# HG changeset patch
# User bebatut
# Date 1461673098 14400
# Node ID 01c2b74b3a21bf6cfb8b71e0a220141a2cca2fbc

planemo upload commit 23ef4b1699065b4f6200c58328bfecfb33dd7fd1-dirty

diff -r 000000000000 -r 01c2b74b3a21 convert_extract_sequence_file.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_extract_sequence_file.py	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,414 @@
+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+
+import sys
+import os
+import argparse
+import copy
+import operator
+
+FASTA_FILE_LAST_POS = None
+
+#################
+# Parse methods #
+#################
+def text_end_of_file(row):
+    if row == '':
+        return True
+    else:
+        return False
+
+def get_new_line(input_file, generate_error = True):
+    row = input_file.readline()
+    if text_end_of_file(row):
+        if generate_error :
+            string = os.path.basename(__file__) + ': '
+            string += ' unexpected end of file'
+            raise ValueError(string)
+        else :
+            return None
+    else:
+        return row[:-1]
+
+def next_fasta_record(input_file):
+    global FASTA_FILE_LAST_POS
+    if FASTA_FILE_LAST_POS != None:
+        input_file.seek(FASTA_FILE_LAST_POS)
+    else:
+        FASTA_FILE_LAST_POS = input_file.tell()
+
+    id_line = get_new_line(input_file, generate_error = False)
+    if id_line == None:
+        return None
+    split_line = id_line[1:].split(' ')
+    seq_id = split_line[0]
+    description = ' '.join(split_line[1:])
+    new_line = get_new_line(input_file, generate_error = False)
+    seq = ''
+    while new_line != None:
+        if new_line[0] != '>':        
+            seq += new_line
+            FASTA_FILE_LAST_POS = input_file.tell()
+            new_line = get_new_line(input_file, generate_error = False)
+        else:
+            new_line = None
+    return SeqRecord(seq_id, seq, description)
+
+def next_fastq_record(input_file):
+    id_line = get_new_line(input_file, generate_error = False)
+    if id_line == None:
+        return None
+    if id_line[0] != '@':
+        string = os.path.basename(__file__) + ': '
+        string += ' issue in fastq file'
+        raise ValueError(string)
+    split_line = id_line[1:].split(' ')
+    seq_id = split_line[0]
+    description = ' '.join(split_line[1:])
+    seq = get_new_line(input_file)
+    spacer = get_new_line(input_file)
+    quals = get_new_line(input_file)
+    return SeqRecord(seq_id, seq, description, quals)
+
+def next_record(input_file, file_format):
+    if file_format == 'fasta':
+        return next_fasta_record(input_file)
+    elif file_format == 'fastq':
+        return next_fastq_record(input_file)
+    else:
+        string = os.path.basename(__file__) + ': '
+        string += file_format + ' is not managed'
+        raise ValueError(string)
+
+def write_fasta_record(record, output_sequence_file):
+    output_sequence_file.write('>' + record.get_id() + ' ' + 
+        record.get_description() + '\n')
+    seq = record.get_sequence()
+    split_seq = [seq[i:i+60] for i in xrange(0,len(seq),60)]
+    for split in split_seq:
+        output_sequence_file.write(split + '\n')
+
+def format_qual_value(qual_score, sliding_value, authorized_range, qual_format):
+    ascii_value = ord(qual_score)
+    score = ascii_value-sliding_value
+    if score < authorized_range[0] or score > authorized_range[1]:
+        string = os.path.basename(__file__) + ': wrong score ('
+        string += str(score) + ') with quality format ('
+        string += qual_format
+        raise ValueError(string)
+    return score
+
+def format_qual_string(qual_string, qual_format):
+    if qual_format == 'sanger':
+        return format_qual_value(qual_string, 33 ,[0,40], qual_format)
+    elif qual_format == "solexa":
+        return format_qual_value(qual_string, 64 ,[-5,40], qual_format)
+    elif qual_format == "illumina_1_3":
+        return format_qual_value(qual_string, 33 ,[0,40], qual_format)
+    elif qual_format == "illumina_1_5":
+        return format_qual_value(qual_string, 33 ,[3,40], qual_format)
+    elif qual_format == "illumina_1_8":
+        return format_qual_value(qual_string, 33 ,[0,41], qual_format)
+    else:
+        string = os.path.basename(__file__) + ': quality format ('
+        string += qual_format + ') is not managed'
+        raise ValueError(string) 
+
+def write_qual_record(record, output_qual_file, qual_format):
+    output_qual_file.write('>' + record.get_id() + ' ' + 
+        record.get_description() + '\n')
+    qual = record.get_quality()
+    qual = [str(format_qual_string(qual_str,qual_format)) for qual_str in qual]
+    split_seq = [qual[i:i+60] for i in xrange(0,len(qual),60)]
+    for split in split_seq:
+        output_qual_file.write(' '.join(split) + '\n')
+
+def write_fastq_record(record, output_sequence_file):
+    output_sequence_file.write('@' + record.get_id() + ' ' + 
+        record.get_description() + '\n')
+    output_sequence_file.write(record.get_sequence() + '\n')
+    output_sequence_file.write('+\n')
+    output_sequence_file.write(record.get_quality() + '\n')
+
+def write_information(record, output_file_formats, output_sequence_file, 
+    output_qual_file, qual_format):
+    if "fasta" in output_file_formats:
+        write_fasta_record(record, output_sequence_file)
+    if "qual" in output_file_formats:
+        write_qual_record(record, output_qual_file, qual_format)
+    if "fastq" in output_file_formats:
+        write_fastq_record(record, output_sequence_file)
+
+def fast_test_element_in_list(element,list_to_test):
+    to_continue = True
+    i = 0
+    while to_continue:
+        if i == len(list_to_test) or list_to_test[i] >= element:
+            to_continue = False
+        else:
+            i += 1
+
+    found = False
+    if i < len(list_to_test):
+        if list_to_test[i] == element:
+            found = True
+
+    return found
+
+#########################
+# Constraint definition #
+#########################
+constraints = {
+    'equal': operator.eq,
+    'different': operator.ne,
+    'lower': operator.le,
+    'strictly_lower': operator.lt,
+    'greater': operator.ge,
+    'strictly_greater': operator.gt,
+    'in': operator.contains,
+    'not_in': 'in'
+}
+
+extractable_information = {
+    'id': str,
+    'length': int,
+    'description': str
+}
+
+###########
+# Classes #
+###########
+class SeqRecord:
+
+    def __init__(self, seq_id, sequence, description, quality = ""):
+        self.id = seq_id
+        self.sequence = sequence
+        self.quality = quality
+        self.description = description
+        self.length = len(self.sequence)
+
+    # Getters
+    def get_id(self):
+        return self.id
+
+    def get_sequence(self):
+        return self.sequence
+
+    def get_quality(self):
+        return self.quality
+
+    def get_length(self):
+        return self.length
+
+    def get_description(self):
+        return self.description
+
+    def get(self, category):
+        if category == 'id':
+            return self.get_id()
+        elif category == 'length':
+            return self.get_length()
+        elif category == 'description':
+            return self.get_description()
+        else:
+            string = os.path.basename(__file__) + ': '
+            string += category + ' can not be extracted from SeqRecord'
+            raise ValueError(string)
+
+    # Other functions
+    def extract_information(self,to_extract):
+        extracted_info = []
+        for info_to_extract in to_extract:
+            extracted_info.append(self.get(info_to_extract))
+        return extracted_info
+
+    def test_conservation(self, constraints):
+        to_conserve = True
+        for constrained_info in constraints:
+            record_value = self.get(constrained_info)
+            for constraint in constraints[constrained_info]:
+                to_conserve &= constraint.test_constraint(record_value)
+        return to_conserve
+
+class Records:
+
+    def __init__(self, input_filepath, file_format, constraints):
+        self.records = []
+        self.conserved_records = []
+        with open(input_filepath, 'r') as input_file:
+            to_continue = True
+            while to_continue:
+                record = next_record(input_file, file_format)
+                if record != None:
+                    self.records.append(record)
+                    to_conserve = record.test_conservation(constraints)
+                    if to_conserve:
+                        self.conserved_records.append(copy.copy(record))
+                else:
+                    to_continue = False           
+
+    # Getters
+    def get_records(self):
+        return copy.copy(self.records)
+
+    def get_record_nb(self):
+        return len(self.records)
+
+    def get_conserved_records(self):
+        return copy.copy(self.conserved_records)
+
+    def get_conserved_record_nb(self):
+        return len(self.conserved_records)
+
+    # Other functions
+    def save_conserved_records(self,args):
+        if args.custom_extraction_type == 'True':
+            to_extract = args.to_extract[1:-1].split(',')
+            with open(args.output_information, 'w') as output_information_file:
+                output_information_file.write('\t'.join(to_extract) + '\n')
+                for record in self.conserved_records:
+                    extracted_info = record.extract_information(to_extract)
+                    string_info = [str(info) for info in extracted_info]
+                    string = '\t'.join(string_info)
+                    output_information_file.write(string + '\n')
+        else:
+            qual_format = None
+            if args.format == 'fasta':
+                output_file_formats = ['fasta']
+            elif args.format == 'fastq':
+                if args.split == 'True':
+                    output_file_formats = ['fasta','qual']
+                    qual_format = args.quality_format
+                else:
+                    output_file_formats = ['fastq']
+
+            with open(args.output_sequence,'w') as output_sequence_file: 
+                if "qual" in output_file_formats:
+                    output_qual_file = open(args.output_quality, 'w')
+                else:
+                    output_qual_file = None
+                for record in self.conserved_records:
+                    write_information(record, output_file_formats,
+                        output_sequence_file, output_qual_file, qual_format)
+                if "qual" in output_file_formats:
+                    output_qual_file.close()
+
+class Constraint:
+
+    def __init__(self, constraint_type, value, constrained_information):
+        if not constraints.has_key(constraint_type):
+            string = os.path.basename(__file__) + ': '
+            string += constraint_type + ' is not a correct type of constraint'
+            raise ValueError(string)
+        self.raw_constraint_type = constraint_type
+        self.type = constraints[constraint_type]
+
+        value_format = extractable_information[constrained_information]
+        if self.raw_constraint_type in ['in', 'not_in']:
+            self.values = []
+            with open(value, 'r') as value_file:
+                for row in value_file.readlines():
+                    value = row[:-1]
+                    self.values.append(value_format(value))
+        else:
+            self.values = [value_format(value)]
+        self.values.sort()
+
+    def get_raw_constraint_type(self):
+        return self.raw_constraint_type
+
+    def get_type(self):
+        return self.type
+
+    def get_values(self):
+        return self.values
+
+    def test_constraint(self, similarity_info_value):
+        to_conserve = True
+        if self.raw_constraint_type == 'in':
+            to_conserve &= fast_test_element_in_list(similarity_info_value, 
+                self.values)
+        elif self.raw_constraint_type == 'not_in':
+            to_conserve &= (not fast_test_element_in_list(similarity_info_value, 
+                self.values))
+        else:
+            to_conserve &= self.type(similarity_info_value, self.values[0])
+        return to_conserve    
+
+################
+# Misc methods #
+################
+def test_input_filepath(input_filepath, tool, file_format):
+    if not os.path.exists(input_filepath):
+        string = os.path.basename(__file__) + ': '
+        string += input_filepath + ' does not exist'
+        raise ValueError(string)
+
+def format_constraints(constraints):
+    formatted_constraints = {}
+    if constraints != None:
+        for constr in constraints:
+            split_constraint = constr.split(': ')
+            constrained_information = split_constraint[0]
+            constraint = Constraint(split_constraint[1], split_constraint[2], 
+                constrained_information)
+            formatted_constraints.setdefault(constrained_information,[]).append(
+                constraint)
+    return formatted_constraints
+
+def convert_extract_sequence_file(args):
+    input_filepath = args.input
+    file_format = args.format
+    constraints = args.constraint
+    formatted_constraints = format_constraints(constraints)
+
+    records = Records(input_filepath, file_format, formatted_constraints)
+    records.save_conserved_records(args)
+    
+    report_filepath = args.report
+    with open(report_filepath, 'w') as report_file:
+
+        report_file.write('Information to extract:\n')
+        if args.custom_extraction_type == 'True':
+            for info in args.to_extract[1:-1].split(','):
+                report_file.write('\t' + info + '\n')
+        else:
+            report_file.write('\tsequences\n')
+
+        if constraints != None:
+            report_file.write('Constraints on extraction:\n')
+            for constrained_info in formatted_constraints:
+                report_file.write('\tInfo to constraint: ' + constrained_info 
+                    + '\n')
+                for constraint in formatted_constraints[constrained_info]:
+                    report_file.write('\t\tType of constraint: ' + 
+                        constraint.get_raw_constraint_type()
+                        + '\n')
+                    report_file.write('\t\tValues:\n')
+                    values = constraint.get_values()
+                    for value in values:
+                        report_file.write('\t\t\t' + str(value) + '\n')
+        report_file.write('Number of similarity records: ' + 
+            str(records.get_record_nb()) + '\n')
+        report_file.write('Number of extracted similarity records: ' +
+            str(records.get_conserved_record_nb()) + '\n')
+
+########
+# Main #
+########
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--input', required=True)
+    parser.add_argument('--format', required=True)
+    parser.add_argument('--custom_extraction_type', required=True)
+    parser.add_argument('--to_extract')
+    parser.add_argument('--output_information')
+    parser.add_argument('--split')
+    parser.add_argument('--quality_format')
+    parser.add_argument('--output_sequence')
+    parser.add_argument('--output_quality')
+    parser.add_argument('--constraint', action='append')
+    parser.add_argument('--report', required=True)
+    args = parser.parse_args()
+
+    convert_extract_sequence_file(args)
diff -r 000000000000 -r 01c2b74b3a21 convert_extract_sequence_file.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/convert_extract_sequence_file.xml	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,249 @@
+<tool id="convert_extract_sequence_file" name="Convert/ Extract information" version="1.0.0">
+
+	<description>from a sequence file, with possible constraints</description>
+
+    <macros>
+        <xml name="extraction_option">
+            <param name="to_extract" type="select" display="checkboxes" multiple="true" label="Information to extract" help="">
+                <option value="id">Identifiant</option>
+                <option value="length">Length</option>
+                <validator type="no_options" message="Select at least one information to extract"/>
+            </param>
+        </xml>
+
+        <xml name="extraction_test">
+            <param name='specific_extraction' type="select" label="Extract specific information?" help="If no is selected, a sequence file is generated. If yes, a text file containing the wanted information is generated">
+                <option value="True">Yes</option>
+                <option value="False" selected="true">No</option>
+            </param>
+        </xml>
+    </macros>
+
+	<requirements>
+  	</requirements>
+
+    <stdio>
+    </stdio>
+
+    <version_command>
+    </version_command>
+
+  	<!--<command>-->
+    <command><![CDATA[
+  		python $__tool_directory__/convert_extract_sequence_file.py 
+      		--input $sequence_file_format.sequence_file
+
+            --custom_extraction_type $sequence_file_format.extraction.specific_extraction
+
+            #if $sequence_file_format.extraction.specific_extraction == "True":
+                --to_extract "{$sequence_file_format.extraction.to_extract}"
+                --output_information $information_file
+            #else if $sequence_file_format.format=="fastq":
+                --split $sequence_file_format.extraction.split.split_test
+                #if $sequence_file_format.extraction.split.split_test :
+                    --quality_format $sequence_file_format.extraction.split.quality_format
+                    --output_sequence $fasta_sequence_file_from_fastq
+                    --output_quality $quality_file
+                #else:
+                    --output_sequence $fastq_sequence_file
+                #end if
+            #else:
+                --output_sequence $fasta_sequence_file
+            #end if
+                
+    		#if $constraints.constrained_extraction == "True" :
+                #for $i, $constrain in enumerate( $constraints.constraint_definition )
+                	#set info_to_constrain=$constrain.constrained_information['info_to_constrain']             
+                    #if $info_to_constrain in ("id"):
+                    	--constraint "$info_to_constrain:
+                    	${constrain.constrained_information.constraint_type.type}:
+                    	${constrain.constrained_information.constraint_type.value}"
+                    #else:
+                    	#for $j, $sub_constrain in enumerate( $constrain.constrained_information.constraint_definition )
+                    		--constraint "$info_to_constrain:
+                    		${sub_constrain.type}:
+                    		${sub_constrain.value}"
+                        #end for
+                    #end if
+                #end for
+            #end if
+
+            --report $report_filepath
+            --format $sequence_file_format.format
+        ]]>
+  	</command>
+
+  	<inputs>
+        <conditional name="sequence_file_format">
+        	<param name="format" type="select" display="radio" 
+                label="Format of the sequence file" help="">
+	            <option value="fasta">Fasta</option>
+                <option value="fastq">FastQ</option>
+	        </param>
+            <when value="fastq">
+                <param name="sequence_file" type="data" format="fastq" 
+                    label="Sequence file" help=""/>
+                <conditional name="extraction">
+                    <expand macro="extraction_test"/> 
+
+                    <when value="True">
+                        <expand macro="extraction_option"/> 
+                    </when>
+                    <when value="False">
+                        <conditional name="split">
+                            <param name='split_test' type="select" label="Split file into sequence and quality files?" help="If yes is selected, a fasta and a quality file are generated. If no, a fastq file is generated">
+                                <option value="True" selected="true">Yes</option>
+                                <option value="False">No</option>
+                            </param>
+
+                            <when value="True">
+                                <param name="quality_format" type="select" display="radio" label="Coding of quality scores?" help="">
+                                    <option value="sanger" selected="true">Sanger (Phred+33)</option>
+                                    <option value="solexa">Solexa (Solexa+64) </option>
+                                    <option value="illumina_1_3">Illumina 1.3+ (Phred+64) </option>
+                                    <option value="illumina_1_5">Illumina 1.5+ (Phred+64) </option>
+                                    <option value="illumina_1_8">Illumina 1.8+ (Phred+33) </option>
+                                </param>
+                            </when>
+                            <when value="False" />
+                        </conditional> 
+                    </when>
+                </conditional> 
+            </when>
+
+            <when value="fasta">
+                <param name="sequence_file" type="data" format="fasta" 
+                    label="Sequence file" help=""/>
+                <conditional name="extraction">
+                    <expand macro="extraction_test"/> 
+
+                    <when value="True">
+                        <expand macro="extraction_option"/>
+                    </when>
+                    <when value="False" />
+                </conditional> 
+            </when>
+        </conditional>
+        
+        <conditional name="constraints">
+            <param name='constrained_extraction' type='select' label="Constrain extraction?" help="">
+                <option value="True">Yes</option>
+                <option value="False" selected="true">No</option>
+            </param>
+
+            <when value="True">
+                <repeat name="constraint_definition" title="Constraints on sequences" min="1">
+                    <conditional name="constrained_information">
+                        <param name="info_to_constrain" type="select" label="Information to constrain" help="">
+                            <option value="id">Identifiant</option>
+                            <option value="length">Length</option>
+                        </param>
+                        <when value="id">
+                            <conditional name="constraint_type">
+                                <param name="type" type="select" display="radio" label="Type of constraint" help="">
+                                    <option value="equal">Equal a value</option>
+                                    <option value="in">In a list</option>
+                                    <option value="not_in">Not in a list</option>
+                                </param>
+                                <when value="equal">
+                                    <param name="value" type="text" size="200" label="Equal to" help=""/>
+                                        <validator type="empty_field" message="Give a value"/>
+                                </when>
+                                <when value="in">
+                                    <param format="txt" name="value" type="data" label="List of constraint" help="Text file with a value per line and nothing else"/>
+                                        <validator type="unspecified_build" message="Select a file"/>
+                                </when>
+                                <when value="not_in">
+                                    <param format="txt" name="value" type="data" label="List of constraint" help="Text file with a value per line and nothing else"/>
+                                        <validator type="unspecified_build" message="Select a file"/>
+                                </when>
+                            </conditional>
+                        </when>  
+                        <when value="length">
+                            <repeat name="constraint_definition" title="Constraint on sequence length" min="1">
+                                <param name="type" type="select" label="Type of constraint" help="">
+                                    <option value="equal">Equal to </option>
+                                    <option value="lower">Lower than </option>
+                                    <option value="strictly_lower">Strictly lower than </option>
+                                    <option value="greater">Greater than </option>
+                                    <option value="strictly_greater">Strictly greater than </option>
+                                </param>
+                                <param name="value" type="integer" min="0" max="3000" value="100" label="Value" help=""/>
+                            </repeat>
+                        </when>  
+                    </conditional>
+                </repeat>
+            </when>
+            <when value="False" />
+        </conditional> />
+  	</inputs>
+
+  	<outputs>
+        <data format="txt" name="information_file" 
+            label="${tool.name} on ${on_string}: Information">
+            <filter>((sequence_file_format['extraction']['specific_extraction'] == "True" ))</filter>
+        </data>
+
+        <data format="fasta" name="fasta_sequence_file"
+            label="${tool.name} on ${on_string}: Extracted sequences" >
+            <filter>((sequence_file_format['format'] == 'fasta' and not sequence_file_format['extraction']['specific_extraction']== "True" ))</filter>
+        </data>
+
+        <data format="fastq" name="fastq_sequence_file"
+            label="${tool.name} on ${on_string}: Extracted sequences">
+            <filter>((sequence_file_format['format'] == 'fastq' and sequence_file_format['extraction']['specific_extraction'] == "False" and sequence_file_format['extraction']['split']['split_test'] == "False" ))</filter>
+        </data>
+
+        <data format="qual" name="quality_file" 
+            label="${tool.name} on ${on_string}: Extracted quality">
+            <filter>((sequence_file_format['format'] == 'fastq' and sequence_file_format['extraction']['specific_extraction'] == "False" and sequence_file_format['extraction']['split']['split_test'] == "True" ))</filter>
+        </data>
+
+        <data format="fasta" name="fasta_sequence_file_from_fastq"
+            label="${tool.name} on ${on_string}: Extracted sequences">
+            <filter>((sequence_file_format['format'] == 'fastq' and sequence_file_format['extraction']['specific_extraction'] == "False" and sequence_file_format['extraction']['split']['split_test'] == "True" ))</filter>
+        </data>
+
+        <data format="txt" name="report_filepath" 
+            label="${tool.name} on ${on_string}: Report"/>
+  	</outputs>
+
+  	<tests>
+        <test>
+            <param name="format" value="fasta"/>
+            <param name="sequence_file" value="input_sequence_file.fasta"/>
+            <param name="specific_extraction" value="True" />
+            <param name="to_extract" value="length" />
+            <param name="constrained_extraction" value="False" />
+            <output name="information_file" file="information_lenght_fasta_output.txt"/>
+            <output name="report_filepath" file="report_length_fasta_output.txt"/>
+        </test>
+        <test>
+            <param name="format" value="fastq"/>
+            <param name="sequence_file" value="input_sequence_file.fastq"/>
+            <param name="specific_extraction" value="False" />
+            <param name="split_test" value="True" />
+            <param name="quality_format" value="illumina_1_3" />
+            <param name="constrained_extraction" value="False" />
+            <output name="quality_file" file="extracted_quality_illumina_1_3_fastq_output.qual"/>
+            <output name="fasta_sequence_file_from_fastq" file="extracted_sequences_illumina_1_3_fastq_output.fasta"/>
+            <output name="report_filepath" file="report_illumina_1_3_fastq_output.txt"/>
+        </test>
+  	</tests>
+
+  	<help><![CDATA[
+
+**What it does**
+
+This tool extracts information (sequences, id, length, ...) from sequence files or convert a FastQ file to Fasta file.
+
+Some constraints could be added to extraction/conversion. For example, only sequences with more than 30 bp could be extracted. Or, a sequences whose the identifiant is in a list. 
+
+The input is a sequence file in fasta or fastq format. The tool generates different outputs given the chosen parameters.
+]]>
+  	</help>
+
+    <citations>
+    </citations>
+</tool>
+
diff -r 000000000000 -r 01c2b74b3a21 test-data/extracted_quality_illumina_1_3_fastq_output.qual
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extracted_quality_illumina_1_3_fastq_output.qual	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,174 @@
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+37 38 38 38 38 31 37 31 29 31 23 35 38 38 38 28 26 31 37 37 37 38 38 34 26 36 21 11 31 31 10 19 25 11 18 16 23 26 24 11 31 37 38 31 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+>HWI-M00234:263:000000000-ADM55:1:1101:24419:6736 1:N:0:ATCACG
+34 34 34 34 34 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 35 38 38 38 38 38 37 38 38 38 38 38 38 38 35 38 38 38 38 38 38 38 38 38
+38 38 38 38 38 38 38 35 37 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 37 38 38 38 37 38 38 38 38 38 38 38 38 35 24 37 37 34 37 36 38 38 38 37 38 38 38
+38 38 22 28 10 19 29 31 36 37 36 36 37 37 38 22 29 36 36 35 36 36 36 37 35 35 35 38 31 23 35 34 37 36 37 35 37 38 38 34 23 28 34 35 34 38 38 37 38 38 35 34 21 29 35 35 38 35 34 37
+35 38 35 38 35 38 37 38 38 31 32 37 33 32 30 37 37 37 37 37 37 37 37 32 33 33 37 24 20 33 31 32 37 37 37 37 37 37 37 37
+>HWI-M00234:263:000000000-ADM55:1:1101:5068:6755 1:N:0:ATCACG
+34 34 34 34 34 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38
+38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 35 37 37 30 37 38 38 38 38 38 35 37 38 38 38 38 38 38 38 38 38 38 37 37 37 37 38 38 38 38 38 37 38 38 37 38 38 38 38 38 38 35
+38 38 38 38 38 38 38 37 38 38 38 36 36 35 38 38 38 24 34 24 36 36 38 38 38 38 38 35 23 31 37 38 38 38 38 38 38 38 38 38 38 38 38 38 29 34 37 38 38 38 38 38 34 37 38 35 38 35 37 38
+37 38 38 37 22 34 37 38 35 37 29 37 37 37 32 37 28 26 32 29 36 35 35 33 37 33 33 37 37 37 31 35 31 35 27 36 30 31 37 15 16 26 31 27 30 34 27 19 22 16 13 17 8 19 23 27 30 30 17 7
+20 19 24 27 33 29 37 35 37 17 19 8 21 21 27 8 8
+>HWI-M00234:263:000000000-ADM55:1:1101:21477:6796 1:N:0:ATCACG
+34 34 11 32 34 25 37 23 27 37 31 34 34 36 35 38 38 34 36 38 38 38 38 38 37 32 38 27 37 38 38 23 31 37 36 37 36 37 37 34 36 38 38 34 37 37 27 27 27 37 31 27 34 10 31 37 37 25 32 37
+34 36 37 36 11 36 34 37 24 32 37 38 34 31 35 36 27 37 36 11 11 20 31 24 33 23 33 37 37 34 36 23 37 11 28 37 37 31 34 38 22 37 34 37 38 35 25 37 37 37 22 36 32 37 35 38 24 37 26 37
+37 37 31 25 37 36 36 38 31 19 28 31 35 36 37 38 21 28 36 38 34 32 35 34 21 31 36 34 34 32 11 31 35 35 37
+>HWI-M00234:263:000000000-ADM55:1:1101:12483:6880 1:N:0:ATCACG
+34 34 34 34 34 38 38 38 38 38 38 38 37 38 38 37 38 38 38 38 38 37 38 35 37 36 38 38 38 38 38 37 37 37 38 38 37 38 38 38 38 38 38 38 38 37 38 38 38 37 38 38 38 38 38 38 38 38 34 36
+38 38 38 38 34 37 38 38 38 38 38 38 38 38 38 38 38 38 37 38 38 38 37 36 38 38 35 38 38 38 38 37 37 37 38 38 38 38 38 38 38 38 37 38 38 38 38 38 38 38 38 38 38 37 38 37 38 34 37 31
+37 36 37 37 38 35 32 38 37 38 37 38 38 38 38 37 38 38 38 38 35 38 38 38 37 37 38 38 38 35 26 36 36 37 38 38 38 38 38 38 38 37 38 38 38 38 38 38 38 38 38 38 37 35 38 35 38 38 38 38
+38 38 38 38 38 38 38 35 38 37 37 37 37 37 37 37 24 26 26 35 37 37 37 37 37 33 37 37 33 35 33 37 37 33 37 35 28 35 35 37 35 37 37 37 36 37 36 37 36 37 36 36 34 36 27 31 36 31 34 37
+37 31 36 33 32 37 37 36 36 36 37 37
+>HWI-M00234:263:000000000-ADM55:1:1101:27958:6935 1:N:0:ATCACG
+34 34 34 34 34 38 38 38 38 38 38 38 38 38 38 38 35 38 38 34 37 38 38 38 38 38 38 38 37 36 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 23 35 34
+27 37 38 38 38 37 37 38 38 38 38 38 38 38 38 38 38 34 38 37 25 37 35 38 38 38 38 38 38 31 37 36 36 36 38 38 38 36 38 35 38 38 38 37 38 38 38 38 38 38 25 37 37 38 38 28 36 38 37 37
+37 34 36 37 38 24 36 36 37 38 35 10 31 31 36 36 35 36 35 23 35 32 29 36 36 34 31 36 37 38 37 32 37 37 38 37 28 37 30 10 19 19 26 34 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
+>HWI-M00234:263:000000000-ADM55:1:1101:6151:7404 1:N:0:ATCACG
+34 34 34 34 34 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 37 38 37 38 38 38 38 38
+38 38 38 38 38 37 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 38 35 37 23 37 38 38 38 37 38 38 38 38 36 38 38 38 22 10 34 38 38 37 38 38 38 38 38 38 38 38 34 25 23 37 38 38
+38 35 37 38 37 36 38 38 38 37 38 38 38 37 38 34 38 38 38 38 38 38 38 38 35 38 30 36 38 38 38 38 38 37 37 11 27 37 38 38 38 38 37 35 38 38 38 38 11 20 11 36 37 38 38 38 35 10 10 9
+20 25 35 38 37 34 35 35 30 21 29 32 37 37 37 19 30 21 8 20 30 36 33 30 35 15 29 35 37 37 37 32 37 15 7 14 13 21 27 35 15 18 26 18 7 8 13 21 19 21 27 32 8 8 13 8 8 7 19 25
+15 27 33 37 33 35 30 37 27 17 27 32 37 37 27 33 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
diff -r 000000000000 -r 01c2b74b3a21 test-data/extracted_sequences_illumina_1_3_fastq_output.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/extracted_sequences_illumina_1_3_fastq_output.fasta	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,174 @@
+>HWI-M00234:263:000000000-ADM55:1:1101:21704:2233 1:N:0:ATCACG
+GTGTACAAGGCCCGGGAACGTATTCACCGCGGCATGCTGATCCGCGATTACTAGCGATTC
+CAACTTCATACAGGCGGGTTTCAGCC
+>HWI-M00234:263:000000000-ADM55:1:1101:21334:2699 1:N:0:ATCACG
+CTTTTGACGGCCTTTTTGTTGTCTTCTGAATTTTGTTTTTTTCGGTTGTAACATAATTCC
+TAAAAATCAAATTCGTTAGCGATTATTTTTCTTTCTTTTGAAGTTCTTTCCGCCATTGTT
+TCCGCTATTGCTTCCACGACC
+>HWI-M00234:263:000000000-ADM55:1:1101:13968:2885 1:N:0:ATCACG
+CCCACTGCTGCCTCCCGTAGGAGCCTGGACCGTGTCTCAGTTCCAATGTGGCCGATCACC
+CTCTCAGGTCGGCTACCCATCGTTGCCCTGGTAAGCCATTACCCTACCAACTAGCTAATG
+GGACGCGGGCACATCTCAAAGCGGATTACCCCTTTGGTTAAAGTTTAATGCGAAACTCTA
+ACTTTATGCGTTATTAACCCTCCTTTCGGAGGGCTATTCCCCTCTTTGATGCAGGTTGCC
+CACGTGTTACTCACCCGTCCGCCGCTAATCCACTTCCCGAAGGCAGATTCAACCCTCGAT
+>HWI-M00234:263:000000000-ADM55:1:1101:11873:2948 1:N:0:ATCACG
+CCCCGTTACATCTTCCGCGCAGGAAGACTCGATCAGTGAGCTATTACGCTTTCTTTGAAG
+GATGGCTGCTTCTAAGCCAACTTCCTGACTGTCTTAGCCTTCCCACTTCGTTTTCCACTT
+AGTCAATATTAGGGACCTTAGCCGGCGGTCTGGGTTGTTTCCCTCTTGAGTCCGGACGTT
+AGCACCCGGTGCTCTGTCCCCCGTGCCCAAACTTCCAAGTATTCGGAGTTTGCCATGGTT
+TGGTAAGACGCTATGTCCCCCTAACCATAACAGTGTTCTACCCTCTGAACACATACTCGA
+>HWI-M00234:263:000000000-ADM55:1:1101:7855:3066 1:N:0:ATCACG
+CGTCAATCTTCCAACGCCCACGGCAGATAGGGACAAAACTGTCTCACGACGTTTTAAACC
+CAGCTCACGTACCTCTTTAAATGGCGAACAGCCATACCCTTGGGACCGGCTACAGC
+>HWI-M00234:263:000000000-ADM55:1:1101:24817:3238 1:N:0:ATCACG
+CCCGTGACCAGATTCATGGCCGCCGGTTAGAACCCCAGTACTGTCAGGGTGGTATCCCAA
+GGA
+>HWI-M00234:263:000000000-ADM55:1:1101:17179:3527 1:N:0:ATCACG
+GTGCTTATTTCACTTCCTCAAAATCAGCATCCTGCACATTATCGCCATGCTTT
+>HWI-M00234:263:000000000-ADM55:1:1101:21254:3571 1:N:0:ATCACG
+GTCGCGGGGAAGATCAACTCCTGCAATTCGAGCCATACCAATTACCTCCTAGCGCCCTGA
+CGCTGTTTATGACGAGGATCGCGGCTGCAGATGACGCGAATGACGCCATTGCGCTTGATC
+ACTCGGCAATACTCACAAATGGGTTTAACAGATTATCTAACCTTCATAGTTTGCACACTC
+CTCATGGACATTCC
+>HWI-M00234:263:000000000-ADM55:1:1101:16569:3709 1:N:0:ATCACG
+CCCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGAATACTTATTG
+CGTTTGCTGCGGCACCGAATGGCTTTGCCACCCGACACCTAGTATTCATCGTTTACGGCG
+TGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGGA
+TCGGAAGAGCACACGTCTGAACTCCAGTCACATCCCG
+>HWI-M00234:263:000000000-ADM55:1:1101:22403:3828 1:N:0:ATCACG
+CCCGGACATCTTCGGCGCAGGATCTCTTGACTAGTGAGCTATTACGCACTCTTTAAATGA
+GTGGCTGCTTCTAAGCCAACATCCTAGTTGTCTTAGAAATCCCACATCCTTTTCCACTTA
+ACTTACACTTTGGGACCTTAGCTGATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+CATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAATATCAATCAAACACAC
+ACACACCAGCTTAC
+>HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG
+GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGG
+TCAGCGGTAGCTGCCATAATGTAATGGTAGTCAAATCCTAAGTCTCCCAATGCACATGGC
+AGTGGAGCGTTCCAATCTTGTGTACCGGCTTTGTCTCCTAATCCCAAGTGCCATTTTCCG
+ATAGCTCCGGTAGCATAACCGGTACTTTTGAACATAACCGCCATGGTATATTGTTCGGGA
+CGGATAATCATTCCGGCATTTCCGGCAGCTACG
+>HWI-M00234:263:000000000-ADM55:1:1101:26232:4161 1:N:0:ATCACG
+CTCTTCTTAAGCTCGAACAGCTTCTTCAGTCTTACCTGCCATTTCATCTAAAATTTTTAA
+AGCTCGCTCTAAAACAGTAGTATCATCAATCATAACCAATCCACCATCTGGTCCAGGTTC
+CAAGTGAATCCCAACACTTTTCCCCTCCTTAAAATTGTGTCCACCGAAAAAATTTCTTAC
+AGTGTCAACATTCAGTCCAAGTTCATCGGCTATTCTATGCATACTACCACTAGGCAATGA
+GT
+>HWI-M00234:263:000000000-ADM55:1:1101:23151:4189 1:N:0:ATCACG
+GCGGATTTTCTCGGGAGTATGATTACCCACACTATTGGATTCTTCCGAAGAAGACTCCAT
+ACTACCAAGTTCAGCTCGGATGGTGGATTTGCCTGCCAAGATCAGAAGAGCACACGTCTG
+AACTCCAGTCACATCACGACTTCGTATGCCGTATTCTGCTTGAAAAAAACAATGAAAACT
+AGTCACCGATGACTCACGTTCGCTGAACATTATCTGACAACTAGCTTAACAATGGACATG
+CTTAGCACTGACAACCAGACG
+>HWI-M00234:263:000000000-ADM55:1:1101:17148:4803 1:N:0:ATCACG
+CCCTTTTCGGCAATGGCGATGTTACGGTACATAAGAGCGATTTCGGGGAAACCTTCTTCG
+TCTGCAATATCAGCAAACTTAGGATAATCCAATGA
+>HWI-M00234:263:000000000-ADM55:1:1101:8939:4808 1:N:0:ATCACG
+CCACAGTTCTGTCATATCGCAGTACAGGAATCTCAACCTGTTGTCCATCGGCTACGGCTC
+TCGCCCTCGCCTTAGGCCCCGACTTACCCAGGGCAGATCAGCTTTA
+>HWI-M00234:263:000000000-ADM55:1:1101:11727:5103 1:N:0:ATCACG
+CTCCCGTATAGGATGGATCGAAAGCAATCGTCAGGAATCCACGTTCTGCCAATGTCTGCG
+CATACAAGCCCGAAGCTTGTTCCTTCACGGCACCAAATGGGCCACTGATGGCAATGGCAG
+GCAATTTACCCGTCACATTCTTGGGTACATACAAATCGGCGGCAAGTGTAATGCCGTAAC
+GGTTGTGGAAAG
+>HWI-M00234:263:000000000-ADM55:1:1101:15029:5173 1:N:0:ATCACG
+GGCCTATTCTCTGCGGCCGCCTTTCGGCGGCACCCCTTCTCCCGAAGTTACGGGGTCATT
+TTGCCGAGTTCCTTAACAATGCTTCTTCCGTCGGCCTTAGGATTCTCTCCTCATCCACCT
+GTGTCGGTTTACGGTACGGGTACAATATAAACAATAGCGGCTTTTCTTGACGGCCGGCTC
+ATGGGCTTCCCTACTTTAGT
+>HWI-M00234:263:000000000-ADM55:1:1101:7330:5248 1:N:0:ATCACG
+TGTGTATGAATGAGCGGCTACAGGCTTAGTCGATTTCTTTACTGCGCAGAAGCGGGACTG
+TGACCGACAAAACAGCCGTCGCCTCTCTACGTTCCGGGACCATACGCCGCTCGCAGTGAT
+TGACCCTTACAACCTTGCGGGCGCTCTC
+>HWI-M00234:263:000000000-ADM55:1:1101:18630:5353 1:N:0:ATCACG
+GGCGTGTTCTGCCAAAATAGTGCTGGGCAATATACGACATAGAAGCGAAAGGCAATACTT
+TTTCTAAGGCCTGCCTGATTTCTACTGTTTTCACAATGGCTTGGGCTTCATTGATTGATT
+GCCTGGCACCATCTTGGAATGCTTGCGCAAACGCTTTTTTATCCTCCGGTGAAAGCGTCT
+GCAGAAAAGCCCTGAAACGTTTTTTATGGTCGGCCACTTCCTCAGGAGTATTG
+>HWI-M00234:263:000000000-ADM55:1:1101:11799:5476 1:N:0:ATCACG
+CCTAAATTTTCGAGTATAAGCAGGACCGAAGCCACCAACTTATACCTTATCCTCTAAATT
+TTCGTAAGAGACATGAAGCGGATCTCTAACTATTCCCGATTTTACTGCACCACTTGATCA
+AACGCTTCGGAACAAGAGCTTTTGAGTGATGTCTCGTTTCCACCACTTTGGCAGAAATAA
+AGCTAATCTACTATGATTCGATTAAGCAGCAAGAGCATAATTTTCGTTGCCAGATAAAAT
+TT
+>HWI-M00234:263:000000000-ADM55:1:1101:11348:5668 1:N:0:ATCACG
+GCCTAAATTTTCGTGCAGCGGCAGAACCAAAGCCATCAACCGTTGCCTTATCCTCTAAAT
+TTTCACCCGCGCCACGAGGCTGACACGAACTATCCCCGATTTGACTGCACCACTTTATCG
+GAATGCTTCGGAGCAACAGCTTCCGAGTGATGTCACGTCCCAGCACCTGGTGCCGGGATT
+AAGCTTCAATCTACTATACTTCGATTAAGCAGCGAGAGCGTAACGAGTTTCGCCAGATAA
+AATTTTGAGGACTGAGATTAAAGTGAAAATC
+>HWI-M00234:263:000000000-ADM55:1:1101:25874:5826 1:N:0:ATCACG
+CCTGCAGTGGATAGGGACCGAACTGTCTCACGACGTTCTGAACCCAGCTCACGTACCTCT
+TTAATGGGCGAACAGCCCAACCCTTGGGACCTTCTCCAGCCCCAGGATGAGATGAGCCGA
+CATCGAGGTGCCAAACTTTCCCGCCGATATGGACGCCCGGGCAAAATCAGCTTGTTATCC
+CCAGGGTAGCTTTTATCCGTTGAGCGACGACCCTTCCATTCGGAATCGCCGGAATACTAT
+GCCCTGCTTTCGCACCTGCCCAACCAGTCCGCCCAGCAGTTAAG
+>HWI-M00234:263:000000000-ADM55:1:1101:26932:5861 1:N:0:ATCACG
+AGCGTCAGTTACAGTCCAGAAAGCCGCCTTCGCCACTGGTGTTCTTCCTAATCTCTACGC
+ATTTCACCGCTACACTAGGAATTCCGCTTTCCTCTCCTGCACTCTAGATATCCAGTTTGG
+AATGCAGCCCCCAGGTTAAGCCCGGGGATTTCACATCCCACTTAAACATCCGCCTACGCA
+CCCTTTACCACCAGTAAATCCGGACAACGCTCGCCACCTACGTATTACCGCGGCTGCTGG
+CACGTAGTTAGCCGTGGCTTCCTCCTCTGGTACCTTCATTATCGTCCCCGAAACC
+>HWI-M00234:263:000000000-ADM55:1:1101:14154:5990 1:N:0:ATCACG
+GTGGGATGTCAAGGTAAGCGGCGGCAGCCTTGGCTACAGCAAGAGATACGCCGAGGATGG
+CATTGGCACCCAGATTGGCTTTCGTTTTGGTTCCGTCCAGTGCAAGCATGGCATGGTCGA
+TACCCATCTGGTCGAGGGCGGACATACCGATGAGCTTGGGAGCAATGATATTATTGATAT
+TGTCCACGGCTTTCAGGAC
+>HWI-M00234:263:000000000-ADM55:1:1101:25022:6229 1:N:0:ATCACG
+CCCGAGAACGTATTCACCGCAACATTGCTGATTTGCGATTACTAGTGATTCCAACTTCAT
+GTACTCGAGTTGCAGAGTACAATCCGAACTACGAACAGCTTTCTGAGGTTTGCTCCTCCT
+CGCAGATTTGCTGATCGGAAGAGCACACGTCTGAACTCCAGTCACATC
+>HWI-M00234:263:000000000-ADM55:1:1101:21023:6286 1:N:0:ATCACG
+GTGTACAAGGCCCGGGAACGTATTCACCGCGCCGTGGCTGATGCGCGATTACTAGCGAAT
+CCAGCTTCATGGAGTCGGGTTGCAGACTCCAATCCGAACTGAGAGAGGCTTTAGGGATTA
+GCATCACGTCGCCGTGTAGCTGCCTTCTGTACCCCCCATTGTAACACGTGTGTAGCCCCG
+GACGTAAGGGCCGTGCTGATTTGCCGTCATCCCCACCTTCCTCAC
+>HWI-M00234:263:000000000-ADM55:1:1101:8138:6336 1:N:0:ATCACG
+TGTGTACAAGGCCCGGGAACGTATTCACCGCGACATTCTGATTCGCGATTACTAGCAACT
+CCAGCTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGAGATAGGTTTTATAAGTTT
+TGCTCCACCTCACGGTCTT
+>HWI-M00234:263:000000000-ADM55:1:1101:11055:6543 1:N:0:ATCACG
+CCTGGACATTTTCGGCGCAGGACCTCCCGACCAGTGAGCTATTACGCACTCTTTGACTGT
+GTGGCTGCTTCTGAGCCAACATCCTGGTTGACTTTGAAATCTCACATACTTTTCCACTTA
+ACACGCACTTTGGGACCTTAGCTGGAGGTCTTGGCTCTTTCCTTTTTGCCTATCCAACTT
+ATCTCGTATAGTCTGACTCCCGG
+>HWI-M00234:263:000000000-ADM55:1:1101:24980:6575 1:N:0:ATCACG
+GCCATTTATCTACGCCTGTTGTCACCAACAGGCTCTAGCGGTCTACCCTCCGACGTGGGG
+CGAGCAACCCTCATA
+>HWI-M00234:263:000000000-ADM55:1:1101:7596:6682 1:N:0:ATCACG
+GCCCCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATACTTA
+ACGCTTTCGCTTGGCGGCTGACAATGTATCGCCAACCGCGAGTATTCATCAGATCGGAAG
+AGCACACGTCTGAACTCCAGTCACATCCCGATCTCGTATGCCGTCCTCGGCTTGAAAAAA
+AAAAATATAAACCATGATGAATTTCGAACACTCACGACCACACACTAAGCGTCGACGTA
+>HWI-M00234:263:000000000-ADM55:1:1101:24419:6736 1:N:0:ATCACG
+CGGGCGTTGGCAAGTACGTTATATCACTTACCCACGCTCGATTCAGAACCCCAGGAGTAA
+ATGCTCGTTTTAAGAGGTTGGGATACACAGGCATGGTGTGATTACTGTCGGTGGTTTTTA
+CGGTTCGCTTAAAAAAGCGGTAACCAATGATGCCATTAAAGCGAAGGATAGCGCGTAAAC
+GTTTGACACCAACTTTCACTCCACGGTGTTGCATCAAAGC
+>HWI-M00234:263:000000000-ADM55:1:1101:5068:6755 1:N:0:ATCACG
+GCAGCGGCAGAACCAAAGCCATCAACCGTTGCCTTATCCTCTAAATTTTCACCCGCGCCA
+CGAGGCTGACACGAACTATCCCCGATTTGACTGCACCACTTTATCGGAATGCTTCGGAGC
+AACAGCTTCCGAGTGATGTCACGTCCCAGCACCTGGTGCCGGGATTAAGCTTCAATCTAC
+TATACTTCGATTAAGCAGCGAGAGCGTAACGAGTTTCGCCAGATAAAATTTTGAGGACTG
+AGATTAAAGTGCAAATC
+>HWI-M00234:263:000000000-ADM55:1:1101:21477:6796 1:N:0:ATCACG
+CCCCACTGCTGCTTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTT
+CCTCTCAGAACCCCTATCCATCGTTGACTAGGTGGGCCGTTACCCCGCCTACTATCTAAT
+GGAACGCATCCCCATCGTCTACCGGAAAATACCTT
+>HWI-M00234:263:000000000-ADM55:1:1101:12483:6880 1:N:0:ATCACG
+CTCCTTGTCTGCCTTCGATTACGGCATTTGCAATCGTTCCTGTAAGTAGTTTTACAGCTC
+TAATGGCATCGTCATTCCCTGGTATTACGTAGTCTATTTCATCAGGATCACAGTTAGTAT
+CAACTATTGCTACAACTGGTATTCCTAATATCTTCGCTTCATTTACTGCAATTCTTTCTT
+TTCTTGGATCTACAACAAATAATACATCAGGAAGACCACCCATATCTTGAATGCCACCTA
+AAAACTTTTCAA
+>HWI-M00234:263:000000000-ADM55:1:1101:27958:6935 1:N:0:ATCACG
+CCATTCGGAAATCCGCGGATCAAAGGTCATTTGCACCTACCCGCAGCTTATCGCAGCTTA
+TCACGTCCTTCATCGCCTCCGAGAGCCAAGAGATCGGAAGAGCACACGTCTGAACTCCAG
+TCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAACCCACAAATTCACACT
+ACACACCCACCTCCCATCACGCATCTCTTTTGTCCGAGTCACGCTGCACGCTACCTGCAC
+ACTACCTGCCTCAGTTACATCTTTTTACTCAATGTCCCACCATTTATCAC
+>HWI-M00234:263:000000000-ADM55:1:1101:6151:7404 1:N:0:ATCACG
+GCACGTAGTTAGCCGGGGCTTCCTCCTAAGGTACCGTCATTATCGTCCCTTAGGACAGAG
+CTTTACGATCCGAAAACCTTCATCGCTCACGCGGCGTCGCTGCATCAGAGTTCCCTCCAT
+TGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTG
+TGGCCGTTCACCCTCCCAGGCCGGCTACCCATCGTCGCCTTGGTTAGCTATTACCTCCCC
+AACTAGCTAATGGGACGCGAGTCCAGCTTATACCACTTAACCGCTTTTGCTTGAAAATCA
diff -r 000000000000 -r 01c2b74b3a21 test-data/information_lenght_fasta_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/information_lenght_fasta_output.txt	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,37 @@
+length
+86
+141
+300
+300
+116
+63
+53
+194
+217
+254
+273
+242
+261
+95
+106
+192
+200
+148
+233
+242
+271
+284
+295
+199
+168
+225
+139
+203
+75
+239
+220
+257
+155
+252
+290
+300
diff -r 000000000000 -r 01c2b74b3a21 test-data/input_sequence_file.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_sequence_file.fasta	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,174 @@
+>HWI-M00234:263:000000000-ADM55:1:1101:21704:2233 1:N:0:ATCACG
+GTGTACAAGGCCCGGGAACGTATTCACCGCGGCATGCTGATCCGCGATTACTAGCGATTC
+CAACTTCATACAGGCGGGTTTCAGCC
+>HWI-M00234:263:000000000-ADM55:1:1101:21334:2699 1:N:0:ATCACG
+CTTTTGACGGCCTTTTTGTTGTCTTCTGAATTTTGTTTTTTTCGGTTGTAACATAATTCC
+TAAAAATCAAATTCGTTAGCGATTATTTTTCTTTCTTTTGAAGTTCTTTCCGCCATTGTT
+TCCGCTATTGCTTCCACGACC
+>HWI-M00234:263:000000000-ADM55:1:1101:13968:2885 1:N:0:ATCACG
+CCCACTGCTGCCTCCCGTAGGAGCCTGGACCGTGTCTCAGTTCCAATGTGGCCGATCACC
+CTCTCAGGTCGGCTACCCATCGTTGCCCTGGTAAGCCATTACCCTACCAACTAGCTAATG
+GGACGCGGGCACATCTCAAAGCGGATTACCCCTTTGGTTAAAGTTTAATGCGAAACTCTA
+ACTTTATGCGTTATTAACCCTCCTTTCGGAGGGCTATTCCCCTCTTTGATGCAGGTTGCC
+CACGTGTTACTCACCCGTCCGCCGCTAATCCACTTCCCGAAGGCAGATTCAACCCTCGAT
+>HWI-M00234:263:000000000-ADM55:1:1101:11873:2948 1:N:0:ATCACG
+CCCCGTTACATCTTCCGCGCAGGAAGACTCGATCAGTGAGCTATTACGCTTTCTTTGAAG
+GATGGCTGCTTCTAAGCCAACTTCCTGACTGTCTTAGCCTTCCCACTTCGTTTTCCACTT
+AGTCAATATTAGGGACCTTAGCCGGCGGTCTGGGTTGTTTCCCTCTTGAGTCCGGACGTT
+AGCACCCGGTGCTCTGTCCCCCGTGCCCAAACTTCCAAGTATTCGGAGTTTGCCATGGTT
+TGGTAAGACGCTATGTCCCCCTAACCATAACAGTGTTCTACCCTCTGAACACATACTCGA
+>HWI-M00234:263:000000000-ADM55:1:1101:7855:3066 1:N:0:ATCACG
+CGTCAATCTTCCAACGCCCACGGCAGATAGGGACAAAACTGTCTCACGACGTTTTAAACC
+CAGCTCACGTACCTCTTTAAATGGCGAACAGCCATACCCTTGGGACCGGCTACAGC
+>HWI-M00234:263:000000000-ADM55:1:1101:24817:3238 1:N:0:ATCACG
+CCCGTGACCAGATTCATGGCCGCCGGTTAGAACCCCAGTACTGTCAGGGTGGTATCCCAA
+GGA
+>HWI-M00234:263:000000000-ADM55:1:1101:17179:3527 1:N:0:ATCACG
+GTGCTTATTTCACTTCCTCAAAATCAGCATCCTGCACATTATCGCCATGCTTT
+>HWI-M00234:263:000000000-ADM55:1:1101:21254:3571 1:N:0:ATCACG
+GTCGCGGGGAAGATCAACTCCTGCAATTCGAGCCATACCAATTACCTCCTAGCGCCCTGA
+CGCTGTTTATGACGAGGATCGCGGCTGCAGATGACGCGAATGACGCCATTGCGCTTGATC
+ACTCGGCAATACTCACAAATGGGTTTAACAGATTATCTAACCTTCATAGTTTGCACACTC
+CTCATGGACATTCC
+>HWI-M00234:263:000000000-ADM55:1:1101:16569:3709 1:N:0:ATCACG
+CCCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGAATACTTATTG
+CGTTTGCTGCGGCACCGAATGGCTTTGCCACCCGACACCTAGTATTCATCGTTTACGGCG
+TGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGGA
+TCGGAAGAGCACACGTCTGAACTCCAGTCACATCCCG
+>HWI-M00234:263:000000000-ADM55:1:1101:22403:3828 1:N:0:ATCACG
+CCCGGACATCTTCGGCGCAGGATCTCTTGACTAGTGAGCTATTACGCACTCTTTAAATGA
+GTGGCTGCTTCTAAGCCAACATCCTAGTTGTCTTAGAAATCCCACATCCTTTTCCACTTA
+ACTTACACTTTGGGACCTTAGCTGATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCA
+CATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAATATCAATCAAACACAC
+ACACACCAGCTTAC
+>HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG
+GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGG
+TCAGCGGTAGCTGCCATAATGTAATGGTAGTCAAATCCTAAGTCTCCCAATGCACATGGC
+AGTGGAGCGTTCCAATCTTGTGTACCGGCTTTGTCTCCTAATCCCAAGTGCCATTTTCCG
+ATAGCTCCGGTAGCATAACCGGTACTTTTGAACATAACCGCCATGGTATATTGTTCGGGA
+CGGATAATCATTCCGGCATTTCCGGCAGCTACG
+>HWI-M00234:263:000000000-ADM55:1:1101:26232:4161 1:N:0:ATCACG
+CTCTTCTTAAGCTCGAACAGCTTCTTCAGTCTTACCTGCCATTTCATCTAAAATTTTTAA
+AGCTCGCTCTAAAACAGTAGTATCATCAATCATAACCAATCCACCATCTGGTCCAGGTTC
+CAAGTGAATCCCAACACTTTTCCCCTCCTTAAAATTGTGTCCACCGAAAAAATTTCTTAC
+AGTGTCAACATTCAGTCCAAGTTCATCGGCTATTCTATGCATACTACCACTAGGCAATGA
+GT
+>HWI-M00234:263:000000000-ADM55:1:1101:23151:4189 1:N:0:ATCACG
+GCGGATTTTCTCGGGAGTATGATTACCCACACTATTGGATTCTTCCGAAGAAGACTCCAT
+ACTACCAAGTTCAGCTCGGATGGTGGATTTGCCTGCCAAGATCAGAAGAGCACACGTCTG
+AACTCCAGTCACATCACGACTTCGTATGCCGTATTCTGCTTGAAAAAAACAATGAAAACT
+AGTCACCGATGACTCACGTTCGCTGAACATTATCTGACAACTAGCTTAACAATGGACATG
+CTTAGCACTGACAACCAGACG
+>HWI-M00234:263:000000000-ADM55:1:1101:17148:4803 1:N:0:ATCACG
+CCCTTTTCGGCAATGGCGATGTTACGGTACATAAGAGCGATTTCGGGGAAACCTTCTTCG
+TCTGCAATATCAGCAAACTTAGGATAATCCAATGA
+>HWI-M00234:263:000000000-ADM55:1:1101:8939:4808 1:N:0:ATCACG
+CCACAGTTCTGTCATATCGCAGTACAGGAATCTCAACCTGTTGTCCATCGGCTACGGCTC
+TCGCCCTCGCCTTAGGCCCCGACTTACCCAGGGCAGATCAGCTTTA
+>HWI-M00234:263:000000000-ADM55:1:1101:11727:5103 1:N:0:ATCACG
+CTCCCGTATAGGATGGATCGAAAGCAATCGTCAGGAATCCACGTTCTGCCAATGTCTGCG
+CATACAAGCCCGAAGCTTGTTCCTTCACGGCACCAAATGGGCCACTGATGGCAATGGCAG
+GCAATTTACCCGTCACATTCTTGGGTACATACAAATCGGCGGCAAGTGTAATGCCGTAAC
+GGTTGTGGAAAG
+>HWI-M00234:263:000000000-ADM55:1:1101:15029:5173 1:N:0:ATCACG
+GGCCTATTCTCTGCGGCCGCCTTTCGGCGGCACCCCTTCTCCCGAAGTTACGGGGTCATT
+TTGCCGAGTTCCTTAACAATGCTTCTTCCGTCGGCCTTAGGATTCTCTCCTCATCCACCT
+GTGTCGGTTTACGGTACGGGTACAATATAAACAATAGCGGCTTTTCTTGACGGCCGGCTC
+ATGGGCTTCCCTACTTTAGT
+>HWI-M00234:263:000000000-ADM55:1:1101:7330:5248 1:N:0:ATCACG
+TGTGTATGAATGAGCGGCTACAGGCTTAGTCGATTTCTTTACTGCGCAGAAGCGGGACTG
+TGACCGACAAAACAGCCGTCGCCTCTCTACGTTCCGGGACCATACGCCGCTCGCAGTGAT
+TGACCCTTACAACCTTGCGGGCGCTCTC
+>HWI-M00234:263:000000000-ADM55:1:1101:18630:5353 1:N:0:ATCACG
+GGCGTGTTCTGCCAAAATAGTGCTGGGCAATATACGACATAGAAGCGAAAGGCAATACTT
+TTTCTAAGGCCTGCCTGATTTCTACTGTTTTCACAATGGCTTGGGCTTCATTGATTGATT
+GCCTGGCACCATCTTGGAATGCTTGCGCAAACGCTTTTTTATCCTCCGGTGAAAGCGTCT
+GCAGAAAAGCCCTGAAACGTTTTTTATGGTCGGCCACTTCCTCAGGAGTATTG
+>HWI-M00234:263:000000000-ADM55:1:1101:11799:5476 1:N:0:ATCACG
+CCTAAATTTTCGAGTATAAGCAGGACCGAAGCCACCAACTTATACCTTATCCTCTAAATT
+TTCGTAAGAGACATGAAGCGGATCTCTAACTATTCCCGATTTTACTGCACCACTTGATCA
+AACGCTTCGGAACAAGAGCTTTTGAGTGATGTCTCGTTTCCACCACTTTGGCAGAAATAA
+AGCTAATCTACTATGATTCGATTAAGCAGCAAGAGCATAATTTTCGTTGCCAGATAAAAT
+TT
+>HWI-M00234:263:000000000-ADM55:1:1101:11348:5668 1:N:0:ATCACG
+GCCTAAATTTTCGTGCAGCGGCAGAACCAAAGCCATCAACCGTTGCCTTATCCTCTAAAT
+TTTCACCCGCGCCACGAGGCTGACACGAACTATCCCCGATTTGACTGCACCACTTTATCG
+GAATGCTTCGGAGCAACAGCTTCCGAGTGATGTCACGTCCCAGCACCTGGTGCCGGGATT
+AAGCTTCAATCTACTATACTTCGATTAAGCAGCGAGAGCGTAACGAGTTTCGCCAGATAA
+AATTTTGAGGACTGAGATTAAAGTGAAAATC
+>HWI-M00234:263:000000000-ADM55:1:1101:25874:5826 1:N:0:ATCACG
+CCTGCAGTGGATAGGGACCGAACTGTCTCACGACGTTCTGAACCCAGCTCACGTACCTCT
+TTAATGGGCGAACAGCCCAACCCTTGGGACCTTCTCCAGCCCCAGGATGAGATGAGCCGA
+CATCGAGGTGCCAAACTTTCCCGCCGATATGGACGCCCGGGCAAAATCAGCTTGTTATCC
+CCAGGGTAGCTTTTATCCGTTGAGCGACGACCCTTCCATTCGGAATCGCCGGAATACTAT
+GCCCTGCTTTCGCACCTGCCCAACCAGTCCGCCCAGCAGTTAAG
+>HWI-M00234:263:000000000-ADM55:1:1101:26932:5861 1:N:0:ATCACG
+AGCGTCAGTTACAGTCCAGAAAGCCGCCTTCGCCACTGGTGTTCTTCCTAATCTCTACGC
+ATTTCACCGCTACACTAGGAATTCCGCTTTCCTCTCCTGCACTCTAGATATCCAGTTTGG
+AATGCAGCCCCCAGGTTAAGCCCGGGGATTTCACATCCCACTTAAACATCCGCCTACGCA
+CCCTTTACCACCAGTAAATCCGGACAACGCTCGCCACCTACGTATTACCGCGGCTGCTGG
+CACGTAGTTAGCCGTGGCTTCCTCCTCTGGTACCTTCATTATCGTCCCCGAAACC
+>HWI-M00234:263:000000000-ADM55:1:1101:14154:5990 1:N:0:ATCACG
+GTGGGATGTCAAGGTAAGCGGCGGCAGCCTTGGCTACAGCAAGAGATACGCCGAGGATGG
+CATTGGCACCCAGATTGGCTTTCGTTTTGGTTCCGTCCAGTGCAAGCATGGCATGGTCGA
+TACCCATCTGGTCGAGGGCGGACATACCGATGAGCTTGGGAGCAATGATATTATTGATAT
+TGTCCACGGCTTTCAGGAC
+>HWI-M00234:263:000000000-ADM55:1:1101:25022:6229 1:N:0:ATCACG
+CCCGAGAACGTATTCACCGCAACATTGCTGATTTGCGATTACTAGTGATTCCAACTTCAT
+GTACTCGAGTTGCAGAGTACAATCCGAACTACGAACAGCTTTCTGAGGTTTGCTCCTCCT
+CGCAGATTTGCTGATCGGAAGAGCACACGTCTGAACTCCAGTCACATC
+>HWI-M00234:263:000000000-ADM55:1:1101:21023:6286 1:N:0:ATCACG
+GTGTACAAGGCCCGGGAACGTATTCACCGCGCCGTGGCTGATGCGCGATTACTAGCGAAT
+CCAGCTTCATGGAGTCGGGTTGCAGACTCCAATCCGAACTGAGAGAGGCTTTAGGGATTA
+GCATCACGTCGCCGTGTAGCTGCCTTCTGTACCCCCCATTGTAACACGTGTGTAGCCCCG
+GACGTAAGGGCCGTGCTGATTTGCCGTCATCCCCACCTTCCTCAC
+>HWI-M00234:263:000000000-ADM55:1:1101:8138:6336 1:N:0:ATCACG
+TGTGTACAAGGCCCGGGAACGTATTCACCGCGACATTCTGATTCGCGATTACTAGCAACT
+CCAGCTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGAGATAGGTTTTATAAGTTT
+TGCTCCACCTCACGGTCTT
+>HWI-M00234:263:000000000-ADM55:1:1101:11055:6543 1:N:0:ATCACG
+CCTGGACATTTTCGGCGCAGGACCTCCCGACCAGTGAGCTATTACGCACTCTTTGACTGT
+GTGGCTGCTTCTGAGCCAACATCCTGGTTGACTTTGAAATCTCACATACTTTTCCACTTA
+ACACGCACTTTGGGACCTTAGCTGGAGGTCTTGGCTCTTTCCTTTTTGCCTATCCAACTT
+ATCTCGTATAGTCTGACTCCCGG
+>HWI-M00234:263:000000000-ADM55:1:1101:24980:6575 1:N:0:ATCACG
+GCCATTTATCTACGCCTGTTGTCACCAACAGGCTCTAGCGGTCTACCCTCCGACGTGGGG
+CGAGCAACCCTCATA
+>HWI-M00234:263:000000000-ADM55:1:1101:7596:6682 1:N:0:ATCACG
+GCCCCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATACTTA
+ACGCTTTCGCTTGGCGGCTGACAATGTATCGCCAACCGCGAGTATTCATCAGATCGGAAG
+AGCACACGTCTGAACTCCAGTCACATCCCGATCTCGTATGCCGTCCTCGGCTTGAAAAAA
+AAAAATATAAACCATGATGAATTTCGAACACTCACGACCACACACTAAGCGTCGACGTA
+>HWI-M00234:263:000000000-ADM55:1:1101:24419:6736 1:N:0:ATCACG
+CGGGCGTTGGCAAGTACGTTATATCACTTACCCACGCTCGATTCAGAACCCCAGGAGTAA
+ATGCTCGTTTTAAGAGGTTGGGATACACAGGCATGGTGTGATTACTGTCGGTGGTTTTTA
+CGGTTCGCTTAAAAAAGCGGTAACCAATGATGCCATTAAAGCGAAGGATAGCGCGTAAAC
+GTTTGACACCAACTTTCACTCCACGGTGTTGCATCAAAGC
+>HWI-M00234:263:000000000-ADM55:1:1101:5068:6755 1:N:0:ATCACG
+GCAGCGGCAGAACCAAAGCCATCAACCGTTGCCTTATCCTCTAAATTTTCACCCGCGCCA
+CGAGGCTGACACGAACTATCCCCGATTTGACTGCACCACTTTATCGGAATGCTTCGGAGC
+AACAGCTTCCGAGTGATGTCACGTCCCAGCACCTGGTGCCGGGATTAAGCTTCAATCTAC
+TATACTTCGATTAAGCAGCGAGAGCGTAACGAGTTTCGCCAGATAAAATTTTGAGGACTG
+AGATTAAAGTGCAAATC
+>HWI-M00234:263:000000000-ADM55:1:1101:21477:6796 1:N:0:ATCACG
+CCCCACTGCTGCTTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTT
+CCTCTCAGAACCCCTATCCATCGTTGACTAGGTGGGCCGTTACCCCGCCTACTATCTAAT
+GGAACGCATCCCCATCGTCTACCGGAAAATACCTT
+>HWI-M00234:263:000000000-ADM55:1:1101:12483:6880 1:N:0:ATCACG
+CTCCTTGTCTGCCTTCGATTACGGCATTTGCAATCGTTCCTGTAAGTAGTTTTACAGCTC
+TAATGGCATCGTCATTCCCTGGTATTACGTAGTCTATTTCATCAGGATCACAGTTAGTAT
+CAACTATTGCTACAACTGGTATTCCTAATATCTTCGCTTCATTTACTGCAATTCTTTCTT
+TTCTTGGATCTACAACAAATAATACATCAGGAAGACCACCCATATCTTGAATGCCACCTA
+AAAACTTTTCAA
+>HWI-M00234:263:000000000-ADM55:1:1101:27958:6935 1:N:0:ATCACG
+CCATTCGGAAATCCGCGGATCAAAGGTCATTTGCACCTACCCGCAGCTTATCGCAGCTTA
+TCACGTCCTTCATCGCCTCCGAGAGCCAAGAGATCGGAAGAGCACACGTCTGAACTCCAG
+TCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAACCCACAAATTCACACT
+ACACACCCACCTCCCATCACGCATCTCTTTTGTCCGAGTCACGCTGCACGCTACCTGCAC
+ACTACCTGCCTCAGTTACATCTTTTTACTCAATGTCCCACCATTTATCAC
+>HWI-M00234:263:000000000-ADM55:1:1101:6151:7404 1:N:0:ATCACG
+GCACGTAGTTAGCCGGGGCTTCCTCCTAAGGTACCGTCATTATCGTCCCTTAGGACAGAG
+CTTTACGATCCGAAAACCTTCATCGCTCACGCGGCGTCGCTGCATCAGAGTTCCCTCCAT
+TGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTG
+TGGCCGTTCACCCTCCCAGGCCGGCTACCCATCGTCGCCTTGGTTAGCTATTACCTCCCC
+AACTAGCTAATGGGACGCGAGTCCAGCTTATACCACTTAACCGCTTTTGCTTGAAAATCA
diff -r 000000000000 -r 01c2b74b3a21 test-data/input_sequence_file.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input_sequence_file.fastq	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,144 @@
+@HWI-M00234:263:000000000-ADM55:1:1101:21704:2233 1:N:0:ATCACG
+GTGTACAAGGCCCGGGAACGTATTCACCGCGGCATGCTGATCCGCGATTACTAGCGATTCCAACTTCATACAGGCGGGTTTCAGCC
++
+BCCCCGGED8DFGC::+@C@9@,,EGFAF@CC7@@@FGAF<@FGGEGD7:<6EDDECCFGGCFGGC<66,F<FFCGFC4BFF?5?<
+@HWI-M00234:263:000000000-ADM55:1:1101:21334:2699 1:N:0:ATCACG
+CTTTTGACGGCCTTTTTGTTGTCTTCTGAATTTTGTTTTTTTCGGTTGTAACATAATTCCTAAAAATCAAATTCGTTAGCGATTATTTTTCTTTCTTTTGAAGTTCTTTCCGCCATTGTTTCCGCTATTGCTTCCACGACC
++
+CCCCCGFGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGG@FGGGGGGGGEADGGGGGGGGGGGGGFGGGGFF@CFFEGGDGGGGGFGGGGGGGGFGFCFGGGGGFGCE=FGFDGFGGCEEGGGGDFGGGFGGGGGC
+@HWI-M00234:263:000000000-ADM55:1:1101:13968:2885 1:N:0:ATCACG
+CCCACTGCTGCCTCCCGTAGGAGCCTGGACCGTGTCTCAGTTCCAATGTGGCCGATCACCCTCTCAGGTCGGCTACCCATCGTTGCCCTGGTAAGCCATTACCCTACCAACTAGCTAATGGGACGCGGGCACATCTCAAAGCGGATTACCCCTTTGGTTAAAGTTTAATGCGAAACTCTAACTTTATGCGTTATTAACCCTCCTTTCGGAGGGCTATTCCCCTCTTTGATGCAGGTTGCCCACGTGTTACTCACCCGTCCGCCGCTAATCCACTTCCCGAAGGCAGATTCAACCCTCGAT
++
+<CC8CEFDGGFDF<,6@F7FCGF,:FFCED@@@,;;,<CFFFA,6C@FC@,<E+87FFCFCGFF8,<<FG7+@F7FEFFGGGCFECF,=<B=EF99F@9<FAFFGDF?=E:=4:,9,,CF9A4,>8>C+>3BFGD;@,7>,==>6?=9,,@+@4<=699C9,@+@<+72;@5;0*9:?82BF85=@2=C###############################################################################################################
+@HWI-M00234:263:000000000-ADM55:1:1101:11873:2948 1:N:0:ATCACG
+CCCCGTTACATCTTCCGCGCAGGAAGACTCGATCAGTGAGCTATTACGCTTTCTTTGAAGGATGGCTGCTTCTAAGCCAACTTCCTGACTGTCTTAGCCTTCCCACTTCGTTTTCCACTTAGTCAATATTAGGGACCTTAGCCGGCGGTCTGGGTTGTTTCCCTCTTGAGTCCGGACGTTAGCACCCGGTGCTCTGTCCCCCGTGCCCAAACTTCCAAGTATTCGGAGTTTGCCATGGTTTGGTAAGACGCTATGTCCCCCTAACCATAACAGTGTTCTACCCTCTGAACACATACTCGA
++
+CCCCCCD;B6C,;<EAFECF@FGGGGAECEG@F@FGGGFAAF9FGGCF>F7<FCFF<6FEFFFCDCFGGGEC<F,<A<EFC@F9BFGE<9DFFGEEGG@FFGFFGF8FDEFC<F,94:EF9,C=EGGGCCFCCE>B+>E9FCGG6+@CC>EFC8D>CEF,E=@=E?C,6=AFG>>9?DCGC>FG>GGCDA5*;+=AFF*A;/?B)-)(;64:)>3<E<3))7<E3=;>FDF?E<<4)3;EF@FFA#######################################################
+@HWI-M00234:263:000000000-ADM55:1:1101:7855:3066 1:N:0:ATCACG
+CGTCAATCTTCCAACGCCCACGGCAGATAGGGACAAAACTGTCTCACGACGTTTTAAACCCAGCTCACGTACCTCTTTAAATGGCGAACAGCCATACCCTTGGGACCGGCTACAGC
++
+CCCCCGGGGGGGGFGGGCBCFGGGGGFGGGGGGGGGGGGGGGG,CEGGGGGGGGGGGGGG@F@FGGGGGGGG@@EGFGGGFGFGCGEGGGGGGGGGGCFGGGGEGEEE7FFGFFGD
+@HWI-M00234:263:000000000-ADM55:1:1101:24817:3238 1:N:0:ATCACG
+CCCGTGACCAGATTCATGGCCGCCGGTTAGAACCCCAGTACTGTCAGGGTGGTATCCCAAGGA
++
+CCCCC7FGFGEGGGGGGDFGGGGGGDGGGGGGGGGGGGGGGGGGGGGFEECGGGGGGFFGGGG
+@HWI-M00234:263:000000000-ADM55:1:1101:17179:3527 1:N:0:ATCACG
+GTGCTTATTTCACTTCCTCAAAATCAGCATCCTGCACATTATCGCCATGCTTT
++
+CCCCCG<FCCGGFGGFGGGGGGGGFGGGGGGDEG?<ECGCFEG<EGGGF,CFG
+@HWI-M00234:263:000000000-ADM55:1:1101:21254:3571 1:N:0:ATCACG
+GTCGCGGGGAAGATCAACTCCTGCAATTCGAGCCATACCAATTACCTCCTAGCGCCCTGACGCTGTTTATGACGAGGATCGCGGCTGCAGATGACGCGAATGACGCCATTGCGCTTGATCACTCGGCAATACTCACAAATGGGTTTAACAGATTATCTAACCTTCATAGTTTGCACACTCCTCATGGACATTCC
++
+CCCCCFEFGGGGGGGGGGGGGGGGGGGGGGGGGGGG<FCCGGFFGGDFGGGFGGCGG7FGGGGGCGGAFFEEGC:FGGGGGGGGGDFGGFAGFGGGG7FEGGGGGGE7FGGG>EGGGFFFCFGGFCEEGGFGCGGGFGFDGFFGGCFGGG7C;,5=EF,CG59DCCG@,5CFFFG=FC*CFFGGGDFGGAFFFF
+@HWI-M00234:263:000000000-ADM55:1:1101:16569:3709 1:N:0:ATCACG
+CCCGTCAATTCCTTTGAGTTTCATTCTTGCGAACGTACTCCCCAGGTGGAATACTTATTGCGTTTGCTGCGGCACCGAATGGCTTTGCCACCCGACACCTAGTATTCATCGTTTACGGCGTGGACTACCAGGGTATCTAATCCTGTTTGCTCCCCACGCTTTCGAGCCTCAACGTCAGGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCCCG
++
+CCCCCGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGG9FGGGGDGGGGGGGECGGGGGEGCGGGGGGGDGGGFGGGGGFGGGGGGFGGGGGGGGGGGACFGGGFGGGGGFGGGGGCFGGGGGGFFFFFFEF:65CFFF8FEF7AFEFEE(,6
+@HWI-M00234:263:000000000-ADM55:1:1101:22403:3828 1:N:0:ATCACG
+CCCGGACATCTTCGGCGCAGGATCTCTTGACTAGTGAGCTATTACGCACTCTTTAAATGAGTGGCTGCTTCTAAGCCAACATCCTAGTTGTCTTAGAAATCCCACATCCTTTTCCACTTAACTTACACTTTGGGACCTTAGCTGATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAATATCAATCAAACACACACACACCAGCTTAC
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGEGGGGGGGGFGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGCGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG>DGGGGGGGGFDFFEDGGGCEEECGGGFGGGGGGFGGGGGGGFFFDGGGGFFGGG=D?DFFFF?CFFF5*:<EFE>+*3886=AAA@##################################
+@HWI-M00234:263:000000000-ADM55:1:1101:7508:4067 1:N:0:ATCACG
+GGTGCACTAGGATCGTAGTTGGCTACTTTCCCGTTTTCAATGTATACGCAAGGTACACGGTCAGCGGTAGCTGCCATAATGTAATGGTAGTCAAATCCTAAGTCTCCCAATGCACATGGCAGTGGAGCGTTCCAATCTTGTGTACCGGCTTTGTCTCCTAATCCCAAGTGCCATTTTCCGATAGCTCCGGTAGCATAACCGGTACTTTTGAACATAACCGCCATGGTATATTGTTCGGGACGGATAATCATTCCGGCATTTCCGGCAGCTACG
++
+CCCCCGFGGF8FFECFFCGE9FFGGGG9CFAFFCC@@CFGFGGCGFGGGGGGFFGDGEFFEFG8FGGF@@FGCFGGCA@FCFFCFGGGGFFGFF9??FFFFGGGGGFFF=FGGGDEF:F8,4@ACEE8CCEEGGGCCFG9FFFAFG6CGGEGE,=3EGC2;=EFFFGFGFGG9@9EGGGGC>8=DCFGGDFEFF+=7<AFFE>>5AAEF8AFE589*)849>524=;8*198?CE?9>59@>6(66@C<.))/5;>(13=EFE60(334:AB?
+@HWI-M00234:263:000000000-ADM55:1:1101:26232:4161 1:N:0:ATCACG
+CTCTTCTTAAGCTCGAACAGCTTCTTCAGTCTTACCTGCCATTTCATCTAAAATTTTTAAAGCTCGCTCTAAAACAGTAGTATCATCAATCATAACCAATCCACCATCTGGTCCAGGTTCCAAGTGAATCCCAACACTTTTCCCCTCCTTAAAATTGTGTCCACCGAAAAAATTTCTTACAGTGTCAACATTCAGTCCAAGTTCATCGGCTATTCTATGCATACTACCACTAGGCAATGAGT
++
+CCCCCGGFGFFFGGGGGGCFGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGGFGEGFGGGGFGFGFGGGFAFDGCFGGGGFGGGFGCGFGGGGCGGGFGGGG:FFGGF@F9FGGGGGFGGGGGGCEGGC?FGGGGGGGFGGDFFGF8DFGGCGGGGCDFGGGGGGGGDFGGCFGFDF7;EFFFFFFFB<FDFFAEDFFFFFF@CEFCCEEFFFFFBEFE@8=@657>
+@HWI-M00234:263:000000000-ADM55:1:1101:23151:4189 1:N:0:ATCACG
+GCGGATTTTCTCGGGAGTATGATTACCCACACTATTGGATTCTTCCGAAGAAGACTCCATACTACCAAGTTCAGCTCGGATGGTGGATTTGCCTGCCAAGATCAGAAGAGCACACGTCTGAACTCCAGTCACATCACGACTTCGTATGCCGTATTCTGCTTGAAAAAAACAATGAAAACTAGTCACCGATGACTCACGTTCGCTGAACATTATCTGACAACTAGCTTAACAATGGACATGCTTAGCACTGACAACCAGACG
++
+CCC8AF,6,FGGCFEEBFGCAFGGGFGGF7FB8,CF,<,;,CEE<,@,8+,,6,,,CFFGGGGG,F<EA@F,B<F6@FC6@CBE9F7F,5:F9AF84A,ABFF,=A,A,4,4AEFEGGGGGD8=EC,,4,C;EF9,9=+4++,+4=8DGG6@#############################################################################################################
+@HWI-M00234:263:000000000-ADM55:1:1101:17148:4803 1:N:0:ATCACG
+CCCTTTTCGGCAATGGCGATGTTACGGTACATAAGAGCGATTTCGGGGAAACCTTCTTCGTCTGCAATATCAGCAAACTTAGGATAATCCAATGA
++
+AACBCDFA@@:+:CCEF7@CC@@AFFDGD;FDA@@6E@FF<,CC;@@+7@FG@F<CCFF@F@F@,<,B@F,CDG<@FEF<@,@,CAF9E<FD<??
+@HWI-M00234:263:000000000-ADM55:1:1101:8939:4808 1:N:0:ATCACG
+CCACAGTTCTGTCATATCGCAGTACAGGAATCTCAACCTGTTGTCCATCGGCTACGGCTCTCGCCCTCGCCTTAGGCCCCGACTTACCCAGGGCAGATCAGCTTTA
++
+CC8C9C6<EFGFEEGGGGGGGDECGFDE@FFAFGFGFGGGGGGGGFGFEE@FFGFEGGCFECDGCCFGC+6@B@@FFG,8F@FFGGGGFEDFCF@FFFGGDFFDFF
+@HWI-M00234:263:000000000-ADM55:1:1101:11727:5103 1:N:0:ATCACG
+CTCCCGTATAGGATGGATCGAAAGCAATCGTCAGGAATCCACGTTCTGCCAATGTCTGCGCATACAAGCCCGAAGCTTGTTCCTTCACGGCACCAAATGGGCCACTGATGGCAATGGCAGGCAATTTACCCGTCACATTCTTGGGTACATACAAATCGGCGGCAAGTGTAATGCCGTAACGGTTGTGGAAAG
++
+CCCCCGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGFGGFDF@GGDGGGGGGGGG4*;CFFF
+@HWI-M00234:263:000000000-ADM55:1:1101:15029:5173 1:N:0:ATCACG
+GGCCTATTCTCTGCGGCCGCCTTTCGGCGGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTAACAATGCTTCTTCCGTCGGCCTTAGGATTCTCTCCTCATCCACCTGTGTCGGTTTACGGTACGGGTACAATATAAACAATAGCGGCTTTTCTTGACGGCCGGCTCATGGGCTTCCCTACTTTAGT
++
+CCCCCGGGGGGGGGGGGGGGGGGGGEGG7FECGFGGGGGEGGGGGEEGGGGGGGGGGGGGGGFGGGGGGGGGGGGFGGGCGGGGGGGGGGGGGGGFFGGGGGGGGGGFFG9FCGGGFGGGGGFFFDGGEECGGGGGGGGGGGGGGGGGGGGECGGGGGD>CCG>=98E79=CDDDD4D5DGF=FGGGDGFFFFFFFF6AC
+@HWI-M00234:263:000000000-ADM55:1:1101:7330:5248 1:N:0:ATCACG
+TGTGTATGAATGAGCGGCTACAGGCTTAGTCGATTTCTTTACTGCGCAGAAGCGGGACTGTGACCGACAAAACAGCCGTCGCCTCTCTACGTTCCGGGACCATACGCCGCTCGCAGTGATTGACCCTTACAACCTTGCGGGCGCTCTC
++
+CCCCCGEGGGGGGFGGGGGEGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGFFGGGGDEGGGGGFGGGGGGGGGGECGGGGEFGDGAFGGGGGGFFG>GGECFFGCF+@CC@FGG++@FFFF,>F,DFFGGFFGCGEFG6CEG54*=@D
+@HWI-M00234:263:000000000-ADM55:1:1101:18630:5353 1:N:0:ATCACG
+GGCGTGTTCTGCCAAAATAGTGCTGGGCAATATACGACATAGAAGCGAAAGGCAATACTTTTTCTAAGGCCTGCCTGATTTCTACTGTTTTCACAATGGCTTGGGCTTCATTGATTGATTGCCTGGCACCATCTTGGAATGCTTGCGCAAACGCTTTTTTATCCTCCGGTGAAAGCGTCTGCAGAAAAGCCCTGAAACGTTTTTTATGGTCGGCCACTTCCTCAGGAGTATTG
++
+CCCCCGGGGGGGGGCGGGGGGGGGGFGGFGFGGGGGGGEGGGGGGGGGGGGGDECDFGGGGGGGGGGFGGGGDGGGGGGGGGGGGFFFGGGGGGGGGGGGGGGGGD8<FGGGFGGGGGGGFAEGGFGC,8EFGGGGFDC9DG9E9DCEE>EGGDGGFGGGGFG?FCFDED6F6DG6C6==DD7=D=D6DFF?F**3;9@?699CDBFF5FEB>>D>:@00>=C*8:;25;59*
+@HWI-M00234:263:000000000-ADM55:1:1101:11799:5476 1:N:0:ATCACG
+CCTAAATTTTCGAGTATAAGCAGGACCGAAGCCACCAACTTATACCTTATCCTCTAAATTTTCGTAAGAGACATGAAGCGGATCTCTAACTATTCCCGATTTTACTGCACCACTTGATCAAACGCTTCGGAACAAGAGCTTTTGAGTGATGTCTCGTTTCCACCACTTTGGCAGAAATAAAGCTAATCTACTATGATTCGATTAAGCAGCAAGAGCATAATTTTCGTTGCCAGATAAAATTT
++
+CCCC<FFFGGF@FFFGFFGCGCCFGGGEFGGD;CFFGFGGGGGGCFF@FFGGC<EEGGGCEFGGGF@E@@,BFFGFGGGGG7+@AFEAEFFGGGGGGGFFEGGFGGGCEGEFDGFGGFGG:=>@EC@@77@E>4DEC8C>DGGG>FGGGGF=DAECDDFDEG8==++=,6=FGDGFGGGGGGGGGGFFGFFFFFFFFFFDFFADFFFEAF@F@C5@EEF5=E;EE4477AFBEFBF;*A4>C
+@HWI-M00234:263:000000000-ADM55:1:1101:11348:5668 1:N:0:ATCACG
+GCCTAAATTTTCGTGCAGCGGCAGAACCAAAGCCATCAACCGTTGCCTTATCCTCTAAATTTTCACCCGCGCCACGAGGCTGACACGAACTATCCCCGATTTGACTGCACCACTTTATCGGAATGCTTCGGAGCAACAGCTTCCGAGTGATGTCACGTCCCAGCACCTGGTGCCGGGATTAAGCTTCAATCTACTATACTTCGATTAAGCAGCGAGAGCGTAACGAGTTTCGCCAGATAAAATTTTGAGGACTGAGATTAAAGTGAAAATC
++
+CCCCCGGGGGGGGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCFGFGGGGGDGGCGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGFGGGGGGDGGGGGGGGGDGGG6>E9CCGGGGGGGGGGGGGGGGGGFGFGFFFFFFFFFFFFFFAFFFFFFFFFFFB199@F=9@DF@?;@FDFFFFFF>274A>B<?FABFF7?F???FB94:<<F26)-69>0
+@HWI-M00234:263:000000000-ADM55:1:1101:25874:5826 1:N:0:ATCACG
+CCTGCAGTGGATAGGGACCGAACTGTCTCACGACGTTCTGAACCCAGCTCACGTACCTCTTTAATGGGCGAACAGCCCAACCCTTGGGACCTTCTCCAGCCCCAGGATGAGATGAGCCGACATCGAGGTGCCAAACTTTCCCGCCGATATGGACGCCCGGGCAAAATCAGCTTGTTATCCCCAGGGTAGCTTTTATCCGTTGAGCGACGACCCTTCCATTCGGAATCGCCGGAATACTATGCCCTGCTTTCGCACCTGCCCAACCAGTCCGCCCAGCAGTTAAG
++
+CCCCCDFGGGG<@F,CE<FGGEGDDFG9EEEF7CGFGGG9<E@D@@EC,@FFFEGGG,C<9C<FGGFGF+@CGEECGEFFGGGG<F<A,,4?F?,?5EDF,,=BEF+,A<A,C,,AE84+F=+F>FFGGFFGD8D>DE,,373++++++6,,3@+++@9*@9>5@C*<::7,*0;CC7+:*39CF*045?8AC=A:BB:5)05/;6:6)86::8@F####################################################################
+@HWI-M00234:263:000000000-ADM55:1:1101:26932:5861 1:N:0:ATCACG
+AGCGTCAGTTACAGTCCAGAAAGCCGCCTTCGCCACTGGTGTTCTTCCTAATCTCTACGCATTTCACCGCTACACTAGGAATTCCGCTTTCCTCTCCTGCACTCTAGATATCCAGTTTGGAATGCAGCCCCCAGGTTAAGCCCGGGGATTTCACATCCCACTTAAACATCCGCCTACGCACCCTTTACCACCAGTAAATCCGGACAACGCTCGCCACCTACGTATTACCGCGGCTGCTGGCACGTAGTTAGCCGTGGCTTCCTCCTCTGGTACCTTCATTATCGTCCCCGAAACC
++
+96BCCFGGEGGGFGGGGG?EFFGGGGGCFG9FDFGGFG8FGGCFGGGGGGGGGFDGGDFEBFGFFGGGGGEEEFGGG<FFFCFCFFGDCFGFGG<8FGEFGGGCCFFAEGGFFGFFFFGG8EEFCEGG@EDEGGFGFFFFGGFCBEE8CF8=CFFAF,=D8F8FGG+@DC86?=CGFDGC9D6FC:FC*+;9*331?+=;ABB49>FDEB=45@@FFFBFF;8@E@FC)/6690(-1)),82?B??B################################################
+@HWI-M00234:263:000000000-ADM55:1:1101:14154:5990 1:N:0:ATCACG
+GTGGGATGTCAAGGTAAGCGGCGGCAGCCTTGGCTACAGCAAGAGATACGCCGAGGATGGCATTGGCACCCAGATTGGCTTTCGTTTTGGTTCCGTCCAGTGCAAGCATGGCATGGTCGATACCCATCTGGTCGAGGGCGGACATACCGATGAGCTTGGGAGCAATGATATTATTGATATTGTCCACGGCTTTCAGGAC
++
+CCCCCGGC<F9DE@EG9FF@@FGFGGFEFGF@E@FAFGGGFGFEE8FFEGGGGD>>=F8FG8?EEDFGGGGGG<FFD?FF@FFGE8F=,>FFEBCEFGGGFGGGGGGCEG8D?FFGGEGGFFEGEE8FFGGGG8++>8E>E5@BDA?FGGGGGGCFF6E==57??86ECFCF@CCCCBFCGDGGGG=*>3)868:7=FF
+@HWI-M00234:263:000000000-ADM55:1:1101:25022:6229 1:N:0:ATCACG
+CCCGAGAACGTATTCACCGCAACATTGCTGATTTGCGATTACTAGTGATTCCAACTTCATGTACTCGAGTTGCAGAGTACAATCCGAACTACGAACAGCTTTCTGAGGTTTGCTCCTCCTCGCAGATTTGCTGATCGGAAGAGCACACGTCTGAACTCCAGTCACATC
++
+CCCCCGGGGGGFGGGFGGGGEGGCFGFGGAEGGGDGGEGGGFGFFGG9FFGEFGGGGGGGGGAEGGG8FFGGG?EFGGGGCFGGGCCFGFFGCFGGGCGGGGGG9EF,EGGCFFGFFGGEEGGGDEGGGAFGGGCEFEEBE8EDFGGGGGGGGCGGGGGGGGFGCFDD
+@HWI-M00234:263:000000000-ADM55:1:1101:21023:6286 1:N:0:ATCACG
+GTGTACAAGGCCCGGGAACGTATTCACCGCGCCGTGGCTGATGCGCGATTACTAGCGAATCCAGCTTCATGGAGTCGGGTTGCAGACTCCAATCCGAACTGAGAGAGGCTTTAGGGATTAGCATCACGTCGCCGTGTAGCTGCCTTCTGTACCCCCCATTGTAACACGTGTGTAGCCCCGGACGTAAGGGCCGTGCTGATTTGCCGTCATCCCCACCTTCCTCAC
++
+CCCCCGGGCFFGGDEGGGGGGFGGGGGGGGGGGGGEGGGGGFEGGGGGGGDFFG9FCGGGGGGGGGGGFFFGGGGGEGCFGDGGGAG8EF<FFGGGGGGGFGGCDGDEGFGGGGGGGFGF?GGDFDFGDDEGD+B=DFFFD9DGFGGGGGEGCFCEGEGGGGFCF>FGGCGGGGCGGFDDG<55CF4CFF;5555>FFFFFA6+0(2,08)00(36,,)5:AB2:
+@HWI-M00234:263:000000000-ADM55:1:1101:8138:6336 1:N:0:ATCACG
+TGTGTACAAGGCCCGGGAACGTATTCACCGCGACATTCTGATTCGCGATTACTAGCAACTCCAGCTTCATGTAGGCGAGTTGCAGCCTACAATCCGAACTGAGATAGGTTTTATAAGTTTTGCTCCACCTCACGGTCTT
++
+CCCCCGGGF<FGGGGED@FGGGFGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCGFGGGCGGGGGGGGGGGGGFGGFEGGGGDGGEFCCGEFFGGGGAFGGGGGFGFFFGGFGGFGDFGGGGGG
+@HWI-M00234:263:000000000-ADM55:1:1101:11055:6543 1:N:0:ATCACG
+CCTGGACATTTTCGGCGCAGGACCTCCCGACCAGTGAGCTATTACGCACTCTTTGACTGTGTGGCTGCTTCTGAGCCAACATCCTGGTTGACTTTGAAATCTCACATACTTTTCCACTTAACACGCACTTTGGGACCTTAGCTGGAGGTCTTGGCTCTTTCCTTTTTGCCTATCCAACTTATCTCGTATAGTCTGACTCCCGG
++
+@B,8BF8EFGFGG77@7+8@@6,FFF<,+@C+6FF99@A@EC,CC,BFFDFGA<@D,C9F@CF7,B7CFGG,C@,B@<F?7FF8<,:,C@,?<EE,C?A,E,ACEFG9,C;@,,A;EEA,,?E9884B8=,9,4,@+7>@,B;=,66+@D,,@,3=EF=:@F,C=886,+6@D8D+6+0==C9+6+5+0;+1+3BC1<A?9>9
+@HWI-M00234:263:000000000-ADM55:1:1101:24980:6575 1:N:0:ATCACG
+GCCATTTATCTACGCCTGTTGTCACCAACAGGCTCTAGCGGTCTACCCTCCGACGTGGGGCGAGCAACCCTCATA
++
+CCCCCGGGGGFGGGGGGGGGGGFGGGGGGGG@G<FFFGGGEEGGGGGGFGGCECFGGGGGD:@FGGGGG7ADGGG
+@HWI-M00234:263:000000000-ADM55:1:1101:7596:6682 1:N:0:ATCACG
+GCCCCCGTCAATTCCTTTGAGTTTCACCGTTGCCGGCGTACTCCCCAGGTGGAATACTTAACGCTTTCGCTTGGCGGCTGACAATGTATCGCCAACCGCGAGTATTCATCAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCCCGATCTCGTATGCCGTCCTCGGCTTGAAAAAAAAAAATATAAACCATGATGAATTTCGAACACTCACGACCACACACTAAGCGTCGACGTA
++
+CCCCCGGGGGGACFGGGGGFFEEGGGGGGFFEGGGGGGGGGGEGFGGGGEFG@FGDFFGGGGGGGEGGGDGFFCC>FGCDFGFGGGCE,E:FCCCC7CGGGGGGFE;FFEFCCGFGG@CEFGGGG@F@>@8DGGG=;@FFFGGC;E6,@@+4:,318;9,@FG@###########################################################################
+@HWI-M00234:263:000000000-ADM55:1:1101:24419:6736 1:N:0:ATCACG
+CGGGCGTTGGCAAGTACGTTATATCACTTACCCACGCTCGATTCAGAACCCCAGGAGTAAATGCTCGTTTTAAGAGGTTGGGATACACAGGCATGGTGTGATTACTGTCGGTGGTTTTTACGGTTCGCTTAAAAAAGCGGTAACCAATGATGCCATTAAAGCGAAGGATAGCGCGTAAACGTTTGACACCAACTTTCACTCCACGGTGTTGCATCAAAGC
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGFGGGGGGGDGGGGGGGGGGGGGGGGDFGGGGGGGGGGGGGGGGGGGGGGGGFGGGFGGGGGGGGD9FFCFEGGGFGGGGG7=+4>@EFEEFFG7>EEDEEEFDDDG@8DCFEFDFGGC8=CDCGGFGGDC6>DDGDCFDGDGDGFGG@AFBA?FFFFFFFFABBF95B@AFFFFFFFF
+@HWI-M00234:263:000000000-ADM55:1:1101:5068:6755 1:N:0:ATCACG
+GCAGCGGCAGAACCAAAGCCATCAACCGTTGCCTTATCCTCTAAATTTTCACCCGCGCCACGAGGCTGACACGAACTATCCCCGATTTGACTGCACCACTTTATCGGAATGCTTCGGAGCAACAGCTTCCGAGTGATGTCACGTCCCAGCACCTGGTGCCGGGATTAAGCTTCAATCTACTATACTTCGATTAAGCAGCGAGAGCGTAACGAGTTTCGCCAGATAAAATTTTGAGGACTGAGATTAAAGTGCAAATC
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDFF?FGGGGGDFGGGGGGGGGGFFFFGGGGGFGGFGGGGGGDGGGGGGGFGGGEEDGGG9C9EEGGGGGD8@FGGGGGGGGGGGGG>CFGGGGGCFGDGDFGFGGF7CFGDF>FFFAF=;A>EDDBFBBFFF@D@D<E?@F01;@<?C<471.2)48<??2(549<B>FDF24)66<))
+@HWI-M00234:263:000000000-ADM55:1:1101:21477:6796 1:N:0:ATCACG
+CCCCACTGCTGCTTCCCGTAGGAGTTTGGACCGTGTCTCAGTTCCAATGTGGGGGACCTTCCTCTCAGAACCCCTATCCATCGTTGACTAGGTGGGCCGTTACCCCGCCTACTATCTAATGGAACGCATCCCCATCGTCTACCGGAAAATACCTT
++
+CC,AC:F8<F@CCEDGGCEGGGGGFAG<FGG8@FEFEFFCEGGCFF<<<F@<C+@FF:AFCEFE,ECF9AFGC@DE<FE,,5@9B8BFFCE8F,=FF@CG7FCFGD:FFF7EAFDG9F;FFF@:FEEG@4=@DEFG6=EGCADC6@ECCA,@DDF
+@HWI-M00234:263:000000000-ADM55:1:1101:12483:6880 1:N:0:ATCACG
+CTCCTTGTCTGCCTTCGATTACGGCATTTGCAATCGTTCCTGTAAGTAGTTTTACAGCTCTAATGGCATCGTCATTCCCTGGTATTACGTAGTCTATTTCATCAGGATCACAGTTAGTATCAACTATTGCTACAACTGGTATTCCTAATATCTTCGCTTCATTTACTGCAATTCTTTCTTTTCTTGGATCTACAACAAATAATACATCAGGAAGACCACCCATATCTTGAATGCCACCTAAAAACTTTTCAA
++
+CCCCCGGGGGGGFGGFGGGGGFGDFEGGGGGFFFGGFGGGGGGGGFGGGFGGGGGGGGCEGGGGCFGGGGGGGGGGGGFGGGFEGGDGGGGFFFGGGGGGGGFGGGGGGGGGGFGFGCF@FEFFGDAGFGFGGGGFGGGGDGGGFFGGGD;EEFGGGGGGGFGGGGGGGGGGFDGDGGGGGGGGGGGDGFFFFFFF9;;DFFFFFBFFBDBFFBFD=DDFDFFFEFEFEFEECE<@E@CFF@EBAFFEEEFF
+@HWI-M00234:263:000000000-ADM55:1:1101:27958:6935 1:N:0:ATCACG
+CCATTCGGAAATCCGCGGATCAAAGGTCATTTGCACCTACCCGCAGCTTATCGCAGCTTATCACGTCCTTCATCGCCTCCGAGAGCCAAGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAACCCACAAATTCACACTACACACCCACCTCCCATCACGCATCTCTTTTGTCCGAGTCACGCTGCACGCTACCTGCACACTACCTGCCTCAGTTACATCTTTTTACTCAATGTCCCACCATTTATCAC
++
+CCCCCGGGGGGGGGGGDGGCFGGGGGGGFEGGGGGGGGGGGGGGGGGGGGGGGGGGG8DC<FGGGFFGGGGGGGGGGCGF:FDGGGGGG@FEEEGGGEGDGGGFGGGGGG:FFGG=EGFFFCEFG9EEFGD+@@EEDED8DA>EEC@EFGFAFFGF=F?+44;C##############################################################################################################################
+@HWI-M00234:263:000000000-ADM55:1:1101:6151:7404 1:N:0:ATCACG
+GCACGTAGTTAGCCGGGGCTTCCTCCTAAGGTACCGTCATTATCGTCCCTTAGGACAGAGCTTTACGATCCGAAAACCTTCATCGCTCACGCGGCGTCGCTGCATCAGAGTTCCCTCCATTGTGCAATATTCCCCACTGCTGCCTCCCGTAGGAGTCTGGACCGTGTCTCAGTTCCAGTGTGGCCGTTCACCCTCCCAGGCCGGCTACCCATCGTCGCCTTGGTTAGCTATTACCTCCCCAACTAGCTAATGGGACGCGAGTCCAGCTTATACCACTTAACCGCTTTTGCTTGAAAATCA
++
+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGFGGGGGGGGGGFGGGGGGGGGGGGGGGGGGDF8FGGGFGGGGEGGG7+CGGFGGGGGGGGC:8FGGGDFGFEGGGFGGGFGCGGGGGGGGDG?EGGGGGFF,<FGGGGFDGGGG,5,EFGGGD++*5:DGFCDD?6>AFFF4?6)5?EB?D0>DFFFAF0(/.6<D03;3().646<A)).))(4:0<BFBD?F<2<AFF<B############################################
\ No newline at end of file
diff -r 000000000000 -r 01c2b74b3a21 test-data/report_illumina_1_3_fastq_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report_illumina_1_3_fastq_output.txt	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,4 @@
+Information to extract:
+	sequences
+Number of similarity records: 36
+Number of extracted similarity records: 36
diff -r 000000000000 -r 01c2b74b3a21 test-data/report_length_fasta_output.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/report_length_fasta_output.txt	Tue Apr 26 08:18:18 2016 -0400
@@ -0,0 +1,4 @@
+Information to extract:
+	length
+Number of similarity records: 36
+Number of extracted similarity records: 36