sub generate_SAM_header{
-  print OUT "\@HD\tVN:1.0\tSO:unsorted\n";          # @HD = header, VN = version, SO = sort order
-  foreach my $chr (keys %chromosomes){
-    my $length = length ($chromosomes{$chr});
-    print OUT "\@SQ\tSN:$chr\tLN:$length\n";        # @SQ = sequence, SN = seq name, LN = length
-  }
-  print OUT "\@PG\tID:Bismark\tVN:$bismark_version\tCL:\"bismark $command_line\"\n";        # @PG = program, ID = unique identifier, PN = program name name, VN = program version
-}
-
-### I would like to thank the following individuals for their valuable contributions to the Bismark SAM output format:
-### O. Tam (Sep 2010), C. Whelan (2011), E. Vidal (2011), T. McBryan (2011), P. Hickey (2011)
-
-sub single_end_SAM_output{
-  my ($id,$actual_seq,$methylation_call_params,$qual) = @_;
-  my $strand            = $methylation_call_params->{$id}->{alignment_strand};
-  my $chr               = $methylation_call_params->{$id}->{chromosome};	
-  my $start             = $methylation_call_params->{$id}->{position};	
-  my $stop              = $methylation_call_params->{$id}->{end_position};	
-  my $ref_seq           = $methylation_call_params->{$id}->{unmodified_genomic_sequence};
-  my $methcall          = $methylation_call_params->{$id}->{methylation_call};
-  my $read_conversion   = $methylation_call_params->{$id}->{read_conversion};
-  my $genome_conversion = $methylation_call_params->{$id}->{genome_conversion};
-  my $number_of_mismatches = $methylation_call_params->{$id}->{number_of_mismatches};	
-  ### This is a description of the bitwise FLAG field which needs to be set for the SAM file taken from: "The SAM Format Specification (v1.4-r985), September 7, 2011"
-  ## FLAG: bitwise FLAG. Each bit is explained in the following table:
-  ## Bit    Description                                                Comment                                Value
-  ## 0x1    template has multiple segments in sequencing               0: single-end 1: paired end            value: 2**0 (  1)
-  ## 0x2    each segment properly aligned according to the aligner     true only for paired-end alignments    value: 2**1 (  2)
-  ## 0x4    segment unmapped                                           ---                                           ---
-  ## 0x8    next segment in the template unmapped                      ---                                           ---
-  ## 0x10   SEQ being reverse complemented                                                                    value: 2**4 ( 16)
-  ## 0x20   SEQ of the next segment in the template being reversed                                            value: 2**5 ( 32)
-  ## 0x40   the first segment in the template                          read 1                                 value: 2**6 ( 64)
-  ## 0x80   the last segment in the template                           read 2                                 value: 2**7 (128)
-  ## 0x100  secondary alignment                                        ---                                           ---
-  ## 0x200  not passing quality controls                               ---                                           ---
-  ## 0x400  PCR or optical duplicate                                   ---                                           ---
-
-  #####
-
-  my $flag;                                                           # FLAG variable used for SAM format.
-  if ($strand eq "+"){
-    if ($read_conversion eq 'CT' and $genome_conversion eq 'CT'){
-      $flag = 0;                                                      # 0 for "+" strand (OT)
-    }
-    elsif ($read_conversion eq 'GA' and $genome_conversion eq 'GA'){
-      $flag = 16;                                                     # 16 for "-" strand (CTOB, yields information for the original bottom strand)
-    }
-    else{
-      die "Unexpected strand and read/genome conversion: strand: $strand, read conversion: $read_conversion, genome_conversion: $genome_conversion\n\n";
-    }
-  }
-  elsif ($strand eq "-"){
-    if ($read_conversion eq 'CT' and $genome_conversion eq 'GA'){
-      $flag = 16;                                                     # 16 for "-" strand (OB)
-    }
-    elsif ($read_conversion eq 'GA' and $genome_conversion eq 'CT'){
-      $flag = 0;                                                      # 0 for "+" strand (CTOT, yields information for the original top strand)
-    }
-    else{
-      die "Unexpected strand and read/genome conversion: strand: $strand, read conversion: $read_conversion, genome_conversion: $genome_conversion\n\n";
-    }
-  }
-  else{
-    die "Unexpected strand information: $strand\n\n";
-  }
-
-  #####
-
-  my $mapq = 255;                                                     # Assume mapping quality is unavailable
-
-  #####
-
-  my $cigar;
-  if ($bowtie2){
-    $cigar = $methylation_call_params->{$id}->{CIGAR};                # Actual CIGAR string reported by Bowtie 2
-  }
-  else{
-    $cigar = length($actual_seq) . "M";                               # Bowtie 1 output does not contain indels (only matches and mismatches)
-  }
-
-  #####	
-
-  my $rnext = "*";                                                    # Paired-end variable
-
-  #####
-
-  my $pnext = 0;                                                      # Paired-end variable
-
-  #####
-
-  my $tlen = 0;                                                       # Paired-end variable
-
-  #####
-
-  if ($read_conversion eq 'CT'){
-    $ref_seq = substr($ref_seq, 0, length($ref_seq) - 2);    # Removes additional nucleotides from the 3' end. This only works for the original top or bottom strands
-  }
-  else{
-    $ref_seq = substr($ref_seq, 2, length($ref_seq) - 2);    # Removes additional nucleotides from the 5' end. This works for the complementary strands in non-directional libraries
-  }
-
-  if ($strand eq '-'){
-    $actual_seq = revcomp($actual_seq);                               # Sequence represented on the forward genomic strand
-    $ref_seq = revcomp($ref_seq);                                     # Required for comparison with actual sequence
-    $qual = reverse $qual;                                            # if the sequence was reverse-complemented the quality string needs to be reversed as well
-  }
-
-  #####
-
-  my $hemming_dist = hemming_dist($actual_seq,$ref_seq);              # Edit distance to the reference, i.e. minimal number of one-nucleotide edits needed to transform the read string
-                                                                      # into the reference string. hemming_dist()
-  if ($bowtie2){
-    $hemming_dist += $methylation_call_params->{$id}->{indels};       # Adding the number of inserted/deleted bases which we parsed while getting the genomic sequence
-  }
-
-  my $NM_tag = "NM:i:$hemming_dist";                                  # Optional tag NM: edit distance based on nucleotide differences
-
-  #####
-
-  my $XX_tag = make_mismatch_string($actual_seq, $ref_seq);           # Optional tag XX: string providing mismatched reference bases in the alignment (NO indel information!)
-
-  #####
-
-  my $XM_tag;                                                         # Optional tag XM: Methylation Call String
-  if ($strand eq '+'){
-    $XM_tag = "XM:Z:$methcall";
-  }
-  elsif ($strand eq '-'){
-    $XM_tag = 'XM:Z:'.reverse $methcall;                              # if the sequence was reverse-complemented the methylation call string needs to be reversed as well
-  }
-
-  #####
-
-  my $XR_tag = "XR:Z:$read_conversion";                               # Optional tag XR: Read Conversion
-
-  #####
-
-  my $XG_tag = "XG:Z:$genome_conversion";                             # Optional tag XG: Genome Conversion
-
-  #####
-
-  # SAM format: QNAME, FLAG, RNAME, 1-based POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN, SEQ, QUAL, optional fields
-  print OUT join("\t",($id,$flag,$chr,$start,$mapq,$cigar,$rnext,$pnext,$tlen,$actual_seq,$qual,$NM_tag,$XX_tag,$XM_tag,$XR_tag,$XG_tag)),"\n";
-}
-
-
-sub paired_end_SAM_output{
-  my ($id,$actual_seq_1,$actual_seq_2,$methylation_call_params,$qual_1,$qual_2) = @_;
-  my $strand_1                = $methylation_call_params->{$id}->{alignment_read_1}; # Bowtie 1 only reports the read 1 alignment strand
-  my $strand_2                = $methylation_call_params->{$id}->{alignment_read_2};
-  my $chr                     = $methylation_call_params->{$id}->{chromosome};	
-  my $ref_seq_1               = $methylation_call_params->{$id}->{unmodified_genomic_sequence_1};
-  my $ref_seq_2               = $methylation_call_params->{$id}->{unmodified_genomic_sequence_2};
-  my $methcall_1              = $methylation_call_params->{$id}->{methylation_call_1};
-  my $methcall_2              = $methylation_call_params->{$id}->{methylation_call_2};
-  my $read_conversion_1       = $methylation_call_params->{$id}->{read_conversion_1};
-  my $read_conversion_2       = $methylation_call_params->{$id}->{read_conversion_2};
-  my $genome_conversion       = $methylation_call_params->{$id}->{genome_conversion};
-  my $number_of_mismatches_1  = $methylation_call_params->{$id}->{number_of_mismatches_1}; # only needed for custom allele-specific output, not the default!
-  my $number_of_mismatches_2  = $methylation_call_params->{$id}->{number_of_mismatches_2};
-
-  my $id_1 = $id.'/1';
-  my $id_2 = $id.'/2';
-
-  # Allows all degenerate nucleotide sequences in reference genome
-  die "Reference sequence ($ref_seq_1) contains invalid nucleotides!\n" if $ref_seq_1 =~ /[^ACTGNRYMKSWBDHV]/i;
-  die "Reference sequence ($ref_seq_2) contains invalid nucleotides!\n" if $ref_seq_2 =~ /[^ACTGNRYMKSWBDHV]/i;
-
-  my $index; # used to store the srand origin of the alignment in a less convoluted way
-
-  if ($read_conversion_1 eq 'CT' and $genome_conversion eq 'CT'){
-    $index = 0; ## this is OT   (original top strand)
-  }	
-  elsif ($read_conversion_1 eq 'GA' and $genome_conversion eq 'GA'){
-    $index = 1; ## this is CTOB (complementary to OB)
-  }
-  elsif ($read_conversion_1 eq 'GA' and $genome_conversion eq 'CT'){
-    $index = 2; ## this is CTOT (complementary to OT)
-  }
-  elsif ($read_conversion_1 eq 'CT' and $genome_conversion eq 'GA'){
-    $index = 3; ## this is OB   (original bottom)
-  }
-  else {
-    die "Unexpected combination of read 1 and genome conversion: $read_conversion_1 / $genome_conversion\n";
-  }
-	
-  ### we need to remove 2 bp of the genomic sequence as we were extracting read + 2bp long fragments to make a methylation call at the
-  ### first or last position.
-
-  if ($index == 0 or $index == 3){ # OT or OB
-    $ref_seq_1 = substr($ref_seq_1,0,length($ref_seq_1)-2);
-    $ref_seq_2 = substr($ref_seq_2,2,length($ref_seq_2)-2);
-  }
-  else{ # CTOT or CTOB
-    $ref_seq_1 = substr($ref_seq_1,2,length($ref_seq_1)-2);
-    $ref_seq_2 = substr($ref_seq_2,0,length($ref_seq_2)-2);
-  }
-
-  #####
-
-  my $start_read_1;
-  my $start_read_2;
-  # adjusting end positions
-
-  if ($bowtie2){
-    $start_read_1 = $methylation_call_params->{$id}->{position_1};
-    $start_read_2 = $methylation_call_params->{$id}->{position_2};
-  }
-  else{ # Bowtie 1 output. $strand_1 stores the alignment of Read 1
-    if ($strand_1 eq '+'){ # Read 1 aligns to the + strand
-      $start_read_1 = $methylation_call_params->{$id}->{start_seq_1};
-      $start_read_2 = $methylation_call_params->{$id}->{alignment_end} - length ($actual_seq_2) + 1;
-    }
-    else{ # read 1 is on the - strand
-      $start_read_1 = $methylation_call_params->{$id}->{alignment_end} - length ($actual_seq_1) + 1;
-      $start_read_2 = $methylation_call_params->{$id}->{start_seq_1};
-    }
-  }
-
-  #####
-
-  my $end_read_1;
-  my $end_read_2;
-  # adjusting end positions
-
-  if ($bowtie2){
-    $end_read_1 = $methylation_call_params->{$id}->{end_position_1};
-    $end_read_2 = $methylation_call_params->{$id}->{end_position_2};
-  }
-  else{ # Bowtie 1 output. $strand_1 stores the alignment of Read 1
-    if ($strand_1 eq '+'){ # Read 1 aligns to the + strand
-      $end_read_1 = $methylation_call_params->{$id}->{start_seq_1} + length ($actual_seq_1)-1;
-      $end_read_2 = $methylation_call_params->{$id}->{alignment_end};
-      }
-    else{
-      $end_read_1 = $methylation_call_params->{$id}->{alignment_end};
-      $end_read_2 = $methylation_call_params->{$id}->{start_seq_1} + length ($actual_seq_2)-1;
-    }
-  }
-
-  #####
-
-  ### This is a description of the bitwise FLAG field which needs to be set for the SAM file taken from: "The SAM Format Specification (v1.4-r985), September 7, 2011"
-  ## FLAG: bitwise FLAG. Each bit is explained in the following table:
-  ## Bit    Description                                                Comment                                Value
-  ## 0x1    template having multiple segments in sequencing            0: single-end 1: paired end            value: 2^^0 (  1)
-  ## 0x2    each segment properly aligned according to the aligner     true only for paired-end alignments    value: 2^^1 (  2)
-  ## 0x4    segment unmapped                                           ---                                           ---
-  ## 0x8    next segment in the template unmapped                      ---                                           ---
-  ## 0x10   SEQ being reverse complemented                             - strand alignment                     value: 2^^4 ( 16)
-  ## 0x20   SEQ of the next segment in the template being reversed     + strand alignment                     value: 2^^5 ( 32)
-  ## 0x40   the first segment in the template                          read 1                                 value: 2^^6 ( 64)
-  ## 0x80   the last segment in the template                           read 2                                 value: 2^^7 (128)
-  ## 0x100  secondary alignment                                        ---                                           ---
-  ## 0x200  not passing quality controls                               ---                                           ---
-  ## 0x400  PCR or optical duplicate                                   ---                                           ---
-
-  ### As the FLAG value do not consider that there might be 4 different bisulfite strands of DNA, we are trying to make FLAG tags which take the strand identity into account
-
-  # strands OT and CTOT will be treated as aligning to the top strand (both sequences are scored as aligning to the top strand)
-  # strands OB and CTOB will be treated as aligning to the bottom strand (both sequences are scored as reverse complemented sequences)
-
-  my $flag_1;                                                          # FLAG variable used for SAM format
-  my $flag_2;
-
-  if ($index == 0){       # OT
-    $flag_1 = 67;                                                      # Read 1 is on the + strand  (1+2+64) (Read 2 is technically reverse-complemented, but we do not score it)
-    $flag_2 = 131;                                                     # Read 2 is on - strand but informative for the OT        (1+2+128)
-  }
-  elsif ($index == 1){    # CTOB
-    $flag_1 = 115;                                                     # Read 1 is on the + strand, we score for OB  (1+2+16+32+64)
-    $flag_2 = 179;                                                     # Read 2 is on the - strand  (1+2+16+32+128)
-  }
-  elsif ($index == 2){    # CTOT
-    $flag_1 = 67;                                                      # Read 1 is on the - strand (CTOT) strand, but we score it for OT (1+2+64)
-    $flag_2 = 131;                                                     # Read 2 is on the + strand, score it for OT (1+2+128)
-  }
-  elsif ($index == 3){    # OB
-    $flag_1 = 115;                                                     # Read 1 is on the - strand, we score for OB  (1+2+16+32+64)
-    $flag_2 = 179;                                                     # Read 2 is on the + strand  (1+2+16+32+128)
-  }
-
-  #####
-
-  my $mapq = 255;                                                      # Mapping quality is unavailable
-
-  #####
-
-  my $cigar_1;
-  my $cigar_2;
-
-  if ($bowtie2){
-    $cigar_1 = $methylation_call_params->{$id}->{CIGAR_1};             # Actual CIGAR string reported by Bowtie 2
-    $cigar_2 = $methylation_call_params->{$id}->{CIGAR_2};
-  }
-  else{
-    $cigar_1 = length($actual_seq_1) . "M";                            # Assume no indels for Bowtie 1  mapping (only matches and mismatches)
-    $cigar_2 = length($actual_seq_2) . "M";
-  }
-
-  #####
-
-  my $rnext = '=';                                                     # Chromosome of mate; applies to both reads
-
-  #####
-
-  my $pnext_1 = $start_read_2;                                         # Leftmost position of mate
-  my $pnext_2 = $start_read_1;
-
-  #####
-
-  my $tlen_1;                                                          # signed observed Template LENgth (or inferred fragment size)
-  my $tlen_2;
-
-  if ($bowtie2){
-
-    if ($start_read_1 <= $start_read_2){
-
-      # Read 1 alignment is leftmost
-
-      if ($end_read_2 >= $end_read_1){
-	
-	# ------------------------->     read 1   reads overlapping
-	#  <-------------------------    read 2
-	#
-	# or
-	#
-	# ------------------------->     read 1
-	#   <-----------------------     read 2   read 2 contained within read 1
-	#
-	# or
-	#
-	# ------------------------->     read 1   reads 1 and 2 exactly overlapping
-	# <-------------------------     read 2
-	#
-
-	# dovetailing of reads is not enabled for Bowtie 2 alignments
-
-	$tlen_1 = $end_read_2 - $start_read_1 + 1;                         # Leftmost read has a + sign,
-	$tlen_2 = $start_read_1 - $end_read_2 - 1;                         # Rightmost read has a - sign
-      }
-      elsif ($end_read_2 < $end_read_1){
-
-	# ------------------------->     read 1
-	#       <-----------             read 2   read 2 contained within read 1
-	#
-	# or
-	#
-	# ------------------------->     read 1
-	# <-----------                   read 2   read 2 contained within read 1
-
-	# start and end of read 2  are fully contained within read 1
-	$tlen_1 = 0;                                                       # Set as 0 when the information is unavailable
-	$tlen_2 = 0;                                                       # Set as 0 when the information is unavailable
-      }
-
-    }
-
-    elsif ($start_read_2 < $start_read_1){
-
-      if ($end_read_1 >= $end_read_2){
-
-      # Read 2 alignment is leftmost
-
-	# ------------------------->     read 2   reads overlapping
-	#  <-------------------------    read 1
-	#
-	# or
-	#
-	# ------------------------->     read 2
-	#   <-----------------------     read 1   read 1 contained within read 2
-	#
-	#
-
-	$tlen_2 = $end_read_1 - $start_read_2 + 1;                         # Leftmost read has a + sign,
-	$tlen_1 = $start_read_2 - $end_read_1 - 1;                         # Rightmost read has a - sign
-      }
-      elsif ($end_read_1 < $end_read_2){
-
-	# ------------------------->     read 2
-	#       <-----------             read 1   read 1 contained within read 2
-	#
-	# or
-	#
-	# ------------------------->     read 2
-	# <-----------                   read 1   read 1 contained within read 2
-	
-	# start and end of read 1  are fully contained within read 2
-	$tlen_1 = 0;                                                       # Set as 0 when the information is unavailable
-	$tlen_2 = 0;                                                       # Set as 0 when the information is unavailable
-      }
-    }
-  }
-
-  else{ # Bowtie 1
-
-    if ($end_read_2 >= $end_read_1){
-      # Read 1 alignment is leftmost
-      # ------------------------->  read 1
-      #  <------------------------- read 2
-      # this is the most extreme case for Bowtie 1 alignments, reads do not contain each other, also no dovetailing
-
-      $tlen_1 = $end_read_2 - $start_read_1 + 1;                         # Leftmost read has a + sign,
-      $tlen_2 = $start_read_1 - $end_read_2 - 1;                         # Rightmost read has a - sign
-    }
-    else{
-      # Read 2 alignment is leftmost
-      # ------------------------->  read 2
-      #  <------------------------- read 1
-      # this is the most extreme case for Bowtie 1 alignments, reads do not contain each other, also no dovetailing
-
-      $tlen_2 = $end_read_1 - $start_read_2 + 1;                         # Leftmost read has a + sign,
-      $tlen_1 = $start_read_2 - $end_read_1 - 1;                         # Rightmost read has a - sign
-    }
-  }
-
-  #####
-
-  # adjusting the strand of the sequence before we use them to generate mismatch strings
-  if ($strand_1 eq '-'){
-    $actual_seq_1 = revcomp($actual_seq_1);                            # Sequence represented on the forward genomic strand
-    $ref_seq_1 = revcomp($ref_seq_1);                                  # Required for comparison with actual sequence
-    $qual_1 = reverse $qual_1;                                         # we need to reverse the quality string as well
-  }
-  if ($strand_2 eq '-'){
-    $actual_seq_2 = revcomp($actual_seq_2);                            # Mate sequence represented on the forward genomic strand
-    $ref_seq_2 = revcomp($ref_seq_2);                                  # Required for comparison with actual sequence
-    $qual_2 = reverse $qual_2;                                         # If the sequence gets reverse complemented we reverse the quality string as well
-  }
-
-  #  print "$actual_seq_1\n$ref_seq_1\n\n";
-  #  print "$actual_seq_2\n$ref_seq_2\n\n";
-
-  #####
-
-  my $hemming_dist_1 = hemming_dist($actual_seq_1,$ref_seq_1);         # Minimal number of one-nucleotide edits needed to transform the read string into the reference sequence
-  my $hemming_dist_2 = hemming_dist($actual_seq_2,$ref_seq_2);
-  if ($bowtie2){
-    $hemming_dist_1 += $methylation_call_params->{$id}->{indels_1};    # Adding the number of inserted/deleted bases which we parsed while getting the genomic sequence
-    $hemming_dist_2 += $methylation_call_params->{$id}->{indels_2};    # Adding the number of inserted/deleted bases which we parsed while getting the genomic sequence
-  }
-  my $NM_tag_1 = "NM:i:$hemming_dist_1";                               # Optional tag NM: edit distance based on nucleotide differences
-  my $NM_tag_2 = "NM:i:$hemming_dist_2";                               # Optional tag NM: edit distance based on nucleotide differences
-
-  #####
-
-  my $XX_tag_1 = make_mismatch_string($actual_seq_1,$ref_seq_1);       # Optional tag XX: String providing mismatched reference bases in the alignment (NO indel information!)
-  my $XX_tag_2 = make_mismatch_string($actual_seq_2,$ref_seq_2);
-
-  #####
-
-  my $XM_tag_1;                                                        # Optional tag XM: Methylation call string
-  my $XM_tag_2;
-
-  if ($strand_1 eq '-'){
-    $XM_tag_1 = 'XM:Z:'.reverse $methcall_1;                           # Needs to be reversed if the sequence was reverse complemented
-  }
-  else{
-    $XM_tag_1 = "XM:Z:$methcall_1";
-  }
-
-  if ($strand_2 eq '-'){
-    $XM_tag_2 = 'XM:Z:'.reverse $methcall_2;                           # Needs to be reversed if the sequence was reverse complemented
-  }
-  else{
-    $XM_tag_2 = "XM:Z:$methcall_2";
-  }
-
-  #####
-
-  my $XR_tag_1 = "XR:Z:$read_conversion_1";                            # Optional tag XR: Read 1 conversion state
-  my $XR_tag_2 = "XR:Z:$read_conversion_2";                            # Optional tag XR: Read 2 conversion state
-
-  #####
-
-  my $XG_tag = "XG:Z:$genome_conversion";                              # Optional tag XG: Genome Conversion state; valid for both reads
-
-  #####
-
-  # SAM format: QNAME, FLAG, RNAME, 1-based POS, MAPQ, CIGAR, RNEXT, PNEXT, TLEN, SEQ, QUAL, optional fields
-  print OUT join("\t", ($id_1, $flag_1, $chr, $start_read_1, $mapq, $cigar_1, $rnext, $pnext_1, $tlen_1, $actual_seq_1, $qual_1, $NM_tag_1, $XX_tag_1, $XM_tag_1,$XR_tag_1,$XG_tag)), "\n";
-  print OUT join("\t", ($id_2, $flag_2, $chr, $start_read_2, $mapq, $cigar_2, $rnext, $pnext_2, $tlen_2, $actual_seq_2, $qual_2, $NM_tag_2, $XX_tag_2, $XM_tag_2,$XR_tag_2,$XG_tag)), "\n";
-}
-
-sub revcomp{
-  my $seq = shift or die "Missing seq to reverse complement\n";
-  $seq = reverse $seq;
-  $seq =~ tr/ACTGactg/TGACTGAC/;
-  return $seq;
-}
-
-sub hemming_dist{
-  my $matches = 0;
-  my @actual_seq = split //,(shift @_);
-  my @ref_seq = split //,(shift @_);
-  foreach (0..$#actual_seq){
-    ++$matches if ($actual_seq[$_] eq $ref_seq[$_]);
-  }
-  return my $hd = scalar @actual_seq - $matches;
-}
-
-sub make_mismatch_string{
-  my $actual_seq = shift or die "Missing actual sequence";
-  my $ref_seq = shift or die "Missing reference sequence";
-  my $XX_tag = "XX:Z:";
-  my $tmp = ($actual_seq ^ $ref_seq);                    # Bitwise comparison
-  my $prev_mm_pos = 0;
-  while($tmp =~ /[^\0]/g){                               # Where bitwise comparison showed a difference
-    my $nuc_match = pos($tmp) - $prev_mm_pos - 1;        # Generate number of nucleotide that matches since last mismatch
-    my $nuc_mm = substr($ref_seq, pos($tmp) - 1, 1) if pos($tmp) <= length($ref_seq);  # Obtain reference nucleotide that was different from the actual read
-    $XX_tag .= "$nuc_match" if $nuc_match > 0;           # Ignore if mismatches are adjacent to each other
-    $XX_tag .= "$nuc_mm" if defined $nuc_mm;             # Ignore if there is no mismatch (prevents uninitialized string concatenation)
-    $prev_mm_pos = pos($tmp);                            # Position of last mismatch
-  }
-  my $end_matches = length($ref_seq) - $prev_mm_pos;     # Provides number of matches from last mismatch till end of sequence
-  $XX_tag .= "$end_matches" if $end_matches > 0;         # Ignore if mismatch is at the end of sequence
-  return $XX_tag;
-}
-
-
-
-sub print_helpfile{
-  print << "HOW_TO";
-
-
-     This program is free software: you can redistribute it and/or modify
-     it under the terms of the GNU General Public License as published by
-     the Free Software Foundation, either version 3 of the License, or
-     (at your option) any later version.
-
-     This program is distributed in the hope that it will be useful,
-     but WITHOUT ANY WARRANTY; without even the implied warranty of
-     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-     GNU General Public License for more details.
-     You should have received a copy of the GNU General Public License
-     along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-
-
-DESCRIPTION
-
-
-The following is a brief description of command line options and arguments to control the Bismark
-bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
-reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
-version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
-Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
-(C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
-forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie (1 or 2)
-are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
-sequence from the genome and determine if there were any protected C's present or not.
-
-As of version 0.7.0 Bismark will only run 2 alignment threads for OT and OB in parallel, the 4 strand mode can be
-re-enabled by using --non_directional.
-
-The final output of Bismark is in SAM format by default. For Bowtie 1 one can alos choose to report the old
-'vanilla' output format, which is a single tab delimited file with all sequences that have a unique best
-alignment to any of the 4 possible strands of a bisulfite PCR product. Both formats are described in more detail below.
-
-
-USAGE: bismark [options] <genome_folder> {-1 <mates1> -2 <mates2> | <singles>}
-
-
-ARGUMENTS:
-
-<genome_folder>          The path to the folder containing the unmodified reference genome
-                         as well as the subfolders created by the Bismark_Genome_Preparation
-                         script (/Bisulfite_Genome/CT_conversion/ and /Bisulfite_Genome/GA_conversion/).
-                         Bismark expects one or more fastA files in this folder (file extension: .fa
-                         or .fasta). The path can be relative or absolute.
-
--1 <mates1>              Comma-separated list of files containing the #1 mates (filename usually includes
-                         "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
-                         correspond file-for-file and read-for-read with those specified in <mates2>.
-                         Reads may be a mix of different lengths. Bismark will produce one mapping result
-                         and one report file per paired-end input file pair.
-
--2 <mates2>              Comma-separated list of files containing the #2 mates (filename usually includes
-                         "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
-                         correspond file-for-file and read-for-read with those specified in <mates1>.
-                         Reads may be a mix of different lengths.
-
-<singles>                A comma- or space-separated list of files containing the reads to be aligned (e.g.
-                         lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
-                         produce one mapping result and one report file per input file.
-
-
-OPTIONS:
-
-
-Input:
-
--q/--fastq               The query input files (specified as <mate1>,<mate2> or <singles> are FASTQ
-                         files (usually having extension .fg or .fastq). This is the default. See also
-                         --solexa-quals.
-
--f/--fasta               The query input files (specified as <mate1>,<mate2> or <singles> are FASTA
-                         files (usually havin extension .fa, .mfa, .fna or similar). All quality values
-                         are assumed to be 40 on the Phred scale.
-
--s/--skip <int>          Skip (i.e. do not align) the first <int> reads or read pairs from the input.
-
--u/--upto <int>          Only aligns the first <int> reads or read pairs from the input. Default: no limit.
-
---phred33-quals          FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
-
---phred64-quals          FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
-
---solexa-quals           Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
-                         (which can't). The formula for conversion is: 
-                         phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
-                         is usually the right option for use with (unconverted) reads emitted by the GA
-                         Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
-
---solexa1.3-quals        Same as --phred64-quals. This is usually the right option for use with (unconverted)
-                         reads emitted by GA Pipeline version 1.3 or later. Default: off.
-
---path_to_bowtie         The full path </../../> to the Bowtie (1 or 2) installation on your system. If not
-                         specified it is assumed that Bowtie (1 or 2) is in the PATH.
-
-
-Alignment:
-
--n/--seedmms <int>       The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
-                         of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the 
-                         default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
-
--l/--seedlen             The "seed length"; i.e., the number of bases of the high quality end of the read to
-                         which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
-                         larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
-
--e/--maqerr <int>        Maximum permitted total of quality values at all mismatched read positions throughout
-                         the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
-                         quality values to the nearest 10 and saturates at 30. This value is not relevant for
-                         Bowtie 2.
-
---chunkmbs <int>         The number of megabytes of memory a given thread is given to store path descriptors in
-                         --best mode. Best-first search must keep track of many paths at once to ensure it is
-                         always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
-                         memory impact of the descriptors, but they can still grow very large in some cases. If
-                         you receive an error message saying that chunk memory has been exhausted in --best mode,
-                         try adjusting this parameter up to dedicate more memory to the descriptors. This value
-                         is not relevant for Bowtie 2. Default: 512.
-
--I/--minins <int>        The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
-                         a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
-                         with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
-                         satisfied). A 19-bp gap would not be valid in that case. Default: 0.
-
--X/--maxins <int>        The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
-                         a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
-                         60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
-                         A 61-bp gap would not be valid in that case. Default: 500.
-
-
-Bowtie 1 Reporting:
-
--k <2>                   Due to the way Bismark works Bowtie will report up to 2 valid alignments. This option
-                         will be used by default.
-
---best                   Make Bowtie guarantee that reported singleton alignments are "best" in terms of stratum
-                         (i.e. number of mismatches, or mismatches in the seed in the case if -n mode) and in
-                         terms of the quality; e.g. a 1-mismatch alignment where the mismatch position has Phred
-                         quality 40 is preferred over a 2-mismatch alignment where the mismatched positions both
-                         have Phred quality 10. When --best is not specified, Bowtie may report alignments that
-                         are sub-optimal in terms of stratum and/or quality (though an effort is made to report
-                         the best alignment). --best mode also removes all strand bias. Note that --best does not
-                         affect which alignments are considered "valid" by Bowtie, only which valid alignments
-                         are reported by Bowtie. Bowtie is about 1-2.5 times slower when --best is specified.
-                         Default: on.
-
---no_best                Disables the --best option which is on by default. This can speed up the alignment process,
-                         e.g. for testing purposes, but for credible results it is not recommended to disable --best.
-
-
-Output:
-
---non_directional        The sequencing library was constructed in a non strand-specific manner, alignments to all four
-                         bisulfite strands will be reported. Default: OFF.
-
-                         (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
-                         to the original strands are merely theoretical and should not exist in reality. Specifying directional
-                         alignments (which is the default) will only run 2 alignment threads to the original top (OT)
-                         or bottom (OB) strands in parallel and report these alignments. This is the recommended option
-                         for sprand-specific libraries).
-
---sam-no-hd              Suppress SAM header lines (starting with @). This might be useful when very large input files are
-                         split up into several smaller files to run concurrently and the output files are to be merged.
-
---quiet                  Print nothing besides alignments.
-
---vanilla                Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
-                         of SAM format output.
-
--un/--unmapped           Write all reads that could not be aligned to a file in the output directory. Written reads will
-                         appear as they did in the input, without any translation of quality values that may have
-                         taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
-                         and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
-                         with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
-                         are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
-
---ambiguous              Write all reads which produce more than one valid alignment with the same number of lowest
-                         mismatches or other reads that fail to align uniquely to a file in the output directory.
-                         Written reads will appear as they did in the input, without any of the translation of quality
-                         values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
-                         parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
-                         _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
-
--o/--output_dir <dir>    Write all output files into this directory. By default the output files will be written into
-                         the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
-                         to create it first. The path to the output folder can be either relative or absolute.
-
---temp_dir <dir>         Write temporary files to this directory instead of into the same directory as the input files. If
-                         the specified folder does not exist, Bismark will attempt to create it first. The path to the
-                         temporary folder can be either relative or absolute.
-
-
-
-Other:
-
--h/--help                Displays this help file.
-
--v/--version             Displays version information.
-
-
-BOWTIE 2 SPECIFIC OPTIONS
-
---bowtie2                Uses Bowtie 2 instead of Bowtie 1. Bismark limits Bowtie 2 to only perform end-to-end
-                         alignments, i.e. searches for alignments involving all read characters (also called 
-                         untrimmed or unclipped alignments). Bismark assumes that raw sequence data is adapter
-                         and/or quality trimmed where appropriate. Default: off.
-
-Bowtie 2 alignment options:
-
--N <int>                 Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
-                         Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
-                         but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
-                         Bowtie 1 see -n).
-
--L <int>                 Sets the length of the seed substrings to align during multiseed alignment. Smaller values
-                         make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
-                         used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
-                         Bowtie 1 see -l).
-
---ignore-quals           When calculating a mismatch penalty, always consider the quality value at the mismatched
-                         position to be the highest possible, regardless of the actual value. I.e. input is treated
-                         as though all quality values are high. This is also the default behavior when the input
-                         doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
-
-
-Bowtie 2 paired-end options:
-
---no-mixed               This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
-                         it cannot find a concordant or discordant alignment for a pair. This option is invariable and
-                         and on by default.
-
---no-discordant          Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
-                         A discordant alignment is an alignment where both mates align uniquely, but that does not
-                         satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
-                         and it is on by default.
-
-
-Bowtie 2 effort options:
-
--D <int>                 Up to <int> consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
-                         the alignments found so far. A seed extension "fails" if it does not yield a new best or a
-                         new second-best alignment. Default: 15.
-
--R <int>                 <int> is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
-                         When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
-                         mismatches allowed) at different offsets and searches for more alignments. A read is considered
-                         to have repetitive seeds if the total number of seed hits divided by the number of seeds
-                         that aligned at least once is greater than 300. Default: 2.
-
-Bowtie 2 parallelization options:
-
-
--p NTHREADS              Launch NTHREADS parallel search threads (default: 1). Threads will run on separate processors/cores
-                         and synchronize when parsing reads and outputting alignments. Searching for alignments is highly
-                         parallel, and speedup is close to linear. Increasing -p increases Bowtie 2's memory footprint.
-                         E.g. when aligning to a human genome index, increasing -p from 1 to 8 increases the memory footprint
-                         by a few hundred megabytes. This option is only available if bowtie is linked with the pthreads
-                         library (i.e. if BOWTIE_PTHREADS=0 is not specified at build time). In addition, this option will
-                         automatically use the option '--reorder', which guarantees that output SAM records are printed in
-                         an order corresponding to the order of the reads in the original input file, even when -p is set
-                         greater than 1 (Bismark requires the Bowtie 2 output to be this way). Specifying --reorder and
-                         setting -p greater than 1 causes Bowtie 2 to run somewhat slower and use somewhat more memory then
-                         if --reorder were not specified. Has no effect if -p is set to 1, since output order will naturally
-                         correspond to input order in that case.
-
-Bowtie 2 Scoring options:
-
---score_min <func>       Sets a function governing the minimum alignment score needed for an alignment to be considered
-                         "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
-                         L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
-                         See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
-                         L,0,-0.2.
-
---rdg <int1>,<int2>      Sets the read gap open (<int1>) and extend (<int2>) penalties. A read gap of length N gets a penalty
-                         of <int1> + N * <int2>. Default: 5, 3.
-
---rfg <int1>,<int2>      Sets the reference gap open (<int1>) and extend (<int2>) penalties. A reference gap of length N gets
-                         a penalty of <int1> + N * <int2>. Default: 5, 3.
-
-
-Bowtie 2 Reporting options:
-
--most_valid_alignments <int> This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is
-                         deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
-                         default mode, but adjusting the -M setting is deprecated.  Use the -D and -R options to adjust the
-                         effort expended to find valid alignments.
-
-                         For reference, this used to be the old (now deprecated) description of -M:
-                         Bowtie 2 searches for at most <int>+1 distinct, valid alignments for each read. The search terminates when it
-                         can't find more distinct valid alignments, or when it finds <int>+1 distinct alignments, whichever
-                         happens first. Only the best alignment is reported. Information from the other alignments is used to
-                         estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes 
-                         Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
-                         aligns many places. For reads that have more than <int>+1 distinct, valid alignments, Bowtie 2 does not
-                         guarantee that the alignment reported is the best possible in terms of alignment score. -M is
-                         always used and its default value is set to 10.
-
-
-'VANILLA' Bismark  OUTPUT:
-
-Single-end output format (tab-separated):
-
- (1) <seq-ID>
- (2) <read alignment strand>
- (3) <chromosome>
- (4) <start position>
- (5) <end position>
- (6) <observed bisulfite sequence>
- (7) <equivalent genomic sequence>
- (8) <methylation call>
- (9) <read conversion
-(10) <genome conversion>
-(11) <read quality score (Phred33)>
-
-
-Paired-end output format (tab-separated):
- (1) <seq-ID>
- (2) <read 1 alignment strand>
- (3) <chromosome>
- (4) <start position>
- (5) <end position>
- (6) <observed bisulfite sequence 1>
- (7) <equivalent genomic sequence 1>
- (8) <methylation call 1>
- (9) <observed bisulfite sequence 2>
-(10) <equivalent genomic sequence 2>
-(11) <methylation call 2>
-(12) <read 1 conversion
-(13) <genome conversion>
-(14) <read 1 quality score (Phred33)>
-(15) <read 2 quality score (Phred33)>
-
-
-Bismark SAM OUTPUT (default):
-
- (1) QNAME  (seq-ID)
- (2) FLAG   (this flag tries to take the strand a bisulfite read originated from into account (this is different from ordinary DNA alignment flags!))
- (3) RNAME  (chromosome)
- (4) POS    (start position)
- (5) MAPQ   (always 255)
- (6) CIGAR
- (7) RNEXT
- (8) PNEXT
- (9) TLEN
-(10) SEQ
-(11) QUAL   (Phred33 scale)
-(12) NM-tag (edit distance to the reference)
-(13) XX-tag (base-by-base mismatches to the reference. This does not include indels)
-(14) XM-tag (methylation call string)
-(15) XR-tag (read conversion state for the alignment)
-(16) XG-tag (genome conversion state for the alignment)
-
-Each read of paired-end alignments is written out in a separate line in the above format.
-
-
-This script was last edited on 21 Aug 2012.
-
-HOW_TO
-}
--- a/bismark_bowtie2_wrapper.xml	Tue Dec 25 05:45:46 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,616 +0,0 @@
-<tool id="bismark_bowtie2" name="Bismark" version="0.7.7.2">
-    <!-- Wrapper compatible with Bismark version 0.7.7 -->
-    <description>bisulfite mapper (bowtie2)</description>
-    <!--<version_command>bismark version</version_command>-->
-    <requirements>
-        <requirement type="set_environment">SCRIPT_PATH</requirement>
-        <requirement type="package" version="0.12.8">bowtie</requirement>
-        <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
-    </requirements>
-    <parallelism method="basic"></parallelism>
-    <command interpreter="python">
-        bismark_wrapper.py
-        
-        ## Change this to accommodate the number of threads you have available.
-        --num-threads 4
-
-        --bismark_path \$SCRIPT_PATH
-
-        --bowtie2
-
-        ##
-        ## Bismark Genome Preparation, if desired.
-        ##
-
-        ## Handle reference file.
-        #if $refGenomeSource.genomeSource == "history":
-            --own-file=$refGenomeSource.ownFile
-        #else:
-            --indexes-path ${refGenomeSource.index.fields.path}
-        #end if
-
-
-        ##
-        ##  Input parameters
-        ##
-
-
-        #if $singlePaired.sPaired == "single":
-            --single-paired $singlePaired.input_singles
-
-            #if $singlePaired.input_singles.ext == "fastqillumina":
-                --phred64-quals
-                --fastq
-            #elif $singlePaired.input_singles.ext == "fastqsanger":
-                --fastq
-            #elif $singlePaired.input_singles.ext == "fasta":
-                --fasta
-            #end if
-        #else:
-            --mate-paired 
-            --mate1 $singlePaired.input_mate1
-            --mate2 $singlePaired.input_mate2
-
-            #if $singlePaired.input_mate1.ext == "fastqillumina":
-                --phred64-quals
-                --fastq
-            #elif $singlePaired.input_mate1.ext == "fastqsanger":
-                --fastq
-            #elif $singlePaired.input_mate1.ext == "fasta":
-                --fasta
-            #end if
-
-            -I $singlePaired.minInsert
-            -X $singlePaired.maxInsert
-        #end if
-
-
-        ## for now hardcode the value for the required memory per thread in --best mode
-        --chunkmbs 512
-
-
-        #if $params.settingsType == "custom":
-
-            ## default 20
-            --seed-len $params.seed_len
-            ## default 0
-            --seed-mismatches $params.seed_mismatches
-            ## default 15
-            --seed-extention-attempts $params.seed_extention_attempts
-            ## default 2
-            --max-reseed $params.max_reseed
-            
-            ## default 70
-            ##--maqerr $params.maqerr
-
-            ## default unlimited
-            #if $params.qupto != 0:
-                --qupto $params.qupto
-            #end if
-            #if $params.skip_reads != 0:
-                --skip-reads $params.skip_reads
-            #end if
-
-            ## if set, disable the original behaviour
-            $params.no_mixed
-            ## if set, disable the original behaviour
-            $params.no_discordant
-
-
-            ###if str($params.isReportOutput) == "yes":
-            ##    --output-report-file $report_file
-            ###end if
-
-        #end if
-
-        ##
-        ## Output parameters.
-        ##
-        --output $output
-        $suppress_header
-
-      #if str( $singlePaired.sPaired ) == "single"
-        #if $output_unmapped_reads_l
-          --output-unmapped-reads $output_unmapped_reads_l
-        #end if
-        #if $output_suppressed_reads_l
-          --output-suppressed-reads $output_suppressed_reads_l
-        #end if
-      #else
-        #if $output_unmapped_reads_l and $output_unmapped_reads_r
-          --output-unmapped-reads-l $output_unmapped_reads_l
-          --output-unmapped-reads-r $output_unmapped_reads_r
-        #end if
-        #if $output_suppressed_reads_l and $output_suppressed_reads_l
-          --output-suppressed-reads-l $output_suppressed_reads_l
-          --output-suppressed-reads-r $output_suppressed_reads_r
-        #end if
-      #end if
-
-    </command>
-    <inputs>
-        <conditional name="refGenomeSource">
-          <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
-            <option value="indexed">Use a built-in index</option>
-            <option value="history">Use one from the history</option>
-          </param>
-          <when value="indexed">
-            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
-              <options from_data_table="bowtie2_indexes">
-                <filter type="sort_by" column="2"/>
-                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-              </options>
-            </param>
-          </when>  <!-- build-in -->
-          <when value="history">
-            <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
-          </when>  <!-- history -->
-        </conditional>  <!-- refGenomeSource -->
-
-        <!-- Input Parameters -->
-        <conditional name="singlePaired">
-            <param name="sPaired" type="select" label="Is this library mate-paired?">
-              <option value="single">Single-end</option>
-              <option value="paired">Paired-end</option>
-            </param>
-            <when value="single">
-                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
-            </when>
-            <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
-                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
-                <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
-                <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
-            </when>
-        </conditional>
-
-
-        <conditional name="params">
-            <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
-              <option value="default">Use Defaults</option>
-              <option value="custom">Full parameter list</option>
-            </param>
-            <when value="default" />
-            <!-- Full/advanced params. -->
-            <when value="custom">
-                <!-- -N -->
-                <param name="seed_mismatches" type="integer" value="0" label="Number of mismatches to be allowed in a seed alignment during multiseed alignment" />
-                <!-- -L -->
-                <param name="seed_len" type="integer" value="20" label="Length of the seed substrings to align during multiseed alignment" />
-                <!--
-                <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." />
-                -->
-                <!-- -D -->
-                <param name="seed_extention_attempts" type="integer" value="15" label="How many consecutive seed extension attempts can fail before Bowtie 2 moves on" />
-                <!-- -R -->
-                <param name="max_reseed" type="integer" value="2" label="Maximum number of times Bowtie 2 will re-seed reads with repetitive seeds" />
-
-                <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." />
-                <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" />
-
-                <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable looking for discordant alignments if it cannot find any concordant alignments" help="" />
-                <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates" help="" />
-
-                <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write ambiguous reads to an extra output file." help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." />
-                <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file" />
-                <!-- output Options -->
-                <!-- 
-                <param name="isReportOutput" type="select" label="Offer all report files concatenated in one file.">
-                    <option value="yes">yes</option>
-                    <option value="no">no</option>
-                </param>
-                -->
-                <!--end output options --> 
-            </when>  <!-- full -->
-      </conditional>  <!-- params -->
-      <param name="suppress_header" type="boolean" truevalue="--suppress-header" falsevalue="" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
-    </inputs>
-    <outputs>
-        <!-- that does not work
-        <data format="txt" name="report_file" label="${tool.name} on ${on_string}: Report">
-            <filter>str($params.isReportOutput) == "yes"</filter>
-        </data>
-        -->
-        <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
-          <actions>
-            <conditional name="refGenomeSource.genomeSource">
-              <when value="indexed">
-                <action type="metadata" name="dbkey">
-                  <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
-                    <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                    <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                  </option>
-                </action>
-              </when>
-              <when value="history">
-                <action type="metadata" name="dbkey">
-                  <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                </action>
-              </when>
-            </conditional>
-          </actions>
-        </data>
-
-    <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
-      <filter>
-        ((
-          params['settingsType'] == "custom" and
-          params['suppressed_read_file'] is True
-        ))
-      </filter>
-      <actions>
-        <conditional name="singlePaired.sPaired">
-          <when value="single">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
-            </action>
-          </when>
-          <when value="paired">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-
-    <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
-      <filter>singlePaired['sPaired'] == "paired"</filter>
-      <filter>params['settingsType'] == "custom"</filter>
-      <filter>params['supressed_read_file'] is True</filter>
-      <actions>
-        <conditional name="singlePaired.sPaired">
-          <when value="single">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
-            </action>
-          </when>
-          <when value="paired">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-
-    <!-- Outout unmapped reads -->
-    <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
-      <filter>
-        ((
-          params['settingsType'] == "custom" and
-          params['unmapped_read_file'] is True
-        ))
-      </filter>
-      <actions>
-        <conditional name="singlePaired.sPaired">
-          <when value="single">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
-            </action>
-          </when>
-          <when value="paired">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-    <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
-      <filter>singlePaired['sPaired'] == "paired"</filter>
-      <filter>params['settingsType'] == "custom"</filter>
-      <filter>params['unmapped_read_file'] is True</filter>
-      <actions>
-        <conditional name="singlePaired.sPaired">
-          <when value="single">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
-            </action>
-          </when>
-          <when value="paired">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-        
-        
-    </outputs>
-
-    <tests>
-    </tests>
-
-    <help>
-
-**What it does**
-
-Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
-reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
-version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
-Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
-(C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
-forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie (1 or 2)
-are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
-sequence from the genome and determine if there were any protected C's present or not.
-
-.. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
-
-As of version 0.7.0 Bismark will only run 2 alignment threads for OT and OB in parallel, the 4 strand mode can be
-re-enabled by using non_directional mode.
-
-It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.
-
-------
-
-**Know what you are doing**
-
-.. class:: warningmark
-
-There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
-
- .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
-
-------
-
-**Input formats**
-
-Bismark accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*), Illumina FASTQ format (galaxy type *fastqillumina*) or FASTA format (galaxy type *fasta*). Use the FASTQ Groomer to prepare your files.
-
-------
-
-**A Note on Built-in Reference Genomes**
-
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
-
-------
-
-The final output of Bismark is in SAM format by default.
-
-**Outputs**
-
-The output is in SAM format, and has the following columns::
-
-    Column  Description
-  --------  --------------------------------------------------------
-  1  QNAME  seq-ID
-  2  FLAG   this flag tries to take the strand a bisulfite read 
-            originated from into account 
-            (this is different from ordinary DNA alignment flags!)
-  3  RNAME  chromosome
-  4  POS    start position
-  5  MAPQ   always 255
-  6  CIGAR  extended CIGAR string
-  7  MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
-  8  MPOS   1-based Mate POSition
-  9  ISIZE  Inferred insert SIZE
-  10 SEQ    query SEQuence on the same strand as the reference
-  11 QUAL   Phred33 scale
-  12 NM-tag edit distance to the reference)
-  13 XX-tag base-by-base mismatches to the reference. 
-            This does not include indels.
-  14 XM-tag methylation call string
-  15 XR-tag read conversion state for the alignment
-  16 XG-tag genome conversion state for the alignment
-  
-
-Each read of paired-end alignments is written out in a separate line in the above format.
-
-
-It looks like this (scroll sideways to see the entire example)::
-
-  QNAME	FLAG	RNAME	POS	MAPQ	CIAGR	MRNM	MPOS	ISIZE	SEQ	QUAL	OPT
-  HWI-EAS91_1_30788AAXX:1:1:1761:343	4	*	0	0	*	*	0	0	AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG	hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
-  HWI-EAS91_1_30788AAXX:1:1:1578:331	4	*	0	0	*	*	0	0	GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG	hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
-
--------
-
-**Bismark settings**
-
-All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.
-
-------
-
-**Bismark parameter list**
-
-This is an exhaustive list of Bismark options:
-
-------
-
-**OPTIONS**
-
-
-Input::
-
-  --singles              A comma- or space-separated list of files containing the reads to be aligned (e.g.
-                         lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
-                         produce one mapping result and one report file per input file.
-
-  -1 mates1              Comma-separated list of files containing the #1 mates (filename usually includes
-                         "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
-                         correspond file-for-file and read-for-read with those specified in mates2.
-                         Reads may be a mix of different lengths. Bismark will produce one mapping result
-                         and one report file per paired-end input file pair.
-
-  -2 mates2              Comma-separated list of files containing the #2 mates (filename usually includes
-                         "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
-                         correspond file-for-file and read-for-read with those specified in mates1.
-                         Reads may be a mix of different lengths.
-
-  -q/--fastq             The query input files (specified as mate1,mate2 or singles are FASTQ
-                         files (usually having extension .fg or .fastq). This is the default. See also
-                         --solexa-quals.
-
-  -f/--fasta             The query input files (specified as mate1,mate2 or singles are FASTA
-                         files (usually havin extension .fa, .mfa, .fna or similar). All quality values
-                         are assumed to be 40 on the Phred scale.
-
-  -s/--skip INT          Skip (i.e. do not align) the first INT reads or read pairs from the input.
-
-  -u/--upto INT          Only aligns the first INT reads or read pairs from the input. Default: no limit.
-
-  --phred33-quals        FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
-
-  --phred64-quals        FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
-
-  --solexa-quals         Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
-                         (which can't). The formula for conversion is: 
-                         phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
-                         is usually the right option for use with (unconverted) reads emitted by the GA
-                         Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
-
-  --solexa1.3-quals      Same as --phred64-quals. This is usually the right option for use with (unconverted)
-                         reads emitted by GA Pipeline version 1.3 or later. Default: off.
-
-
-Alignment::
-
-  -n/--seedmms INT       The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
-                         of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the 
-                         default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
-
-  -l/--seedlen           The "seed length"; i.e., the number of bases of the high quality end of the read to
-                         which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
-                         larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
-
-  -e/--maqerr INT        Maximum permitted total of quality values at all mismatched read positions throughout
-                         the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
-                         quality values to the nearest 10 and saturates at 30. This value is not relevant for
-                         Bowtie 2.
-
-  --chunkmbs INT         The number of megabytes of memory a given thread is given to store path descriptors in
-                         --best mode. Best-first search must keep track of many paths at once to ensure it is
-                         always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
-                         memory impact of the descriptors, but they can still grow very large in some cases. If
-                         you receive an error message saying that chunk memory has been exhausted in --best mode,
-                         try adjusting this parameter up to dedicate more memory to the descriptors. This value
-                         is not relevant for Bowtie 2. Default: 512.
-
-  -I/--minins INT        The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
-                         a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
-                         with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
-                         satisfied). A 19-bp gap would not be valid in that case. Default: 0.
-
-  -X/--maxins INT        The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
-                         a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
-                         60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
-                         A 61-bp gap would not be valid in that case. Default: 500.
-
-
-
-Output::
-
-  --non_directional      The sequencing library was constructed in a non strand-specific manner, alignments to all four
-                         bisulfite strands will be reported. Default: OFF.
-
-                         (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
-                         to the original strands are merely theoretical and should not exist in reality. Specifying directional
-                         alignments (which is the default) will only run 2 alignment threads to the original top (OT)
-                         or bottom (OB) strands in parallel and report these alignments. This is the recommended option
-                         for sprand-specific libraries).
-
-  --sam-no-hd            Suppress SAM header lines (starting with @). This might be useful when very large input files are
-                         split up into several smaller files to run concurrently and the output files are to be merged.
-
-  --quiet                Print nothing besides alignments.
-
-  --vanilla              Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
-                         of SAM format output.
-
-  -un/--unmapped         Write all reads that could not be aligned to a file in the output directory. Written reads will
-                         appear as they did in the input, without any translation of quality values that may have
-                         taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
-                         and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
-                         with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
-                         are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
-
-  --ambiguous            Write all reads which produce more than one valid alignment with the same number of lowest
-                         mismatches or other reads that fail to align uniquely to a file in the output directory.
-                         Written reads will appear as they did in the input, without any of the translation of quality
-                         values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
-                         parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
-                         _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
-
-  -o/--output_dir DIR    Write all output files into this directory. By default the output files will be written into
-                         the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
-                         to create it first. The path to the output folder can be either relative or absolute.
-
-  --temp_dir DIR          Write temporary files to this directory instead of into the same directory as the input files. If
-                         the specified folder does not exist, Bismark will attempt to create it first. The path to the
-                         temporary folder can be either relative or absolute.
-
-------
-
-Bowtie 2 alignment options::
-
-  -N INT                 Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
-                         Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
-                         but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
-                         Bowtie 1 see -n).
-
-  -L INT                   Sets the length of the seed substrings to align during multiseed alignment. Smaller values
-                         make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
-                         used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
-                         Bowtie 1 see -l).
-
-  --ignore-quals         When calculating a mismatch penalty, always consider the quality value at the mismatched
-                         position to be the highest possible, regardless of the actual value. I.e. input is treated
-                         as though all quality values are high. This is also the default behavior when the input
-                         doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
-
-
-Bowtie 2 paired-end options::
-
-  --no-mixed             This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
-                         it cannot find a concordant or discordant alignment for a pair. This option is invariable and
-                         and on by default.
-
-  --no-discordant        Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
-                         A discordant alignment is an alignment where both mates align uniquely, but that does not
-                         satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
-                         and it is on by default.
-
-
-Bowtie 2 effort options::
-
-  -D INT                 Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
-                         the alignments found so far. A seed extension "fails" if it does not yield a new best or a
-                         new second-best alignment. Default: 15.
-
-  -R INT                 INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
-                         When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
-                         mismatches allowed) at different offsets and searches for more alignments. A read is considered
-                         to have repetitive seeds if the total number of seed hits divided by the number of seeds
-                         that aligned at least once is greater than 300. Default: 2.
-
-
-Bowtie 2 Scoring options::
-
-  --score_min "func"     Sets a function governing the minimum alignment score needed for an alignment to be considered
-                         "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
-                         L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
-                         See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
-                         L,0,-0.2.
-
-
-Bowtie 2 Reporting options::
-
- --most_valid_alignments INT This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is
-                         deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
-                         default mode, but adjusting the -M setting is deprecated.  Use the -D and -R options to adjust the
-                         effort expended to find valid alignments.
-
-                         For reference, this used to be the old (now deprecated) description of -M:
-                         Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
-                         can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
-                         happens first. Only the best alignment is reported. Information from the other alignments is used to
-                         estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes 
-                         Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
-                         aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
-                         guarantee that the alignment reported is the best possible in terms of alignment score. -M is
-                         always used and its default value is set to 10.
-
-  </help>
-</tool>
--- a/bismark_bowtie_wrapper.xml	Tue Dec 25 05:45:46 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,614 +0,0 @@
-<tool id="bismark_bowtie" name="Bismark" version="0.7.7.2">
-    <!-- Wrapper compatible with Bismark version 0.7.7 -->
-    <description>bisulfite mapper (bowtie)</description>
-    <!--<version_command>bismark version</version_command>-->
-    <requirements>
-        <requirement type="set_environment">SCRIPT_PATH</requirement>
-        <requirement type="package" version="0.12.8">bowtie</requirement>
-        <requirement type="package" version="2.0.0-beta7">bowtie2</requirement>
-    </requirements>
-    <parallelism method="basic"></parallelism>
-    <command interpreter="python">
-        bismark_wrapper.py
-        
-        ## Change this to accommodate the number of threads you have available.
-        --num-threads 4
-
-        --bismark_path \$SCRIPT_PATH
-
-        ##
-        ## Bismark Genome Preparation, if desired.
-        ##
-
-        ## Handle reference file.
-        #if $refGenomeSource.genomeSource == "history":
-            --own-file=$refGenomeSource.ownFile
-        #else:
-            --indexes-path ${refGenomeSource.index.fields.path}
-        #end if
-
-
-        ##
-        ##  Input parameters
-        ##
-
-
-        #if $singlePaired.sPaired == "single":
-            --single-paired $singlePaired.input_singles
-
-            #if $singlePaired.input_singles.ext == "fastqillumina":
-                --phred64-quals
-                --fastq
-            #elif $singlePaired.input_singles.ext == "fastqsanger":
-                --fastq
-            #elif $singlePaired.input_singles.ext == "fasta":
-                --fasta
-            #end if
-        #else:
-            --mate-paired 
-            --mate1 $singlePaired.input_mate1
-            --mate2 $singlePaired.input_mate2
-
-            #if $singlePaired.input_mate1.ext == "fastqillumina":
-                --phred64-quals
-                --fastq
-            #elif $singlePaired.input_mate1.ext == "fastqsanger":
-                --fastq
-            #elif $singlePaired.input_mate1.ext == "fasta":
-                --fasta
-            #end if
-
-            -I $singlePaired.minInsert
-            -X $singlePaired.maxInsert
-        #end if
-
-
-        ## for now hardcode the value for the required memory per thread in --best mode
-        --chunkmbs 512
-
-
-        #if $params.settingsType == "custom":
-
-            ## default 20
-            --seed-len $params.seed_len
-            ## default 0
-            --seed-mismatches $params.seed_mismatches
-            ## default 15
-            --seed-extention-attempts $params.seed_extention_attempts
-            ## default 2
-            --max-reseed $params.max_reseed
-            
-            ## default 70
-            ##--maqerr $params.maqerr
-
-            ## default unlimited
-            #if $params.qupto != 0:
-                --qupto $params.qupto
-            #end if
-            #if $params.skip_reads != 0:
-                --skip-reads $params.skip_reads
-            #end if
-
-            ## if set, disable the original behaviour
-            $params.no_mixed
-            ## if set, disable the original behaviour
-            $params.no_discordant
-
-
-            ###if str($params.isReportOutput) == "yes":
-            ##    --output-report-file $report_file
-            ###end if
-
-        #end if
-
-        ##
-        ## Output parameters.
-        ##
-        --output $output
-        $suppress_header
-
-      #if str( $singlePaired.sPaired ) == "single"
-        #if $output_unmapped_reads_l
-          --output-unmapped-reads $output_unmapped_reads_l
-        #end if
-        #if $output_suppressed_reads_l
-          --output-suppressed-reads $output_suppressed_reads_l
-        #end if
-      #else
-        #if $output_unmapped_reads_l and $output_unmapped_reads_r
-          --output-unmapped-reads-l $output_unmapped_reads_l
-          --output-unmapped-reads-r $output_unmapped_reads_r
-        #end if
-        #if $output_suppressed_reads_l and $output_suppressed_reads_l
-          --output-suppressed-reads-l $output_suppressed_reads_l
-          --output-suppressed-reads-r $output_suppressed_reads_r
-        #end if
-      #end if
-
-    </command>
-    <inputs>
-        <conditional name="refGenomeSource">
-          <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
-            <option value="indexed">Use a built-in index</option>
-            <option value="history">Use one from the history</option>
-          </param>
-          <when value="indexed">
-            <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
-              <options from_data_table="bowtie_indexes">
-                <filter type="sort_by" column="2"/>
-                <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-              </options>
-            </param>
-          </when>  <!-- build-in -->
-          <when value="history">
-            <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
-          </when>  <!-- history -->
-        </conditional>  <!-- refGenomeSource -->
-
-        <!-- Input Parameters -->
-        <conditional name="singlePaired">
-            <param name="sPaired" type="select" label="Is this library mate-paired?">
-              <option value="single">Single-end</option>
-              <option value="paired">Paired-end</option>
-            </param>
-            <when value="single">
-                <param name="input_singles" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
-            </when>
-            <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
-                <param name="input_mate2" type="data" format="fastqsanger,fastqillumina,fastq,fasta" label="FASTQ/FASTA file" help="FASTQ or FASTA files." />
-                <param name="minInsert" type="integer" value="0" label="Minimum insert size for valid paired-end alignments" />
-                <param name="maxInsert" type="integer" value="250" label="Maximum insert size for valid paired-end alignments" />
-            </when>
-        </conditional>
-
-
-        <conditional name="params">
-            <param name="settingsType" type="select" label="Bismark settings to use" help="You can use the default settings or set custom values for any of Bismark's parameters.">
-              <option value="default">Use Defaults</option>
-              <option value="custom">Full parameter list</option>
-            </param>
-            <when value="default" />
-            <!-- Full/advanced params. -->
-            <when value="custom">
-                <!-- -n -->
-                <param name="seed_mismatches" type="select" label="The maximum number of mismatches permitted in the 'seed'.">
-                    <option value="0">0</option>
-                    <option value="1">1</option>
-                    <option value="2" selected="true">2</option>
-                    <option value="3">3</option>
-                </param>
-                <!-- -l -->
-                <param name="seed_len" type="integer" value="28" label="The 'seed length'; The number of bases of the high quality end of the read to which the maximum number of mismatches applies." />
-                <!--
-                <param name="maqerr" type="integer" value="70" label="Maximum permitted total of quality values at all mismatched read positions throughout the entire alignment, not just in the 'seed'." />
-                -->
-                <param name="qupto" type="integer" value="0" label="Only aligns the first N reads or read pairs from the input" help="Default is 0 and means 'no-limit'." />
-                <param name="skip_reads" type="integer" value="0" label="Skip (i.e. do not align) the first N reads or read pairs from the input" />
-
-                <param name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable looking for discordant alignments if it cannot find any concordant alignments" help="" />
-                <param name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable Bowtie 2's behaviour to try to find alignments for the individual mates" help="" />
-
-                <param name="suppressed_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write ambiguous reads to an extra output file." help="Write all reads which produce more than one valid alignment with the same number of lowest mismatches or other reads that fail to align uniquely." />
-                <param name="unmapped_read_file" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Write all reads that could not be aligned to a file" />
-                <!-- output Options -->
-                <!-- 
-                <param name="isReportOutput" type="select" label="Offer all report files concatenated in one file.">
-                    <option value="yes">yes</option>
-                    <option value="no">no</option>
-                </param>
-                -->
-                <!--end output options --> 
-            </when>  <!-- full -->
-      </conditional>  <!-- params -->
-      <param name="suppress_header" type="boolean" truevalue="--suppress-header" falsevalue="" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" />
-    </inputs>
-    <outputs>
-        <!-- that does not work
-        <data format="txt" name="report_file" label="${tool.name} on ${on_string}: Report">
-            <filter>str($params.isReportOutput) == "yes"</filter>
-        </data>
-        -->
-        <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads">
-          <actions>
-            <conditional name="refGenomeSource.genomeSource">
-              <when value="indexed">
-                <action type="metadata" name="dbkey">
-                  <option type="from_data_table" name="bowtie2_indexes" column="1" offset="0">
-                    <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
-                    <filter type="param_value" ref="refGenomeSource.index" column="0"/>
-                  </option>
-                </action>
-              </when>
-              <when value="history">
-                <action type="metadata" name="dbkey">
-                  <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
-                </action>
-              </when>
-            </conditional>
-          </actions>
-        </data>
-
-    <data format="fastq" name="output_suppressed_reads_l" label="${tool.name} on ${on_string}: suppressed reads (L)">
-      <filter>
-        ((
-          params['settingsType'] == "custom" and
-          params['suppressed_read_file'] is True
-        ))
-      </filter>
-      <actions>
-        <conditional name="singlePaired.sPaired">
-          <when value="single">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
-            </action>
-          </when>
-          <when value="paired">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-
-    <data format="fastq" name="output_suppressed_reads_r" label="${tool.name} on ${on_string}: suppressed reads (R)">
-      <filter>singlePaired['sPaired'] == "paired"</filter>
-      <filter>params['settingsType'] == "custom"</filter>
-      <filter>params['supressed_read_file'] is True</filter>
-      <actions>
-        <conditional name="singlePaired.sPaired">
-          <when value="single">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
-            </action>
-          </when>
-          <when value="paired">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-
-    <!-- Outout unmapped reads -->
-    <data format="fastq" name="output_unmapped_reads_l" label="${tool.name} on ${on_string}: unmapped reads (L)">
-      <filter>
-        ((
-          params['settingsType'] == "custom" and
-          params['unmapped_read_file'] is True
-        ))
-      </filter>
-      <actions>
-        <conditional name="singlePaired.sPaired">
-          <when value="single">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
-            </action>
-          </when>
-          <when value="paired">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-    <data format="fastq" name="output_unmapped_reads_r" label="${tool.name} on ${on_string}: unmapped reads (R)">
-      <filter>singlePaired['sPaired'] == "paired"</filter>
-      <filter>params['settingsType'] == "custom"</filter>
-      <filter>params['unmapped_read_file'] is True</filter>
-      <actions>
-        <conditional name="singlePaired.sPaired">
-          <when value="single">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_singles" param_attribute="ext" />
-            </action>
-          </when>
-          <when value="paired">
-            <action type="format">
-              <option type="from_param" name="singlePaired.input_mate1" param_attribute="ext" />
-            </action>
-          </when>
-        </conditional>
-      </actions>
-    </data>
-        
-        
-    </outputs>
-
-    <tests>
-    </tests>
-
-    <help>
-
-**What it does**
-
-Bismark_ is a bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
-reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
-version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
-Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
-(C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
-forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie (1 or 2)
-are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
-sequence from the genome and determine if there were any protected C's present or not.
-
-.. _Bismark: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
-
-As of version 0.7.0 Bismark will only run 2 alignment threads for OT and OB in parallel, the 4 strand mode can be
-re-enabled by using non_directional mode.
-
-It is developed by Krueger F and Andrews SR. at the Babraham Institute. Krueger F, Andrews SR. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571-2.
-
-------
-
-**Know what you are doing**
-
-.. class:: warningmark
-
-There is no such thing (yet) as an automated gearshift in short read mapping. It is all like stick-shift driving in San Francisco. In other words = running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.
-
- .. __: http://www.bioinformatics.babraham.ac.uk/projects/bismark/
-
-------
-
-**Input formats**
-
-Bismark accepts files in either Sanger FASTQ format (galaxy type *fastqsanger*), Illumina FASTQ format (galaxy type *fastqillumina*) or FASTA format (galaxy type *fasta*). Use the FASTQ Groomer to prepare your files.
-
-------
-
-**A Note on Built-in Reference Genomes**
-
-The default variant for all genomes is "Full", defined as all primary chromosomes (or scaffolds/contigs) including mitochondrial plus associated unmapped, plasmid, and other segments. When only one version of a genome is available in this tool, it represents the default "Full" variant. Some genomes will have more than one variant available. The "Canonical Male" or sometimes simply "Canonical" variant contains the primary chromosomes for a genome. For example a human "Canonical" variant contains chr1-chr22, chrX, chrY, and chrM. The "Canonical Female" variant contains the primary chromosomes excluding chrY.
-
-------
-
-The final output of Bismark is in SAM format by default.
-
-**Outputs**
-
-The output is in SAM format, and has the following columns::
-
-    Column  Description
-  --------  --------------------------------------------------------
-  1  QNAME  seq-ID
-  2  FLAG   this flag tries to take the strand a bisulfite read 
-            originated from into account 
-            (this is different from ordinary DNA alignment flags!)
-  3  RNAME  chromosome
-  4  POS    start position
-  5  MAPQ   always 255
-  6  CIGAR  extended CIGAR string
-  7  MRNM   Mate Reference sequence NaMe ('=' if same as RNAME)
-  8  MPOS   1-based Mate POSition
-  9  ISIZE  Inferred insert SIZE
-  10 SEQ    query SEQuence on the same strand as the reference
-  11 QUAL   Phred33 scale
-  12 NM-tag edit distance to the reference)
-  13 XX-tag base-by-base mismatches to the reference. 
-            This does not include indels.
-  14 XM-tag methylation call string
-  15 XR-tag read conversion state for the alignment
-  16 XG-tag genome conversion state for the alignment
-  
-
-Each read of paired-end alignments is written out in a separate line in the above format.
-
-
-It looks like this (scroll sideways to see the entire example)::
-
-  QNAME	FLAG	RNAME	POS	MAPQ	CIAGR	MRNM	MPOS	ISIZE	SEQ	QUAL	OPT
-  HWI-EAS91_1_30788AAXX:1:1:1761:343	4	*	0	0	*	*	0	0	AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG	hhhhhhh;;hhhhhhhhhhh^hOhhhhghhhfhhhgh;;h;;hhhh;h;;;;;;;hhhhhhghhhh;;Phhh
-  HWI-EAS91_1_30788AAXX:1:1:1578:331	4	*	0	0	*	*	0	0	GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG	hhhhhhh;;hhhhhhhhhhhhhhhhhhhhhhhhhhhh;;h;;hhhh;h;;;;;;;hhhhhhhhhhh;;hhVh
-
--------
-
-**Bismark settings**
-
-All of the options have a default value. You can change any of them. If any Bismark function is missing please contact the tool author or your Galaxy admin.
-
-------
-
-**Bismark parameter list**
-
-This is an exhaustive list of Bismark options:
-
-------
-
-**OPTIONS**
-
-
-Input::
-
-  --singles              A comma- or space-separated list of files containing the reads to be aligned (e.g.
-                         lane1.fq,lane2.fq lane3.fq). Reads may be a mix of different lengths. Bismark will
-                         produce one mapping result and one report file per input file.
-
-  -1 mates1              Comma-separated list of files containing the #1 mates (filename usually includes
-                         "_1"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
-                         correspond file-for-file and read-for-read with those specified in mates2.
-                         Reads may be a mix of different lengths. Bismark will produce one mapping result
-                         and one report file per paired-end input file pair.
-
-  -2 mates2              Comma-separated list of files containing the #2 mates (filename usually includes
-                         "_2"), e.g. flyA_1.fq,flyB_1.fq). Sequences specified with this option must
-                         correspond file-for-file and read-for-read with those specified in mates1.
-                         Reads may be a mix of different lengths.
-
-  -q/--fastq             The query input files (specified as mate1,mate2 or singles are FASTQ
-                         files (usually having extension .fg or .fastq). This is the default. See also
-                         --solexa-quals.
-
-  -f/--fasta             The query input files (specified as mate1,mate2 or singles are FASTA
-                         files (usually havin extension .fa, .mfa, .fna or similar). All quality values
-                         are assumed to be 40 on the Phred scale.
-
-  -s/--skip INT          Skip (i.e. do not align) the first INT reads or read pairs from the input.
-
-  -u/--upto INT          Only aligns the first INT reads or read pairs from the input. Default: no limit.
-
-  --phred33-quals        FASTQ qualities are ASCII chars equal to the Phred quality plus 33. Default: on.
-
-  --phred64-quals        FASTQ qualities are ASCII chars equal to the Phred quality plus 64. Default: off.
-
-  --solexa-quals         Convert FASTQ qualities from solexa-scaled (which can be negative) to phred-scaled
-                         (which can't). The formula for conversion is: 
-                         phred-qual = 10 * log(1 + 10 ** (solexa-qual/10.0)) / log(10). Used with -q. This
-                         is usually the right option for use with (unconverted) reads emitted by the GA
-                         Pipeline versions prior to 1.3. Works only for Bowtie 1. Default: off.
-
-  --solexa1.3-quals      Same as --phred64-quals. This is usually the right option for use with (unconverted)
-                         reads emitted by GA Pipeline version 1.3 or later. Default: off.
-
-
-Alignment::
-
-  -n/--seedmms INT       The maximum number of mismatches permitted in the "seed", i.e. the first L base pairs
-                         of the read (where L is set with -l/--seedlen). This may be 0, 1, 2 or 3 and the 
-                         default is 1. This option is only available for Bowtie 1 (for Bowtie 2 see -N).
-
-  -l/--seedlen           The "seed length"; i.e., the number of bases of the high quality end of the read to
-                         which the -n ceiling applies. The default is 28. Bowtie (and thus Bismark) is faster for
-                         larger values of -l. This option is only available for Bowtie 1 (for Bowtie 2 see -L).
-
-  -e/--maqerr INT        Maximum permitted total of quality values at all mismatched read positions throughout
-                         the entire alignment, not just in the "seed". The default is 70. Like Maq, bowtie rounds
-                         quality values to the nearest 10 and saturates at 30. This value is not relevant for
-                         Bowtie 2.
-
-  --chunkmbs INT         The number of megabytes of memory a given thread is given to store path descriptors in
-                         --best mode. Best-first search must keep track of many paths at once to ensure it is
-                         always extending the path with the lowest cumulative cost. Bowtie tries to minimize the
-                         memory impact of the descriptors, but they can still grow very large in some cases. If
-                         you receive an error message saying that chunk memory has been exhausted in --best mode,
-                         try adjusting this parameter up to dedicate more memory to the descriptors. This value
-                         is not relevant for Bowtie 2. Default: 512.
-
-  -I/--minins INT        The minimum insert size for valid paired-end alignments. E.g. if -I 60 is specified and
-                         a paired-end alignment consists of two 20-bp alignments in the appropriate orientation
-                         with a 20-bp gap between them, that alignment is considered valid (as long as -X is also
-                         satisfied). A 19-bp gap would not be valid in that case. Default: 0.
-
-  -X/--maxins INT        The maximum insert size for valid paired-end alignments. E.g. if -X 100 is specified and
-                         a paired-end alignment consists of two 20-bp alignments in the proper orientation with a
-                         60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied).
-                         A 61-bp gap would not be valid in that case. Default: 500.
-
-
-
-Output::
-
-  --non_directional      The sequencing library was constructed in a non strand-specific manner, alignments to all four
-                         bisulfite strands will be reported. Default: OFF.
-
-                         (The current Illumina protocol for BS-Seq is directional, in which case the strands complementary
-                         to the original strands are merely theoretical and should not exist in reality. Specifying directional
-                         alignments (which is the default) will only run 2 alignment threads to the original top (OT)
-                         or bottom (OB) strands in parallel and report these alignments. This is the recommended option
-                         for sprand-specific libraries).
-
-  --sam-no-hd            Suppress SAM header lines (starting with @). This might be useful when very large input files are
-                         split up into several smaller files to run concurrently and the output files are to be merged.
-
-  --quiet                Print nothing besides alignments.
-
-  --vanilla              Performs bisulfite mapping with Bowtie 1 and prints the 'old' output (as in Bismark 0.5.X) instead
-                         of SAM format output.
-
-  -un/--unmapped         Write all reads that could not be aligned to a file in the output directory. Written reads will
-                         appear as they did in the input, without any translation of quality values that may have
-                         taken place within Bowtie or Bismark. Paired-end reads will be written to two parallel files with _1
-                         and _2 inserted in their filenames, i.e. _unmapped_reads_1.txt and unmapped_reads_2.txt. Reads
-                         with more than one valid alignment with the same number of lowest mismatches (ambiguous mapping)
-                         are also written to _unmapped_reads.txt unless the option --ambiguous is specified as well.
-
-  --ambiguous            Write all reads which produce more than one valid alignment with the same number of lowest
-                         mismatches or other reads that fail to align uniquely to a file in the output directory.
-                         Written reads will appear as they did in the input, without any of the translation of quality
-                         values that may have taken place within Bowtie or Bismark. Paired-end reads will be written to two
-                         parallel files with _1 and _2 inserted in theit filenames, i.e. _ambiguous_reads_1.txt and
-                         _ambiguous_reads_2.txt. These reads are not written to the file specified with --un.
-
-  -o/--output_dir DIR    Write all output files into this directory. By default the output files will be written into
-                         the same folder as the input file(s). If the specified folder does not exist, Bismark will attempt
-                         to create it first. The path to the output folder can be either relative or absolute.
-
-  --temp_dir DIR          Write temporary files to this directory instead of into the same directory as the input files. If
-                         the specified folder does not exist, Bismark will attempt to create it first. The path to the
-                         temporary folder can be either relative or absolute.
-
-------
-
-Bowtie 2 alignment options::
-
-  -N INT                 Sets the number of mismatches to allowed in a seed alignment during multiseed alignment.
-                         Can be set to 0 or 1. Setting this higher makes alignment slower (often much slower)
-                         but increases sensitivity. Default: 0. This option is only available for Bowtie 2 (for
-                         Bowtie 1 see -n).
-
-  -L INT                   Sets the length of the seed substrings to align during multiseed alignment. Smaller values
-                         make alignment slower but more senstive. Default: the --sensitive preset of Bowtie 2 is
-                         used by default, which sets -L to 20. This option is only available for Bowtie 2 (for
-                         Bowtie 1 see -l).
-
-  --ignore-quals         When calculating a mismatch penalty, always consider the quality value at the mismatched
-                         position to be the highest possible, regardless of the actual value. I.e. input is treated
-                         as though all quality values are high. This is also the default behavior when the input
-                         doesn't specify quality values (e.g. in -f mode). This option is invariable and on by default.
-
-
-Bowtie 2 paired-end options::
-
-  --no-mixed             This option disables Bowtie 2's behavior to try to find alignments for the individual mates if
-                         it cannot find a concordant or discordant alignment for a pair. This option is invariable and
-                         and on by default.
-
-  --no-discordant        Normally, Bowtie 2 looks for discordant alignments if it cannot find any concordant alignments.
-                         A discordant alignment is an alignment where both mates align uniquely, but that does not
-                         satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior
-                         and it is on by default.
-
-
-Bowtie 2 effort options::
-
-  -D INT                 Up to INT consecutive seed extension attempts can "fail" before Bowtie 2 moves on, using
-                         the alignments found so far. A seed extension "fails" if it does not yield a new best or a
-                         new second-best alignment. Default: 15.
-
-  -R INT                 INT is the maximum number of times Bowtie 2 will "re-seed" reads with repetitive seeds.
-                         When "re-seeding," Bowtie 2 simply chooses a new set of reads (same length, same number of
-                         mismatches allowed) at different offsets and searches for more alignments. A read is considered
-                         to have repetitive seeds if the total number of seed hits divided by the number of seeds
-                         that aligned at least once is greater than 300. Default: 2.
-
-
-Bowtie 2 Scoring options::
-
-  --score_min "func"     Sets a function governing the minimum alignment score needed for an alignment to be considered
-                         "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying
-                         L,0,-0.2 sets the minimum-score function f to f(x) = 0 + -0.2 * x, where x is the read length.
-                         See also: setting function options at http://bowtie-bio.sourceforge.net/bowtie2. The default is
-                         L,0,-0.2.
-
-
-Bowtie 2 Reporting options::
-
- --most_valid_alignments INT This used to be the Bowtie 2 parameter -M. As of Bowtie 2 version 2.0.0 beta7 the option -M is
-                         deprecated. It will be removed in subsequent versions. What used to be called -M mode is still the
-                         default mode, but adjusting the -M setting is deprecated.  Use the -D and -R options to adjust the
-                         effort expended to find valid alignments.
-
-                         For reference, this used to be the old (now deprecated) description of -M:
-                         Bowtie 2 searches for at most INT+1 distinct, valid alignments for each read. The search terminates when it
-                         can't find more distinct valid alignments, or when it finds INT+1 distinct alignments, whichever
-                         happens first. Only the best alignment is reported. Information from the other alignments is used to
-                         estimate mapping quality and to set SAM optional fields, such as AS:i and XS:i. Increasing -M makes 
-                         Bowtie 2 slower, but increases the likelihood that it will pick the correct alignment for a read that
-                         aligns many places. For reads that have more than INT+1 distinct, valid alignments, Bowtie 2 does not
-                         guarantee that the alignment reported is the best possible in terms of alignment score. -M is
-                         always used and its default value is set to 10.
-
-  </help>
-</tool>
--- a/bismark_genome_preparation	Tue Dec 25 05:45:46 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,492 +0,0 @@
-#!/usr/bin/perl --
-use strict;
-use warnings;
-use Cwd;
-use File::Path qw(rmtree);
-$|++;
-
-
-## This program is Copyright (C) 2010-12, Felix Krueger (felix.krueger@bbsrc.ac.uk)
-
-## This program is free software: you can redistribute it and/or modify
-## it under the terms of the GNU General Public License as published by
-## the Free Software Foundation, either version 3 of the License, or
-## (at your option) any later version.
-
-## This program is distributed in the hope that it will be useful,
-## but WITHOUT ANY WARRANTY; without even the implied warranty of
-## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-## GNU General Public License for more details.
-
-## You should have received a copy of the GNU General Public License
-## along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-use Getopt::Long;
-use Cwd;
-
-my $verbose;
-my $help;
-my $version;
-my $man;
-my $path_to_bowtie;
-my $multi_fasta;
-my $single_fasta;
-my $bowtie2;
-
-my $bismark_version = 'v0.7.7';
-
-GetOptions ('verbose' => \$verbose,
-	    'help' => \$help,
-	    'man' => \$man,
-	    'version' => \$version,
-	    'path_to_bowtie:s' => \$path_to_bowtie,
-	    'single_fasta' => \$single_fasta,
-	    'bowtie2' => \$bowtie2,
-	   );
-
-my $genome_folder = shift @ARGV; # mandatory
-my $CT_dir;
-my $GA_dir;
-
-if ($help or $man){
-  print_helpfile();
-  exit;
-}
-
-if ($version){
-  print << "VERSION";
-
-          Bismark - Bisulfite Mapper and Methylation Caller.
-
-          Bismark Genome Preparation Version: $bismark_version
-        Copyright 2010-12 Felix Krueger, Babraham Bioinformatics
-              www.bioinformatics.babraham.ac.uk/projects/
-
-VERSION
-    exit;
-}
-
-if ($single_fasta){
-  print "Writing individual genomes out into single-entry fasta files (one per chromosome)\n\n";
-  $multi_fasta = 0;
-}
-else{
-  print "Writing bisulfite genomes out into a single MFA (multi FastA) file\n\n";
-  $single_fasta = 0;
-  $multi_fasta = 1;
-}
-
-my @filenames = create_bisulfite_genome_folders();
-
-process_sequence_files ();
-
-launch_bowtie_indexer();
-
-sub launch_bowtie_indexer{
-  if ($bowtie2){
-    print "Bismark Genome Preparation - Step III: Launching the Bowtie 2 indexer\n";
-  }
-  else{
-    print "Bismark Genome Preparation - Step III: Launching the Bowtie (1) indexer\n";
-  }
-  print "Please be aware that this process can - depending on genome size - take up to several hours!\n";
-  sleep(5);
-
-  ### if the path to bowtie was specfified explicitely
-  if ($path_to_bowtie){
-    if ($bowtie2){
-      $path_to_bowtie =~ s/$/bowtie2-build/;
-    }
-    else{
-      $path_to_bowtie =~ s/$/bowtie-build/;
-    }
-  }
-  ### otherwise we assume that bowtie-build is in the path
-  else{
-    if ($bowtie2){
-      $path_to_bowtie = 'bowtie2-build';
-    }
-    else{
-      $path_to_bowtie = 'bowtie-build';
-    }
-  }
-
-  $verbose and print "\n";
-
-  ### Forking the program to run 2 instances of Bowtie-build or Bowtie2-build (= the Bowtie (1/2) indexer)
-  my $pid = fork();
-
-  # parent process
-  if ($pid){
-    sleep(1);
-    chdir $CT_dir or die "Unable to change directory: $!\n";
-    $verbose and warn "Preparing indexing of CT converted genome in $CT_dir\n";
-    my @fasta_files = <*.fa>;
-    my $file_list = join (',',@fasta_files);
-    $verbose and print "Parent process: Starting to index C->T converted genome with the following command:\n\n";
-    $verbose and print "$path_to_bowtie -f $file_list BS_CT\n\n";
-
-    sleep (11);
-    exec ("$path_to_bowtie","-f","$file_list","BS_CT");
-  }
-
-  # child process
-  elsif ($pid == 0){
-    sleep(2);
-    chdir $GA_dir or die "Unable to change directory: $!\n";
-    $verbose and warn "Preparing indexing of GA converted genome in $GA_dir\n";
-    my @fasta_files = <*.fa>;
-    my $file_list = join (',',@fasta_files);
-    $verbose and print "Child process: Starting to index G->A converted genome with the following command:\n\n";
-    $verbose and print "$path_to_bowtie -f $file_list BS_GA\n\n";
-    $verbose and print "(starting in 10 seconds)\n";
-    sleep(10);
-    exec ("$path_to_bowtie","-f","$file_list","BS_GA");
-  }
-
-  # if the platform doesn't support the fork command we will run the indexing processes one after the other
-  else{
-    print "Forking process was not successful, therefore performing the indexing sequentially instead\n";
-    sleep(10);
-
-    ### moving to CT genome folder
-    $verbose and warn "Preparing to index CT converted genome in $CT_dir\n";
-    chdir $CT_dir or die "Unable to change directory: $!\n";
-    my @fasta_files = <*.fa>;
-    my $file_list = join (',',@fasta_files);
-    $verbose and print "$file_list\n\n";
-    sleep(2);
-    system ("$path_to_bowtie","-f","$file_list","BS_CT");
-    @fasta_files=();
-    $file_list= '';
-
-    ### moving to GA genome folder
-    $verbose and warn "Preparing to index GA converted genome in $GA_dir\n";
-    chdir $GA_dir or die "Unable to change directory: $!\n";
-    @fasta_files = <*.fa>;
-    $file_list = join (',',@fasta_files);
-    $verbose and print "$file_list\n\n";
-    sleep(2);
-    exec ("$path_to_bowtie","-f","$file_list","BS_GA");
-  }
-}
-
-
-sub process_sequence_files {
-
-  my ($total_CT_conversions,$total_GA_conversions) = (0,0);
-  $verbose and print "Bismark Genome Preparation - Step II: Bisulfite converting reference genome\n\n";
-  sleep (3);
-
-  $verbose and print "conversions performed:\n";
-  $verbose and print join("\t",'chromosome','C->T','G->A'),"\n";
-
-
-  ### If someone wants to index a genome which consists of thousands of contig and scaffold files we need to write the genome conversions into an MFA file
-  ### Otherwise the list of comma separated chromosomes we provide for bowtie-build will get too long for the kernel to handle
-  ### This is now the default option
-
-  if ($multi_fasta){
-    ### Here we just use one multi FastA file name, append .CT_conversion or .GA_conversion and print all sequence conversions into these files
-    my $bisulfite_CT_conversion_filename = "$CT_dir/genome_mfa.CT_conversion.fa";
-    open (CT_CONVERT,'>',$bisulfite_CT_conversion_filename) or die "Can't write to file $bisulfite_CT_conversion_filename: $!\n";
-
-    my $bisulfite_GA_conversion_filename = "$GA_dir/genome_mfa.GA_conversion.fa";
-    open (GA_CONVERT,'>',$bisulfite_GA_conversion_filename) or die "Can't write to file $bisulfite_GA_conversion_filename: $!\n";
-  }
-
-  foreach my $filename(@filenames){
-    my ($chromosome_CT_conversions,$chromosome_GA_conversions) = (0,0);
-    open (IN,$filename) or die "Failed to read from sequence file $filename $!\n";
-    # warn "Reading chromosome information from $filename\n\n";
-
-    ### first line needs to be a fastA header
-    my $first_line = <IN>;
-    chomp $first_line;
-
-    ### Extracting chromosome name from the FastA header
-    my $chromosome_name = extract_chromosome_name($first_line);
-
-    ### alternatively, chromosomes can be written out into single-entry FastA files. This will only work for genomes with up to a few hundred chromosomes.
-    unless ($multi_fasta){
-      my $bisulfite_CT_conversion_filename = "$CT_dir/$chromosome_name";
-      $bisulfite_CT_conversion_filename =~ s/$/.CT_conversion.fa/;
-      open (CT_CONVERT,'>',$bisulfite_CT_conversion_filename) or die "Can't write to file $bisulfite_CT_conversion_filename: $!\n";
-
-      my $bisulfite_GA_conversion_filename = "$GA_dir/$chromosome_name";
-      $bisulfite_GA_conversion_filename =~ s/$/.GA_conversion.fa/;
-      open (GA_CONVERT,'>',$bisulfite_GA_conversion_filename) or die "Can't write to file $bisulfite_GA_conversion_filename: $!\n";
-    }
-
-    print CT_CONVERT ">",$chromosome_name,"_CT_converted\n"; # first entry
-    print GA_CONVERT ">",$chromosome_name,"_GA_converted\n"; # first entry
-
-
-    while (<IN>){
-
-      ### in case the line is a new fastA header
-      if ($_ =~ /^>/){
-	### printing out the stats for the previous chromosome
-	$verbose and print join ("\t",$chromosome_name,$chromosome_CT_conversions,$chromosome_GA_conversions),"\n";
-	### resetting the chromosome transliteration counters
-	($chromosome_CT_conversions,$chromosome_GA_conversions) = (0,0);
-	
-	### Extracting chromosome name from the additional FastA header
-	$chromosome_name = extract_chromosome_name($_);
-
-	### alternatively, chromosomes can be written out into single-entry FastA files. This will only work for genomes with up to a few hundred chromosomes.
-	unless ($multi_fasta){
-	  my $bisulfite_CT_conversion_filename = "$CT_dir/$chromosome_name";
-	  $bisulfite_CT_conversion_filename =~ s/$/.CT_conversion.fa/;
-	  open (CT_CONVERT,'>',$bisulfite_CT_conversion_filename) or die "Can't write to file $bisulfite_CT_conversion_filename: $!\n";
-	
-	  my $bisulfite_GA_conversion_filename = "$GA_dir/$chromosome_name";
-	  $bisulfite_GA_conversion_filename =~ s/$/.GA_conversion.fa/;
-	  open (GA_CONVERT,'>',$bisulfite_GA_conversion_filename) or die "Can't write to file $bisulfite_GA_conversion_filename: $!\n";
-	}
-
-	print CT_CONVERT ">",$chromosome_name,"_CT_converted\n";
-	print GA_CONVERT ">",$chromosome_name,"_GA_converted\n";
-      }
-
-      else{
-	my $sequence = uc$_;
-
-	### (I) First replacing all ambiguous sequence characters (such as M,S,R....) by N (G,A,T,C,N and the line endings \r and \n are added to a character group)
-	
-	$sequence =~ s/[^ATCGN\n\r]/N/g;
-	
-	### (II) Writing the chromosome out into a C->T converted version (equals forward strand conversion)
-	
-	my $CT_sequence = $sequence;
-	my $CT_transliterations_performed = ($CT_sequence =~ tr/C/T/); # converts all Cs into Ts
-	$total_CT_conversions += $CT_transliterations_performed;
-	$chromosome_CT_conversions += $CT_transliterations_performed;
-	
-	print CT_CONVERT $CT_sequence;
-	
-	### (III) Writing the chromosome out in a G->A converted version of the forward strand (this is equivalent to reverse-
-	### complementing the forward strand and then C->T converting it)
-	
-	my $GA_sequence = $sequence;
-	my $GA_transliterations_performed = ($GA_sequence =~ tr/G/A/); # converts all Gs to As on the forward strand
-	$total_GA_conversions += $GA_transliterations_performed;
-	$chromosome_GA_conversions += $GA_transliterations_performed;
-	
-	print GA_CONVERT $GA_sequence;
-	
-      }
-    }
-    $verbose and print join ("\t",$chromosome_name,$chromosome_CT_conversions,$chromosome_GA_conversions),"\n";
-  }
-  close (CT_CONVERT) or die "Failed to close filehandle: $!\n";
-  close (GA_CONVERT) or die "Failed to close filehandle: $!\n";
-
-
-  print "\nTotal number of conversions performed:\n";
-  print "C->T:\t$total_CT_conversions\n";
-  print "G->A:\t$total_GA_conversions\n";
-
-  warn "\nStep II - Genome bisulfite conversions - completed\n\n\n";
-}
-
-sub extract_chromosome_name {
-
-  my $header = shift;
-
-  ## Bowtie extracts the first string after the initial > in the FASTA file, so we are doing this as well
-
-  if ($header =~ s/^>//){
-    my ($chromosome_name) = split (/\s+/,$header);
-    return $chromosome_name;
-  }
-  else{
-    die "The specified chromosome file doesn't seem to be in FASTA format as required! $!\n";
-  }
-}
-
-sub create_bisulfite_genome_folders{
-
-  $verbose and print "Bismark Genome Preparation - Step I: Preparing folders\n\n";
-
-  # Ensuring a genome folder has been specified
-  if ($genome_folder){
-    unless ($genome_folder =~ /\/$/){
-      $genome_folder =~ s/$/\//;
-    }
-    $verbose and print "Path to genome folder specified: $genome_folder\n";
-    chdir $genome_folder or die "Could't move to directory $genome_folder. Make sure the directory exists! $!";
-
-    # making the genome folder path abolsolute so it won't break if the path was specified relative
-    $genome_folder = getcwd;
-    unless ($genome_folder =~ /\/$/){
-      $genome_folder =~ s/$/\//;
-    }
-  }
-
-  else{
-    $verbose and print "Genome folder was not provided as argument ";
-    while (1){
-      print "Please specify a genome folder to be bisulfite converted:\n";
-      $genome_folder = <STDIN>;
-      chomp $genome_folder;
-
-      # adding a trailing slash unless already present
-      unless ($genome_folder =~ /\/$/){
-	$genome_folder =~ s/$/\//;
-      }
-      if (chdir $genome_folder){
-	last;
-      }
-      else{
-	warn "Could't move to directory $genome_folder! $!";
-      }
-    }
-  }
-
-  if ($path_to_bowtie){
-    unless ($path_to_bowtie =~ /\/$/){
-      $path_to_bowtie =~ s/$/\//;
-    }
-    if (chdir $path_to_bowtie){
-      if ($bowtie2){
-	$verbose and print "Path to Bowtie 2 specified: $path_to_bowtie\n";
-      }
-      else{
-	$verbose and print "Path to Bowtie (1) specified: $path_to_bowtie\n";
-      }
-    }
-    else{
-      die "There was an error with the path to bowtie: $!\n";
-    }
-  }
-
-  chdir $genome_folder or die "Could't move to directory $genome_folder. Make sure the directory exists! $!";
-
-
-  # Exiting unless there are fastA files in the folder
-  my @filenames = <*.fa>;
-
-  ### if there aren't any genomic files with the extension .fa we will look for files with the extension .fasta
-  unless (@filenames){
-    @filenames =  <*.fasta>;
-  }
-
-  unless (@filenames){
-    die "The specified genome folder $genome_folder does not contain any sequence files in FastA format (with .fa or .fasta file extensions\n";
-  }
-
-  warn "Bisulfite Genome Indexer version $bismark_version (last modified 17 Nov 2011)\n\n";
-  sleep (3);
-
-  # creating a directory inside the genome folder to store the bisfulfite genomes unless it already exists
-  my $bisulfite_dir = "${genome_folder}Bisulfite_Genome/";
-  unless (-d $bisulfite_dir){
-    mkdir $bisulfite_dir or die "Unable to create directory $bisulfite_dir $!\n";
-    $verbose and print "Created Bisulfite Genome folder $bisulfite_dir\n";
-  }
-  else{
-    while (1){
-      print "\nA directory called $bisulfite_dir already exists. Bisulfite converted sequences and/or already existing Bowtie (1 or 2) indexes might be overwritten!\nDo you want to continue anyway?\t";
-      my $proceed = <STDIN>;
-      chomp $proceed;
-      if ($proceed =~ /^y/i ){
-	last;
-      }
-      elsif ($proceed =~ /^n/i){
-	die "Terminated by user\n\n";
-      }
-    }
-  }
-
-  ### as of version 0.6.0 the Bismark indexer will no longer delete the Bisulfite_Genome directory if it was present already, since it could store the Bowtie 1 or 2  indexes already
-  # removing any existing files and subfolders in the bisulfite directory (the specified directory won't be deleted)
-  # rmtree($bisulfite_dir, {verbose => 1,keep_root => 1});
-  #  unless (-d $bisulfite_dir){ #  had to add this after changing remove_tree to rmtree // suggested by Samantha Cooper @ Illumina
-  #    mkdir $bisulfite_dir or die "Unable to create directory $bisulfite_dir $!\n";
-  #  }
-  # }
-
-  chdir $bisulfite_dir or die "Unable to move to $bisulfite_dir\n";
-  $CT_dir = "${bisulfite_dir}CT_conversion/";
-  $GA_dir = "${bisulfite_dir}GA_conversion/";
-
-  # creating 2 subdirectories to store a C->T (forward strand conversion) and a G->A (reverse strand conversion)
-  # converted version of the genome
-  unless (-d $CT_dir){
-    mkdir $CT_dir or die "Unable to create directory $CT_dir $!\n";
-    $verbose and print "Created Bisulfite Genome folder $CT_dir\n";
-  }
-  unless (-d $GA_dir){
-    mkdir $GA_dir or die "Unable to create directory $GA_dir $!\n";
-    $verbose and print "Created Bisulfite Genome folder $GA_dir\n";
-  }
-
-  # moving back to the original genome folder
-  chdir $genome_folder or die "Could't move to directory $genome_folder $!";
-  # $verbose and print "Moved back to genome folder folder $genome_folder\n";
-  warn "\nStep I - Prepare genome folders - completed\n\n\n";
-  return @filenames;
-}
-
-sub print_helpfile{
-  print << 'HOW_TO';
-
-
-DESCRIPTION
-
-This script is supposed to convert a specified reference genome into two different bisulfite
-converted versions and index them for alignments with Bowtie 1 (default), or Bowtie 2. The first
-bisulfite genome will have all Cs converted to Ts (C->T), and the other one will have all Gs
-converted to As (G->A). Both bisulfite genomes will be stored in subfolders within the reference
-genome folder. Once the bisulfite conversion has been completed the program will fork and launch
-two simultaneous instances of the bowtie 1 or 2 indexer (bowtie-build or bowtie2-build). Be aware
-that the indexing process can take up to several hours; this will mainly depend on genome size
-and system resources.
-
-
-
-
-The following is a brief description of command line options and arguments to control the
-Bismark Genome Preparation script:
-
-
-USAGE: bismark_genome_preparation [options] <arguments>
-
-
-OPTIONS:
-
---help/--man             Displays this help filea and exits.
-
---version                Displays version information and exits.
-
---verbose                Print verbose output for more details or debugging.
-
---path_to_bowtie         The full path to the Bowtie 1 or Bowtie 2 installation on your system.If
-                         the path </../../> is not provided as an option you will be prompted for it.
-
---bowtie2                This will create bisulfite indexes for Bowtie 2. (Default: Bowtie 1).
-
---single_fasta           Instruct the Bismark Indexer to write the converted genomes into
-                         single-entry FastA files instead of making one multi-FastA file (MFA)
-                         per chromosome. This might be useful if individual bisulfite converted
-                         chromosomes are needed (e.g. for debugging), however it can cause a
-                         problem with indexing if the number of chromosomes is vast (this is likely
-                         to be in the range of several thousand files; the operating system can
-                         only handle lists up to a certain length, and some newly assembled
-                         genomes may contain 20000-50000 contigs of scaffold files which do exceed
-                         this list length limit).
-
-
-ARGUMENTS:
-
-<path_to_genome_folder>  The path to the folder containing the genome to be bisulfite converted.
-                         At the current time Bismark Genome Preparation expects one or more fastA
-                         files in the folder (with the file extension: .fa or .fasta). If the path
-                         is not provided as an argument you will be prompted for it.
-
-
-
-This script was last modified on 18 Nov 2011.
-HOW_TO
-}
--- a/bismark_methylation_extractor	Tue Dec 25 05:45:46 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3537 +0,0 @@
-#!/usr/bin/perl
-use warnings;
-use strict;
-$|++;
-use Getopt::Long;
-use Cwd;
-use Carp;
-
-my @filenames; # input files
-my %counting;
-my $parent_dir = getcwd();
-
-my %fhs;
-
-my $version = 'v0.7.7';
-my ($ignore,$genomic_fasta,$single,$paired,$full,$report,$no_overlap,$merge_non_CpG,$vanilla,$output_dir,$no_header,$bedGraph,$remove,$coverage_threshold,$counts,$cytosine_report,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome) = process_commandline();
-
-
-### only needed for bedGraph output
-my @sorting_files; # if files are to be written to bedGraph format, these are the methylation extractor output files
-my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total
-my @bedfiles;
-
-### only needed for genome-wide cytosine methylation report
-my %chromosomes;
-
-##############################################################################################
-### Summarising Run Parameters
-##############################################################################################
-
-### METHYLATION EXTRACTOR
-
-warn "Summarising Bismark methylation extractor parameters:\n";
-warn '='x63,"\n";
-
-if ($single){
-  if ($vanilla){
-    warn "Bismark single-end vanilla format specified\n";
-  }
-  else{
-    warn "Bismark single-end SAM format specified (default)\n"; # default
-  }
-}
-elsif ($paired){
-  if ($vanilla){
-    warn "Bismark paired-end vanilla format specified\n";
-  }
-  else{
-    warn "Bismark paired-end SAM format specified (default)\n"; # default
-  }
-}
-
-if ($ignore){
-  warn "First $ignore bases will be disregarded when processing the methylation call string\n";
-}
-
-if ($full){
-  warn "Strand-specific outputs will be skipped. Separate output files for cytosines in CpG, CHG and CHH context will be generated\n";
-}
-if ($merge_non_CpG){
-  warn "Merge CHG and CHH context to non-CpG context specified\n";
-}
-### output directory
-if ($output_dir eq ''){
-  warn "Output will be written to the current directory ('$parent_dir')\n";
-}
-else{
-  warn "Output path specified as: $output_dir\n";
-}
-
-
-sleep (1);
-
-### BEDGRAPH
-
-if ($bedGraph){
-  warn "\n\nSummarising bedGraph parameters:\n";
-  warn '='x63,"\n";
-
-  if ($counts){
-    warn "Generating additional output in bedGraph format including methylating counts (output format: <Chromosome> <Start Position> <End Position> <Methylation Percentage> <count methylated> <count non-methylated>)\n";
-  }
-  else{
-    warn "Generating additional sorted output in bedGraph format (output format: <Chromosome> <Start Position> <End Position> <Methylation Percentage>)\n";
-  }
-
-  warn "Using a cutoff of $coverage_threshold read(s) to report cytosine positions\n";
-
-  if ($CX_context){
-    warn "Reporting and sorting methylation information for all cytosine context (sorting may take a long time, you have been warned ...)\n";
-  }
-  else{ # default
-    $CpG_only = 1;
-    warn "Reporting and sorting cytosine methylation information in CpG context only (default)\n";
-  }
-
-  if ($remove){
-    warn "White spaces in read ID names will be removed prior to sorting\n";
-  }
-
-  sleep (1);
-
-  if ($cytosine_report){
-    warn "\n\nSummarising genome-wide cytosine methylation report parameters:\n";
-    warn '='x63,"\n";
-    warn "Generating comprehensive genome-wide cytosine report (output format: <Chromosome> <Start Position> <End Position> <Methylation Percentage> )\n";
-
-
-    if ($CX_context){
-      warn "Reporting methylation for all cytosine contexts. Be aware that this will generate enormous files\n";
-    }
-    else{ # default
-      $CpG_only = 1;
-      warn "Reporting cytosine methylation in CpG context only (default)\n";
-    }
-
-    if ($split_by_chromosome){
-      warn "Splitting the cytosine report output up into individual files for each chromosome\n";
-    }
-
-    ### Zero-based coordinates
-    if ($zero){
-      warn "Using zero-based genomic coordinates (user-defined)\n";
-    }
-    else{ # default, 1-based coords
-      warn "Using 1-based genomic coordinates (default)\n";
-    }
-
-    ### GENOME folder
-    if ($genome_folder){
-      unless ($genome_folder =~/\/$/){
-	$genome_folder =~ s/$/\//;
-      }
-      warn "Genome folder was specified as $genome_folder\n";
-    }
-    else{
-      $genome_folder  = '/data/public/Genomes/Mouse/NCBIM37/';
-      warn "Using the default genome folder /data/public/Genomes/Mouse/NCBIM37/\n";
-    }
-    sleep (1);
-  }
-}
-
-warn "\n";
-sleep (5);
-
-######################################################
-### PROCESSING FILES
-######################################################
-
-foreach my $filename (@filenames){
-  # resetting counters and filehandles
-  %fhs = ();
-  %counting =(
-	      total_meCHG_count => 0,
-	      total_meCHH_count => 0,
-	      total_meCpG_count => 0,
-	      total_unmethylated_CHG_count => 0,
-	      total_unmethylated_CHH_count => 0,
-	      total_unmethylated_CpG_count => 0,
-	      sequences_count => 0,
-	     );
-  @sorting_files = ();
-  @bedfiles = ();
-
-  process_Bismark_results_file($filename);
-
-  if ($bedGraph){
-    my $out = $filename;
-    $out =~ s/sam$//;
-    $out =~ s/txt$//;
-    $out =~ s/$/bedGraph/;
-
-    my $bedGraph_output = $out;
-    open (OUT,'>',$output_dir.$out) or die $!;
-    # warn "Writing bedGraph to file: $out\n";
-
-    process_bedGraph_output();
-    close OUT or die $!;
-
-    ### genome-wide cytosine methylation report requires bedGraph processing anyway
-    if ($cytosine_report){
-      my $cytosine_out = $out;
-      $cytosine_out =~ s/bedGraph$//;
-
-      read_genome_into_memory();
-      generate_genome_wide_cytosine_report($bedGraph_output,$cytosine_out);
-    }
-  }
-}
-
-
-sub process_commandline{
-  my $help;
-  my $single_end;
-  my $paired_end;
-  my $ignore;
-  my $genomic_fasta;
-  my $full;
-  my $report;
-  my $extractor_version;
-  my $no_overlap;
-  my $merge_non_CpG;
-  my $vanilla;
-  my $output_dir;
-  my $no_header;
-  my $bedGraph;
-  my $coverage_threshold = 1; # Minimum number of reads covering before calling methylation status
-  my $remove;
-  my $counts;
-  my $cytosine_report;
-  my $genome_folder;
-  my $zero;
-  my $CpG_only;
-  my $CX_context;
-  my $split_by_chromosome;
-
-
-  my $command_line = GetOptions ('help|man' => \$help,
-				 'p|paired-end' => \$paired_end,
-				 's|single-end' => \$single_end,
-				 'fasta' => \$genomic_fasta,
-				 'ignore=i' => \$ignore,
-				 'comprehensive' => \$full,
-				 'report' => \$report,
-				 'version' => \$extractor_version,
-				 'no_overlap' => \$no_overlap,
-				 'merge_non_CpG' => \$merge_non_CpG, 
-				 'vanilla' => \$vanilla,
-				 'o|output=s' => \$output_dir,
-				 'no_header' => \$no_header,
-				 'bedGraph' => \$bedGraph,
-				 "cutoff=i" => \$coverage_threshold,
-				 "remove_spaces" => \$remove,
-				 "counts" => \$counts,
-				 "cytosine_report" => \$cytosine_report,
-				 'g|genome_folder=s' => \$genome_folder,
-				 "zero_based" => \$zero,	
-				 "CX|CX_context" => \$CX_context,
-				 "split_by_chromosome" => \$split_by_chromosome,
-				);
-
-  ### EXIT ON ERROR if there were errors with any of the supplied options
-  unless ($command_line){
-    die "Please respecify command line options\n";
-  }
-
-  ### HELPFILE
-  if ($help){
-    print_helpfile();
-    exit;
-  }
-
-  if ($extractor_version){
-    print << "VERSION";
-
-
-                           Bismark Methylation Extractor
-
-   Bismark Extractor Version: $version Copyright 2010-12 Felix Krueger, Babraham Bioinformatics
-                www.bioinformatics.babraham.ac.uk/projects/bismark/
-
-
-VERSION
-    exit;
-  }
-
-
-  ### no files provided
-  unless (@ARGV){
-    die "You need to provide one or more Bismark files to create an individual C methylation output. Please respecify!\n";
-  }
-  @filenames = @ARGV;
-
-  warn "\n *** Bismark methylation extractor version $version ***\n\n";
-
-  ### IGNORING <INT> bases at the start of the read when processing the methylation call string
-  unless ($ignore){
-    $ignore = 0;
-  }
-  ### PRINT A REPORT
-  unless ($report){
-    $report = 0;
-  }
-
-  ### OUTPUT DIR PATH
-  if ($output_dir){
-    unless ($output_dir =~ /\/$/){
-      $output_dir =~ s/$/\//;
-    }
-  }
-  else{
-    $output_dir = '';
-  }
-
-  ### NO HEADER
-  unless ($no_header){
-    $no_header = 0;
-  }
-
-  ### OLD (VANILLA) OUTPUT FORMAT
-  unless ($vanilla){
-    $vanilla = 0;
-  }
-
-  if ($single_end){
-    $paired_end = 0;   ### SINGLE END ALIGNMENTS
-  }
-  elsif ($paired_end){
-    $single_end = 0;   ### PAIRED-END ALIGNMENTS
-  }
-  else{
-    die "Please specify whether the supplied file(s) are in Bismark single-end or paired-end format\n\n";
-  }
-
-  ### NO OVERLAP
-  if ($no_overlap){
-    die "The option '--no_overlap' can only be specified for paired-end input!\n" unless ($paired_end);
-  }
-  else{
-    $no_overlap = 0;
-  }
-
-  ### COMPREHENSIVE OUTPUT
-  unless ($full){
-    $full = 0;
-  }
-
-  ### MERGE NON-CpG context
-  unless ($merge_non_CpG){
-    $merge_non_CpG = 0;
-  }
-
-  ### remove white spaces in read ID (needed for sorting using the sort command
-  unless ($remove){
-    $remove = 0;
-  }
-
-  ### COVERAGE THRESHOLD FOR gedGraph OUTPUT
-  unless (defined $coverage_threshold){
-    unless ($coverage_threshold > 0){
-      die "Please select a coverage greater than 0 (positive integers only)\n";
-    }
-    $coverage_threshold = 1;
-  }
-
-  if ($zero){
-    die "Option '--zero' is only available if  '--cytosine_report' is specified as well. Please respecify\n" unless ($cytosine_report);
-  }
-
-  if ($CX_context){
-    die "Option '--CX_context' is only available if  '--cytosine_report' or '--bedGraph' is specified as well. Please respecify\n" unless ($cytosine_report or $bedGraph);
-  }
-
-  if ($cytosine_report){
-
-    ### GENOME folder
-    if ($genome_folder){
-      unless ($genome_folder =~/\/$/){
-	$genome_folder =~ s/$/\//;
-      }
-    }
-    else{
-      die "Please specify a genome folder to proceed (full path only)\n";
-    }
-
-    unless ($bedGraph){
-      warn "Setting the option '--bedGraph' since this is required for the genome-wide cytosine report\n";
-      $bedGraph = 1;
-    }
-    unless ($counts){
-      warn "Setting the option '--counts' since this is required for the genome-wide cytosine report\n";
-      $counts = 1;
-    }
-    warn "\n";
-  }
-
-  return ($ignore,$genomic_fasta,$single_end,$paired_end,$full,$report,$no_overlap,$merge_non_CpG,$vanilla,$output_dir,$no_header,$bedGraph,$remove,$coverage_threshold,$counts,$cytosine_report,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome);
-}
-
-
-sub process_Bismark_results_file{
-  my $filename = shift;
-
-  warn "\nNow reading in Bismark result file $filename\n\n";
-
-  if ($filename =~ /\.gz$/) {
-    open (IN,"zcat $filename |") or die "Can't open gzipped file $filename: $!\n";
-  } else {
-    open (IN,$filename) or die "Can't open file $filename: $!\n";
-  }
-
-  ### Vanilla and SAM output need to read different numbers of header lines
-  if ($vanilla) {
-    my $bismark_version = <IN>; ## discarding the Bismark version info
-    chomp $bismark_version;
-    $bismark_version =~ s/\r//; # replaces \r line feed
-    $bismark_version =~  s/Bismark version: //;
-    if ($bismark_version =~ /^\@/) {
-      warn "Detected \@ as the first character of the version information. Is it possible that the file is in SAM format?\n\n";
-      sleep (2);
-    }
-
-    unless ($version eq $bismark_version){
-      die "The methylation extractor and Bismark itself need to be of the same version!\n\nVersions used:\nmethylation extractor: '$version'\nBismark: '$bismark_version'\n";
-    }
-  } else {
-    # If the read is in SAM format (default) it can either start with @ header lines or start with alignments directly.
-    # We are reading from it further down
-  }
-
-  my $output_filename = (split (/\//,$filename))[-1];
-
-  ### OPENING OUTPUT-FILEHANDLES
-  if ($report) {
-    my $report_filename = $output_filename;
-    $report_filename =~ s/[\.sam|\.txt]$//;
-    $report_filename =~ s/$/_splitting_report.txt/;
-    $report_filename = $output_dir . $report_filename;
-    open (REPORT,'>',$report_filename) or die "Failed to write to file $report_filename $!\n";
-  }
-
-  if ($report) {
-    print REPORT "$output_filename\n\n";
-    print REPORT "Parameters used to extract methylation information:\n";
-    if ($paired) {
-      if ($vanilla) {
-	print REPORT "Bismark result file: paired-end (vanilla Bismark format)\n";
-      } else {
-	print REPORT "Bismark result file: paired-end (SAM format)\n"; # default
-      }
-    }
-
-    if ($single) {
-      if ($vanilla) {
-	print REPORT "Bismark result file: single-end (vanilla Bismark format)\n";
-      } else {
-	print REPORT "Bismark result file: single-end (SAM format)\n"; # default
-      }
-    }
-
-    if ($ignore) {
-      print REPORT "Ignoring first $ignore bases\n";
-    }
-
-    if ($full) {
-      print REPORT "Output specified: comprehensive\n";
-    } else {
-      print REPORT "Output specified: strand-specific (default)\n";
-    }
-
-    if ($no_overlap) {
-      print REPORT "No overlapping methylation calls specified\n";
-    }
-    if ($genomic_fasta) {
-      print REPORT "Genomic equivalent sequences will be printed out in FastA format\n";
-    }
-    if ($merge_non_CpG) {
-      print REPORT "Methylation in CHG and CHH context will be merged into \"non-CpG context\" output\n";
-    }
-
-    print REPORT "\n";
-  }
-
-  ### CpG-context and non-CpG context. THIS SECTION IS OPTIONAL
-  ### if --comprehensive AND --merge_non_CpG was specified we are only writing out one CpG-context and one Any-Other-context result file
-  if ($full and $merge_non_CpG) {
-    my $cpg_output = my $other_c_output = $output_filename;
-    ### C in CpG context
-    $cpg_output =~ s/^/CpG_context_/;
-    $cpg_output =~ s/sam$/txt/;
-    $cpg_output =~ s/$/.txt/ unless ($cpg_output =~ /\.txt$/);
-    $cpg_output = $output_dir . $cpg_output;
-    push @sorting_files,$cpg_output;
-    open ($fhs{CpG_context},'>',$cpg_output) or die "Failed to write to $cpg_output $! \n";
-    print "Writing result file containing methylation information for C in CpG context to $cpg_output\n";
-
-    unless ($no_header) {
-      print {$fhs{CpG_context}} "Bismark methylation extractor version $version\n";
-    }
-
-    ### C in any other context than CpG
-    $other_c_output =~ s/^/Non_CpG_context_/;
-    $other_c_output =~ s/sam$/txt/;
-    $other_c_output =~ s/$/.txt/ unless ($other_c_output =~ /\.txt$/);