From f69f2174f2ddecdc8f7e58c5755e3370c4d5e203 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Carn=C3=AB=20Draug?= <carandraug+dev@gmail.com>
Date: Fri, 8 Feb 2019 13:45:16 +0000
Subject: [PATCH] Initial commit.

Imported from 334b1b593f9f97c1393e997b45e48cb89782007a
---
 .gitignore                      |  10 +
 Changes                         |   5 +
 dist.ini                        |  12 +
 lib/Bio/Tools/Run/Maq.pm        | 650 ++++++++++++++++++++++++++++++++
 lib/Bio/Tools/Run/Maq/Config.pm | 335 ++++++++++++++++
 t/Maq.t                         | 196 ++++++++++
 t/data/campycoli.fas            |  50 +++
 t/data/r1.fq                    | 500 ++++++++++++++++++++++++
 t/data/r2.fq                    | 500 ++++++++++++++++++++++++
 9 files changed, 2258 insertions(+)
 create mode 100644 .gitignore
 create mode 100644 Changes
 create mode 100644 dist.ini
 create mode 100755 lib/Bio/Tools/Run/Maq.pm
 create mode 100755 lib/Bio/Tools/Run/Maq/Config.pm
 create mode 100755 t/Maq.t
 create mode 100755 t/data/campycoli.fas
 create mode 100644 t/data/r1.fq
 create mode 100644 t/data/r2.fq

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..618cad3
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,10 @@
+.*
+*~
+!.gitignore
+
+# ignore build
+Bio-Tools-Run-Maq-*
+
+# ignore text editors stuff
+.emacs.*
+*.komodoproject
diff --git a/Changes b/Changes
new file mode 100644
index 0000000..bbee184
--- /dev/null
+++ b/Changes
@@ -0,0 +1,5 @@
+Summary of important user-visible changes for Bio-Tools-Run-Maq
+---------------------------------------------------------------
+
+{{$NEXT}}
+  * First release after split from bioperl-run.
diff --git a/dist.ini b/dist.ini
new file mode 100644
index 0000000..9d62b35
--- /dev/null
+++ b/dist.ini
@@ -0,0 +1,12 @@
+name = Bio-Tools-Run-Maq
+version = 1.7.3
+author = Mark A. Jensen
+copyright_holder = Mark A. Jensen <maj@fortinbras.us>
+license = Perl_5
+
+;; Modules should be fixed so that these don't have to be removed.
+[@BioPerl]
+-remove = PodCoverageTests
+-remove = PodWeaver
+-remove = Test::EOL
+-remove = Test::NoTabs
diff --git a/lib/Bio/Tools/Run/Maq.pm b/lib/Bio/Tools/Run/Maq.pm
new file mode 100755
index 0000000..66d3657
--- /dev/null
+++ b/lib/Bio/Tools/Run/Maq.pm
@@ -0,0 +1,650 @@
+#
+# BioPerl module for Bio::Tools::Run::Maq
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Cared for by Mark A. Jensen <maj@fortinbras.us>
+#
+# Copyright Mark A. Jensen
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Run::Maq - Run wrapper for the Maq short-read assembler *BETA*
+
+=head1 SYNOPSIS
+
+ # create an assembly
+ $maq_fac = Bio::Tools::Run::Maq->new();
+ $maq_assy = $maq_fac->run( 'reads.fastq', 'refseq.fas' );
+ # if IO::Uncompress::Gunzip is available...
+ $maq_assy = $maq_fac->run( 'reads.fastq.gz', 'refseq.gz');
+ # paired-end 
+ $maq_assy = $maq_fac->run( 'reads.fastq', 'refseq.fas', 'paired-reads.fastq');
+ # be more strict
+ $maq_fac->set_parameters( -c2q_min_map_quality => 60 );
+ $maq_assy = $maq_fac->run( 'reads.fastq', 'refseq.fas', 'paired-reads.fastq');
+
+ # run maq commands separately
+ $maq_fac = Bio::Tools::Run::Maq->new(
+    -command => 'pileup',
+    -single_end_quality => 1 );
+ $maq_fac->run_maq( -bfa => 'refseq.bfa',
+                    -map => 'maq_assy.map',
+                    -txt => 'maq_assy.pup.txt' );
+
+=head1 DESCRIPTION
+
+This module provides a wrapper interface for Heng Li's
+reference-directed short read assembly suite C<maq> (see
+L<http://maq.sourceforge.net/maq-man.shtml> for manuals and
+downloads).
+
+There are two modes of action. 
+
+=over 
+
+=item * EasyMaq
+
+The first is a simple pipeline through the C<maq> commands, taking
+your read data in and squirting out an assembly object of type
+L<Bio::Assembly::IO::maq>. The pipeline is based on the one performed
+by C<maq.pl easyrun>:
+
+ Action                  maq commands
+ ------                  ------------
+ data conversion to      fasta2bfa, fastq2bfq
+ maq binary formats
+
+ map sequence reads      map
+ to reference seq
+
+ assemble, creating      assemble
+ consensus
+
+ convert map & cns       mapview, cns2fq
+ files to plaintext
+ (for B:A:IO:maq)
+
+Command-line options can be directed to the C<map>, C<assemble>, and
+C<cns2fq> steps. See L</OPTIONS> below.
+
+=item * BigMaq
+
+The second mode is direct access to C<maq> commands. To run a C<maq>
+command, construct a run factory, specifying the desired command using
+the C<-command> argument in the factory constructor, along with
+options specific to that command (see L</OPTIONS>):
+
+ $maqfac->Bio::Tools::Run::Maq->new( -command => 'fasta2bfa' );
+
+To execute, use the C<run_maq> methods. Input and output files are
+specified in the arguments of C<run_maq> (see L</FILES>):
+
+ $maqfac->run_maq( -fas => "myref.fas", -bfa => "myref.bfa" );
+
+=back
+
+=head1 OPTIONS
+
+C<maq> is complex, with many subprograms (commands) and command-line
+options and file specs for each. This module attempts to provide
+commands and options comprehensively. You can browse the choices like so:
+
+ $maqfac = Bio::Tools::Run::Maq->new( -command => 'assemble' );
+ # all maq commands
+ @all_commands = $maqfac->available_parameters('commands'); 
+ @all_commands = $maqfac->available_commands; # alias
+ # just for assemble
+ @assemble_params = $maqfac->available_parameters('params');
+ @assemble_switches = $maqfac->available_parameters('switches');
+ @assemble_all_options = $maqfac->available_parameters();
+
+Reasonably mnemonic names have been assigned to the single-letter
+command line options. These are the names returned by
+C<available_parameters>, and can be used in the factory constructor
+like typical BioPerl named parameters.
+
+See L<http://maq.sourceforge.net/maq-manpage.shtml> for the gory details.
+
+=head1 FILES
+
+When a command requires filenames, these are provided to the C<run_maq> method, not
+the constructor (C<new()>). To see the set of files required by a command, use
+C<available_parameters('filespec')> or the alias C<filespec()>:
+
+  $maqfac = Bio::Tools::Run::Maq->new( -command => 'map' );
+  @filespec = $maqfac->filespec;
+
+This example returns the following array:
+
+ map
+ bfa 
+ bfq1 
+ #bfq2 
+ 2>#log
+
+This indicates that map (C<maq> binary mapfile), bfa (C<maq> binary
+fasta), and bfq (C<maq> binary fastq) files MUST be specified, another
+bfq file MAY be specified, and a log file receiving STDERR also MAY be
+specified. Use these in the C<run_maq> call like so:
+
+ $maqfac->run_maq( -map => 'my.map', -bfa => 'myrefseq.bfa',
+                   -bfq1 => 'reads1.bfq', -bfq2 => 'reads2.bfq' );
+
+Here, the C<log> parameter was unspecified. Therefore, the object will store
+the programs STDERR output for you in the C<stderr()> attribute:
+
+ handle_map_warning($maqfac) if ($maqfac->stderr =~ /warning/);
+
+STDOUT for a run is also saved, in C<stdout()>, unless a file is specified
+to slurp it according to the filespec. C<maq> STDOUT usually contains useful
+information on the run. 
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  bioperl-l@bioperl.org                  - General discussion
+http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+L<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+  http://redmine.open-bio.org/projects/bioperl/
+
+=head1 AUTHOR - Mark A. Jensen
+
+ Email maj -at- fortinbras -dot- us
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+
+
+package Bio::Tools::Run::Maq;
+use strict;
+our $HAVE_IO_UNCOMPRESS;
+
+BEGIN {
+    eval {require IO::Uncompress::Gunzip; $HAVE_IO_UNCOMPRESS = 1};
+}
+
+use IPC::Run;
+
+# Object preamble - inherits from Bio::Root::Root
+
+use lib '../../..';
+use Bio::Root::Root;
+use Bio::Tools::Run::Maq::Config;
+use Bio::Tools::GuessSeqFormat;
+use File::Basename qw(fileparse);
+
+use base qw(Bio::Root::Root Bio::Tools::Run::AssemblerBase );
+
+## maq ( from tigr )
+our $program_name = 'maq'; # name of the executable
+
+# Note:
+#  other globals required by Bio::Tools::Run::AssemblerBase are
+#  imported from Bio::Tools::Run::Maq::Config
+
+our $qual_param = 'quality_file';
+our $use_dash = 1;
+our $join = ' ';
+
+our $asm_format = 'maq';
+
+=head2 new()
+
+ Title   : new
+ Usage   : my $obj = new Bio::Tools::Run::Maq();
+ Function: Builds a new Bio::Tools::Run::Maq object
+ Returns : an instance of Bio::Tools::Run::Maq
+ Args    :
+
+=cut
+
+sub new {
+  my ($class,@args) = @_;
+  my $self = $class->SUPER::new(@args);
+  $self->parameters_changed(1); 
+  $self->_register_program_commands( \@program_commands, \%command_prefixes );
+  unless (grep /command/, @args) {
+      push @args, '-command', 'run';
+  }
+  $self->_set_program_options(\@args, \@program_params, \@program_switches,
+    \%param_translation, $qual_param, $use_dash, $join);
+  $self->program_name($program_name) if not defined $self->program_name();
+  if ($^O =~ /cygwin/) {
+      my @kludge = `PATH=\$PATH:/usr/bin:/usr/local/bin which $program_name`;
+      chomp $kludge[0];
+      $self->program_name($kludge[0]);
+  }
+  $self->parameters_changed(1); # set on instantiation, per Bio::ParameterBaseI
+  $self->_assembly_format($asm_format);
+  return $self;
+}
+
+=head2 run
+
+ Title   : run
+ Usage   : $assembly = $maq_assembler->run($read1_fastq_file, 
+                                           $refseq_fasta_file,
+                                           $read2_fastq_file);
+ Function: Run the maq assembly pipeline. 
+ Returns : Assembly results (file, IO object or Assembly object)
+ Args    : - fastq file containing single-end reads
+           - fasta file containing the reference sequence
+           - [optional] fastq file containing paired-end reads 
+ Note    : gzipped inputs are allowed if IO::Uncompress::Gunzip
+           is available
+             
+=cut
+
+sub run {
+  my ($self, $rd1_file, $ref_file, $rd2_file) = @_;
+
+  # Sanity checks
+  $self->_check_executable();
+  $rd1_file or $self->throw("Fastq reads file required at arg 1");
+  $ref_file or $self->throw("Fasta refseq file required at arg 2");
+  # expand gzipped files as nec.
+  for ($rd1_file, $ref_file, $rd2_file) {
+      next unless $_;
+      if (/\.gz[^.]*$/) {
+	  unless ($HAVE_IO_UNCOMPRESS) {
+	      croak( "IO::Uncompress::Gunzip not available, can't expand '$_'" );
+	  }
+	  my ($tfh, $tf) = $self->io->tempfile;
+	  my $z = IO::Uncompress::Gunzip->new($_);
+	  while (<$z>) { print $tfh $_ }
+	  close $tfh;
+	  $_ = $tf;
+      }
+  }
+  my $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$rd1_file);
+
+  $guesser->guess eq 'fastq' or $self->throw("Reads file doesn't look like fastq at arg 1");
+  $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$ref_file);
+  $guesser->guess eq 'fasta' or $self->throw("Refseq file doesn't look like fasta at arg 2");
+  if ($rd2_file) {
+      $guesser = Bio::Tools::GuessSeqFormat->new(-file=>$rd2_file);
+      $guesser->guess eq 'fastq' or $self->throw("Reads file doesn't look like fastq at arg 3");
+  }
+
+  # maq format conversion
+  ($rd1_file, $ref_file, $rd2_file) = $self->_prepare_input_sequences($rd1_file, $ref_file, $rd2_file);
+
+  # Assemble
+  my ($maq_file, $faq_file) = $self->_run($rd1_file, $ref_file, $rd2_file);
+
+  # Export results in desired object type
+  my $asm  = $self->_export_results($maq_file);
+  return $asm;
+}
+
+=head2 run_maq()
+
+ Title   : run_maq
+ Usage   : $obj->run_maq( @file_args )
+ Function: Run a maq command as specified during object contruction
+ Returns : 
+ Args    : a specification of the files to operate on:
+
+=cut
+
+sub run_maq {
+    my ($self, @args) = @_;
+    # _translate_params will provide an array of command/parameters/switches
+    # -- these are set at object construction
+    # to set up the run, need to add the files to the call
+    # -- provide these as arguments to this function
+
+    my $cmd = $self->command if $self->can('command');
+    $self->throw("No maq command specified for the object") unless $cmd;
+    # setup files necessary for this command
+    my $filespec = $command_files{$cmd};
+    $self->throw("No command-line file specification is defined for command '$cmd'; check Bio::Tools::Run::Maq::Config") unless $filespec;
+
+    # parse args based on filespec
+    # require named args
+    $self->throw("Named args are required") unless !(@args % 2);
+    s/^-// for @args;
+    my %args = @args; 
+    # validate
+    my @req = map { 
+	my $s = $_; 
+	$s =~ s/^[012]?[<>]//;
+	$s =~ s/[^a-zA-Z0-9_]//g; 
+	$s
+    } grep !/[#]/, @$filespec;
+    !defined($args{$_}) && $self->throw("Required filearg '$_' not specified") for @req;
+    # set up redirects
+    my ($in, $out, $err);
+    for (@$filespec) {
+	m/^1?>(.*)/ && do {
+	    defined($args{$1}) && ( open($out,">", $args{$1}) or $self->throw("Open for write error : $!"));
+	    next;
+	};
+	m/^2>#?(.*)/ && do {
+	    defined($args{$1}) && (open($err, ">", $args{$1}) or $self->throw("Open for write error : $!"));
+	    next;
+	};
+	m/^<#?(.*)/ && do {
+	    defined($args{$1}) && (open($in, "<", $args{$1}) or $self->throw("Open for read error : $!"));
+	    next;
+	}
+    }
+    my $dum;
+    $in || ($in = \$dum);
+    $out || ($out = \$self->{'stdout'});
+    $err || ($err = \$self->{'stderr'});
+    
+    # Get program executable
+    my $exe = $self->executable;
+    # Get command-line options
+    my $options = $self->_translate_params();
+    # Get file specs sans redirects in correct order
+    my @specs = map { 
+	my $s = $_; 
+	$s =~ s/[^a-zA-Z0-9_]//g; 
+	$s
+    } grep !/[<>]/, @$filespec;
+    my @files = @args{@specs};
+    # expand arrayrefs
+    my $l = $#files;
+    for (0..$l) {
+	splice(@files, $_, 1, @{$files[$_]}) if (ref($files[$_]) eq 'ARRAY');
+    }
+    @files = map { defined $_ ? $_ : () } @files; # squish undefs
+    my @ipc_args = ( $exe, @$options, @files );
+
+    eval {
+	IPC::Run::run(\@ipc_args, $in, $out, $err) or
+	    die ("There was a problem running $exe : $!");
+    };
+    if ($@) {
+	$self->throw("$exe call crashed: $@");
+    }
+
+    # return arguments as specified on call
+    return @args;
+}
+
+=head2 stdout()
+
+ Title   : stdout
+ Usage   : $fac->stdout()
+ Function: store the output from STDOUT for the run, 
+           if no file specified in run_maq()
+ Example : 
+ Returns : scalar string
+ Args    : on set, new value (a scalar or undef, optional)
+
+=cut
+
+sub stdout {
+    my $self = shift;
+    
+    return $self->{'stdout'} = shift if @_;
+    return $self->{'stdout'};
+}
+
+=head2 stderr()
+
+ Title   : stderr
+ Usage   : $fac->stderr()
+ Function: store the output from STDERR for the run, 
+           if no file is specified in run_maq()
+ Example : 
+ Returns : scalar string
+ Args    : on set, new value (a scalar or undef, optional)
+
+=cut
+
+sub stderr {
+    my $self = shift;
+    
+    return $self->{'stderr'} = shift if @_;
+    return $self->{'stderr'};
+}
+
+
+
+=head1 Bio::Tools::Run::AssemblerBase overrides
+
+=head2 _check_sequence_input()
+
+ No-op.
+
+=cut
+
+sub _check_sequence_input {
+    return 1;
+}
+
+=head2 _check_optional_quality_input()
+
+ No-op.
+
+=cut
+
+sub _check_optional_quality_input {
+    return 1;
+}
+
+=head2 _prepare_input_sequences
+
+ Convert input fastq and fasta to maq format.
+
+=cut
+
+sub _prepare_input_sequences {
+
+    my ($self, @args) = @_;
+    my (%args, $read1, $read2, $refseq);
+    if (grep /^-/, @args) { # named parms
+	$self->throw("Input args not an even number") unless !(@args % 2);
+	%args = @args;
+	($read1, $refseq, $read2) = @args{qw( -read1 -refseq -read2 )};
+    }
+    else {
+	($read1, $refseq, $read2) = @args;
+    }
+    # just handle file input for now...
+    $self->throw("maq requires at least one FASTQ read file and one FASTA reference sequence") 
+	unless (defined $read1 && defined $refseq);
+    $self->throw("File cannot be found")
+	unless ( -e $read1 && -e $refseq && (!defined $read2 || -e $read2) );
+
+    # maq needs its own fasta/fastq format. Use its own converters to 
+    # create tempfiles in bfa, bfq format.
+    my ($ref_h, $ref_file, $rd1_h, $rd1_file, $rd2_h, $rd2_file);
+    ($ref_h, $ref_file) = $self->io->tempfile( -dir => $self->tempdir() );
+    ($rd1_h, $rd1_file) = $self->io->tempfile( -dir => $self->tempdir() );
+    $ref_h->close;
+    $rd1_h->close;
+    my $fac = Bio::Tools::Run::Maq->new( -command => 'fasta2bfa' );
+    $fac->run_maq( -bfa => $ref_file, -fas => $refseq );
+    $fac->set_parameters( -command => 'fastq2bfq' );
+    $fac->run_maq( -bfq => $rd1_file, -faq => $read1 );
+    if (defined $read2) {
+	($rd2_h, $rd2_file) = $self->io->tempfile( -dir => $self->tempdir() );
+	$rd2_h->close;
+	$fac->run_maq( -bfq => $rd2_file, -faq => $read2);
+    }
+    return ($rd1_file, $ref_file, $rd2_file);
+}
+
+=head2 _collate_subcmd_args()
+
+ Title   : _collate_subcmd_args
+ Usage   : $args_hash = $self->_collate_subcmd_args
+ Function: collate parameters and switches into command-specific
+           arg lists for passing to new()
+ Returns : hash of named argument lists
+ Args    : [optional] composite cmd prefix (scalar string) 
+           [default is 'run']
+
+=cut
+
+sub _collate_subcmd_args {
+    my $self = shift;
+    my $cmd = shift;
+    my %ret;
+    # default command is 'run'
+    $cmd ||= 'run';
+    my @subcmds = @{$composite_commands{$cmd}};
+    my %subcmds;
+    my $cur_options = $self->{'_options'};
+
+    # collate
+    foreach my $subcmd (@subcmds) {
+	# find the composite cmd form of the argument in 
+	# the current params and switches
+	# e.g., map_max_mismatches
+	my @params = grep /^${subcmd}_/, @{$$cur_options{'_params'}};
+	my @switches = grep /^${subcmd}_/, @{$$cur_options{'_switches'}};
+	$ret{$subcmd} = [];
+	# create an argument list suitable for passing to new() of
+	# the subcommand factory...
+	foreach my $opt (@params, @switches) {
+	    my $subopt = $opt; 
+	    $subopt =~ s/^${subcmd}_//; 
+	    push(@{$ret{$subcmd}}, '-'.$subopt => $self->$opt) if defined $self->$opt;
+	}
+    }
+    return \%ret;
+}
+
+=head2 _run()
+
+ Title   :   _run
+ Usage   :   $factory->_run()
+ Function:   Run a maq assembly pipeline
+ Returns :   depends on call (An assembly file)
+ Args    :   - single end read file in maq bfq format
+             - reference seq file in maq bfa format
+             - [optional] paired end read file in maq bfq format
+
+=cut
+
+sub _run {
+  my ($self, $rd1_file, $ref_file, $rd2_file) = @_;
+  my ($cmd, $filespec, @ipc_args);
+  # Get program executable
+  my $exe = $self->executable;
+
+  # treat run() as a separate command and duplicate the component-specific
+  # parameters in the config globals
+
+  # Setup needed files and filehandles first
+  my $tdir = $self->tempdir();
+  my ($maph, $mapf) = $self->io->tempfile( -template => 'mapXXXX', -dir => $tdir ); #map
+  my ($cnsh, $cnsf) = $self->io->tempfile( -template => 'cnsXXXX', -dir => $tdir ); #consensus
+  my ($maqh, $maqf) = $self->_prepare_output_file();
+  my ($nm,$dr,$suf) = fileparse($maqf,".maq");
+  my $faqf = $dr.$nm.".cns.fastq";
+
+  $_->close for ($maph, $cnsh, $maqh);
+
+  # Get command-line options for the component commands:
+  my $subcmd_args = $self->_collate_subcmd_args();
+  # map reads to ref seq
+  # set up subcommand options
+  
+  my $maq = Bio::Tools::Run::Maq->new( 
+      -command => 'map',
+      @{$subcmd_args->{map}}
+      );
+  $maq->run_maq( -map => $mapf, -bfa => $ref_file, -bfq1 => $rd1_file,
+		 -bfq2 => $rd2_file );
+  # assemble reads into consensus
+  $maq = Bio::Tools::Run::Maq->new(
+      -command => 'assemble',
+      @{$subcmd_args->{asm}}
+      );
+  $maq->run_maq( -cns => $cnsf, -bfa => $ref_file, -map => $mapf );
+  # convert map into plain text
+  $maq = Bio::Tools::Run::Maq->new(
+      -command => 'mapview'
+      );
+  $maq->run_maq( -map => $mapf, -txt => $maqf );
+
+  # convert consensus into plain text fastq
+  $maq = Bio::Tools::Run::Maq->new(
+      -command => 'cns2fq',
+      @{$subcmd_args->{c2q}}
+      );
+  $maq->run_maq( -cns => $cnsf, -faq => $faqf );
+  
+  return ($maqf, $faqf);
+
+}
+
+=head2 available_parameters()
+
+ Title   : available_parameters
+ Usage   : @cmds = $fac->available_commands('commands');
+ Function: Use to browse available commands, params, or switches
+ Returns : array of scalar strings
+ Args    : 'commands' : all maq commands
+           'params'   : parameters for this object's command
+           'switches' : boolean switches for this object's command
+           'filespec' : the filename spec for this object's command
+ 4Geeks  : Overrides Bio::ParameterBaseI via 
+           Bio::Tools::Run::AssemblerBase
+
+=cut
+
+sub available_parameters {
+    my $self = shift;
+    my $subset = shift;
+    for ($subset) { # get commands
+	!defined && do { # delegate
+	    return $self->SUPER::available_parameters($subset);
+	};	    
+	m/^c/i && do {
+	    return grep !/^run$/, @program_commands;
+	};
+	m/^f/i && do { # get file spec
+	    return @{$command_files{$self->command}};
+	};
+	do { #else delegate...
+	    return $self->SUPER::available_parameters($subset);
+	};
+    }
+}
+
+sub available_commands { shift->available_parameters('commands') };
+
+sub filespec { shift->available_parameters('filespec') };
+	
+1;
diff --git a/lib/Bio/Tools/Run/Maq/Config.pm b/lib/Bio/Tools/Run/Maq/Config.pm
new file mode 100755
index 0000000..77d4a20
--- /dev/null
+++ b/lib/Bio/Tools/Run/Maq/Config.pm
@@ -0,0 +1,335 @@
+# $Id$
+#
+# BioPerl module for Bio::Tools::Run::Maq::Config
+#
+# Please direct questions and support issues to <bioperl-l@bioperl.org>
+#
+# Cared for by Mark A. Jensen <maj@fortinbras.us>
+#
+# Copyright Mark A. Jensen
+#
+# You may distribute this module under the same terms as perl itself
+
+# POD documentation - main docs before the code
+
+=head1 NAME
+
+Bio::Tools::Run::Maq::Config - Configuration data for maq commands
+
+=head1 SYNOPSIS
+
+Used internally by L<Bio::Tools::Run::Maq>.
+
+=head1 DESCRIPTION
+
+This package exports information describing maq commands, parameters,
+switches, and input and output filetypes for individual maq commands.
+
+=head1 FEEDBACK
+
+=head2 Mailing Lists
+
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to
+the Bioperl mailing list.  Your participation is much appreciated.
+
+  bioperl-l@bioperl.org                  - General discussion
+http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
+
+=head2 Support
+
+Please direct usage questions or support issues to the mailing list:
+
+L<bioperl-l@bioperl.org>
+
+rather than to the module maintainer directly. Many experienced and
+reponsive experts will be able look at the problem and quickly
+address it. Please include a thorough description of the problem
+with code and data examples if at all possible.
+
+=head2 Reporting Bugs
+
+Report bugs to the Bioperl bug tracking system to help us keep track
+of the bugs and their resolution. Bug reports can be submitted via
+the web:
+
+  http://redmine.open-bio.org/projects/bioperl/
+
+=head1 AUTHOR - Mark A. Jensen
+
+Email maj@fortinbras.us
+
+Describe contact details here
+
+=head1 CONTRIBUTORS
+
+Additional contributors names and emails here
+
+=head1 APPENDIX
+
+The rest of the documentation details each of the object methods.
+Internal methods are usually preceded with a _
+
+=cut
+
+# Let the code begin...
+
+
+package Bio::Tools::Run::Maq::Config;
+use strict;
+use warnings;
+no warnings qw(qw);
+use Bio::Root::Root;
+use Exporter;
+use base qw(Bio::Root::Root );
+
+our (@ISA, @EXPORT, @EXPORT_OK);
+push @ISA, 'Exporter';
+@EXPORT = qw(
+             @program_commands
+             %command_prefixes
+             %composite_commands
+             @program_params
+             @program_switches
+             %param_translation
+             %command_files
+            );
+
+@EXPORT_OK = qw();
+
+
+
+our @program_commands = qw(
+    run
+    fasta2bfa
+    fastq2bfq
+    map
+    mapmerge
+    rmdup
+    assemble
+    indelpe
+    indelsoa
+    sol2sanger
+    bfq2fastq
+    mapass2maq
+    mapview
+    mapcheck
+    pileup
+    cns2fq
+    cns2snp
+    cns2view
+    cns2ref
+    cns2win
+    fasta2csfa
+    csmap2nt
+    submap
+    eland2maq
+    export2maq
+);
+
+# composite commands: pseudo-commands that run a 
+# sequence of commands
+# composite command prefix => list of prefixes of commands this
+#  composite command runs
+#
+
+our %composite_commands = (
+    'run'        => [qw( map asm c2q )]
+    );
+
+# prefixes only for commands that take params/switches...
+our %command_prefixes = (
+    'fastq2bfq'  => 'q2q',
+    'map'        => 'map',
+    'assemble'   => 'asm',
+    'mapview'    => 'mv',
+    'mapcheck'   => 'mck',
+    'pileup'     => 'pup',
+    'cns2fq'     => 'c2q',
+    'cns2win'    => 'c2w',
+    'submap'     => 'sub',
+    'eland2maq'  => 'l2m',
+    'export2maq' => 'x2m',
+    'run'        => 'run'
+    );
+
+our @program_params = qw(
+    command
+    q2q|n
+    map|adaptor_file         
+    map|first_read_length    
+    map|max_hits             
+    map|max_mismatches       
+    map|max_outer_distance   
+    map|max_outer_distance_rf
+    map|mismatch_dump        
+    map|mismatch_posn_dump   
+    map|mismatch_thr         
+    map|mutation_rate        
+    map|second_read_length   
+    map|unmapped_dump        
+    asm|error_dep_coeff      
+    asm|het_fraction         
+    asm|max_mismatches       
+    asm|max_quality_sum      
+    asm|min_map_quality      
+    asm|num_haplotypes       
+    mck|max_mismatches       
+    mck|min_map_quality      
+    pup|max_mismatches       
+    pup|max_quality_vals     
+    pup|min_map_quality      
+    pup|site_input_file      
+    c2q|min_map_quality      
+    c2q|min_read_depth       
+    c2q|min_nbr_quality      
+    c2q|max_read_depth       
+    c2w|window_size          
+    c2w|ref_seq              
+    c2w|start_posn           
+    c2w|end_posn             
+    c2w|min_cons_quality     
+    sub|max_mismatches       
+    sub|max_quality_sum      
+    sub|min_map_quality      
+    l2q|def_qual             
+    x2m|max_outer_distance   
+    x2m|first_read_length    
+    x2m|second_read_length   
+    );
+
+our @program_switches = qw(
+    asm|single_end_quality 
+    asm|discard_wrong_pairs
+    mv|omit_seq_qual       
+    mv|show_mismatch_posns 
+    mck|single_end_quality 
+    pup|single_end_quality 
+    pup|discard_wrong_pairs
+    pup|verbose            
+    pup|show_base_posn     
+    sub|discard_wrong_pairs
+    x2m|retain_filt_reads  
+);
+
+our %param_translation = (
+    'q2q|n'                        => 'n',
+    'map|max_mismatches'           => 'n',
+    'map|max_outer_distance'       => 'a',
+    'map|max_outer_distance_rf'    => 'A',
+    'map|first_read_length'        => '1',
+    'map|second_read_length'       => '2',
+    'map|mutation_rate'            => 'm',
+    'map|adaptor_file'             => 'd',
+    'map|unmapped_dump'            => 'u',
+    'map|mismatch_thr'             => 'e',
+    'map|mismatch_dump'            => 'H',
+    'map|max_hits'                 => 'C',
+    'map|mismatch_posn_dump'       => 'N',
+    'asm|error_dep_coeff'          => 't',
+    'asm|het_fraction'             => 'r',
+    'asm|max_mismatches'           => 'm',
+    'asm|max_quality_sum'          => 'Q',
+    'asm|min_map_quality'          => 'q',
+    'asm|num_haplotypes'           => 'N',
+    'mck|max_mismatches'           => 'm',
+    'mck|min_map_quality'          => 'q',
+    'pup|max_mismatches'           => 'm',
+    'pup|max_quality_vals'         => 'Q',
+    'pup|min_map_quality'          => 'q',
+    'pup|site_input_file'          => 'l',
+    'c2q|min_map_quality'          => 'Q',
+    'c2q|min_read_depth'           => 'd',
+    'c2q|min_nbr_quality'          => 'n',
+    'c2q|max_read_depth'           => 'D',
+    'c2w|window_size'              => 'w',
+    'c2w|ref_seq'                  => 'c',
+    'c2w|start_posn'               => 'b',
+    'c2w|end_posn'                 => 'e',
+    'c2w|min_cons_quality'         => 'q',
+    'sub|max_mismatches'           => 'm',
+    'sub|max_quality_sum'          => 'Q',
+    'sub|min_map_quality'          => 'q',
+    'l2q|def_qual'                 => 'q',
+    'x2m|max_outer_distance'       => 'a',
+    'x2m|first_read_length'        => '1',
+    'x2m|second_read_length'       => '2',
+    'asm|single_end_quality'       => 's',
+    'asm|discard_wrong_pairs'      => 'p',
+    'mv|omit_seq_qual'             => 'b',
+    'mv|show_mismatch_posns'       => 'N',
+    'mck|single_end_quality'       => 's',
+    'pup|single_end_quality'       => 's',
+    'pup|discard_wrong_pairs'      => 'p',
+    'pup|verbose'                  => 'v',
+    'pup|show_base_posn'           => 'P',
+    'sub|discard_wrong_pairs'      => 'p',
+    'x2m|retain_filt_reads'        => 'n'
+    );
+
+#
+# the order in the arrayrefs is the order required
+# on the command line
+#
+# the strings in the arrayrefs (less special chars)
+# become the keys for named parameters to run_maq
+# 
+# special chars:
+#
+# '#' implies optional
+# '*' implies variable number of this type
+# <|> implies stdin/stdout redirect
+#
+
+our %command_files = (
+    'run'        => [qw( faq fas faq )],
+    'fastq2bfq'  => [qw( faq bfq )],
+    'fasta2bfa'  => [qw( fas bfa )],
+    'map'        => [qw( map bfa bfq1 #bfq2 2>#log )],
+    'mapmerge'   => [qw( out_map *in_map )],
+    'rmdup'      => [qw( out_map in_map )],
+    'assemble'   => [qw( cns bfa map 2>#log )],
+    'indelpe'    => [qw( bfa map >txt )],
+    'indelsoa'   => [qw( bfa map >txt )],
+    'sol2sanger' => [qw( in_faq out_faq )],
+    'bfq2fastq'  => [qw( bfq faq )],
+    'mapass2maq' => [qw( in_map out_map )],
+    'mapview'    => [qw( map >txt )],
+    'mapcheck'   => [qw( bfa map >txt )],
+    'pileup'     => [qw( bfa map >txt )],
+    'cns2fq'     => [qw( cns >faq )],
+    'cns2snp'    => [qw( cns >txt )],
+    'cns2view'   => [qw( cns >txt )],
+    'cns2ref'    => [qw( cns >fas )],
+    'cns2win'    => [qw( cns >txt )],
+    'fasta2csfa' => [qw( in_fas >out_fas )],
+    'csmap2nt'   => [qw( out_map bfa in_map )],
+    'submap'     => [qw( out_map in_map )],
+    'eland2maq'  => [qw( map lis eld )],
+    'export2maq' => [qw( map lis xpt )]
+    );
+
+INIT {
+    # add subcommand params and switches for
+    # composite commands
+    my @sub_params;
+    my @sub_switches;
+    foreach my $cmd (keys %composite_commands) {
+	foreach my $subcmd ( @{$composite_commands{$cmd}} ) {
+	    my @sub_program_params = grep /^$subcmd\|/, @program_params;
+	    my @sub_program_switches = grep /^$subcmd\|/, @program_switches;
+	    for (@sub_program_params) {
+		m/^$subcmd\|(.*)/;
+		push @sub_params, "$cmd\|${subcmd}_".$1;
+	    }
+	    for (@sub_program_switches) {
+		m/^$subcmd\|(.*)/;
+		push @sub_switches, "$cmd\|${subcmd}_".$1;
+	    }
+	}
+    }
+    push @program_params, @sub_params;
+    push @program_switches, @sub_switches;
+    # translations for subcmd params/switches not necessary
+}
+1;
diff --git a/t/Maq.t b/t/Maq.t
new file mode 100755
index 0000000..255e47a
--- /dev/null
+++ b/t/Maq.t
@@ -0,0 +1,196 @@
+#-*-perl-*-
+
+
+use strict;
+use warnings;
+no warnings qw(once);
+our $home;
+BEGIN {
+    $home = '.'; # set to '.' for Build use, 
+                      # '..' for debugging from .t file
+    unshift @INC, $home;
+    use Bio::Root::Test;
+    test_begin(-tests => 52,
+	       -requires_modules => [qw(IPC::Run Bio::Tools::Run::Maq)]);
+}
+
+use File::Temp qw(tempfile tempdir);
+use Bio::Tools::Run::WrapperBase;
+
+# test command functionality
+
+ok my $maqfac = Bio::Tools::Run::Maq->new(
+    -command            => 'assemble',
+    -single_end_quality => 1,
+    -het_fraction       => 0.005,
+    -max_mismatches     => 4
+    ), "make a factory using command 'assemble'";
+# ParameterBaseI compliance : really AssemblerBase tests...
+ok $maqfac->parameters_changed, "parameters changed on construction";
+ok $maqfac->het_fraction, "access parameter";
+ok !$maqfac->parameters_changed, "parameters_changed cleared on read";
+ok $maqfac->set_parameters( -error_dep_coeff => 0.5 ), "set a param not set in constructor";
+ok $maqfac->parameters_changed, "parameters_changed set";
+is ($maqfac->error_dep_coeff, 0.5, "parameter really set");
+is ($maqfac->het_fraction, 0.005, "original parameter unchanged");
+ok !$maqfac->parameters_changed, "parameters_changed cleared on read";
+ok $maqfac->set_parameters( -het_fraction => 0.01 ), "change an original parameter";
+is ($maqfac->het_fraction, 0.01, "parameter really changed");
+ok $maqfac->reset_parameters( -het_fraction => 0.05 ), "reset parameters with arg";
+ok !$maqfac->max_mismatches, "original parameters undefined";
+is ($maqfac->het_fraction, 0.05, "parameter really reset via arg");
+#back to beginning
+$maqfac->set_parameters(
+    -command            => 'assemble',
+    -single_end_quality => 1,
+    -het_fraction       => 0.005,
+    -max_mismatches     => 4
+    );
+ok $maqfac->parameters_changed, "parameters changed";
+
+is( scalar $maqfac->available_parameters, 9, "all available options");
+is( scalar $maqfac->available_parameters('params'), 7, "available parameters" );
+is( scalar $maqfac->available_parameters('switches'), 2, "available switches" );
+my %pms = $maqfac->get_parameters;
+is_deeply( \%pms, 
+	   { command            => 'assemble',
+             het_fraction       => 0.005,
+             max_mismatches     => 4,
+             single_end_quality => 1}, "get_parameters correct");
+is( $maqfac->command, 'assemble', "command attribute set");
+
+is_deeply( $maqfac->{_options}->{_commands}, 
+	   [@Bio::Tools::Run::Maq::program_commands], 
+	   "internal command array set" );
+
+is_deeply( $maqfac->{_options}->{_prefixes},
+	   {%Bio::Tools::Run::Maq::command_prefixes}, 
+	   "internal prefix hash set");
+
+is_deeply( $maqfac->{_options}->{_params}, 
+	   [qw( command error_dep_coeff het_fraction max_mismatches max_quality_sum min_map_quality num_haplotypes)], 
+	   "commands filtered by prefix");
+
+
+my @a = @{$maqfac->_translate_params};
+is shift @a, 'assemble', 'translate_params: command correct';
+my ($k, %h);
+for (@a) {
+    (/^-/) ? ( $h{$k = $_} = undef ) : ( $h{$k} = $_ );
+}
+is_deeply( \%h, { '-m' => 4, '-r' => 0.005, '-s' => undef }, 'translate_params: options correct');
+
+# test run_maq filearg parsing
+# a pipeline...
+
+SKIP : {
+    test_skip( -requires_executable => $maqfac,
+	       -tests => 27 );
+    my $rd1 = test_input_file('r1.fq');
+    my $rd2 = test_input_file('r2.fq');
+    my $refseq = test_input_file('campycoli.fas');
+    
+    my $tdir = tempdir( "maqXXXX", CLEANUP => 1);
+    my ($r1h, $r1f) = tempfile( "rd1XXXX", DIR => $tdir );
+    $r1h->close;
+    my ($r2h, $r2f) = tempfile( "rd2XXXX", DIR => $tdir );
+    $r2h->close;
+    my ($refh, $reff) = tempfile( "refXXXX", DIR => $tdir );
+    $refh->close;
+    my ($map1h, $map1f) = tempfile( "mapXXXX", DIR => $tdir );
+    $map1h->close;
+    my ($map2h, $map2f) = tempfile( "mapXXXX", DIR => $tdir );
+    $map2h->close;
+    my ($mmaph, $mmapf) = tempfile( "mapXXXX", DIR => $tdir );
+    $mmaph->close;
+    my ($cnsh, $cnsf) = tempfile( "cnsXXXX", DIR => $tdir );
+    $cnsh->close;
+    my ($maqh, $maqf) = tempfile( "maqXXXX", DIR => $tdir );
+    $maqh->close;
+    my ($fqh, $fqf) = tempfile( "faqXXXX", DIR => $tdir );
+    $fqh->close;
+    
+    ok $maqfac = Bio::Tools::Run::Maq->new(
+	-command            => 'fasta2bfa'
+	), "make fasta2bfa conversion factory";
+    
+    ok $maqfac->run_maq( -fas => $refseq,
+			 -bfa => $reff ), "convert refseq to bfa";
+    
+    like($maqfac->stderr, qr/1 sequence/, "maq success");
+    
+    ok $maqfac = Bio::Tools::Run::Maq->new(
+	-command            => 'fastq2bfq'
+	), "make fastq2bfq conversion factory";
+    
+    ok $maqfac->run_maq( -faq => $rd1,
+			 -bfq => $r1f ), "convert r1.fq to bfa";
+    like($maqfac->stderr, qr/125 sequences were loaded/, "maq success");
+    ok $maqfac->run_maq( -faq => $rd2,
+			 -bfq => $r2f ), "convert r2.fq to bfa";
+    like($maqfac->stderr, qr/125 sequences were loaded/, "maq success");
+    
+    ok $maqfac = Bio::Tools::Run::Maq->new(
+	-command            => 'map',
+	), "make map factory";
+    
+    ok $maqfac->run_maq( -map => $map1f,
+			 -bfa => $reff,
+			 -bfq1 => $r1f ), "map single-end reads";
+    ok $maqfac->run_maq( -map => $map2f,
+			 -bfa => $reff,
+			 -bfq2 => $r2f,
+			 -bfq1 => $r1f ), "map paired-end reads";
+    
+    ok $maqfac = Bio::Tools::Run::Maq->new(
+	-command            => 'mapmerge'
+	), "make mapmerge factory";
+    
+    ok $maqfac->run_maq( -out_map => $mmapf,
+			 -in_map => [$map1f, $map2f] ), "merge maps";
+    
+    ok $maqfac = Bio::Tools::Run::Maq->new(
+	-command            => 'assemble'
+	), "make assemble factory";
+    
+    ok $maqfac->run_maq( -cns => $cnsf,
+			 -bfa => $reff,
+			 -map => $mmapf ), "assemble consensus";
+    
+    ok $maqfac = Bio::Tools::Run::Maq->new(
+	-command            => 'mapview'
+	), "make mapview converter";
+    
+    
+    ok $maqfac->run_maq( -map => $mmapf,
+			 -txt => $maqf ), "convert mmap";
+    
+    ok $maqfac = Bio::Tools::Run::Maq->new(
+	-command            => 'cns2fq'
+	), "make consensus->fastq converter";
+    ok $maqfac->run_maq( -cns => $cnsf,
+			 -faq => $fqf ), "convert consensus -> fastq";
+
+    # test run (assembly pipeline) 
+    # these parms are the maq defaults for the respective programs
+    ok $maqfac = Bio::Tools::Run::Maq->new(
+	-map_max_mismatches => 2,
+	-asm_max_mismatches => 7,
+	-c2q_min_map_quality => 40
+	), "make an assembly factory";
+    
+    is( $maqfac->command, 'run', "command attribute set");
+    is( $maqfac->map_max_mismatches, 2, "map param set");
+    is( $maqfac->asm_max_mismatches, 7, "asm param set");
+    is( $maqfac->c2q_min_map_quality, 40, "c2q param set");
+    ok my $assy = $maqfac->run($rd1,$refseq,$rd2), "make full assy";
+    #some fuzziness in these: sometimes maq gives 41+4, sometimes 42+6.
+    cmp_ok( $assy->get_nof_contigs, '>=', 37, "number of contigs");
+    cmp_ok( $assy->get_nof_singlets,'>=',4, "number of singlets");
+
+}
+1;
+
+#  sub test_input_file {
+#      return "./data/".shift;
+#  }
diff --git a/t/data/campycoli.fas b/t/data/campycoli.fas
new file mode 100755
index 0000000..b02e6a5
--- /dev/null
+++ b/t/data/campycoli.fas
@@ -0,0 +1,50 @@
+>gi|65306796|gb|AY948116.1| Campylobacter coli plasmid p3384, complete sequence
+AAGCTTTTAAAACACCAAAAAAGGAAAAATTTAAAAATGCAAAAACCAATATCCCGAAGTGCATAGCTTA
+GAAGAAAGCCTTGCAATACTTAAAAAAATATAAAGATGATGTAAATAAGGAAAGATTATGAAGGTATAAA
+ATCTGTTATAAGTAATCATGCGATAGAGAGTATTTACATGAATGAATTAGATATTATCGCTATGATAAAA
+CAAAGTGCTTTAAAGTTAAGTGCTGATGAAATCATTGCTGAATATAAGGAAAAGGGATTTGTAGAATATG
+TCAAAAGTTGCCACCGCTCATTGCAATCCTAAAAAACAACCTGCATTAAACCACAATGATAGAACCAACG
+ATAATGCTAAGACAATCACTAAAGAACTTACGCATTTAAATGAATACTCTTGCACTAGCGATGAAGTGCG
+TAAGAACATAGAAAGGCTTTATAAAAAAGCTTATGAAAATTTTTATAAATATTGTGAAAATAAGAATGGT
+TTAGCTAAAAGTGGAAAGCCTAAAGGACTTCAAAATTTTACTAAAAAAGAAAAATGTTATCACGAGTTTA
+TATACGAAATCGGCGAAAATACTACAATGGAGCAATGCCAAGAGCTTACGCAAAAAATCGCAGAGCTTAC
+AGGATTTACACCTTTACAAGTTGTAATCCATAGAGATGAAGTAAGTGAGAATGCTAAAGGGGAAAAACAA
+ACCCATTATCACGCCCACGCGGTATTTTTTACACTCGATAACAATGGCTTACAACTTGCTAGACGTGAAG
+CAAGTTTGAATAAAGCCAATCTTAGCAAAATACAAACCCTAACCGCACAAAGTTTAAAAATGGAGCGTGG
+AGCTAATCGCTACGAGAATAACGAAAAGCAACCTCAATACATACAAGATTATAAAACATACGCTCAATTT
+AAAGAACAAGAAAAAGCATTACTTCAAAGAATACAAGAACAAGAGCATAAATTAACGCAAATGGCCCTAG
+AATTGAAAAAAAAAGAAAAAGAGATACAAGACAAGGCTAAAGAGTTAAAATCGAAAGAAAACGAATTACA
+AGCGAAAATAGAGCAACATCAAAAACATATACAAAATTTAGAACTAGGACACGAAAGAGCTTTAAAGGAA
+CTTACACAAGAGTTTGAAAAGCGTTTAAGCCTATGGAAAAACATTTTAACCTTTGGAAAATACAACGCCA
+AAGTAAGAGAAGACTATCAGTTAACAAAGAATGCTTTTTTAATTAGCACAGATGAAAGCAGGAGAGAAGC
+TAACAAAGAGCTTGAATATTTAAAATTTGAATATCATAAAGTCAAAGATGAACGAGATAATTTAAAAACT
+TTGTTTGAGGCACACAAAACAAAAAATGTTAAATTAGAAACTCGACTAAAAGAAATAGGCAAATGGTGTG
+AAAAAAATTTAAGCGTGGAGCAGTTAAAAGAAATATTTCCATTAAAAGCCGAAAGAATAGAAAAAGAGCT
+TAAATATCAAAGAGCTTTTGAAAATTCTTTTGAACAAGCAAAAAGAAACGATAGAGGGTTTGGGTTTAGC
+AGATAGTTTTCTTTTTTGGTGCTTTAGCAAATCGCACCTGTTAAGGTGCTATGATTTGCGAAAAGGGGGT
+GCGGGGGCTGTCTGAGTGCGTAGCACGGAAGACGGACAAAGCCCACCGCCCTAGAAAAAAAATTACTCAA
+CTTTTTTTGTTTTTTCTCTCGCGCGCGTACGCGTACGCGATTTTTTTTATTTTTTATATATTTTTCTTAT
+TTTTAGGGGGCTTTCTAAGCCCTATATGATGGGGGCTAGCGAAATATTAAAACGACAAAATTCTACTATT
+AAAACGACAAAATTCTACTATTAAAACGACAAAATTCTACTATTAAAACGACAAAATTCTACTATTAAGG
+GGAGAAAATTCTACTATTAAAACGACAAAATATTTGACAAATATTGTTTTAATATGCTACAATAAAAAAT
+CCGCCTTGAGTTTTCACTCTTGGCGGAAATTTATCAATCAAGGCTAACTATGAAACGACATAGTAAGCGT
+TTTGTGAGATTATACCTAAAATTTAGGTTTTTTAAGCTTAAAGTTGAAGTATTTTTCTAGCAAAACCGCA
+GGGGCAGAGAAGCCCCTTGCCTTGATTGTCTTACTTTGGATATGCAAATGAGCGAAATAGTTAAATATAA
+TAATGATTTTAATCTTTTACCTATGCCTGAACTTAAAGCCATACAAATGGATATGTTTATGGCTATTATC
+TCACTAACCAAAGACAAAAAAGAAAATACGCCATTTTTAAAAAAGTTTTTTAACCCTGATAAAAGAAAAA
+TAATTATTCCGCAAAAGAAGTTTATTGAATTATGTCGGTTAAACGATAGTAAAATGGACTATAAAGAAAT
+TTTCTTTGCCATTGATGATTGCTTGAAAAAACTTTGCAATTTTCTTATTTCATACCAAAAAGATGAAAGA
+ACGATTTATAATTTTGTTTGTTTTGAAGAAGCAAATATTATTGCTGATGAAGTGCATATAACTTTACAAA
+GTCGTTTTTACGATATGATAATAAATAAAAAATTTGGTTTCACAGCCTTTGAATTAGCCGAATTTGCAGA
+ACTTAGCGGTAAATATACAAAAACTTTATACAGACTTTTAAAGCAATTTAGAACCACAGGCAAAGCTTAT
+TTTGAGTGGGAAGAATTTTGCAGGATTATGAAAATACCTGAAAATTATCGTCAAATAGATATAGACCAAA
+GAATTTTAAAACCTGCTATCAAAGAACTTTCTAAAGAACGCAATCTTTTTGACCAAATCAGAGTGCCTTT
+TAAAAATCTTGCTTATGAAAAAGAAAAAACCGCAGGGCGTGGGCGTGGCGGTAAAGTTTCAGGTATTAGC
+TTTACTTTTAAACCTGAAAATATCCAAATGCAAAAGCTAGAAAATGAAAGTCAAAAAATAATGAGCGATG
+AGCAAAAATATTTAAAGATTTTAAACAATATGAAACTTAATCAAGTTAGATTTGATTATAATGACAAGCT
+TTGGCAATTTAACGATTTTGATTTTGATGAATTTAAAATTATTGCAATAGAGCTTGTAAGAGATGAATAC
+GAGAATTTAAACTTTGGAAATCATATGCACTTTAATGCTAAAAATCAAGAGCAGTTTTTTAAAATGATTG
+AAACCTTTAGAAAAGGTATTAGGTAAAAATTTGCTATAATTATATCTTTAAAGGATACAAGCTATCCGCC
+ACTTGTGCCAAGTGTCGAGCTTGTAAGGGGTGCAACCCCTTAACCCCACTAATAAAAATCAACTAAAATC
+AATAAATGATTTTTTTGATTTTTATT
+
diff --git a/t/data/r1.fq b/t/data/r1.fq
new file mode 100644
index 0000000..d49d778
--- /dev/null
+++ b/t/data/r1.fq
@@ -0,0 +1,500 @@
+@gi|65306796|gb|AY948116.1|_1951_2136_0/1
+AAGTAAGACAATCAAGGCAAGGGGC
++
+YYYYYYYYYYYYYYYYWYYSYWYSY
+@gi|65306796|gb|AY948116.1|_1531_1682_1/1
+AGTTGAGTAATTTTTTTTCTAGGGC
++
+YYYYYYYYYYWYYYYWYYWYWYYWW
+@gi|65306796|gb|AY948116.1|_603_785_2/1
+CTTTATTCAAACTTGCTTCACGTCT
++
+YYYYYYYYYWYYYYYYWYWYWYYSU
+@gi|65306796|gb|AY948116.1|_1888_2018_3/1
+TCGTTTCATAGTTAGCCTTGATTGA
++
+YYYYYYYYYYWYYYYYYYYSYYYWW
+@gi|65306796|gb|AY948116.1|_1990_2157_4/1
+TTTATCAATCAAGGCTAACTATGAA
++
+YYYYYYYYYYYYYYYWYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_1165_1307_5/1
+TTTAACCTTTGGAAAATACAACGCC
++
+YYYYYYYYYYYYYYYYWYYSYWYSU
+@gi|65306796|gb|AY948116.1|_1622_1777_6/1
+ATATAGGGCTTAGAAAGCCCCCTAA
++
+YYYYYYYYYWYYYYWWYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_1116_1298_7/1
+AGGAACTTACACAAGAGTTTGAAAA
++
+YYYYYYYYYYYYYYWWYYYWWYYWW
+@gi|65306796|gb|AY948116.1|_63_202_8/1
+TAGCGATAATATCTAATTCATTCAT
++
+YYYYYYYYYYYYYYYYYYYWWYYSY
+@gi|65306796|gb|AY948116.1|_2908_3068_9/1
+TAGAAAATGAAAGTCAAAAAATAAT
++
+YYYYYYYYYYYYYYYYYYWYWWYSU
+@gi|65306796|gb|AY948116.1|_2909_3032_a/1
+ATCAAAATCGTTAAATTGCCAAAGC
++
+YYYYYYYYYYYYYYYYYYYWWWYSY
+@gi|65306796|gb|AY948116.1|_3096_3266_b/1
+GGGTTAAGGGGTTGCACCCCTTACA
++
+YYYYYYYYYYYYYWYYYYYSYWYWY
+@gi|65306796|gb|AY948116.1|_479_649_c/1
+AATAAGAATGGTTTAGCTAAAAGTG
++
+YYYYYYYYYYWYYYWWYWWYWWWQQ
+@gi|65306796|gb|AY948116.1|_1502_1651_d/1
+CTTTGTCCGTCTTCCGTGCTACGCA
++
+YYYYYYYYYYYYYYWWYYWUWYYSY
+@gi|65306796|gb|AY948116.1|_944_1116_e/1
+CAAGAACAAGAGCATAAATTAACGC
++
+YYYYYYYYYYYYYWYYWYYSYYYSY
+@gi|65306796|gb|AY948116.1|_3061_3240_f/1
+AGCTTGTAAGAGATGAATACGAGAA
++
+YYYYYYYYYYYYYYYYYYWYWYYWW
+@gi|65306796|gb|AY948116.1|_1955_2172_10/1
+TATTATATTTAACTATTTCGCTCAT
++
+YYYYYYYYYYYYYYYWYWWYWWYWW
+@gi|65306796|gb|AY948116.1|_2987_3171_11/1
+TAATACCTTTTCTAAAGGTTTCAAT
++
+YYYYYYYYYYYYYWYYYYYSYYYSU
+@gi|65306796|gb|AY948116.1|_2261_2430_12/1
+AAATAAGAAAATTGCAAAGTTTTTT
++
+YYYYYYYYYYYYYWYYWYYWYYYWW
+@gi|65306796|gb|AY948116.1|_57_240_13/1
+TTCATCAGCACTTAACTTTAAAGCA
++
+YYYYYYYYYYYYYYYYYWWYWYYWW
+@gi|65306796|gb|AY948116.1|_1168_1364_14/1
+AACCTTTGGAAAATACAACGCCAAA
++
+YYYYYYYYYYYYYYYYWYYSYWYSY
+@gi|65306796|gb|AY948116.1|_673_829_15/1
+AAGTGAGAATGCTAAAGGGGAAAAA
++
+YYYYYYYYYWYYYWYYWYYWWWYWY
+@gi|65306796|gb|AY948116.1|_275_459_16/1
+AATATGTCAAAAGTTGCCACCGCTC
++
+YYYYYYYYYWYYYWYYWYWYWWYWY
+@gi|65306796|gb|AY948116.1|_3145_3288_17/1
+TGATTGAAACCTTTAGAAAAGGTAT
++
+YYYYYYYYYWYYYYYYWYWUWYYWY
+@gi|65306796|gb|AY948116.1|_1295_1444_18/1
+TAATGGAAATATTTCTTTTAACTGC
++
+YYYYYYYYYYYYYYWWYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_2129_2328_19/1
+TCTTACTTTGGATATGCAAATGAGC
++
+YYYYYYYYYYYYYYYYWYWUWWYWY
+@gi|65306796|gb|AY948116.1|_1462_1646_1a/1
+TCCGTCTTCCGTGCTACGCACTCAG
++
+YYYYYYYYYYYYYYYYWYYSYWYSU
+@gi|65306796|gb|AY948116.1|_2770_2956_1b/1
+TTTAAATATTTTTGCTCATCGCTCA
++
+YYYYYYYYYYWYYYYYYYYSYWYWW
+@gi|65306796|gb|AY948116.1|_1336_1508_1c/1
+CTTGTTCAAAAGAATTTTCAAAAGC
++
+YYYYYYYYYYYYYYWWYYYSYYYWW
+@gi|65306796|gb|AY948116.1|_2153_2336_1d/1
+CGAAATAGTTAAATATAATAATGAT
++
+YYYYYYYYYYWYYWYYYYWYWWWQQ
+@gi|65306796|gb|AY948116.1|_844_1031_1e/1
+ATTTTAACTCTTTAGCCTTGTCTTG
++
+YYYYYYYYYYWYYYWWYYWYWYYWW
+@gi|65306796|gb|AY948116.1|_2821_2986_1f/1
+AAGAAAAAACCGCAGGGCGTGGGCG
++
+YYYYYYYYYYYYYYYWYWWYWYYSY
+@gi|65306796|gb|AY948116.1|_58_177_20/1
+AGTGCATAGCTTAGAAGAAAGCCTT
++
+YYYYYYYYYWYYYYYYYWWYWWYWY
+@gi|65306796|gb|AY948116.1|_2612_2792_21/1
+TCTGATTTGGTCAAAAAGATAGCGT
++
+YYYYYYYYYYYYYYWWYWWWYWYSU
+@gi|65306796|gb|AY948116.1|_2081_2254_22/1
+ATTTTTCTAGCAAAACCGCAGGGGC
++
+YYYYYYYYYYYYYYYYYYYSYWYWW
+@gi|65306796|gb|AY948116.1|_963_1092_23/1
+TAACGCAAATGGCCCTAGAATTGAA
++
+YYYYYYYYYYWYYWYWYYYSYYYWW
+@gi|65306796|gb|AY948116.1|_1802_1954_24/1
+ACGACAAAATTCTACTATTAAAACG
++
+YYYYYYYYYYWYYWYYYWWYWWWQQ
+@gi|65306796|gb|AY948116.1|_125_324_25/1
+GCAGGTTGTTTTTTAGGATTGCAAT
++
+YYYYYYYYYWYYYYYWYYWUWWYWW
+@gi|65306796|gb|AY948116.1|_2801_2960_26/1
+AATCTTTAAATATTTTTGCTCATCG
++
+YYYYYYYYYYYYYYYYWYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_1744_1934_27/1
+TTCTTATTTTTAGGGGGCTTTCTAA
++
+YYYYYYYYYYYYYYYYYYWYWWWQQ
+@gi|65306796|gb|AY948116.1|_2759_2911_28/1
+TCTAGCTTTTGCATTTGGATATTTT
++
+YYYYYYYYYYYYYYYYYYWUWWYWY
+@gi|65306796|gb|AY948116.1|_1201_1398_29/1
+CACCATTTGCCTATTTCTTTTAGTC
++
+YYYYYYYYYYWYYYYYYYWYWWWQQ
+@gi|65306796|gb|AY948116.1|_1966_2156_2a/1
+TTGAGTTTTCACTCTTGGCGGAAAT
++
+YYYYYYYYYWYYYYYYYYWYWWYSY
+@gi|65306796|gb|AY948116.1|_1691_1870_2b/1
+TTTTTCTCTCGCGCGCGTACGCGTA
++
+YYYYYYYYYYWYYYYYYWWYWYYSU
+@gi|65306796|gb|AY948116.1|_2329_2493_2c/1
+AGTTTATTGAATTATGTCGGTTAAA
++
+YYYYYYYYYYYYYYYYYWWUWWYWY
+@gi|65306796|gb|AY948116.1|_145_306_2d/1
+GTTATAAGTAATCATGCGATAGAGA
++
+YYYYYYYYYYYYYWYYYYWUWWYWY
+@gi|65306796|gb|AY948116.1|_930_1108_2e/1
+TACTTCAAAGAATACAAGAACAAGA
++
+YYYYYYYYYYYYYYYYYYYSYYYSY
+@gi|65306796|gb|AY948116.1|_580_743_2f/1
+TACTACAATGGAGCAATGCCAAGAG
++
+YYYYYYYYYWYYYYYWYWWYWWWQQ
+@gi|65306796|gb|AY948116.1|_1032_1194_30/1
+ACTTTGGCGTTGTATTTTCCAAAGG
++
+YYYYYYYYYYYYYWYWYYWUWYYWY
+@gi|65306796|gb|AY948116.1|_2128_2314_31/1
+ATTATTTTTCTTCTATCAGGGTTAA
++
+YYYYYYYYYYYYYYWWYYYSYWYWY
+@gi|65306796|gb|AY948116.1|_196_351_32/1
+TCGTTGGTTCTATCATTGTGGTTTA
++
+YYYYYYYYYWYYYYYYYWWUWYYWW
+@gi|65306796|gb|AY948116.1|_1339_1491_33/1
+GGCACACAAAACAAAAAATGTTAAA
++
+YYYYYYYYYYWYYYYYYYWWWYYSY
+@gi|65306796|gb|AY948116.1|_2509_2658_34/1
+TAACTTTACAAAGTCGTTTTTACGA
++
+YYYYYYYYYYYYYYYYWYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_1940_2118_35/1
+AAGGGGCTTCTCTGCCCCTGCGGTT
++
+YYYYYYYYYYYYYYYYYWWUWYYSU
+@gi|65306796|gb|AY948116.1|_216_381_36/1
+GTAAGTTCTTTAGTGATTGTCTTAG
++
+YYYYYYYYYYYYYYWWYYYWWWYWW
+@gi|65306796|gb|AY948116.1|_461_636_37/1
+AATCCTGTAAGCTCTGCGATTTTTT
++
+YYYYYYYYYYYYYWYYYYYWYYYWW
+@gi|65306796|gb|AY948116.1|_325_461_38/1
+ATTAAACCACAATGATAGAACCAAC
++
+YYYYYYYYYYYYYWYYYYWYWWWQQ
+@gi|65306796|gb|AY948116.1|_2304_2478_39/1
+CTTCAAAACAAACAAAATTATAAAT
++
+YYYYYYYYYYWYYYWWYYWWWWWQQ
+@gi|65306796|gb|AY948116.1|_278_467_3a/1
+ATGTCAAAAGTTGCCACCGCTCATT
++
+YYYYYYYYYYYYYYYYYWWUWWYSU
+@gi|65306796|gb|AY948116.1|_2717_2903_3b/1
+AGATATAGACCAAAGAATTTTAAAA
++
+YYYYYYYYYYYYYYYYYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_1389_1563_3c/1
+GCAAATGGTGTGAAAAAAATTTAAG
++
+YYYYYYYYYYYYYYYYYYWYWWWQQ
+@gi|65306796|gb|AY948116.1|_3000_3167_3d/1
+ACCTTTTCTAAAGGTTTCAATCATT
++
+YYYYYYYYYYYYYYYYYYWYWWYSY
+@gi|65306796|gb|AY948116.1|_360_547_3e/1
+ACATTTTTCTTTTTTAGTAAAATTT
++
+YYYYYYYYYYWYYYYYYYYSYYYWY
+@gi|65306796|gb|AY948116.1|_143_319_3f/1
+TTGTTTTTTAGGATTGCAATGAGCG
++
+YYYYYYYYYWYYYYYWYYWWYYYWW
+@gi|65306796|gb|AY948116.1|_1382_1538_40/1
+TAAACCCAAACCCTCTATCGTTTCT
++
+YYYYYYYYYYWYYYYWYYYSYWYSU
+@gi|65306796|gb|AY948116.1|_2707_2804_41/1
+TTTAAAAGGCACTCTGATTTGGTCA
++
+YYYYYYYYYYWYYYYWYWWYWYYSU
+@gi|65306796|gb|AY948116.1|_430_615_42/1
+AGAAAGGCTTTATAAAAAAGCTTAT
++
+YYYYYYYYYYWYYYWWYWWYWWYSU
+@gi|65306796|gb|AY948116.1|_2383_2537_43/1
+CATATCGTAAAAACGACTTTGTAAA
++
+YYYYYYYYYYYYYYYWYYYWYYYWY
+@gi|65306796|gb|AY948116.1|_839_973_44/1
+GGAGCTAATCGCTACGAGAATAACG
++
+YYYYYYYYYYWYYYWWYYWYWYYWY
+@gi|65306796|gb|AY948116.1|_2761_2927_45/1
+TTTTTGACTTTCATTTTCTAGCTTT
++
+YYYYYYYYYYWYYYYYWYWWWWYWY
+@gi|65306796|gb|AY948116.1|_375_561_46/1
+ATAAACTCGTGATAACATTTTTCTT
++
+YYYYYYYYYWYYYYWWYYYSYWYWW
+@gi|65306796|gb|AY948116.1|_2751_2931_47/1
+TTATTTTTTGACTTTCATTTTCTAG
++
+YYYYYYYYYWYYYWYYWYWWYWYSU
+@gi|65306796|gb|AY948116.1|_2312_2478_48/1
+CTTCAAAACAAACAAAATTATAAAT
++
+YYYYYYYYYYYYYYYWYYYWYWYSY
+@gi|65306796|gb|AY948116.1|_1934_2078_49/1
+TTGTTTTAATATACTACAATAAAAA
++
+YYYYYYYYYWYYYYYWYWWYWWWQQ
+@gi|65306796|gb|AY948116.1|_263_431_4a/1
+AGGGATTTGTAGAATATGTCAAAAG
++
+YYYYYYYYYYYYYYWWYYWYWWYWW
+@gi|65306796|gb|AY948116.1|_452_644_4b/1
+AAGGTGTAAATCCTGTAAGCTCTGC
++
+YYYYYYYYYYYYYYWWYWWUWWYWY
+@gi|65306796|gb|AY948116.1|_2570_2722_4c/1
+TGAATTAGCCGAATTTGCAGAACTT
++
+YYYYYYYYYYWYYYYYYWWYWYYSU
+@gi|65306796|gb|AY948116.1|_2549_2708_4d/1
+ATAATTTTCAGGTATTTTCATAATC
++
+YYYYYYYYYYYYYYYYYWWUWWYWY
+@gi|65306796|gb|AY948116.1|_1498_1676_4e/1
+GTAATTTTTTTTCTAGGGCGGTGGG
++
+YYYYYYYYYYYYYYWWYYWUWWYWW
+@gi|65306796|gb|AY948116.1|_2890_3076_4f/1
+TCATCTCTTACAAGCTCTATTGCAA
++
+YYYYYYYYYYYYYYYYYYWWWWYWW
+@gi|65306796|gb|AY948116.1|_3149_3310_50/1
+AATCAAAAAAATCATTTATTGATTT
++
+YYYYYYYYYYWYYYYWYYYSYYYSU
+@gi|65306796|gb|AY948116.1|_1992_2129_51/1
+ACAATCAAGGCAAGGGGCTTCTCTG
++
+YYYYYYYYYYYYYYWWYWWYWWYSU
+@gi|65306796|gb|AY948116.1|_945_1120_52/1
+AAGAACAAGAGCATAAATTAACGCA
++
+YYYYYYYYYYWYYYYYWYYWYWWQQ
+@gi|65306796|gb|AY948116.1|_2526_2710_53/1
+CGATAATTTTCAGGTATTTTCATAA
++
+YYYYYYYYYWYYYWYYYWWUWYYSU
+@gi|65306796|gb|AY948116.1|_2414_2548_54/1
+TTGCAATTTTCTTATTTCATACCAA
++
+YYYYYYYYYYWYYYYYYWWWWYYSU
+@gi|65306796|gb|AY948116.1|_1957_2161_55/1
+AAATCCGCCTTGAGTTTTCACTCTT
++
+YYYYYYYYYYYYYYYYWYWYWWWQQ
+@gi|65306796|gb|AY948116.1|_299_483_56/1
+TTATTTTCACAATATTTATAAAAAT
++
+YYYYYYYYYYYYYWYYYWWYWWYWY
+@gi|65306796|gb|AY948116.1|_2162_2328_57/1
+TAAATATAATAATGATTTTAATCTT
++
+YYYYYYYYYYYYYYYYYYYWWWYSU
+@gi|65306796|gb|AY948116.1|_292_484_58/1
+CTTATTTTCACAATATTTATAAAAA
++
+YYYYYYYYYYWYYYYYWYYWWYYSU
+@gi|65306796|gb|AY948116.1|_1558_1716_59/1
+GTACGCGTACGCGCGCGAGAGAAAA
++
+YYYYYYYYYYWYYYYYYYYWYWYSU
+@gi|65306796|gb|AY948116.1|_171_331_5a/1
+TATTTACATGAATGAATTAGATATT
++
+YYYYYYYYYYYYYYYYWYYSYYYWW
+@gi|65306796|gb|AY948116.1|_2624_2822_5b/1
+ACTTTTAAAGCAATTTAGAACCACA
++
+YYYYYYYYYYYYYYYYYYYWWYYSY
+@gi|65306796|gb|AY948116.1|_2024_2222_5c/1
+ATCCATTTGTATGGCTTTAAGTTCA
++
+YYYYYYYYYYYYYYWWYYYWWYYSY
+@gi|65306796|gb|AY948116.1|_2196_2392_5d/1
+CCTGAACTTAAAGCCATACAAATGG
++
+YYYYYYYYYYWYYYYYYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_2377_2544_5e/1
+AAATTTTCTTTGCCATTGATGATTG
++
+YYYYYYYYYWYYYWYYWYWWYYYWY
+@gi|65306796|gb|AY948116.1|_3111_3290_5f/1
+TTTAATGCTAAAAATCAAGAGCAGT
++
+YYYYYYYYYYYYYWYWYYWYWWYSY
+@gi|65306796|gb|AY948116.1|_910_1065_60/1
+TAAGAACAAGAAAAAGCATTACTTC
++
+YYYYYYYYYYYYYWYYYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_2966_3121_61/1
+TTAGCATTAAAGTGCATATGATTTC
++
+YYYYYYYYYYYYYYYYYWWWWWYSY
+@gi|65306796|gb|AY948116.1|_1321_1511_62/1
+TTTAAAAACTTTGTTTGAGGCACAC
++
+YYYYYYYYYWYYYWYYWYYWWYYSY
+@gi|65306796|gb|AY948116.1|_1873_2073_63/1
+CTTTAAGCTTAAAAAACCTAAATTT
++
+YYYYYYYYYYYYYYYYYWWUWYYSU
+@gi|65306796|gb|AY948116.1|_2702_2884_64/1
+AAATTATCGTCAAATAGATATAGAC
++
+YYYYYYYYYYYYYYYYWYWWWYYSY
+@gi|65306796|gb|AY948116.1|_672_807_65/1
+GTTTGTATTTTGCTAAGATTGGCTT
++
+YYYYYYYYYYWYYYYYYYYSYYYWY
+@gi|65306796|gb|AY948116.1|_2165_2331_66/1
+ACTTCTTTTGCGGAATAATTATTTT
++
+YYYYYYYYYYWYYYYWYWWUWWYWW
+@gi|65306796|gb|AY948116.1|_1998_2143_67/1
+TCAAGGCTAACTATGAAACGACATA
++
+YYYYYYYYYYYYYYYYYYWUWYYSY
+@gi|65306796|gb|AY948116.1|_904_1068_68/1
+TCAATTTAAGAACAAGAAAAAGCAT
++
+YYYYYYYYYYYYYYYWYWWYWWWQQ
+@gi|65306796|gb|AY948116.1|_2994_3156_69/1
+AGGTTTCAATCATTTTAAAAAACTG
++
+YYYYYYYYYYYYYYYYYYYSYWYWY
+@gi|65306796|gb|AY948116.1|_2715_2892_6a/1
+TATTTTCAGGTTTAAAAGTAAAGCT
++
+YYYYYYYYYYYYYYYYYWWYWWYWW
+@gi|65306796|gb|AY948116.1|_633_845_6b/1
+TAGCTCCACGCTCCATTTTTAAACT
++
+YYYYYYYYYYYYYYYYYYYWYWYSU
+@gi|65306796|gb|AY948116.1|_319_475_6c/1
+ACAATATTTATAAAAATTTTCATAA
++
+YYYYYYYYYYYYYYWWYWWUWWWQQ
+@gi|65306796|gb|AY948116.1|_2202_2401_6d/1
+CTTAAAGCCATACAAATGGATATGT
++
+YYYYYYYYYYWYYYYYWYWWYWYWY
+@gi|65306796|gb|AY948116.1|_2825_2992_6e/1
+AATCTAACTTGATTAAGTTTCATAT
++
+YYYYYYYYYWYYYYWWYYYWYYYWY
+@gi|65306796|gb|AY948116.1|_1262_1447_6f/1
+TTTTAATGGAAATATTTCTTTTAAC
++
+YYYYYYYYYWYYYWYYWYYWYWYWW
+@gi|65306796|gb|AY948116.1|_2751_2927_70/1
+TTTTTGACTTTCATTTTCTAGCTTT
++
+YYYYYYYYYYYYYYYYYYYSYWYWY
+@gi|65306796|gb|AY948116.1|_3034_3217_71/1
+TTGATGAATTTAAAATTATTGCAAT
++
+YYYYYYYYYYYYYYYYYYWWYYYWY
+@gi|65306796|gb|AY948116.1|_678_858_72/1
+AGAATGCTAAAGGGGAAAAACAAAC
++
+YYYYYYYYYWYYYYYYYYWUWWWQQ
+@gi|65306796|gb|AY948116.1|_149_317_73/1
+GTTTTTTAGGATTGCAATGAGCGGT
++
+YYYYYYYYYYWYYYWWYWWWWYYSU
+@gi|65306796|gb|AY948116.1|_2458_2654_74/1
+TTTGCCTGTGGTTCTAAATTGCTTT
++
+YYYYYYYYYWYYYYYYYYYWWYYWW
+@gi|65306796|gb|AY948116.1|_315_506_75/1
+TTCCACTTTTAGCTAAACCATTCTT
++
+YYYYYYYYYWYYYYYYWYYSYYYSY
+@gi|65306796|gb|AY948116.1|_916_1071_76/1
+TGATGTTGCTCTATTTTCGCTTGTA
++
+YYYYYYYYYYYYYYYYYYYWWWYWY
+@gi|65306796|gb|AY948116.1|_1530_1707_77/1
+TTGGGTTTAGCAGATAGTTTTCTTT
++
+YYYYYYYYYYYYYWYWYYYWWWWQQ
+@gi|65306796|gb|AY948116.1|_227_417_78/1
+TAAGTGCTGATGAAATCATTGCTGA
++
+YYYYYYYYYYYYYYYYYYWUWWYWY
+@gi|65306796|gb|AY948116.1|_792_964_79/1
+TAATTTATGCTCTTGTTCTTGTATT
++
+YYYYYYYYYYYYYYYYYYWUWWYWW
+@gi|65306796|gb|AY948116.1|_2506_2676_7a/1
+ATATAACTTTACAAAGTCGTTTTTA
++
+YYYYYYYYYWYYYYYWYYWYWWYWY
+@gi|65306796|gb|AY948116.1|_881_1061_7b/1
+CTATTTTCGCTTGTAATTCGTTTTC
++
+YYYYYYYYYWYYYYWWYYWYWWYWW
+@gi|65306796|gb|AY948116.1|_998_1182_7c/1
+AAAGAGATACAAGACAAGGCTAAAG
++
+YYYYYYYYYYWYYWYWYYYWWWYWY
diff --git a/t/data/r2.fq b/t/data/r2.fq
new file mode 100644
index 0000000..6094a3b
--- /dev/null
+++ b/t/data/r2.fq
@@ -0,0 +1,500 @@
+@gi|65306796|gb|AY948116.1|_1951_2136_0/2
+AATAAAAAATCCGCCTTGAGTTTTC
++
+YYYYYYYYYYWYYYYYYYWWWWWQQ
+@gi|65306796|gb|AY948116.1|_1531_1682_1/2
+TGGGTTTAGCAGATAGTTTTCTTTT
++
+YYYYYYYYYWYYYYYYYWWYWYYSU
+@gi|65306796|gb|AY948116.1|_603_785_2/2
+AGCTTACGCAAAAAATCGCAGAGCT
++
+YYYYYYYYYWYYYYYYYYWYWYYSU
+@gi|65306796|gb|AY948116.1|_1888_2018_3/2
+AGGGGAGAAAATTCTACTATTAAAA
++
+YYYYYYYYYYYYYWYYYWWYWYYWY
+@gi|65306796|gb|AY948116.1|_1990_2157_4/2
+TTTCGCTCATTTGCATATCCAAAGT
++
+YYYYYYYYYWYYYYYWYYYWYYYSY
+@gi|65306796|gb|AY948116.1|_1165_1307_5/2
+CTTTGACTTTATGATATTCAAATTT
++
+YYYYYYYYYYYYYWYYWYYWWWYSY
+@gi|65306796|gb|AY948116.1|_1622_1777_6/2
+CTGAGTGCGTAGCACGGAAGACGGA
++
+YYYYYYYYYYYYYYYYYWWWYWYWY
+@gi|65306796|gb|AY948116.1|_1116_1298_7/2
+TATGATATTCAAATTTTAAATATTC
++
+YYYYYYYYYWYYYYWWYYYSYYYSU
+@gi|65306796|gb|AY948116.1|_63_202_8/2
+ATAGCTTAGAAGAAAGCCTTGCAAT
++
+YYYYYYYYYYWYYYYYYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_2908_3068_9/2
+TACAAGCTCTATTGCAATAATTTTA
++
+YYYYYYYYYWYYYWYYYYWWWWWQQ
+@gi|65306796|gb|AY948116.1|_2909_3032_a/2
+AGAAAATGAAAGTCAAAAAATAATG
++
+YYYYYYYYYYYYYYWWYYWWYWWQQ
+@gi|65306796|gb|AY948116.1|_3096_3266_b/2
+GGAAATCATATGCACTTTAATGCTA
++
+YYYYYYYYYYYYYYYYYYWUWWWQQ
+@gi|65306796|gb|AY948116.1|_479_649_c/2
+TTGTAAAGGTGTAAATCCTGTAAGC
++
+YYYYYYYYYWYYYYYYYYWWWWWQQ
+@gi|65306796|gb|AY948116.1|_1502_1651_d/2
+GAACAAGCAAAAAGAAACGATAGAG
++
+YYYYYYYYYYWYYYYYYWWYWYYSY
+@gi|65306796|gb|AY948116.1|_944_1116_e/2
+TTTAAAGCTCTTTCGTGTCCTAGTT
++
+YYYYYYYYYWYYYYYYYYWYWWYWY
+@gi|65306796|gb|AY948116.1|_3061_3240_f/2
+GCTCGACACTTGGCACAAGTGGCGG
++
+YYYYYYYYYYYYYYYYWYYSYYYWW
+@gi|65306796|gb|AY948116.1|_1955_2172_10/2
+AAAAATCCGCCTTGAGTTTTCACTC
++
+YYYYYYYYYYYYYYYWYYYSYWYWY
+@gi|65306796|gb|AY948116.1|_2987_3171_11/2
+TAGATTTGATTATAATGACAAGCTT
++
+YYYYYYYYYYYYYYWWYYYSYWYSU
+@gi|65306796|gb|AY948116.1|_2261_2430_12/2
+AGAAAATACGCCATTTTTAAAAAAG
++
+YYYYYYYYYYYYYWYWYYWWYYYWY
+@gi|65306796|gb|AY948116.1|_57_240_13/2
+AAGTGCATAGCTTAGAAGAAAGCCT
++
+YYYYYYYYYWYYYYWWYWWUWYYWW
+@gi|65306796|gb|AY948116.1|_1168_1364_14/2
+ATTTAACATTTTTTGTTTTGTGTGC
++
+YYYYYYYYYWYYYYWWYWWWWWWQQ
+@gi|65306796|gb|AY948116.1|_673_829_15/2
+TTTTAAACTTTGTGCGGTTAGGGTT
++
+YYYYYYYYYYYYYYYWYYYSYYYWY
+@gi|65306796|gb|AY948116.1|_275_459_16/2
+TTTTCATAAGCTTTTTTATAAAGCC
++
+YYYYYYYYYWYYYWYWYWWUWWYWY
+@gi|65306796|gb|AY948116.1|_3145_3288_17/2
+TTTTAGTTGATTTTTATTAGTGGGG
++
+YYYYYYYYYYYYYYYWYYWUWWYSU
+@gi|65306796|gb|AY948116.1|_1295_1444_18/2
+CATAAAGTCAAAGATGAACGAGATA
++
+YYYYYYYYYYYYYYYYYWWYWYYSY
+@gi|65306796|gb|AY948116.1|_2129_2328_19/2
+TCTTTTGCGGAATAATTATTTTTCT
++
+YYYYYYYYYYYYYYWWYYWWYWYWY
+@gi|65306796|gb|AY948116.1|_1462_1646_1a/2
+AAAAGAGCTTAAATATCAAAGAGCT
++
+YYYYYYYYYYWYYYYYYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_2770_2956_1b/2
+GCTATCTTTTTGACCAAATCAGAGT
++
+YYYYYYYYYYYYYWYYYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_1336_1508_1c/2
+TGAGGCACACAAAACAAAAAATGTT
++
+YYYYYYYYYYYYYWYWYYYWWWYSU
+@gi|65306796|gb|AY948116.1|_2153_2336_1d/2
+AATAAACTTCTTTTGCGGAATAATT
++
+YYYYYYYYYYYYYYWWYYWWWYYSY
+@gi|65306796|gb|AY948116.1|_844_1031_1e/2
+TAATCGCTACGAGAATAACGAAAAG
++
+YYYYYYYYYWYYYWYYYYYWYYYSY
+@gi|65306796|gb|AY948116.1|_2821_2986_1f/2
+ACTTGATTAAGTTTCATATTGTTTA
++
+YYYYYYYYYYYYYYYWYYWUWWYSU
+@gi|65306796|gb|AY948116.1|_58_177_20/2
+GTAAATACTCTCTATCGCATGATTA
++
+YYYYYYYYYWYYYYWWYYWWYWWQQ
+@gi|65306796|gb|AY948116.1|_2612_2792_21/2
+AACTTTATACAGACTTTTAAAGCAA
++
+YYYYYYYYYYYYYYYYWYYWWWYSU
+@gi|65306796|gb|AY948116.1|_2081_2254_22/2
+TCTTTGGTTAGTGAGATAATAGCCA
++
+YYYYYYYYYYYYYYYYWYYWYWYWY
+@gi|65306796|gb|AY948116.1|_963_1092_23/2
+TCTAAATTTTGTATATGTTTTTGAT
++
+YYYYYYYYYYYYYYWWYYWYWWYSY
+@gi|65306796|gb|AY948116.1|_1802_1954_24/2
+TATTGTAGTATATTAAAACAATATT
++
+YYYYYYYYYYYYYYWWYYWWYYYSU
+@gi|65306796|gb|AY948116.1|_125_324_25/2
+ATTATGAAGGTATAAAATCTGTTAT
++
+YYYYYYYYYYYYYYYWYWWYWYYWW
+@gi|65306796|gb|AY948116.1|_2801_2960_26/2
+TAAAAATCTTGCTTATGAAAAAGAA
++
+YYYYYYYYYWYYYYWWYYYWWWYSU
+@gi|65306796|gb|AY948116.1|_1744_1934_27/2
+ATATTTGTCAAATATTTTGTCGTTT
++
+YYYYYYYYYYYYYYYYYYWUWWWQQ
+@gi|65306796|gb|AY948116.1|_2759_2911_28/2
+TTCTAAAGAACGCTATCTTTTTGAC
++
+YYYYYYYYYYYYYWYYYYYSYWYWY
+@gi|65306796|gb|AY948116.1|_1201_1398_29/2
+AGACTATCAGTTAACAAAGAATGCT
++
+YYYYYYYYYYYYYYYYWYWUWWYWW
+@gi|65306796|gb|AY948116.1|_1966_2156_2a/2
+TTCGCTCATTTGCATATCCAAAGTA
++
+YYYYYYYYYWYYYYYWYYYSYWYSU
+@gi|65306796|gb|AY948116.1|_1691_1870_2b/2
+CGTTTTAATAGTAGAATTTTGTCGT
++
+YYYYYYYYYYWYYYYWYYYSYWYWY
+@gi|65306796|gb|AY948116.1|_2329_2493_2c/2
+CAATAATATTTGCTTCTTCAAAACA
++
+YYYYYYYYYYWYYYYYWYYWYYYSU
+@gi|65306796|gb|AY948116.1|_145_306_2d/2
+TTGCAATGAGCGGTGGCAACTTTTG
++
+YYYYYYYYYYYYYYYYWYWYWYYWY
+@gi|65306796|gb|AY948116.1|_930_1108_2e/2
+TCTTTCGTGTCCTAGTTCTAAATTT
++
+YYYYYYYYYYYYYYYYYYWYWWWQQ
+@gi|65306796|gb|AY948116.1|_580_743_2f/2
+TGTTATCGAGTGTAAAAAATACCGC
++
+YYYYYYYYYYYYYYYYWYWYWWYSU
+@gi|65306796|gb|AY948116.1|_1032_1194_30/2
+CGAAAGAAAACGAATTACAAGCGAA
++
+YYYYYYYYYYYYYYYYYYWWWWYSY
+@gi|65306796|gb|AY948116.1|_2128_2314_31/2
+GTCTTACTTTGGATATGCAAATGAG
++
+YYYYYYYYYYWYYYYWYYWUWWYSY
+@gi|65306796|gb|AY948116.1|_196_351_32/2
+ATCGCTATGATAAAACAAAGTGCTT
++
+YYYYYYYYYYYYYYYYWYYWYWWQQ
+@gi|65306796|gb|AY948116.1|_1339_1491_33/2
+TCAAAAGCTCTTTGATATTTAAGCT
++
+YYYYYYYYYWYYYYYYYYWYWWYWW
+@gi|65306796|gb|AY948116.1|_2509_2658_34/2
+AAGCTTTGCCTGTGGTTCTAAATTG
++
+YYYYYYYYYWYYYYYYYYYSYYYSY
+@gi|65306796|gb|AY948116.1|_1940_2118_35/2
+TAATATACTACAATAAAAAATCCGC
++
+YYYYYYYYYYYYYYYYYWWUWWWQQ
+@gi|65306796|gb|AY948116.1|_216_381_36/2
+TGCTTTAAAGTTAAGTGCTGATGAA
++
+YYYYYYYYYYYYYYYYYWWYWYYWW
+@gi|65306796|gb|AY948116.1|_461_636_37/2
+TTTTATAAATATTGTGAAAATAAGA
++
+YYYYYYYYYYYYYYWWYWWUWWYSU
+@gi|65306796|gb|AY948116.1|_325_461_38/2
+AATTTTCATAAGCTTTTTTATAAAG
++
+YYYYYYYYYYYYYYYYYWWUWWYSY
+@gi|65306796|gb|AY948116.1|_2304_2478_39/2
+AGAAAAATAATTATTCCGCAAAAGA
++
+YYYYYYYYYWYYYYYWYYWYWYYSY
+@gi|65306796|gb|AY948116.1|_278_467_3a/2
+TATAAAAATTTTCATAAGCTTTTTT
++
+YYYYYYYYYYYYYYYYYYWWWWYSU
+@gi|65306796|gb|AY948116.1|_2717_2903_3b/2
+TTGCATTTGGATATTTTCAGGTTTA
++
+YYYYYYYYYYWYYYYWYWWUWYYWW
+@gi|65306796|gb|AY948116.1|_1389_1563_3c/2
+AGCACCAAAAAAGAAAACTATCTGC
++
+YYYYYYYYYYWYYWYWYWWWYWWQQ
+@gi|65306796|gb|AY948116.1|_3000_3167_3d/2
+AATGACAAGCTTTGGCAATTTAACG
++
+YYYYYYYYYWYYYYWWYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_360_547_3e/2
+AGACAATCACTAAAGAACTTACGCA
++
+YYYYYYYYYYWYYYYYYYYSYWYSY
+@gi|65306796|gb|AY948116.1|_143_319_3f/2
+CTGTTATAAGTAATCATGCGATAGA
++
+YYYYYYYYYYYYYYYYYYYSYWYSY
+@gi|65306796|gb|AY948116.1|_1382_1538_40/2
+GAAATAGGCAAATGGTGTGAAAAAA
++
+YYYYYYYYYYWYYYYYYYYSYWWQQ
+@gi|65306796|gb|AY948116.1|_2707_2804_41/2
+ATCGTCAAATAGATATAGACCAAAG
++
+YYYYYYYYYYYYYYWWYYYSYYYSU
+@gi|65306796|gb|AY948116.1|_430_615_42/2
+TTTTGCGTAAGCTCTTGGCATTGCT
++
+YYYYYYYYYYYYYYWWYWWYWWYWW
+@gi|65306796|gb|AY948116.1|_2383_2537_43/2
+TCTTTGCCATTGATGATTGCTTGAA
++
+YYYYYYYYYYYYYYWWYWWUWWYSU
+@gi|65306796|gb|AY948116.1|_839_973_44/2
+CATTTGCGTTAATTTATGCTCTTGT
++
+YYYYYYYYYYYYYWYYWYWYWWYSU
+@gi|65306796|gb|AY948116.1|_2761_2927_45/2
+CTAAAGAACGCTATCTTTTTGACCA
++
+YYYYYYYYYYYYYYYWYWWUWWYSY
+@gi|65306796|gb|AY948116.1|_375_561_46/2
+AACTTACGCATTTAAATGAATACTC
++
+YYYYYYYYYWYYYYYYYWWUWWYSY
+@gi|65306796|gb|AY948116.1|_2751_2931_47/2
+AAAGAACTTTCTAAAGAACGCTATC
++
+YYYYYYYYYWYYYYYYWYYSYWYSU
+@gi|65306796|gb|AY948116.1|_2312_2478_48/2
+AATTATTCCGCAAAAGAAGTTTATT
++
+YYYYYYYYYWYYYYYYWYYWYWWQQ
+@gi|65306796|gb|AY948116.1|_1934_2078_49/2
+TTCAACTTTAAGCTTAAAAAACCTA
++
+YYYYYYYYYYWYYYYWYYWUWWYSU
+@gi|65306796|gb|AY948116.1|_263_431_4a/2
+CTATGTTCTTACGCACTTCATCGCT
++
+YYYYYYYYYYYYYYYYWYWUWYYWY
+@gi|65306796|gb|AY948116.1|_452_644_4b/2
+TATGAAAATTTTTATAAATATTGTG
++
+YYYYYYYYYYYYYWYYYYYSYWYWY
+@gi|65306796|gb|AY948116.1|_2570_2722_4c/2
+ATATCTATTTGACGATAATTTTCAG
++
+YYYYYYYYYYYYYYYYYWWYWWYWY
+@gi|65306796|gb|AY948116.1|_2549_2708_4d/2
+AAAATTTGGTTTCACAGCCTTTGAA
++
+YYYYYYYYYYYYYYYYYYYSYWYSU
+@gi|65306796|gb|AY948116.1|_1498_1676_4e/2
+TTTTGAACAAGCAAAAAGAAACGAT
++
+YYYYYYYYYYWYYYYYYWWYWYYSU
+@gi|65306796|gb|AY948116.1|_2890_3076_4f/2
+ATATCCAAATGCAAAAGCTAGAAAA
++
+YYYYYYYYYYYYYYWWYYYSYYYSY
+@gi|65306796|gb|AY948116.1|_3149_3310_50/2
+TGAAACCTTTAGAAAAGGTATTAGG
++
+YYYYYYYYYYYYYYYYYYYSYYYWY
+@gi|65306796|gb|AY948116.1|_1992_2129_51/2
+TATCAATCAAGGCTAACTATGAAAC
++
+YYYYYYYYYYWYYYYYYYYSYYYSU
+@gi|65306796|gb|AY948116.1|_945_1120_52/2
+TTCCTTTAAAGCTCTTTCGTGTCCT
++
+YYYYYYYYYYYYYYWWYYYWYYYWW
+@gi|65306796|gb|AY948116.1|_2526_2710_53/2
+TTTTACGATATGATAATAAATAAAA
++
+YYYYYYYYYYYYYWYYWYYWYYYSU
+@gi|65306796|gb|AY948116.1|_2414_2548_54/2
+TTATTTATTATCATATCGTAAAAAC
++
+YYYYYYYYYYYYYYYYWYWUWYYWY
+@gi|65306796|gb|AY948116.1|_1957_2161_55/2
+ACTATTTCGCTCATTTGCATATCCA
++
+YYYYYYYYYYYYYYYYYYWWYWYWY
+@gi|65306796|gb|AY948116.1|_299_483_56/2
+CATTGCAATCCTAAAAAACAACCTG
++
+YYYYYYYYYYWYYYWWYYWUWYYSY
+@gi|65306796|gb|AY948116.1|_2162_2328_57/2
+TCTTTTGCGGAATAATTATTTTTCT
++
+YYYYYYYYYYYYYYYYYYYWWWYSU
+@gi|65306796|gb|AY948116.1|_292_484_58/2
+CACCGCTCATTGCAATCCTAAAAAA
++
+YYYYYYYYYYYYYYWWYYYSYYYWW
+@gi|65306796|gb|AY948116.1|_1558_1716_59/2
+GGTGCTTTAGCAAATCGCACCTGTT
++
+YYYYYYYYYYYYYYYYYYWWWWYWY
+@gi|65306796|gb|AY948116.1|_171_331_5a/2
+GTTTAATGCAGGTTGTTTTTTAGGA
++
+YYYYYYYYYYYYYYWWYWWYWWWQQ
+@gi|65306796|gb|AY948116.1|_2624_2822_5b/2
+TTTTTCATAAGCAAGATTTTTAAAA
++
+YYYYYYYYYYWYYYYYWYYSYYYWW
+@gi|65306796|gb|AY948116.1|_2024_2222_5c/2
+TAAGCGTTTTGTGAGATTATACCTA
++
+YYYYYYYYYYYYYYYWYWWWYWYWW
+@gi|65306796|gb|AY948116.1|_2196_2392_5d/2
+ATGGCAAAGAAAATTTCTTTATAGT
++
+YYYYYYYYYYWYYYYYYWWUWWYSY
+@gi|65306796|gb|AY948116.1|_2377_2544_5e/2
+TTATTATCATATCGTAAAAACGACT
++
+YYYYYYYYYYYYYYYYYYYSYWYWW
+@gi|65306796|gb|AY948116.1|_3111_3290_5f/2
+GATTTTAGTTGATTTTTATTAGTGG
++
+YYYYYYYYYYYYYYYYYWWWYYYWW
+@gi|65306796|gb|AY948116.1|_910_1065_60/2
+TGCTCTATTTTCGCTTGTAATTCGT
++
+YYYYYYYYYYYYYYWWYYWYWYYWW
+@gi|65306796|gb|AY948116.1|_2966_3121_61/2
+CAATATGAAACTTAATCAAGTTAGA
++
+YYYYYYYYYYWYYYWWYYYWYYYSY
+@gi|65306796|gb|AY948116.1|_1321_1511_62/2
+TTGCTTGTTCAAAAGAATTTTCAAA
++
+YYYYYYYYYYYYYYYYYYYSYWYWY
+@gi|65306796|gb|AY948116.1|_1873_2073_63/2
+AAAATTCTACTATTAAGGGGAGAAA
++
+YYYYYYYYYWYYYYYYWYWYWYYWW
+@gi|65306796|gb|AY948116.1|_2702_2884_64/2
+GGTTTAAAAGTAAAGCTAATACCTG
++
+YYYYYYYYYYYYYYYYYYYWYYYWW
+@gi|65306796|gb|AY948116.1|_672_807_65/2
+TAAGTGAGAATGCTAAAGGGGAAAA
++
+YYYYYYYYYYWYYWYWYYYSYYYSY
+@gi|65306796|gb|AY948116.1|_2165_2331_66/2
+ATATAATAATGATTTTAATCTTTTA
++
+YYYYYYYYYWYYYYWWYYWUWYYWY
+@gi|65306796|gb|AY948116.1|_1998_2143_67/2
+ATATCCAAAGTAAGACAATCAAGGC
++
+YYYYYYYYYYWYYYYYWYWYWWYWY
+@gi|65306796|gb|AY948116.1|_904_1068_68/2
+TGTTGCTCTATTTTCGCTTGTAATT
++
+YYYYYYYYYYYYYYWWYYWUWWWQQ
+@gi|65306796|gb|AY948116.1|_2994_3156_69/2
+GATTATAATGACAAGCTTTGGCAAT
++
+YYYYYYYYYYWYYWYYWYWUWWYWW
+@gi|65306796|gb|AY948116.1|_2715_2892_6a/2
+ATAGATATAGACCAAAGAATTTTAA
++
+YYYYYYYYYWYYYYYWYYWWYYYSY
+@gi|65306796|gb|AY948116.1|_633_845_6b/2
+GATTTACACCTTTACAAGTTGTAAT
++
+YYYYYYYYYYYYYWYYWYWWWYYSU
+@gi|65306796|gb|AY948116.1|_319_475_6c/2
+ACCTGCATTAAACCACAATGATAGA
++
+YYYYYYYYYYYYYYYYWYWUWWYWY
+@gi|65306796|gb|AY948116.1|_2202_2401_6d/2
+CAATCATCAATGGCAAAGAAAATTT
++
+YYYYYYYYYYYYYYYYYYYWWWWQQ
+@gi|65306796|gb|AY948116.1|_2825_2992_6e/2
+AAAAACCGCAGGGCGTGGGCGCGGC
++
+YYYYYYYYYWYYYYWWYYWUWWYSY
+@gi|65306796|gb|AY948116.1|_1262_1447_6f/2
+AACAAAGAGCTTGAATATTTAAAAT
++
+YYYYYYYYYWYYYYWWYYYSYYYSU
+@gi|65306796|gb|AY948116.1|_2751_2927_70/2
+AAAGAACTTTCTAAAGAACGCTATC
++
+YYYYYYYYYWYYYYYWYWWWWYYWW
+@gi|65306796|gb|AY948116.1|_3034_3217_71/2
+GGATAGCTTGTATCCTTTAAAGATA
++
+YYYYYYYYYWYYYWYYYYWUWWYWW
+@gi|65306796|gb|AY948116.1|_678_858_72/2
+TTCTCGTAGCGATTAGCTCCACGCT
++
+YYYYYYYYYYYYYYYYYYWYWWYSU
+@gi|65306796|gb|AY948116.1|_149_317_73/2
+TAAGTAATCATGCGATAGAGAGTAT
++
+YYYYYYYYYWYYYYYWYYWWYYYSY
+@gi|65306796|gb|AY948116.1|_2458_2654_74/2
+ATAATTTTGTTTGTTTTGAAGAAGC
++
+YYYYYYYYYWYYYWYYYWWYWYYSU
+@gi|65306796|gb|AY948116.1|_315_506_75/2
+AACAACCTGCATTAAACCACAATGA
++
+YYYYYYYYYWYYYYWWYYWWYWYWY
+@gi|65306796|gb|AY948116.1|_916_1071_76/2
+ACAAGAAAAAGCATTACTTCAAAGA
++
+YYYYYYYYYWYYYYWWYWWWYWWQQ
+@gi|65306796|gb|AY948116.1|_1530_1707_77/2
+CGCGCGCGAGAGAAAAAACAAAAAA
++
+YYYYYYYYYWYYYYWWYYYSYYYSY
+@gi|65306796|gb|AY948116.1|_227_417_78/2
+ACTTCATCGCTAGTGCAAGAGTATT
++
+YYYYYYYYYYYYYYWWYYYWWWWQQ
+@gi|65306796|gb|AY948116.1|_792_964_79/2
+TTAGCAAAATACAAACCCTAACCGC
++
+YYYYYYYYYYWYYYYYYYWUWWYWY
+@gi|65306796|gb|AY948116.1|_2506_2676_7a/2
+ATTCTTCCCACTCAAAATAAGCTTT
++
+YYYYYYYYYYWYYWYYWYYSYYYSY
+@gi|65306796|gb|AY948116.1|_881_1061_7b/2
+ATACAAGATTATAAAACATACGCTC
++
+YYYYYYYYYYWYYYYWYYWYWWWQQ
+@gi|65306796|gb|AY948116.1|_998_1182_7c/2
+TATTTTCCAAAGGTTAAAATGTTTT
++
+YYYYYYYYYYWYYYYYWYWWWWWQQ