First commit

2025-12-08 16:50:27 +00:00 · 2022-01-13 23:27:39 +01:00
parent dab6549cad
commit f53bf1b804
93 changed files with 11042 additions and 0 deletions
--- a/pkg/obiformats/ecopcr_read.go
+++ b/pkg/obiformats/ecopcr_read.go
@@ -0,0 +1,238 @@
+package obiformats
+
+import (
+	"compress/gzip"
+	"encoding/csv"
+	"fmt"
+	"io"
+	"log"
+	"os"
+	"strconv"
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+type __ecopcr_file__ struct {
+	file           io.Reader
+	csv            *csv.Reader
+	names          map[string]int
+	version        int
+	mode           string
+	forward_primer string
+	reverse_primer string
+}
+
+func __readline__(stream io.Reader) string {
+	line := make([]byte, 1024)
+	char := make([]byte, 1)
+
+	i := 0
+	for n, err := stream.Read(char); err == nil && n == 1 && char[0] != '\n'; n, err = stream.Read(char) {
+		line[i] = char[0]
+		i++
+	}
+	return string(line[0:i])
+}
+
+func __read_ecopcr_bioseq__(file *__ecopcr_file__) (obiseq.BioSequence, error) {
+
+	record, err := file.csv.Read()
+
+	if err != nil {
+		return obiseq.NilBioSequence, err
+	}
+
+	name := strings.TrimSpace(record[0])
+
+	// Ensure that sequence name is unique accross a file.
+	if val, ok := file.names[name]; ok {
+		file.names[name]++
+		name = fmt.Sprintf("%s_%d", name, val)
+	} else {
+		file.names[name] = 1
+	}
+
+	var sequence []byte
+	var comment string
+
+	if file.version == 2 {
+		sequence = []byte(strings.TrimSpace(record[20]))
+		comment = strings.TrimSpace(record[21])
+
+	} else {
+		sequence = []byte(strings.TrimSpace(record[18]))
+		comment = strings.TrimSpace(record[19])
+	}
+
+	bseq := obiseq.MakeBioSequence(name, sequence, comment)
+	annotation := bseq.Annotations()
+
+	annotation["ac"] = name
+	annotation["seq_length"], _ = strconv.Atoi(strings.TrimSpace(record[1]))
+	annotation["taxid"], _ = strconv.Atoi(strings.TrimSpace(record[2]))
+	annotation["rank"] = strings.TrimSpace(record[3])
+	annotation["species_taxid"], _ = strconv.Atoi(strings.TrimSpace(record[4]))
+	annotation["species_name"] = strings.TrimSpace(record[5])
+	annotation["genus_taxid"], _ = strconv.Atoi(strings.TrimSpace(record[6]))
+	annotation["genus_name"] = strings.TrimSpace(record[7])
+	annotation["family_taxid"], _ = strconv.Atoi(strings.TrimSpace(record[8]))
+	annotation["family_name"] = strings.TrimSpace(record[9])
+	k_m_taxid := file.mode + "_taxid"
+	k_m_name := file.mode + "_name"
+	annotation[k_m_taxid], _ = strconv.Atoi(strings.TrimSpace(record[10]))
+	annotation[k_m_name] = strings.TrimSpace(record[11])
+	annotation["strand"] = strings.TrimSpace(record[12])
+	annotation["forward_primer"] = file.forward_primer
+	annotation["forward_match"] = strings.TrimSpace(record[13])
+	annotation["forward_mismatch"], _ = strconv.Atoi(strings.TrimSpace(record[14]))
+
+	delta := 0
+	if file.version == 2 {
+		value, err := strconv.ParseFloat(strings.TrimSpace(record[15]), 64)
+		if err != nil {
+			annotation["forward_tm"] = value
+		} else {
+			annotation["forward_tm"] = -1
+		}
+		delta++
+	}
+
+	annotation["reverse_primer"] = file.reverse_primer
+	annotation["reverse_match"] = strings.TrimSpace(record[15+delta])
+	annotation["reverse_mismatch"], _ = strconv.Atoi(strings.TrimSpace(record[16+delta]))
+
+	if file.version == 2 {
+		value, err := strconv.ParseFloat(strings.TrimSpace(record[17+delta]), 64)
+		if err != nil {
+			annotation["reverse_tm"] = value
+		} else {
+			annotation["reverse_tm"] = -1
+		}
+		delta++
+	}
+
+	annotation["amplicon_length"], _ = strconv.Atoi(strings.TrimSpace(record[17+delta]))
+
+	return bseq, nil
+}
+
+func ReadEcoPCRBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenceBatch {
+	tag := make([]byte, 11)
+	n, _ := reader.Read(tag)
+
+	version := 1
+	if n == 11 && string(tag) == "#@ecopcr-v2" {
+		version = 2
+	}
+
+	line := __readline__(reader)
+	for !strings.HasPrefix(line, "# direct  strand oligo1") {
+		line = __readline__(reader)
+	}
+	forward_primer := (strings.Split(line, " "))[6]
+
+	line = __readline__(reader)
+	for !strings.HasPrefix(line, "# reverse strand oligo2") {
+		line = __readline__(reader)
+	}
+	reverse_primer := (strings.Split(line, " "))[5]
+
+	line = __readline__(reader)
+	for !strings.HasPrefix(line, "# output in") {
+		line = __readline__(reader)
+	}
+	mode := (strings.Split(line, " "))[3]
+
+	file := csv.NewReader(reader)
+	file.Comma = '|'
+	file.Comment = '#'
+	file.TrimLeadingSpace = true
+	file.ReuseRecord = true
+
+	log.Printf("EcoPCR file version : %d  Mode : %s\n", version, mode)
+
+	ecopcr := __ecopcr_file__{
+		file:           reader,
+		csv:            file,
+		names:          make(map[string]int),
+		version:        version,
+		mode:           mode,
+		forward_primer: forward_primer,
+		reverse_primer: reverse_primer}
+
+	opt := MakeOptions(options)
+
+	new_iter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
+	new_iter.Add(1)
+
+	go func() {
+		new_iter.Wait()
+		close(new_iter.Channel())
+	}()
+
+	go func() {
+
+		seq, err := __read_ecopcr_bioseq__(&ecopcr)
+		slice := make(obiseq.BioSequenceSlice, 0, opt.BatchSize())
+		i := 0
+		ii := 0
+		for err == nil {
+			slice = append(slice, seq)
+			ii++
+			if ii >= opt.BatchSize() {
+				new_iter.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
+				slice = make(obiseq.BioSequenceSlice, 0, opt.BatchSize())
+
+				i++
+				ii = 0
+			}
+
+			seq, err = __read_ecopcr_bioseq__(&ecopcr)
+		}
+
+		if len(slice) > 0 {
+			new_iter.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
+		}
+
+		new_iter.Done()
+
+		if err != nil && err != io.EOF {
+			log.Panicf("%+v", err)
+		}
+
+	}()
+
+	return new_iter
+}
+
+func ReadEcoPCR(reader io.Reader, options ...WithOption) obiseq.IBioSequence {
+	ib := ReadEcoPCRBatch(reader, options...)
+	return ib.SortBatches().IBioSequence()
+}
+
+func ReadEcoPCRBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	var reader io.Reader
+	var greader io.Reader
+	var err error
+
+	reader, err = os.Open(filename)
+	if err != nil {
+		log.Printf("open file error: %+v", err)
+		return obiseq.NilIBioSequenceBatch, err
+	}
+
+	// Test if the flux is compressed by gzip
+	greader, err = gzip.NewReader(reader)
+	if err == nil {
+		reader = greader
+	}
+
+	return ReadEcoPCRBatch(reader, options...), nil
+}
+
+func ReadEcoPCRFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
+	ib, err := ReadEcoPCRBatchFromFile(filename, options...)
+	return ib.SortBatches().IBioSequence(), err
+
+}
--- a/pkg/obiformats/embl_read.go
+++ b/pkg/obiformats/embl_read.go
@@ -0,0 +1,246 @@
+package obiformats
+
+import (
+	"bufio"
+	"bytes"
+	"compress/gzip"
+	"io"
+	"log"
+	"os"
+	"strconv"
+	"strings"
+	"time"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+var __FILE_CHUNK_SIZE__ = 1 << 20
+
+func __slice_grow__(slice []string) []string {
+	return slice
+}
+
+type __embl_chunk__ struct {
+	entries [][]string
+	order   int
+}
+
+type __file_chunk__ struct {
+	raw   io.Reader
+	order int
+}
+
+func __end_of_last_entry__(buff []byte) int {
+	//  6    5  43 2    1
+	// <CR>?<LF>//<CR>?<LF>
+	var i int
+	var state = 0
+	var start = 0
+	for i = len(buff) - 1; i >= 0 && state < 5; i-- {
+		switch state {
+		case 0: // outside of the pattern
+			if buff[i] == '\n' {
+				state = 1
+			}
+		case 1: // a \n have been matched
+			start = i + 2
+			switch buff[i] {
+			case '\r':
+				state = 2
+			case '/':
+				state = 3
+			case '\n':
+				state = 1
+			default:
+				state = 0
+			}
+		case 2: // a \r have been matched
+			switch buff[i] {
+			case '/':
+				state = 3
+			case '\n':
+				state = 1
+			default:
+				state = 0
+			}
+		case 3: // the first / have been matched
+			switch buff[i] {
+			case '/':
+				state = 4
+			case '\n':
+				state = 1
+			default:
+				state = 0
+			}
+		case 4: // the second / have been matched
+			switch buff[i] {
+			case '\n':
+				state = 5
+			default:
+				state = 0
+			}
+		}
+
+	}
+
+	if i > 0 {
+		return start
+	} else {
+		return -1
+	}
+}
+
+func __parse_embl_file__(input <-chan __file_chunk__, out obiseq.IBioSequenceBatch) {
+
+	for chunks := range input {
+		scanner := bufio.NewScanner(chunks.raw)
+		order := chunks.order
+		sequences := make(obiseq.BioSequenceSlice, 0, 100)
+		id := ""
+		scientific_name := ""
+		def_bytes := new(bytes.Buffer)
+		feat_bytes := new(bytes.Buffer)
+		seq_bytes := new(bytes.Buffer)
+		taxid := 1
+		for scanner.Scan() {
+
+			line := scanner.Text()
+
+			switch {
+			case strings.HasPrefix(line, "ID   "):
+				id = strings.SplitN(line[5:], ";", 2)[0]
+			case strings.HasPrefix(line, "OS   "):
+				scientific_name = strings.TrimSpace(line[5:])
+			case strings.HasPrefix(line, "DE   "):
+				if def_bytes.Len() > 0 {
+					def_bytes.WriteByte(' ')
+				}
+				def_bytes.WriteString(strings.TrimSpace(line[5:]))
+			case strings.HasPrefix(line, "FH   "):
+				feat_bytes.WriteString(line)
+			case line == "FH":
+				feat_bytes.WriteByte('\n')
+				feat_bytes.WriteString(line)
+			case strings.HasPrefix(line, "FT   "):
+				feat_bytes.WriteByte('\n')
+				feat_bytes.WriteString(line)
+				if strings.HasPrefix(line, `FT                   /db_xref="taxon:`) {
+					taxid, _ = strconv.Atoi(strings.SplitN(line[37:], `"`, 2)[0])
+				}
+			case strings.HasPrefix(line, "     "):
+				parts := strings.SplitN(line[5:], " ", 7)
+				for i := 0; i < 6; i++ {
+					seq_bytes.WriteString(parts[i])
+				}
+			case line == "//":
+				sequence := obiseq.MakeBioSequence(id,
+					seq_bytes.Bytes(),
+					def_bytes.String())
+
+				sequence.SetFeatures(feat_bytes.String())
+
+				annot := sequence.Annotations()
+				annot["scientific_name"] = scientific_name
+				annot["taxid"] = taxid
+				// log.Println(FormatFasta(sequence, FormatFastSeqJsonHeader))
+				sequences = append(sequences, sequence)
+				def_bytes = new(bytes.Buffer)
+				feat_bytes = new(bytes.Buffer)
+				seq_bytes = new(bytes.Buffer)
+			}
+		}
+		out.Channel() <- obiseq.MakeBioSequenceBatch(order, sequences...)
+
+	}
+
+	out.Done()
+
+}
+
+func __read_flat_file_chunk__(reader io.Reader, readers chan __file_chunk__) {
+	var err error
+	var buff []byte
+
+	size := 0
+	l := 0
+	i := 0
+
+	buff = make([]byte, 1<<20)
+	for err == nil {
+		for ; err == nil && l < len(buff); l += size {
+			size, err = reader.Read(buff[l:])
+		}
+		buff = buff[:l]
+		end := __end_of_last_entry__(buff)
+		remains := buff[end:]
+		buff = buff[:end]
+		io := bytes.NewBuffer(buff)
+		readers <- __file_chunk__{io, i}
+		i++
+		buff = make([]byte, __FILE_CHUNK_SIZE__)
+		copy(buff, remains)
+		l = len(remains)
+	}
+
+	close(readers)
+}
+
+//  6    5  43 2    1
+// <CR>?<LF>//<CR>?<LF>
+func ReadEMBLBatch(reader io.Reader, options ...WithOption) obiseq.IBioSequenceBatch {
+	opt := MakeOptions(options)
+	entry_channel := make(chan __file_chunk__, opt.BufferSize())
+
+	new_iter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
+
+	// new_iter.Add(opt.ParallelWorkers())
+	new_iter.Add(2)
+
+	go func() {
+		new_iter.Wait()
+		for len(new_iter.Channel()) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(new_iter.Channel())
+	}()
+
+	// for j := 0; j < opt.ParallelWorkers(); j++ {
+	for j := 0; j < 2; j++ {
+		go __parse_embl_file__(entry_channel, new_iter)
+	}
+
+	go __read_flat_file_chunk__(reader, entry_channel)
+
+	return new_iter
+}
+
+func ReadEMBL(reader io.Reader, options ...WithOption) obiseq.IBioSequence {
+	ib := ReadEMBLBatch(reader, options...)
+	return ib.SortBatches().IBioSequence()
+}
+
+func ReadEMBLBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	var reader io.Reader
+	var greader io.Reader
+	var err error
+
+	reader, err = os.Open(filename)
+	if err != nil {
+		log.Printf("open file error: %+v", err)
+		return obiseq.NilIBioSequenceBatch, err
+	}
+
+	// Test if the flux is compressed by gzip
+	greader, err = gzip.NewReader(reader)
+	if err == nil {
+		reader = greader
+	}
+
+	return ReadEMBLBatch(reader, options...), nil
+}
+
+func ReadEMBLFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
+	ib, err := ReadEMBLBatchFromFile(filename, options...)
+	return ib.SortBatches().IBioSequence(), err
+
+}
--- a/pkg/obiformats/fastseq_header.go
+++ b/pkg/obiformats/fastseq_header.go
@@ -0,0 +1,30 @@
+package obiformats
+
+import (
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func ParseGuessedFastSeqHeader(sequence obiseq.BioSequence) {
+	if strings.HasPrefix(sequence.Definition(), "{") {
+		ParseFastSeqJsonHeader(sequence)
+	} else {
+		ParseFastSeqOBIHeader(sequence)
+	}
+}
+
+func IParseFastSeqHeaderBatch(iterator obiseq.IBioSequenceBatch, options ...WithOption) obiseq.IBioSequenceBatch {
+	opt := MakeOptions(options)
+	return iterator.MakeIWorker(obiseq.AnnotatorToSeqWorker(opt.ParseFastSeqHeader()),
+		opt.ParallelWorkers(),
+		opt.BufferSize())
+}
+
+func IParseFastSeqHeader(iterator obiseq.IBioSequence, options ...WithOption) obiseq.IBioSequence {
+	opt := MakeOptions(options)
+
+	return IParseFastSeqHeaderBatch(iterator.IBioSequenceBatch(opt.BatchSize(),
+		opt.BufferSize()),
+		options...).SortBatches().IBioSequence()
+}
--- a/pkg/obiformats/fastseq_interface.go
+++ b/pkg/obiformats/fastseq_interface.go
@@ -0,0 +1,5 @@
+package obiformats
+
+import "git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+
+type FormatHeader func(sequence obiseq.BioSequence) string
--- a/pkg/obiformats/fastseq_json_header.go
+++ b/pkg/obiformats/fastseq_json_header.go
@@ -0,0 +1,66 @@
+package obiformats
+
+import (
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"github.com/goccy/go-json"
+)
+
+func _parse_json_header_(header string, annotations obiseq.Annotation) string {
+
+	start := -1
+	stop := -1
+	level := 0
+	lh := len(header)
+
+	for i := 0; (i < lh) && (stop < 0); i++ {
+		// fmt.Printf("[%d,%d-%d] : %d (%c) (%d,%c)\n", i, start, stop, header[i], header[i], '{', '{')
+		if level == 0 && header[i] == '{' {
+			start = i
+		}
+
+		if header[i] == '{' {
+			level++
+		}
+
+		if header[i] == '}' {
+			level--
+		}
+
+		if start >= 0 && level == 0 {
+			stop = i
+		}
+
+	}
+
+	if start < 0 || stop < 0 {
+		return header
+	}
+
+	stop++
+
+	json.Unmarshal([]byte(header)[start:stop], annotations)
+	return strings.TrimSpace(header[stop:])
+}
+
+func ParseFastSeqJsonHeader(sequence obiseq.BioSequence) {
+	sequence.SetDefinition(_parse_json_header_(sequence.Definition(),
+		sequence.Annotations()))
+}
+
+func FormatFastSeqJsonHeader(sequence obiseq.BioSequence) string {
+	annotations := sequence.Annotations()
+
+	if annotations != nil {
+		text, err := json.Marshal(sequence.Annotations())
+
+		if err != nil {
+			panic(err)
+		}
+
+		return string(text)
+	}
+
+	return ""
+}
--- a/pkg/obiformats/fastseq_obi_header.go
+++ b/pkg/obiformats/fastseq_obi_header.go
@@ -0,0 +1,288 @@
+package obiformats
+
+import (
+	"bytes"
+	"fmt"
+	"regexp"
+	"strconv"
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+	"github.com/goccy/go-json"
+)
+
+var __obi_header_value_string_pattern__ = regexp.MustCompile(`^'\s*([^']*'|"[^"]*")\s*;`)
+var __obi_header_value_numeric_pattern__ = regexp.MustCompile(`^\s*([+-]?\.\d+|[+-]?\d+(\.\d*)?([eE][+-]?\d+)?)\s*;`)
+
+func __match__dict__(text []byte) []int {
+
+	state := 0
+	level := 0
+	start := 0
+	instring := byte(0)
+
+	for i, r := range text {
+		if state == 2 {
+			if r == ';' {
+				// end of the pattern
+				return []int{start, i + 1}
+			}
+
+			if r != ' ' && r != '\t' {
+				// Bad character at the end of the pattern
+				return []int{}
+			}
+		}
+
+		if r == '{' && instring == 0 { // Beginning of dict
+			level++
+			if state == 0 {
+				// Beginning of the main dict
+				state++
+				start = i
+			}
+
+			continue
+		}
+
+		if state == 0 && r != ' ' && r != '\t' {
+			// It's not a dict
+			return []int{}
+		}
+
+		if state == 1 {
+			if r == '"' || r == '\'' {
+				if instring == 0 {
+					// start of a string
+					instring = r
+				} else {
+					if instring == r {
+						// end of a string
+						instring = 0
+					}
+				}
+
+				continue
+			}
+		}
+
+		if r == '}' && instring == 0 {
+			// end of a dict
+			level--
+
+			if level == 0 {
+				// end of the main dict
+				state++
+			}
+		}
+
+	}
+
+	return []int{}
+}
+
+func __match__key__(text []byte) []int {
+
+	state := 0
+	start := 0
+
+	for i, r := range text {
+
+		if state == 0 {
+			if (r >= 'A' && r <= 'Z') || (r >= 'a' && r <= 'z') {
+				// Beginning of the key
+				// fmt.Printf("Beginning of the key (%c) %d\n", r, i)
+				state++
+				start = i
+				continue
+			}
+
+			if r != ' ' && r != '\t' {
+				// It's not a key
+				return []int{}
+			}
+
+			continue
+		}
+
+		if state > 0 && r == '=' {
+			// End of thee pattern
+			// fmt.Printf("End of the pattern (%c) %d\n", r, i)
+			return []int{start, i + 1}
+		}
+
+		if state == 1 {
+			if r == ' ' || r == '\t' {
+				// End of the key
+				state++
+				continue
+			}
+
+			if (r >= 'A' && r <= 'Z') || (r >= 'a' && r <= 'z') ||
+				(r >= '0' && r <= '9') ||
+				r == '_' || r == '-' || r == '.' {
+				// Continuing the key
+				continue
+			}
+
+			// Not allowed character in a key
+			// fmt.Printf("Not allowed char (%c) %d\n", r, i)
+			return []int{}
+		}
+
+		if state == 2 && r != ' ' && r != '\t' {
+			// fmt.Printf("Not allowed char 2 (%c) %d\n", r, i)
+			// Not allowed character after a key
+			return []int{}
+		}
+	}
+
+	return []int{} // Not a key
+}
+
+func __match__general__(text []byte) []int {
+
+	for i, r := range text {
+		if r == ';' {
+			return []int{0, i + 1}
+		}
+	}
+
+	return []int{} // Not generic value
+}
+
+var __false__ = []byte{'f', 'a', 'l', 's', 'e'}
+var __False__ = []byte{'F', 'a', 'l', 's', 'e'}
+var __FALSE__ = []byte{'F', 'A', 'L', 'S', 'E'}
+
+var __true__ = []byte{'t', 'r', 'u', 'e'}
+var __True__ = []byte{'T', 'r', 'u', 'e'}
+var __TRUE__ = []byte{'T', 'R', 'U', 'E'}
+
+func __is_true__(text []byte) bool {
+	return (len(text) == 1 && (text[0] == 't' || text[0] == 'T')) ||
+		bytes.Equal(text, __true__) ||
+		bytes.Equal(text, __True__) ||
+		bytes.Equal(text, __TRUE__)
+}
+
+func __is_false__(text []byte) bool {
+	return (len(text) == 1 && (text[0] == 'f' || text[0] == 'F')) ||
+		bytes.Equal(text, __false__) ||
+		bytes.Equal(text, __False__) ||
+		bytes.Equal(text, __FALSE__)
+}
+
+func ParseFastSeqOBIHeader(sequence obiseq.BioSequence) {
+	definition := []byte(sequence.Definition())
+	annotations := sequence.Annotations()
+
+	// all_matches := __obi_header_pattern__.FindAllSubmatchIndex(definition, -1)
+
+	d := definition
+
+	//for m := __obi_header_key_pattern__.FindIndex(definition); len(m) > 0; {
+	//fmt.Println(string(definition[0:20]), __match__key__(definition))
+	for m := __match__key__(definition); len(m) > 0; {
+		var bvalue []byte
+		var value interface{}
+		start := m[0]
+		stop := -1
+		key := string(bytes.TrimSpace(d[start:(m[1] - 1)]))
+		part := d[m[1]:]
+
+		// numeric value
+		m = __obi_header_value_numeric_pattern__.FindIndex(part)
+		if len(m) > 0 {
+			bvalue = bytes.TrimSpace(part[m[0]:(m[1] - 1)])
+			value, _ = strconv.ParseFloat(string(bvalue), 64)
+			stop = m[1] + 1
+		} else {
+			// string value
+
+			m = __obi_header_value_string_pattern__.FindIndex(part)
+			if len(m) > 0 {
+				bvalue = bytes.TrimSpace(part[m[0]:(m[1] - 1)])
+				value = string(bvalue[1:(len(bvalue) - 1)])
+				stop = m[1] + 1
+			} else {
+
+				// dict value
+				m = __match__dict__(part)
+				if len(m) > 0 {
+					bvalue = bytes.TrimSpace(part[m[0]:(m[1] - 1)])
+					j := bytes.ReplaceAll(bvalue, []byte("'"), []byte(`"`))
+					var err error
+					if strings.HasPrefix(key, "merged_") ||
+						strings.HasSuffix(key, "_count") {
+						dict := make(map[string]int)
+						err = json.Unmarshal(j, &dict)
+						value = dict
+					} else {
+						dict := make(map[string]interface{})
+						err = json.Unmarshal(j, &dict)
+						value = dict
+					}
+
+					if err != nil {
+						value = string(bvalue)
+					}
+					stop = m[1] + 1
+				} else {
+
+					// Generic value
+
+					// m = __obi_header_value_general_pattern__.FindIndex(part)
+					m = __match__general__(part)
+					if len(m) > 0 {
+						bvalue = bytes.TrimSpace(part[m[0]:(m[1] - 1)])
+
+						if __is_false__(bvalue) {
+							value = false
+						} else {
+							if __is_true__(bvalue) {
+								value = true
+							} else {
+								value = string(bvalue)
+							}
+						}
+
+						stop = m[1] + 1
+					} else {
+						// no value
+						break
+					} // End of No value
+				} // End of not dict
+			} // End of not string
+		} // End of not numeric
+
+		annotations[key] = value
+
+		d = part[stop:]
+		//m = __obi_header_key_pattern__.FindIndex(d)
+		m = __match__key__(d)
+	}
+
+	sequence.SetDefinition(string(bytes.TrimSpace(d)))
+}
+
+func FormatFastSeqOBIHeader(sequence obiseq.BioSequence) string {
+	annotations := sequence.Annotations()
+
+	if annotations != nil {
+		var text strings.Builder
+
+		for key, value := range annotations {
+			switch t := value.(type) {
+			case string:
+				text.WriteString(fmt.Sprintf("%s=%s; ", key, t))
+			default:
+				text.WriteString(fmt.Sprintf("%s=%v; ", key, value))
+			}
+		}
+
+		return text.String()
+	}
+
+	return ""
+}
--- a/pkg/obiformats/fastseq_read.c
+++ b/pkg/obiformats/fastseq_read.c
@@ -0,0 +1,104 @@
+#include "fastseq_read.h"
+
+
+static fast_kseq_t* _open_fast_sek(gzFile fp, int shift) {
+    fast_kseq_t* iterator;
+
+    iterator = (fast_kseq_t*)malloc(sizeof(fast_kseq_t));
+
+
+    if (iterator == NULL)
+        return NULL;
+
+    iterator->filez = fp;
+    iterator->finished = false;
+    iterator->shift = shift;
+
+    if (fp != Z_NULL) {
+        iterator->seq = kseq_init(fp);
+
+        if (iterator->seq == NULL) {
+            free(iterator);
+            iterator=NULL;
+        }
+    }
+    else {
+        free(iterator);
+        iterator=NULL;
+    }
+
+    return iterator;
+}
+
+/**
+ * @brief open a FastA or FastQ file gizzed or not 
+ * 
+ * @param filename a const char* indicating the path of the 
+ *        fast* file
+ * @return kseq_t* a pointer to a kseq_t structure or NULL on
+ *         failing
+ */
+fast_kseq_t* open_fast_sek_file(const char* filename, int shift) {
+    gzFile fp;  
+
+    fp = gzopen(filename, "r");  
+    return _open_fast_sek(fp, shift);
+}
+
+fast_kseq_p open_fast_sek_fd(int fd, bool keep_open, int shift) {
+    gzFile fp;  
+
+    if (keep_open)
+        fd = dup(fd);
+
+    fp = gzdopen(fd, "r"); 
+    return _open_fast_sek(fp, shift);
+}
+
+fast_kseq_p open_fast_sek_stdin(int shift) {
+    return open_fast_sek_fd(fileno(stdin), true, shift);
+}
+
+
+int64_t next_fast_sek(fast_kseq_t* iterator) {
+    int64_t l;
+
+    if (iterator == NULL || iterator->seq == NULL)
+        return -3;
+
+    l = kseq_read(iterator->seq);
+    iterator->finished = l==0;
+    if (l>0) l = gzoffset(iterator->filez);
+    return l;
+}
+
+int rewind_fast_sek(fast_kseq_t* iterator) {
+    if (iterator == NULL || iterator->seq == NULL)
+        return -3;
+
+    kseq_rewind(iterator->seq);
+    return 0;
+}
+
+int close_fast_sek(fast_kseq_t* iterator) {
+    gzFile fp;  
+    kseq_t *seq;
+    int rep = -3;
+
+    if (iterator == NULL)
+        return rep;
+
+    fp  = iterator->filez;
+    seq = iterator->seq;
+
+    free(iterator);
+
+    if (seq != NULL)
+        kseq_destroy(iterator->seq);
+
+    if (fp != Z_NULL)
+        rep = gzclose(fp);
+
+    return rep;
+}
+    
--- a/pkg/obiformats/fastseq_read.go
+++ b/pkg/obiformats/fastseq_read.go
@@ -0,0 +1,153 @@
+package obiformats
+
+// #cgo CFLAGS: -g -Wall
+// #cgo LDFLAGS: -lz
+// #include <stdlib.h>
+// #include "fastseq_read.h"
+import "C"
+
+import (
+	"errors"
+	"fmt"
+	"log"
+	"os"
+	"time"
+	"unsafe"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/cutils"
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func __fastseq_reader__(seqfile C.fast_kseq_p,
+	iterator obiseq.IBioSequenceBatch,
+	batch_size int) {
+	var comment string
+	i := 0
+	ii := 0
+
+	slice := make(obiseq.BioSequenceSlice, 0, batch_size)
+
+	for l := int64(C.next_fast_sek(seqfile)); l > 0; l = int64(C.next_fast_sek(seqfile)) {
+
+		s := seqfile.seq
+
+		sequence := C.GoBytes(unsafe.Pointer(s.seq.s),
+			C.int(s.seq.l))
+
+		name := C.GoString(s.name.s)
+
+		if s.comment.l > C.ulong(0) {
+			comment = C.GoString(s.comment.s)
+		} else {
+			comment = ""
+		}
+
+		rep := obiseq.MakeBioSequence(name, sequence, comment)
+
+		if s.qual.l > C.ulong(0) {
+			cquality := cutils.ByteSlice(unsafe.Pointer(s.qual.s), int(s.qual.l))
+			quality := make(obiseq.Quality, s.qual.l)
+			l := int(s.qual.l)
+			shift := uint8(seqfile.shift)
+			for j := 0; j < l; j++ {
+				quality[j] = uint8(cquality[j]) - shift
+			}
+
+			rep.SetQualities(quality)
+		}
+		slice = append(slice, rep)
+		ii++
+		if ii >= batch_size {
+			// log.Printf("\n==> Pushing sequence batch\n")
+			// start := time.Now()
+
+			iterator.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
+			// elapsed := time.Since(start)
+			// log.Printf("\n==>sequences pushed after %s\n", elapsed)
+
+			slice = make(obiseq.BioSequenceSlice, 0, batch_size)
+			i++
+			ii = 0
+		}
+	}
+	if len(slice) > 0 {
+		iterator.Channel() <- obiseq.MakeBioSequenceBatch(i, slice...)
+	}
+	iterator.Done()
+
+}
+
+func ReadFastSeqBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	opt := MakeOptions(options)
+
+	name := C.CString(filename)
+	defer C.free(unsafe.Pointer(name))
+
+	pointer := C.open_fast_sek_file(name, C.int32_t(opt.QualityShift()))
+
+	var err error
+	err = nil
+
+	if pointer == nil {
+		err = errors.New(fmt.Sprintf("Cannot open file %s", filename))
+		return obiseq.NilIBioSequenceBatch, err
+	}
+
+	size := int64(-1)
+	fi, err := os.Stat(filename)
+	if err == nil {
+		size = fi.Size()
+		log.Printf("File size of %s is %d bytes\n", filename, size)
+	} else {
+		size = -1
+	}
+
+	new_iter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
+	new_iter.Add(1)
+
+	go func() {
+		new_iter.Wait()
+		for len(new_iter.Channel()) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(new_iter.Channel())
+
+		log.Println("End of the fastq file reading")
+	}()
+
+	log.Println("Start of the fastq file reading")
+
+	go __fastseq_reader__(pointer, new_iter, opt.BatchSize())
+	parser := opt.ParseFastSeqHeader()
+	if parser != nil {
+		return IParseFastSeqHeaderBatch(new_iter, options...), err
+	}
+
+	return new_iter, err
+}
+
+func ReadFastSeqFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
+	ib, err := ReadFastSeqBatchFromFile(filename, options...)
+	return ib.SortBatches().IBioSequence(), err
+}
+
+func ReadFastSeqBatchFromStdin(options ...WithOption) obiseq.IBioSequenceBatch {
+	opt := MakeOptions(options)
+	new_iter := obiseq.MakeIBioSequenceBatch(opt.BufferSize())
+
+	new_iter.Add(1)
+
+	go func() {
+		new_iter.Wait()
+		close(new_iter.Channel())
+	}()
+
+	go __fastseq_reader__(C.open_fast_sek_stdin(C.int32_t(opt.QualityShift())), new_iter, opt.BatchSize())
+
+	return new_iter
+}
+
+func ReadFastSeqFromStdin(options ...WithOption) obiseq.IBioSequence {
+	ib := ReadFastSeqBatchFromStdin(options...)
+	return ib.SortBatches().IBioSequence()
+}
--- a/pkg/obiformats/fastseq_read.h
+++ b/pkg/obiformats/fastseq_read.h
@@ -0,0 +1,41 @@
+#ifndef _READ_H
+#define _READ_H
+
+#include <zlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <stdbool.h> 
+
+#include "kseq/kseq.h"
+
+KSEQ_INIT(gzFile, gzread)
+
+typedef struct {
+  kseq_t  *seq;
+  bool    finished;
+  int16_t shift;
+  gzFile filez;
+} fast_kseq_t, *fast_kseq_p;
+ 
+
+fast_kseq_t* open_fast_sek_file(const char* filename, int shift);
+fast_kseq_t* open_fast_sek_fd(int fd, bool keep_open, int shift);
+fast_kseq_t* open_fast_sek_stdin(int shift);
+
+/**
+ * @brief read the next sequence on the fast* stream
+ * 
+ * @param seq a kseq_t* created using function open_fast_sek
+ * @return int if greater than 0 represents the length of the
+ *             sequence, otherwise indicates an error
+ *              - -1 : no more sequence in the stream
+ *              - -2 : too short quality sequence
+ *              - -3 : called with NULL pointer
+ */ 
+int64_t next_fast_sek(fast_kseq_t* iterator);
+
+
+int close_fast_sek(fast_kseq_t* iterator);
+int rewind_fast_sek(fast_kseq_t* iterator);
+
+#endif
--- a/pkg/obiformats/fastseq_write_fasta.go
+++ b/pkg/obiformats/fastseq_write_fasta.go
@@ -0,0 +1,164 @@
+package obiformats
+
+import (
+	"bytes"
+	"fmt"
+	"io"
+	"log"
+	"os"
+	"strings"
+	"sync"
+	"time"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func min(x, y int) int {
+	if x < y {
+		return x
+	}
+	return y
+}
+
+func FormatFasta(seq obiseq.BioSequence, formater FormatHeader) string {
+	var fragments strings.Builder
+
+	s := seq.Sequence()
+	l := len(s)
+
+	fragments.Grow(l + int(l/60) + 10)
+
+	for i := 0; i < l; i += 60 {
+		to := min(i+60, l)
+		fmt.Fprintf(&fragments, "%s\n", string(s[i:to]))
+	}
+
+	folded := fragments.String()
+	folded = folded[:fragments.Len()-1]
+	info := formater(seq)
+	return fmt.Sprintf(">%s %s %s\n%s",
+		seq.Id(), info,
+		seq.Definition(),
+		folded)
+}
+
+func FormatFastaBatch(batch obiseq.BioSequenceBatch, formater FormatHeader) []byte {
+	var bs bytes.Buffer
+	for _, seq := range batch.Slice() {
+		bs.WriteString(FormatFasta(seq, formater))
+		bs.WriteString("\n")
+	}
+	return bs.Bytes()
+}
+
+func WriteFasta(iterator obiseq.IBioSequence, file io.Writer, options ...WithOption) error {
+	opt := MakeOptions(options)
+
+	header_format := opt.FormatFastSeqHeader()
+
+	for iterator.Next() {
+		seq := iterator.Get()
+		fmt.Fprintln(file, FormatFasta(seq, header_format))
+	}
+
+	return nil
+}
+
+func WriteFastaToFile(iterator obiseq.IBioSequence,
+	filename string,
+	options ...WithOption) error {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return err
+	}
+
+	return WriteFasta(iterator, file, options...)
+}
+
+func WriteFastaToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
+	return WriteFasta(iterator, os.Stdout, options...)
+}
+
+func WriteFastaBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options ...WithOption) error {
+	buffsize := iterator.BufferSize()
+	new_iter := obiseq.MakeIBioSequenceBatch(buffsize)
+
+	opt := MakeOptions(options)
+	nwriters := 4
+
+	chunkchan := make(chan FileChunck)
+	chunkwait := sync.WaitGroup{}
+
+	header_format := opt.FormatFastSeqHeader()
+
+	chunkwait.Add(nwriters)
+
+	go func() {
+		chunkwait.Wait()
+		for len(chunkchan) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(chunkchan)
+	}()
+
+	ff := func(iterator obiseq.IBioSequenceBatch) {
+		for iterator.Next() {
+			batch := iterator.Get()
+			chunkchan <- FileChunck{
+				FormatFastaBatch(batch, header_format),
+				batch.Order(),
+			}
+			new_iter.Channel() <- batch
+		}
+		new_iter.Done()
+	}
+
+	for i := 0; i < nwriters; i++ {
+		go ff(iterator.Split())
+	}
+
+	next_to_send := 0
+	received := make(map[int]FileChunck, 100)
+
+	go func() {
+		for chunk := range chunkchan {
+			if chunk.order == next_to_send {
+				file.Write(chunk.text)
+				next_to_send++
+				chunk, ok := received[next_to_send]
+				for ok {
+					file.Write(chunk.text)
+					delete(received, next_to_send)
+					next_to_send++
+					chunk, ok = received[next_to_send]
+				}
+			} else {
+				received[chunk.order] = chunk
+			}
+
+		}
+	}()
+
+	return nil
+}
+
+func WriteFastaBatchToStdout(iterator obiseq.IBioSequenceBatch, options ...WithOption) error {
+	return WriteFastaBatch(iterator, os.Stdout, options...)
+}
+
+func WriteFastaBatchToFile(iterator obiseq.IBioSequenceBatch,
+	filename string,
+	options ...WithOption) error {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return err
+	}
+
+	return WriteFastaBatch(iterator, file, options...)
+}
--- a/pkg/obiformats/fastseq_write_fastq.go
+++ b/pkg/obiformats/fastseq_write_fastq.go
@@ -0,0 +1,168 @@
+package obiformats
+
+import (
+	"bytes"
+	"fmt"
+	"io"
+	"log"
+	"os"
+	"time"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func FormatFastq(seq obiseq.BioSequence, quality_shift int, formater FormatHeader) string {
+
+	l := seq.Length()
+	q := seq.Qualities()
+	ascii := make([]byte, seq.Length())
+
+	for j := 0; j < l; j++ {
+		ascii[j] = uint8(q[j]) + uint8(quality_shift)
+	}
+
+	info := ""
+	if formater != nil {
+		info = formater(seq)
+	}
+
+	return fmt.Sprintf("@%s %s %s\n%s\n+\n%s",
+		seq.Id(), info,
+		seq.Definition(),
+		string(seq.Sequence()),
+		string(ascii),
+	)
+}
+
+func FormatFastqBatch(batch obiseq.BioSequenceBatch, quality_shift int,
+	formater FormatHeader) []byte {
+	var bs bytes.Buffer
+	for _, seq := range batch.Slice() {
+		bs.WriteString(FormatFastq(seq, quality_shift, formater))
+		bs.WriteString("\n")
+	}
+	return bs.Bytes()
+}
+
+func WriteFastq(iterator obiseq.IBioSequence, file io.Writer, options ...WithOption) error {
+	opt := MakeOptions(options)
+
+	header_format := opt.FormatFastSeqHeader()
+	quality := opt.QualityShift()
+
+	for iterator.Next() {
+		seq := iterator.Get()
+		fmt.Fprintln(file, FormatFastq(seq, quality, header_format))
+	}
+
+	return nil
+}
+
+func WriteFastqToFile(iterator obiseq.IBioSequence,
+	filename string,
+	options ...WithOption) error {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return err
+	}
+
+	return WriteFastq(iterator, file, options...)
+}
+
+func WriteFastqToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
+	return WriteFastq(iterator, os.Stdout, options...)
+}
+
+type FileChunck struct {
+	text  []byte
+	order int
+}
+
+func WriteFastqBatch(iterator obiseq.IBioSequenceBatch, file io.Writer, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	buffsize := iterator.BufferSize()
+	new_iter := obiseq.MakeIBioSequenceBatch(buffsize)
+
+	opt := MakeOptions(options)
+	nwriters := 4
+
+	chunkchan := make(chan FileChunck)
+
+	header_format := opt.FormatFastSeqHeader()
+	quality := opt.QualityShift()
+
+	new_iter.Add(nwriters)
+
+	go func() {
+		new_iter.Wait()
+		for len(chunkchan) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(chunkchan)
+		for len(new_iter.Channel()) > 0 {
+			time.Sleep(time.Millisecond)
+		}
+		close(new_iter.Channel())
+	}()
+
+	ff := func(iterator obiseq.IBioSequenceBatch) {
+		for iterator.Next() {
+			batch := iterator.Get()
+			chunkchan <- FileChunck{
+				FormatFastqBatch(batch, quality, header_format),
+				batch.Order(),
+			}
+			new_iter.Channel() <- batch
+		}
+		new_iter.Done()
+	}
+
+	log.Println("Start of the fastq file reading")
+	for i := 0; i < nwriters; i++ {
+		go ff(iterator.Split())
+	}
+
+	next_to_send := 0
+	received := make(map[int]FileChunck, 100)
+
+	go func() {
+		for chunk := range chunkchan {
+			if chunk.order == next_to_send {
+				file.Write(chunk.text)
+				next_to_send++
+				chunk, ok := received[next_to_send]
+				for ok {
+					file.Write(chunk.text)
+					delete(received, next_to_send)
+					next_to_send++
+					chunk, ok = received[next_to_send]
+				}
+			} else {
+				received[chunk.order] = chunk
+			}
+
+		}
+	}()
+
+	return new_iter, nil
+}
+
+func WriteFastqBatchToStdout(iterator obiseq.IBioSequenceBatch, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	return WriteFastqBatch(iterator, os.Stdout, options...)
+}
+
+func WriteFastqBatchToFile(iterator obiseq.IBioSequenceBatch,
+	filename string,
+	options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return obiseq.NilIBioSequenceBatch, err
+	}
+
+	return WriteFastqBatch(iterator, file, options...)
+}
--- a/pkg/obiformats/kseq/Makefile
+++ b/pkg/obiformats/kseq/Makefile
@@ -0,0 +1,5 @@
+all:kseq.h kseq_test.c
+		$(CC) -g -O2 kseq_test.c -o kseq_test -lz
+
+clean:
+		rm -f *.o kseq_test
--- a/pkg/obiformats/kseq/kseq.h
+++ b/pkg/obiformats/kseq/kseq.h
@@ -0,0 +1,223 @@
+/* The MIT License
+
+   Copyright (c) 2008 Genome Research Ltd (GRL).
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/
+
+/* Contact: Heng Li <lh3@sanger.ac.uk> */
+
+/* Last Modified: 12APR2009 */
+
+#ifndef AC_KSEQ_H
+#define AC_KSEQ_H
+
+#include <ctype.h>
+#include <string.h>
+#include <stdlib.h>
+
+#define KS_SEP_SPACE 0 // isspace(): \t, \n, \v, \f, \r
+#define KS_SEP_TAB   1 // isspace() && !' '
+#define KS_SEP_MAX   1
+
+#define __KS_TYPE(type_t)						\
+	typedef struct __kstream_t {				\
+		char *buf;								\
+		int begin, end, is_eof;					\
+		type_t f;								\
+	} kstream_t;
+
+#define ks_eof(ks) ((ks)->is_eof && (ks)->begin >= (ks)->end)
+#define ks_rewind(ks) ((ks)->is_eof = (ks)->begin = (ks)->end = 0)
+
+#define __KS_BASIC(type_t, __bufsize)								\
+	static inline kstream_t *ks_init(type_t f)						\
+	{																\
+		kstream_t *ks = (kstream_t*)calloc(1, sizeof(kstream_t));	\
+		ks->f = f;													\
+		ks->buf = (char*)malloc(__bufsize);							\
+		return ks;													\
+	}																\
+	static inline void ks_destroy(kstream_t *ks)					\
+	{																\
+		if (ks) {													\
+			free(ks->buf);											\
+			free(ks);												\
+		}															\
+	}
+
+#define __KS_GETC(__read, __bufsize)						\
+	static inline int ks_getc(kstream_t *ks)				\
+	{														\
+		if (ks->is_eof && ks->begin >= ks->end) return -1;	\
+		if (ks->begin >= ks->end) {							\
+			ks->begin = 0;									\
+			ks->end = __read(ks->f, ks->buf, __bufsize);	\
+			if (ks->end < __bufsize) ks->is_eof = 1;		\
+			if (ks->end == 0) return -1;					\
+		}													\
+		return (int)ks->buf[ks->begin++];					\
+	}
+
+#ifndef KSTRING_T
+#define KSTRING_T kstring_t
+typedef struct __kstring_t {
+	size_t l, m;
+	char *s;
+} kstring_t;
+#endif
+
+#ifndef kroundup32
+#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
+#endif
+
+#define __KS_GETUNTIL(__read, __bufsize)								\
+	static int ks_getuntil(kstream_t *ks, int delimiter, kstring_t *str, int *dret) \
+	{																	\
+		if (dret) *dret = 0;											\
+		str->l = 0;														\
+		if (ks->begin >= ks->end && ks->is_eof) return -1;				\
+		for (;;) {														\
+			int i;														\
+			if (ks->begin >= ks->end) {									\
+				if (!ks->is_eof) {										\
+					ks->begin = 0;										\
+					ks->end = __read(ks->f, ks->buf, __bufsize);		\
+					if (ks->end < __bufsize) ks->is_eof = 1;			\
+					if (ks->end == 0) break;							\
+				} else break;											\
+			}															\
+			if (delimiter > KS_SEP_MAX) {								\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (ks->buf[i] == delimiter) break;					\
+			} else if (delimiter == KS_SEP_SPACE) {						\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (isspace(ks->buf[i])) break;						\
+			} else if (delimiter == KS_SEP_TAB) {						\
+				for (i = ks->begin; i < ks->end; ++i)					\
+					if (isspace(ks->buf[i]) && ks->buf[i] != ' ') break; \
+			} else i = 0; /* never come to here! */						\
+			if (str->m - str->l < i - ks->begin + 1) {					\
+				str->m = str->l + (i - ks->begin) + 1;					\
+				kroundup32(str->m);										\
+				str->s = (char*)realloc(str->s, str->m);				\
+			}															\
+			memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
+			str->l = str->l + (i - ks->begin);							\
+			ks->begin = i + 1;											\
+			if (i < ks->end) {											\
+				if (dret) *dret = ks->buf[i];							\
+				break;													\
+			}															\
+		}																\
+		if (str->l == 0) {												\
+			str->m = 1;													\
+			str->s = (char*)calloc(1, 1);								\
+		}																\
+		str->s[str->l] = '\0';											\
+		return str->l;													\
+	}
+
+#define KSTREAM_INIT(type_t, __read, __bufsize) \
+	__KS_TYPE(type_t)							\
+	__KS_BASIC(type_t, __bufsize)				\
+	__KS_GETC(__read, __bufsize)				\
+	__KS_GETUNTIL(__read, __bufsize)
+
+#define __KSEQ_BASIC(type_t)											\
+	static inline kseq_t *kseq_init(type_t fd)							\
+	{																	\
+		kseq_t *s = (kseq_t*)calloc(1, sizeof(kseq_t));					\
+		s->f = ks_init(fd);												\
+		return s;														\
+	}																	\
+	static inline void kseq_rewind(kseq_t *ks)							\
+	{																	\
+		ks->last_char = 0;												\
+		ks->f->is_eof = ks->f->begin = ks->f->end = 0;					\
+	}																	\
+	static inline void kseq_destroy(kseq_t *ks)							\
+	{																	\
+		if (!ks) return;												\
+		free(ks->name.s); free(ks->comment.s); free(ks->seq.s);	free(ks->qual.s); \
+		ks_destroy(ks->f);												\
+		free(ks);														\
+	}
+
+/* Return value:
+   >=0  length of the sequence (normal)
+   -1   end-of-file
+   -2   truncated quality string
+ */
+#define __KSEQ_READ														\
+	static int kseq_read(kseq_t *seq)									\
+	{																	\
+		int c;															\
+		kstream_t *ks = seq->f;											\
+		if (seq->last_char == 0) { /* then jump to the next header line */ \
+			while ((c = ks_getc(ks)) != -1 && c != '>' && c != '@');	\
+			if (c == -1) return -1; /* end of file */					\
+			seq->last_char = c;											\
+		} /* the first header char has been read */						\
+		seq->comment.l = seq->seq.l = seq->qual.l = 0;					\
+		if (ks_getuntil(ks, 0, &seq->name, &c) < 0) return -1;			\
+		if (c != '\n') ks_getuntil(ks, '\n', &seq->comment, 0);			\
+		while ((c = ks_getc(ks)) != -1 && c != '>' && c != '+' && c != '@') { \
+			if (isgraph(c)) { /* printable non-space character */		\
+				if (seq->seq.l + 1 >= seq->seq.m) { /* double the memory */ \
+					seq->seq.m = seq->seq.l + 2;						\
+					kroundup32(seq->seq.m); /* rounded to next closest 2^k */ \
+					seq->seq.s = (char*)realloc(seq->seq.s, seq->seq.m); \
+				}														\
+				seq->seq.s[seq->seq.l++] = (char)c;						\
+			}															\
+		}																\
+		if (c == '>' || c == '@') seq->last_char = c; /* the first header char has been read */	\
+		seq->seq.s[seq->seq.l] = 0;	/* null terminated string */		\
+		if (c != '+') return seq->seq.l; /* FASTA */					\
+		if (seq->qual.m < seq->seq.m) {	/* allocate enough memory */	\
+			seq->qual.m = seq->seq.m;									\
+			seq->qual.s = (char*)realloc(seq->qual.s, seq->qual.m);		\
+		}																\
+		while ((c = ks_getc(ks)) != -1 && c != '\n'); /* skip the rest of '+' line */ \
+		if (c == -1) return -2; /* we should not stop here */			\
+		while ((c = ks_getc(ks)) != -1 && seq->qual.l < seq->seq.l)		\
+			if (c >= 33 && c <= 127) seq->qual.s[seq->qual.l++] = (unsigned char)c;	\
+		seq->qual.s[seq->qual.l] = 0; /* null terminated string */		\
+		seq->last_char = 0;	/* we have not come to the next header line */ \
+		if (seq->seq.l != seq->qual.l) return -2; /* qual string is shorter than seq string */ \
+		return seq->seq.l;												\
+	}
+
+#define __KSEQ_TYPE(type_t)						\
+	typedef struct {							\
+		kstring_t name, comment, seq, qual;		\
+		int last_char;							\
+		kstream_t *f;							\
+	} kseq_t;
+
+#define KSEQ_INIT(type_t, __read)				\
+	KSTREAM_INIT(type_t, __read, 4096)			\
+	__KSEQ_TYPE(type_t)							\
+	__KSEQ_BASIC(type_t)						\
+	__KSEQ_READ
+
+#endif
--- a/pkg/obiformats/kseq/kseq_test
+++ b/pkg/obiformats/kseq/kseq_test
--- a/pkg/obiformats/kseq/kseq_test.c
+++ b/pkg/obiformats/kseq/kseq_test.c
@@ -0,0 +1,27 @@
+#include <zlib.h>
+#include <stdio.h>
+#include "kseq.h"
+KSEQ_INIT(gzFile, gzread)
+
+int main(int argc, char *argv[])
+{
+	gzFile fp;
+	kseq_t *seq;
+	int l;
+	if (argc == 1) {
+		fprintf(stderr, "Usage: %s <in.seq>\n", argv[0]);
+		return 1;
+	}
+	fp = gzopen(argv[1], "r");
+	seq = kseq_init(fp);
+	while ((l = kseq_read(seq)) >= 0) {
+		printf("name: %s\n", seq->name.s);
+		if (seq->comment.l) printf("comment: %s\n", seq->comment.s);
+		printf("seq: %s\n", seq->seq.s);
+		if (seq->qual.l) printf("qual: %s\n", seq->qual.s);
+	}
+	printf("return value: %d\n", l);
+	kseq_destroy(seq);
+	gzclose(fp);
+	return 0;
+}
--- a/pkg/obiformats/kseq/kseq_test.dSYM/Contents/Info.plist
+++ b/pkg/obiformats/kseq/kseq_test.dSYM/Contents/Info.plist
@@ -0,0 +1,20 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+	<dict>
+		<key>CFBundleDevelopmentRegion</key>
+		<string>English</string>
+		<key>CFBundleIdentifier</key>
+		<string>com.apple.xcode.dsym.kseq_test</string>
+		<key>CFBundleInfoDictionaryVersion</key>
+		<string>6.0</string>
+		<key>CFBundlePackageType</key>
+		<string>dSYM</string>
+		<key>CFBundleSignature</key>
+		<string>????</string>
+		<key>CFBundleShortVersionString</key>
+		<string>1.0</string>
+		<key>CFBundleVersion</key>
+		<string>1</string>
+	</dict>
+</plist>
--- a/pkg/obiformats/kseq/kseq_test.dSYM/Contents/Resources/DWARF/kseq_test
+++ b/pkg/obiformats/kseq/kseq_test.dSYM/Contents/Resources/DWARF/kseq_test
--- a/pkg/obiformats/kseq/s1.fasta
+++ b/pkg/obiformats/kseq/s1.fasta
@@ -0,0 +1,291 @@
+>HWI-D00393:103:C6KCUANXX:2:2309:18209:70743_CONS_SUB_SUB reverse_score=72.0; count=2; direction=forward; experiment=australie; seq_a_mismatch=0; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; status=full; seq_a_deletion=0; seq_length=98; start=aaaac; merged_sample={'AN5-30_b': 1, 'AML-33_b': 1}; seq_a_insertion=0; mode=alignment; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+aaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagagtt
+ggcataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2209:18639:37342_CONS_SUB_SUB_CMP ali_length=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-45_b': 1, 'AN2-30_a': 1}; forward_score=72.0; seq_b_mismatch=0; start=ataaa; experiment=australie; seq_a_single=33; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=2; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ataaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2115:3400:66119_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-03_a': 1}; forward_score=72.0; score=367.38470594; seq_a_mismatch=0; forward_tag=gtacgact; seq_b_mismatch=0; start=ccaaa; experiment=australie; mid_quality=62.0797101449; avg_quality=58.9050632911; seq_a_single=33; score_norm=3.99331202109; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=gtgtacat; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=03_03A; seq_b_single=33; 
+ccaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:2310:20070:75862_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=23.1; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-12_b': 1}; forward_score=72.0; score=360.189837214; seq_a_mismatch=0; forward_tag=catcagtc; seq_b_mismatch=0; start=ccaaa; experiment=australie; mid_quality=53.0507246377; avg_quality=49.6265822785; seq_a_single=33; score_norm=3.91510692624; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=cgagtcgt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=28.9; position=11_11D; seq_b_single=33; 
+ccaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggaataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2114:5633:21903_CONS_SUB_SUB merged_sample={'ABR-15_a': 1, 'AN5-12_b': 1, 'AW2-35_b': 1}; forward_score=72.0; seq_b_insertion=0; seq_a_insertion=0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; count=3; seq_length=100; start=ccaaa; experiment=australie; reverse_score=72.0; mode=alignment; status=full; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ccaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1112:5602:81492_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-12_b': 1}; forward_score=72.0; score=367.699098517; seq_a_mismatch=0; forward_tag=catcagtc; seq_b_mismatch=0; start=ccaaa; experiment=australie; mid_quality=62.2463768116; avg_quality=59.0506329114; seq_a_single=33; score_norm=3.9967293317; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=cgagtcgt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_11D; seq_b_single=33; 
+ccaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtcttgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1101:4074:21538_CONS_SUB_SUB merged_sample={'AN4-36_b': 51, 'AW2-04_b': 11, 'AW2-04_a': 10, 'AN4-38_b': 158, 'AN5-43_b': 2, 'ADR-14_b': 2, 'AW2-34_b': 10, 'AW2-34_a': 1, 'AN3-38_b': 1, 'ABR-30_b': 1, 'AW2-36_b': 17, 'AN2-15_a': 11, 'AN4-34_b': 44, 'AN5-45_b': 5, 'AW2-27_b': 1, 'AW2-27_a': 3, 'ADR-25_a': 1, 'AN4-19_b': 30, 'ABR-44_a': 2, 'ABR-31_b': 1, 'AN2-20_b': 1, 'AN1-43_a': 2, 'AN2-13_b': 21, 'AN5-11_b': 2, 'AN4-22_b': 16, 'AN3-14_b': 1, 'AN3-14_a': 3, 'AW2-35_b': 101, 'AN2-19_b': 1, 'ABR-33_a': 1, 'ABR-29_a': 11, 'AW1-40_b': 9, 'ADR-13_a': 5, 'ADR-06_b': 1, 'AN4-26_a': 1, 'AN5-15_b': 20, 'AN2-01_a': 5, 'ADR-21_b': 1, 'AW2-23_b': 29, 'AW2-23_a': 3, 'ADR-13_b': 1, 'AW2-21_a': 1, 'AWO-27_b': 1, 'AW2-21_b': 20, 'AN2-10_a': 9, 'AN5-13_b': 19, 'AN4-20_b': 1, 'AN2-30_a': 1, 'AN3-22_b': 4, 'AN3-25_b': 3, 'AN3-25_a': 5, 'AN4-24_b': 26, 'ABR-15_a': 34, 'AW2-36_a': 5, 'AW2-12_b': 7, 'AW2-12_a': 5, 'AN5-48_a': 1, 'AW1-06_a': 6, 'AN5-21_a': 1, 'AN5-21_b': 20, 'AN2-09_b': 11, 'ABR-13_b': 2, 'ABR-13_a': 23, 'AN2-09_a': 7, 'AN3-20_b': 2, 'AN2-07_a': 4, 'AN2-07_b': 8, 'AN4-44_b': 26, 'AN4-21_b': 19, 'AW2-03_a': 28, 'AN4-42_b': 30, 'AW2-03_b': 47, 'ADR-26_b': 1, 'AN1-03_a': 6, 'AML-47_a': 1, 'AWO-30_b': 1, 'AN1-03_b': 3, 'ADR-30_b': 1, 'AN4-37_b': 40, 'AW2-07_b': 43, 'AN4-40_a': 1, 'AN3-44_b': 1, 'AN4-40_b': 36, 'AW2-01_b': 32, 'AW2-01_a': 13, 'AN5-10_b': 64, 'AW1-11_a': 29, 'AN2-43_a': 1, 'AN2-43_b': 2, 'AN1-17_a': 6, 'AN5-37_b': 1, 'blk-12_b': 1, 'ABR-35_b': 1, 'blk-02_b': 1, 'AN2-45_b': 8, 'AN3-40_a': 1, 'AW1-17_a': 5, 'AN2-45_a': 7, 'AW2-17_b': 4, 'ABR-25_a': 1, 'ABR-08_b': 1, 'AN5-14_b': 6, 'AWO-10_b': 1, 'AN2-38_a': 3, 'AN5-33_b': 15, 'AN2-12_a': 7, 'blk-04_b': 1, 'AN3-08_b': 4, 'AN3-01_b': 2, 'AN5-12_b': 106, 'ABR-23_a': 2, 'AN3-42_b': 19, 'AN4-23_b': 96, 'AN2-35_b': 1, 'ABR-02_a': 7, 'AN5-35_a': 1, 'ABR-17_a': 5, 'AML-42_a': 1, 'ADR-10_b': 1, 'ABR-39_a': 14, 'AN3-20_a': 3, 'pos-01_a': 1, 'AN5-03_b': 13, 'AN3-05_a': 1, 'AWO-42_b': 1, 'ABR-14_b': 1, 'AW2-13_b': 2, 'AW2-13_a': 5, 'blk-06_b': 2, 'AML-24_a': 1, 'ADR-12_b': 1, 'ABR-09_a': 3, 'ABR-12_b': 1, 'AN3-03_b': 3, 'AN3-03_a': 4, 'ABR-12_a': 34, 'ABR-27_b': 1, 'AN4-11_b': 15, 'AN5-22_b': 11, 'AN3-47_b': 2, 'AN3-47_a': 1, 'AN4-13_b': 35, 'AN2-41_b': 1, 'AN4-41_b': 14, 'AN4-22_a': 1, 'AN2-02_b': 5, 'ADR-37_b': 1, 'AN4-15_b': 2, 'AN5-20_a': 1, 'AN5-20_b': 18, 'AN3-45_b': 4, 'AW2-40_b': 20, 'AN5-09_b': 2, 'AN5-09_a': 1, 'AW2-40_a': 5, 'AN4-47_b': 11, 'AWO-19_b': 1, 'ABR-41_a': 12, 'AW1-32_b': 1, 'AW1-30_a': 15, 'AN4-05_a': 1, 'AN3-41_a': 1, 'AN3-46_b': 2, 'AN5-24_b': 35, 'ABR-43_a': 1, 'AW1-34_b': 1, 'AN5-30_b': 20, 'AN5-30_a': 1, 'AW2-28_a': 10, 'AW2-28_b': 5, 'AN5-25_b': 16, 'AN4-01_a': 1, 'AN2-04_b': 2, 'AW2-30_a': 22, 'AML-19_a': 1, 'AN2-34_a': 2, 'AN2-38_b': 3, 'pos-06_a': 1, 'AN5-19_b': 4, 'blk-07_b': 1, 'ABR-47_a': 1, 'AN2-02_a': 7, 'AN3-43_b': 12, 'AW1-20_a': 2, 'AW2-39_a': 3, 'AW2-43_a': 1, 'AWO-41_a': 10, 'AN5-38_a': 1, 'AW2-43_b': 3, 'AN4-17_b': 12, 'AW2-07_a': 48, 'AN3-04_b': 2, 'AN4-35_b': 86, 'AW1-26_a': 8, 'AWO-34_b': 1, 'ABR-14_a': 13, 'AN2-13_a': 4, 'AN4-39_a': 1, 'ABR-01_a': 78, 'AN5-44_b': 1, 'AN4-39_b': 85, 'AW1-30_b': 4, 'AN2-31_b': 7, 'AN3-37_a': 1, 'AN4-12_b': 142, 'AN3-35_b': 12, 'ABR-42_a': 9, 'ABR-03_b': 1, 'AN3-17_b': 19, 'AML-08_a': 2, 'AW1-29_a': 4, 'AN2-05_b': 3, 'AN4-46_b': 39, 'AN2-05_a': 5, 'AN4-14_b': 4, 'AN5-23_b': 24, 'AN4-25_a': 1, 'AML-12_a': 1, 'AN3-34_a': 1, 'AN5-28_b': 31, 'AN3-34_b': 2, 'AN5-27_b': 3, 'ABR-32_b': 1, 'AWO-15_b': 1, 'ABR-46_a': 8, 'AW1-18_a': 76, 'AN3-13_b': 1, 'AN4-18_b': 2, 'AN4-24_a': 1, 'AWO-06_b': 1, 'AN5-42_b': 14, 'ABR-28_a': 2, 'AN2-40_a': 2, 'AW1-40_a': 9, 'AW2-35_a': 70, 'ABR-40_b': 2, 'AN2-10_b': 3, 'AN3-27_b': 3, 'ABR-44_b': 1, 'ADR-38_b': 1, 'AN3-19_b': 2, 'ABR-40_a': 22, 'AN4-06_b': 17, 'ADR-05_b': 1, 'AN2-12_b': 1, 'ABR-08_a': 6, 'AN5-41_b': 10, 'AWO-37_b': 1, 'AN4-29_b': 40, 'AW2-42_b': 3, 'AW1-27_a': 6, 'ADR-34_b': 1, 'AN4-45_b': 115, 'AWO-13_b': 1, 'AN5-34_b': 73, 'ABR-22_b': 2, 'AN5-39_b': 2, 'AW2-42_a': 1, 'AN2-04_a': 4, 'AN4-43_b': 19, 'AW1-08_b': 1, 'AW1-08_a': 1, 'AW1-11_b': 1, 'AN4-48_a': 1, 'AML-04_a': 1, 'AML-41_a': 1, 'AW1-35_a': 2}; count=3190; seq_b_insertion=0; status=full; seq_a_deletion=0; seq_length=100; start=ctaaa; experiment=australie; seq_a_insertion=0; mode=alignment; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1102:20365:63690_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'ABR-13_a': 1}; forward_score=72.0; score=367.706336455; seq_a_mismatch=0; forward_tag=tagtcgca; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3333333333; avg_quality=59.1265822785; seq_a_single=33; score_norm=3.99680800494; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=cgctctcg; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=01_09E; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgctcgttga
+>HWI-D00393:103:C6KCUANXX:2:1109:5898:71477_CONS_SUB_SUB_CMP merged_sample={'AW2-04_a': 1, 'AN4-38_b': 1, 'AW1-07_b': 1, 'AN4-34_b': 5, 'AN4-19_b': 1, 'AN2-20_b': 1, 'AN2-13_b': 3, 'AN5-11_b': 1, 'AN3-14_a': 1, 'ABR-29_a': 1, 'AW2-23_b': 3, 'AW2-23_a': 1, 'AN4-28_b': 1, 'AW2-21_b': 3, 'AN4-24_b': 1, 'AN5-21_b': 1, 'ABR-13_a': 2, 'AN3-20_b': 1, 'ADR-11_b': 1, 'AN4-44_b': 1, 'AN3-46_b': 2, 'AN4-42_b': 1, 'AW2-03_b': 2, 'AN1-03_a': 1, 'AN4-37_b': 2, 'AW2-07_b': 3, 'AN4-40_b': 3, 'AW2-01_a': 1, 'AW1-11_a': 5, 'AN2-43_b': 2, 'pos-09_a': 1, 'ABR-25_a': 1, 'AN2-38_b': 1, 'AN3-08_a': 1, 'AN3-01_b': 1, 'AN5-12_b': 2, 'AN3-42_b': 3, 'AN4-23_b': 1, 'ABR-02_a': 1, 'ABR-17_a': 1, 'ABR-39_a': 1, 'ABR-14_a': 3, 'AW2-13_b': 1, 'ABR-12_a': 4, 'AN4-13_b': 2, 'AN2-41_b': 1, 'AN4-15_b': 1, 'AN5-20_b': 1, 'AW2-40_b': 3, 'ABR-41_a': 1, 'AN3-35_a': 1, 'AN3-43_b': 1, 'AN5-24_b': 2, 'AN5-30_b': 1, 'AN5-34_b': 3, 'AN5-19_b': 1, 'AWO-41_a': 1, 'AN5-38_a': 1, 'AW2-07_a': 1, 'AN4-35_b': 5, 'ABR-01_a': 4, 'AN4-39_b': 2, 'AN2-31_b': 1, 'AW1-30_a': 1, 'AN4-12_b': 2, 'ABR-42_a': 2, 'AN3-17_a': 1, 'AN3-17_b': 1, 'AN2-05_b': 1, 'AN4-46_b': 1, 'AN4-14_b': 4, 'AN5-23_b': 4, 'ABR-32_a': 1, 'ABR-46_a': 2, 'AW1-18_a': 4, 'AN4-18_b': 1, 'AW1-35_a': 1, 'AW2-35_b': 6, 'AW1-40_b': 3, 'AW2-35_a': 2, 'AN2-10_a': 2, 'AN2-02_a': 1, 'AN4-29_b': 1, 'AN4-45_b': 3, 'AW2-44_b': 1, 'ABR-22_b': 1, 'AW1-28_b': 1, 'AW2-42_b': 1, 'AN4-43_b': 2, 'AW1-27_a': 1}; count=159; status=full; seq_a_deletion=0; seq_length=100; start=ctaaa; experiment=australie; seq_a_insertion=0; mode=alignment; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:1116:11515:15328_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-44_b': 1, 'AN4-39_b': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=2; seq_length=100; status=full; mode=alignment; head_quality=37.0; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttactaggttaaggtctcgtttgttaa
+>HWI-D00393:103:C6KCUANXX:2:1206:17870:33853_CONS_SUB_SUB ali_length=92; seq_ab_match=92; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW1-30_a': 7}; forward_score=72.0; seq_a_mismatch=0; forward_tag=cgctctcg; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=gactgatg; goodAli=Alignement; count=7; seq_length=100; status=full; mode=alignment; position=02_12A; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcttaactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2106:7652:12042_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-40_b': 1, 'AW2-35_b': 1, 'ABR-01_a': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=3; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcgtaactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2115:4325:51738_CONS_SUB_SUB_CMP status=full; merged_sample={'AW1-29_a': 1, 'ABR-41_a': 1, 'AN2-02_a': 1, 'AN4-39_b': 1, 'AN2-07_a': 1}; seq_b_insertion=0; seq_a_insertion=0; seq_a_mismatch=0; forward_score=72.0; tail_quality=37.0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; count=5; seq_length=100; start=ctaaa; experiment=australie; reverse_score=72.0; mode=alignment; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgctaa
+>HWI-D00393:103:C6KCUANXX:2:2211:17027:90962_CONS_SUB_SUB status=full; merged_sample={'AML-46_a': 1, 'AN4-46_b': 7}; seq_b_insertion=0; seq_a_insertion=0; seq_a_mismatch=0; forward_score=72.0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; count=8; seq_length=100; start=ctaaa; experiment=australie; reverse_score=72.0; mode=alignment; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcattcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1113:14380:43631_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-34_b': 1}; forward_score=72.0; score=367.706336455; seq_a_mismatch=0; forward_tag=atgatcgc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3333333333; avg_quality=59.1265822785; seq_a_single=33; score_norm=3.99680800494; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_08B; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagtatgtaaaggtctcgatcgttat
+>HWI-D00393:103:C6KCUANXX:2:1116:10928:36920_CONS_SUB_SUB_CMP ali_length=92; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-38_b': 1, 'AN5-25_b': 1, 'AW2-01_a': 1}; forward_score=72.0; seq_a_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=3; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgtttgttaa
+>HWI-D00393:103:C6KCUANXX:2:1204:11153:34132_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-38_b': 1, 'AN4-39_b': 1, 'AN2-31_b': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; status=full; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=3; seq_length=100; mode=alignment; head_quality=37.0; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactattcagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2106:2429:2922_CONS_SUB_SUB_CMP ali_length=93; seq_ab_match=93; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-38_b': 1}; forward_score=72.0; score=371.700731814; seq_a_mismatch=0; forward_tag=tctactga; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.7299270073; avg_quality=59.4522292994; seq_a_single=32; score_norm=3.99678206251; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=99; status=full; mode=alignment; head_quality=37.0; position=11_08F; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggtaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2201:17654:97503_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=34.6; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-34_b': 1}; forward_score=72.0; score=307.231253197; seq_a_mismatch=0; forward_tag=tcagtgtc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=53.8115942029; avg_quality=51.4113924051; seq_a_single=33; score_norm=3.33947014344; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tcagtgtc; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=35.1; position=12_02B; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgtgaa
+>HWI-D00393:103:C6KCUANXX:2:2206:15790:49247_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-24_b': 1, 'AWO-41_a': 1, 'AW2-35_a': 1, 'AN4-35_b': 1, 'AW2-07_a': 1, 'AN3-04_b': 1, 'AN2-13_a': 1, 'AN4-22_b': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=8; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttagggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2301:12930:40102_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'ABR-15_a': 1, 'AN4-39_b': 1}; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=2; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttaacaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2315:17692:90977_CONS_SUB_SUB_CMP ali_length=93; seq_a_deletion=0; reverse_score=72.0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-38_b': 1, 'ABR-41_a': 1, 'AN3-17_b': 1}; forward_score=72.0; seq_a_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=32; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; goodAli=Alignement; count=3; seq_length=99; mode=alignment; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactattagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1207:9047:41800_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'ABR-13_a': 2, 'AN5-19_a': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=3; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgctcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2210:14421:16016_CONS_SUB_SUB_CMP reverse_score=66.0; count=7; direction=reverse; seq_b_insertion=0; experiment=australie; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; seq_length=99; start=ctaaa; merged_sample={'AW2-12_b': 1, 'AN4-41_b': 1, 'AW2-07_a': 1, 'AN5-21_b': 1, 'AN2-15_a': 1, 'AN4-23_b': 1, 'AN4-37_b': 1}; seq_a_insertion=0; mode=alignment; status=full; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgtta
+>HWI-D00393:103:C6KCUANXX:2:2211:13367:14752_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=32.6; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW1-18_a': 1}; forward_score=72.0; score=367.610399661; seq_a_mismatch=0; forward_tag=gtcacgtc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=61.0434782609; avg_quality=57.6329113924; seq_a_single=33; score_norm=3.9957652137; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=gtcgtaga; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=35.6; position=02_10C; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaagatctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:2307:6880:68904_CONS_SUB_SUB_CMP ali_length=81; seq_ab_match=56; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-37_b': 1}; forward_score=72.0; score=59.9384545346; seq_a_mismatch=1; forward_tag=atcagtca; seq_b_mismatch=22; start=ctaaa; experiment=australie; mid_quality=52.6666666667; avg_quality=50.6835443038; seq_a_single=33; score_norm=0.73998092018; reverse_score=72.0; direction=reverse; seq_b_insertion=2; seq_b_deletion=13; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_08E; seq_b_single=44; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaagtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1312:11682:89893_CONS_SUB_SUB_CMP ali_length=92; seq_a_deletion=0; reverse_score=72.0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-19_b': 1, 'AN5-10_b': 1, 'AN5-15_b': 1, 'AW2-34_b': 1, 'AN5-45_b': 1, 'AN4-40_b': 1}; forward_score=72.0; seq_a_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; status=full; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=6; seq_length=100; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcattaa
+>HWI-D00393:103:C6KCUANXX:2:2109:18223:83128_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'ABR-15_a': 1, 'ABR-13_a': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=cgctctcg; goodAli=Alignement; count=2; seq_length=100; status=full; mode=alignment; head_quality=37.0; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttggcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2204:19781:26262_CONS_SUB_SUB_CMP ali_length=95; seq_ab_match=95; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'ABR-01_a': 1}; forward_score=72.0; score=379.691935178; seq_a_mismatch=0; forward_tag=gatcgcga; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=63.5703703704; avg_quality=60.1419354839; seq_a_single=30; score_norm=3.9967572124; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=155; reverse_tag=actagatc; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=01_07H; seq_b_single=30; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaagatctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2215:4598:28592_CONS_SUB_SUB_CMP status=full; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-40_b': 1, 'AW2-35_b': 1, 'AN5-03_b': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; goodAli=Alignement; count=3; seq_length=100; mode=alignment; head_quality=37.0; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggcctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2304:13327:3228_CONS_SUB_SUB merged_sample={'AN4-36_b': 1, 'AN4-29_b': 1, 'AW2-01_b': 1, 'AW2-35_a': 1, 'ABR-46_a': 1, 'AW1-18_a': 1, 'AW1-40_b': 1, 'AN4-24_b': 1, 'AW2-07_b': 2}; forward_score=72.0; seq_b_insertion=0; seq_a_insertion=0; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; count=10; seq_length=100; start=ctaaa; experiment=australie; reverse_score=72.0; mode=alignment; status=full; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtcccgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1208:20375:7918_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; seq_a_deletion=0; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-37_b': 1, 'AW2-30_a': 1, 'AN4-35_b': 1}; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=3; seq_length=100; status=full; mode=alignment; head_quality=37.0; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcatagctatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1215:20045:28654_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-12_b': 1, 'AN5-42_b': 1, 'AN4-23_b': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=3; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcctaactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1302:19280:14816_CONS_SUB_SUB_CMP status=full; merged_sample={'ABR-01_a': 1, 'AWO-46_b': 1, 'AN4-22_b': 1}; seq_b_insertion=0; seq_a_mismatch=0; forward_score=72.0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; count=3; seq_length=100; start=ctaaa; experiment=australie; seq_a_insertion=0; mode=alignment; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgtacgttaa
+>HWI-D00393:103:C6KCUANXX:2:2214:8779:29491_CONS_SUB_SUB_CMP status=full; merged_sample={'AN5-24_b': 1, 'ADR-13_a': 2, 'AW2-35_a': 1}; seq_b_insertion=0; seq_a_insertion=0; forward_score=72.0; reverse_match=tttgtctgcttaattgcg; seq_b_mismatch=0; seq_a_deletion=0; count=4; seq_length=100; start=ctaaa; experiment=australie; reverse_score=72.0; mode=alignment; seq_b_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; head_quality=37.0; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggctaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2104:3449:54357_CONS_SUB_SUB_CMP status=full; merged_sample={'AN4-13_b': 1, 'AN4-42_b': 1, 'AN4-38_b': 1, 'AN5-21_b': 1, 'AN4-46_b': 1, 'AN4-12_b': 6}; seq_b_insertion=0; seq_a_mismatch=0; forward_score=72.0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; count=11; seq_length=100; start=ctaaa; experiment=australie; seq_a_insertion=0; mode=alignment; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgttag
+>HWI-D00393:103:C6KCUANXX:2:1102:14455:71108_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-23_b': 1}; forward_score=72.0; score=367.706336455; seq_a_mismatch=0; forward_tag=actagatc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3333333333; avg_quality=59.1265822785; seq_a_single=33; score_norm=3.99680800494; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=ctatgcta; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=09_05G; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgtcag
+>HWI-D00393:103:C6KCUANXX:2:1110:14996:73808_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-43_b': 1, 'AW2-40_b': 1, 'AW2-07_b': 2}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=4; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagtaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1204:14078:1983_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-13_b': 1}; forward_score=72.0; score=367.706336455; seq_a_mismatch=0; forward_tag=tagtcgca; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3333333333; avg_quality=59.1265822785; seq_a_single=33; score_norm=3.99680800494; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=atatagcg; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=09_04E; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttactaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1212:8502:98185_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-37_b': 1, 'AW2-35_a': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=2; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcatgactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1305:7874:81774_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-07_a': 1, 'AN4-34_b': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=2; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtcttgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1103:10874:79989_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-35_b': 1}; forward_score=72.0; score=367.706336455; seq_a_mismatch=0; forward_tag=gtgtacat; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3333333333; avg_quality=59.1265822785; seq_a_single=33; score_norm=3.99680800494; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=agcacagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=09_07C; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttcaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1207:7817:59077_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-38_b': 1}; forward_score=72.0; score=366.948065081; seq_a_mismatch=0; forward_tag=tctactga; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=60.9420289855; avg_quality=57.9113924051; seq_a_single=33; score_norm=3.9885659248; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_08F; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgatcgttat
+>HWI-D00393:103:C6KCUANXX:2:1308:2120:40513_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN3-42_b': 1}; forward_score=72.0; score=367.703923809; seq_a_mismatch=0; forward_tag=atgatcgc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3043478261; avg_quality=59.1012658228; seq_a_single=33; score_norm=3.99678178053; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=actctgct; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_03B; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcattcgttat
+>HWI-D00393:103:C6KCUANXX:2:2206:6280:74968_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=acacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-40_a': 1}; forward_score=66.0; score=367.706336455; seq_a_mismatch=0; forward_tag=gatcgcga; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3333333333; avg_quality=59.1265822785; seq_a_single=33; score_norm=3.99680800494; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=catcagtc; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=05_08H; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttgaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1215:13979:31122_CONS_SUB_SUB_CMP ali_length=93; seq_ab_match=93; tail_quality=37.0; reverse_match=tttgttgcttaattgcga; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-34_b': 1}; forward_score=72.0; score=371.70314446; seq_a_mismatch=0; forward_tag=atgatcgc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.6861313869; avg_quality=59.4140127389; seq_a_single=32; score_norm=3.99680800494; reverse_score=66.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=99; status=full; mode=alignment; head_quality=37.0; position=11_08B; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggtaagggtctcgttcgtta
+>HWI-D00393:103:C6KCUANXX:2:2208:15903:75212_CONS_SUB_SUB ali_length=92; seq_ab_match=91; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-01_b': 1}; forward_score=72.0; score=359.811368897; seq_a_mismatch=1; forward_tag=actagatc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.0072463768; avg_quality=58.8417721519; seq_a_single=33; score_norm=3.91099314019; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tcagtgtc; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=09_02G; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagtaggttaaggtctcgtttgttaa
+>HWI-D00393:103:C6KCUANXX:2:1203:16969:99847_CONS_SUB_SUB ali_length=92; seq_ab_match=91; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-40_b': 1}; forward_score=72.0; score=359.526419012; seq_a_mismatch=0; forward_tag=ctgcgtac; seq_b_mismatch=1; start=ctaaa; experiment=australie; mid_quality=60.9782608696; avg_quality=57.9430379747; seq_a_single=33; score_norm=3.90789585883; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_08H; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataacaatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2213:12449:50581_CONS_SUB_SUB_CMP status=full; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-45_b': 1, 'AN5-25_b': 1, 'AN4-22_b': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; goodAli=Alignement; count=3; seq_length=100; mode=alignment; head_quality=37.0; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggtataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2310:15600:75905_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-03_a': 1}; forward_score=72.0; score=367.701511163; seq_a_mismatch=0; forward_tag=gtacgact; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.2753623188; avg_quality=59.0759493671; seq_a_single=33; score_norm=3.99675555612; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=gtgtacat; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=03_03A; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggtaagggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:1214:16466:5047_CONS_SUB_SUB status=full; merged_sample={'AN2-07_b': 1, 'AN1-17_a': 1, 'AN3-25_b': 1, 'AN4-23_b': 1, 'AW2-35_a': 1}; seq_b_insertion=0; seq_a_insertion=0; seq_a_mismatch=0; forward_score=72.0; seq_b_deletion=0; seq_a_deletion=0; count=5; seq_length=100; start=ctaaa; experiment=australie; reverse_score=72.0; mode=alignment; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcgggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1306:6166:18686_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=24.8; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-39_b': 1}; forward_score=72.0; score=200.442729055; seq_a_mismatch=0; forward_tag=gatgatct; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=40.5289855072; avg_quality=38.6898734177; seq_a_single=33; score_norm=2.17872531582; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=27.2; position=11_08G; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggctagagtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2312:19984:25051_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-03_b': 1}; forward_score=72.0; score=367.703923809; seq_a_mismatch=0; forward_tag=acacacac; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3043478261; avg_quality=59.1012658228; seq_a_single=33; score_norm=3.99678178053; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=actctgct; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=09_03A; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttagagtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:1209:10424:5048_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-43_b': 1}; forward_score=72.0; score=367.706336455; seq_a_mismatch=0; forward_tag=acgacgag; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3333333333; avg_quality=59.1265822785; seq_a_single=33; score_norm=3.99680800494; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=agtgctac; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_09C; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggataaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:1306:10017:29340_CONS_SUB_SUB_CMP merged_sample={'AN4-36_b': 1, 'AN4-12_b': 1, 'AW2-07_a': 1}; forward_score=72.0; direction=reverse; seq_b_insertion=0; seq_a_insertion=0; seq_a_mismatch=0; seq_b_deletion=0; status=full; seq_a_deletion=0; count=3; seq_length=100; start=ctaaa; experiment=australie; reverse_score=72.0; mode=alignment; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttagcataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1116:1609:19254_CONS_SUB_SUB ali_length=93; seq_ab_match=93; tail_quality=34.4; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-45_b': 1}; forward_score=72.0; score=365.502727331; seq_a_mismatch=0; forward_tag=atcagtca; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=55.8905109489; avg_quality=52.9936305732; seq_a_single=32; score_norm=3.93013685302; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=agtgctac; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=31.9; position=11_09E; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgtttt
+>HWI-D00393:103:C6KCUANXX:2:1116:18814:29744_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-35_a': 1}; forward_score=72.0; score=367.048675141; seq_a_mismatch=0; forward_tag=acgacgag; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=61.7101449275; avg_quality=58.582278481; seq_a_single=33; score_norm=3.9896595124; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=actagatc; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=03_07C; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcagattaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1301:18017:5670_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=91; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-29_b': 1}; forward_score=72.0; score=307.503017136; seq_a_mismatch=0; forward_tag=atcagtca; seq_b_mismatch=1; start=ctaaa; experiment=australie; mid_quality=48.0362318841; avg_quality=46.0632911392; seq_a_single=33; score_norm=3.3424240993; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=agcacagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=27.9; position=11_07E; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagccggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2304:14057:23271_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'ADR-47_b': 1, 'AN3-35_b': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=2; seq_length=100; status=full; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataattatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1105:1482:86390_CONS_SUB_SUB_CMP ali_length=94; seq_ab_match=94; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-13_b': 1}; forward_score=72.0; score=375.690301881; seq_a_mismatch=0; forward_tag=atcagtca; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=63.0735294118; avg_quality=59.7307692308; seq_a_single=31; score_norm=3.99670533916; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=156; reverse_tag=cgagtcgt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_11E; seq_b_single=31; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgtaaa
+>HWI-D00393:103:C6KCUANXX:2:1214:1498:16792_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=36.4; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-01_a': 1}; forward_score=72.0; score=367.691974388; seq_a_mismatch=0; forward_tag=gatgatct; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.2608695652; avg_quality=59.0253164557; seq_a_single=33; score_norm=3.99665189552; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=acagcaca; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=03_02G; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggctgaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2112:6296:18402_CONS_SUB_SUB_CMP reverse_score=72.0; count=2; direction=reverse; seq_b_insertion=0; experiment=australie; seq_b_deletion=0; status=full; seq_a_deletion=0; seq_length=100; start=ctaaa; merged_sample={'AN4-11_b': 1, 'AN4-17_b': 1}; seq_a_insertion=0; mode=alignment; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggaataactatttagcaggttaaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:2202:15115:92220_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-35_b': 1}; forward_score=72.0; score=367.703923809; seq_a_mismatch=0; forward_tag=gtgtacat; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3043478261; avg_quality=59.1012658228; seq_a_single=33; score_norm=3.99678178053; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=agcacagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=09_07C; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggtccgggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2308:15218:31319_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=35.1; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-30_a': 1}; forward_score=72.0; score=367.379880648; seq_a_mismatch=0; forward_tag=gcgtcagc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=61.7463768116; avg_quality=58.4936708861; seq_a_single=33; score_norm=3.99325957226; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=agactatg; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=06_01F; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactagttagcaggttaaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:1303:8962:10788_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=91; tail_quality=35.6; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-40_b': 1}; forward_score=72.0; score=328.577396734; seq_a_mismatch=0; forward_tag=ctgcgtac; seq_b_mismatch=1; start=ctaaa; experiment=australie; mid_quality=51.2898550725; avg_quality=49.2721518987; seq_a_single=33; score_norm=3.57149344276; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=35.1; position=11_08H; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactttttagcaggttaaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:1309:18593:53694_CONS_SUB_SUB_CMP ali_length=92; seq_a_deletion=0; reverse_score=72.0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-43_b': 1, 'ABR-41_a': 1, 'AW2-35_a': 1}; forward_score=72.0; seq_a_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; status=full; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=3; seq_length=100; mode=alignment; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactacttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1208:4517:87099_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-03_a': 1}; forward_score=72.0; score=367.701511163; seq_a_mismatch=0; forward_tag=gtacgact; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.2753623188; avg_quality=59.0759493671; seq_a_single=33; score_norm=3.99675555612; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=gtgtacat; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=03_03A; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagaaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1115:14275:7184_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-45_b': 1}; forward_score=72.0; score=367.706336455; seq_a_mismatch=0; forward_tag=atcagtca; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3333333333; avg_quality=59.1265822785; seq_a_single=33; score_norm=3.99680800494; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=agtgctac; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_09E; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttagagtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1209:11513:82442_CONS_SUB_SUB_CMP ali_length=94; seq_ab_match=94; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-39_a': 1}; forward_score=72.0; score=375.685590398; seq_a_mismatch=0; forward_tag=gatgatct; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=63.0294117647; avg_quality=59.6923076923; seq_a_single=31; score_norm=3.996655217; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=156; reverse_tag=actagatc; goodAli=Alignement; count=1; seq_length=98; status=full; mode=alignment; head_quality=37.0; position=03_07G; seq_b_single=31; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1214:6399:72570_CONS_SUB_SUB ali_length=92; seq_ab_match=88; tail_quality=24.5; reverse_match=tttgtctgcttaattacg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-30_a': 1}; forward_score=72.0; score=255.892896628; seq_a_mismatch=3; forward_tag=tctactga; seq_b_mismatch=1; start=ctaaa; experiment=australie; mid_quality=40.4057971014; avg_quality=38.5253164557; seq_a_single=33; score_norm=2.78144452857; reverse_score=66.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tactatac; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=26.6; position=03_06F; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgtgcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1305:3473:19356_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-07_b': 1}; forward_score=72.0; score=367.635869076; seq_a_mismatch=0; forward_tag=tactatac; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=61.9782608696; avg_quality=58.8164556962; seq_a_single=33; score_norm=3.99604205518; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=actctgct; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=09_03F; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcgtaactatttagcaggttaaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:2302:5940:68325_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-37_b': 1}; forward_score=72.0; score=367.706336455; seq_a_mismatch=0; forward_tag=atcagtca; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3333333333; avg_quality=59.1265822785; seq_a_single=33; score_norm=3.99680800494; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_08E; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggtcgaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:2309:13769:62059_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=91; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-35_a': 1}; forward_score=72.0; score=359.470664833; seq_a_mismatch=0; forward_tag=acgacgag; seq_b_mismatch=1; start=ctaaa; experiment=australie; mid_quality=61.7536231884; avg_quality=58.6202531646; seq_a_single=33; score_norm=3.90728983514; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=actagatc; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=03_07C; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaagttctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2315:8947:22476_CONS_SUB_SUB ali_length=93; seq_ab_match=93; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN3-25_a': 1}; forward_score=72.0; score=368.159719936; seq_a_mismatch=0; forward_tag=acacacac; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=58.4744525547; avg_quality=55.7388535032; seq_a_single=32; score_norm=3.95870666598; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=agactatg; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=05_01A; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactgtttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1301:19819:95569_CONS_SUB_SUB_CMP ali_length=94; seq_ab_match=94; tail_quality=37.0; reverse_match=tttgtctttaattccgat; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-34_b': 1}; forward_score=72.0; score=375.699952465; seq_a_mismatch=0; forward_tag=tcagtgtc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=63.1911764706; avg_quality=59.8333333333; seq_a_single=31; score_norm=3.99680800494; reverse_score=60.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=156; reverse_tag=tcagtgtc; goodAli=Alignement; count=1; seq_length=98; status=full; mode=alignment; head_quality=37.0; position=12_02B; seq_b_single=31; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgtt
+>HWI-D00393:103:C6KCUANXX:2:1313:4613:34271_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=32.3; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW1-11_a': 1}; forward_score=72.0; score=313.551003229; seq_a_mismatch=0; forward_tag=gtcacgtc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=56.6594202899; avg_quality=53.1518987342; seq_a_single=33; score_norm=3.40816307858; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=cgctctcg; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=25.6; position=02_09C; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggtcaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2113:10988:9799_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=30.2; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-13_b': 1}; forward_score=72.0; score=361.020650934; seq_a_mismatch=0; forward_tag=atcagtca; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=55.6086956522; avg_quality=52.4936708861; seq_a_single=33; score_norm=3.92413751015; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=cgagtcgt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=31.8; position=11_11E; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaatgtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2113:5686:82397_CONS_SUB_SUB_CMP ali_length=93; seq_ab_match=93; tail_quality=36.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'blk-12_b': 1}; forward_score=72.0; score=371.343139227; seq_a_mismatch=0; forward_tag=ctatgcta; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.1532846715; avg_quality=58.7643312102; seq_a_single=32; score_norm=3.99293698094; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=ctgcgtac; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=35.1; position=08_12E; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggatagggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:2311:15976:57660_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=91; tail_quality=30.1; reverse_match=tttgtctggttaattccg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-39_b': 1}; forward_score=72.0; score=346.55597612; seq_a_mismatch=0; forward_tag=gatgatct; seq_b_mismatch=1; start=ctaaa; experiment=australie; mid_quality=56.8550724638; avg_quality=53.8037974684; seq_a_single=33; score_norm=3.76691278391; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=35.4; position=11_08G; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggtgaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2205:20527:78743_CONS_SUB_SUB ali_length=95; seq_ab_match=93; tail_quality=29.1; reverse_match=tttgtctgcttaatggcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-12_b': 1}; forward_score=72.0; score=351.353534518; seq_a_mismatch=1; forward_tag=catcagtc; seq_b_mismatch=1; start=ctaaa; experiment=australie; mid_quality=50.2074074074; avg_quality=47.8709677419; seq_a_single=30; score_norm=3.69845825808; reverse_score=66.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=155; reverse_tag=ctatgcta; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=35.1; position=11_05D; seq_b_single=30; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtcgcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1104:5688:6100_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-46_b': 1}; forward_score=72.0; score=367.370471331; seq_a_mismatch=0; forward_tag=tctactga; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.0362318841; avg_quality=58.8670886076; seq_a_single=33; score_norm=3.99315729707; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=agtgctac; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_09F; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtcccattcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1111:18652:56309_CONS_SUB_SUB ali_length=93; seq_ab_match=93; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN2-12_a': 1}; forward_score=72.0; score=371.700731814; seq_a_mismatch=0; forward_tag=atatagcg; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.7299270073; avg_quality=59.4522292994; seq_a_single=32; score_norm=3.99678206251; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=tatgtcag; goodAli=Alignement; count=1; seq_length=99; status=full; mode=alignment; head_quality=37.0; position=04_04D; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttgttaa
+>HWI-D00393:103:C6KCUANXX:2:1211:20612:10566_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-38_b': 1}; forward_score=72.0; score=367.703923809; seq_a_mismatch=0; forward_tag=tctactga; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3043478261; avg_quality=59.1012658228; seq_a_single=33; score_norm=3.99678178053; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_08F; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataaccatttagctggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2113:19027:63568_CONS_SUB_SUB_CMP ali_length=93; seq_ab_match=93; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-38_b': 1}; forward_score=72.0; score=371.700731814; seq_a_mismatch=0; forward_tag=tctactga; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.7299270073; avg_quality=59.4267515924; seq_a_single=32; score_norm=3.99678206251; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=36.6; position=11_08F; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagtaggctagagtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:2201:15565:85738_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=32.1; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-23_b': 1}; forward_score=72.0; score=365.670520501; seq_a_mismatch=0; forward_tag=actagatc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=59.5289855072; avg_quality=56.3670886076; seq_a_single=33; score_norm=3.97467957066; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=ctatgcta; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=09_05G; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcatatctatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2215:13270:16769_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-01_b': 1}; forward_score=72.0; score=367.703923809; seq_a_mismatch=0; forward_tag=actagatc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3043478261; avg_quality=59.1012658228; seq_a_single=33; score_norm=3.99678178053; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tcagtgtc; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=09_02G; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgtccgttaa
+>HWI-D00393:103:C6KCUANXX:2:1102:18567:11128_CONS_SUB_SUB_CMP ali_length=93; seq_ab_match=93; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN2-10_b': 1}; forward_score=72.0; score=370.995083415; seq_a_mismatch=0; forward_tag=gtcgtaga; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=61.8248175182; avg_quality=58.5732484076; seq_a_single=32; score_norm=3.98919444533; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=atatagcg; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=35.6; position=10_04B; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttgacataactatttagcaggttaaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:1106:7644:40758_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=90; tail_quality=34.2; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-35_b': 1}; forward_score=72.0; score=296.115079326; seq_a_mismatch=2; forward_tag=acgacgag; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=54.1449275362; avg_quality=51.6075949367; seq_a_single=33; score_norm=3.21864216659; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=tagctagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=34.0; position=11_08C; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgttac
+>HWI-D00393:103:C6KCUANXX:2:1111:17524:16890_CONS_SUB_SUB ali_length=94; seq_ab_match=94; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN2-12_b': 1}; forward_score=72.0; score=375.680651297; seq_a_mismatch=0; forward_tag=gactgatg; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.9264705882; avg_quality=59.6025641026; seq_a_single=31; score_norm=3.99660267337; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=156; reverse_tag=atatagcg; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=10_04D; seq_b_single=31; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttgtcataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2109:4640:21588_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN5-10_b': 1}; forward_score=72.0; score=367.701511163; seq_a_mismatch=0; forward_tag=atgatcgc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.2173913043; avg_quality=59.0253164557; seq_a_single=33; score_norm=3.99675555612; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=cgagtcgt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_11B; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcggtcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2212:14824:56282_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW1-11_a': 1}; forward_score=72.0; score=367.703923809; seq_a_mismatch=0; forward_tag=gtcacgtc; seq_b_mismatch=0; start=ctaaa; experiment=australie; mid_quality=62.3043478261; avg_quality=59.1012658228; seq_a_single=33; score_norm=3.99678178053; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=cgctctcg; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=02_09C; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggtcaaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:2306:10336:10418_CONS_SUB_SUB ali_length=92; seq_ab_match=92; tail_quality=37.0; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW2-35_b': 1, 'AN4-23_b': 1}; forward_score=72.0; seq_a_mismatch=0; seq_b_mismatch=0; start=ctaaa; experiment=australie; seq_a_single=33; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; goodAli=Alignement; count=2; seq_length=100; status=full; mode=alignment; head_quality=37.0; seq_b_single=33; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataaccatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2216:11206:55822_CONS_SUB_SUB_CMP ali_length=93; seq_ab_match=92; tail_quality=29.8; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AW1-30_a': 1}; forward_score=72.0; score=357.173125277; seq_a_mismatch=0; forward_tag=cgctctcg; seq_b_mismatch=1; start=ctaaa; experiment=australie; mid_quality=54.6642335766; avg_quality=51.4777070064; seq_a_single=32; score_norm=3.84057123954; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=gactgatg; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=29.5; position=02_12A; seq_b_single=32; 
+ctaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcttaactatttagcaggttaaggtctcgttcgttat
+>HWI-D00393:103:C6KCUANXX:2:2303:4215:99753_CONS_SUB_SUB ali_length=93; seq_ab_match=93; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgtattgcc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-41_b': 1}; forward_score=66.0; score=371.70314446; seq_a_mismatch=0; forward_tag=gtacgact; seq_b_mismatch=0; start=gaaaa; experiment=australie; mid_quality=62.7591240876; avg_quality=59.4522292994; seq_a_single=32; score_norm=3.99680800494; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=157; reverse_tag=agtgctac; goodAli=Alignement; count=1; seq_length=99; status=full; mode=alignment; head_quality=36.6; position=11_09A; seq_b_single=32; 
+gaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagagt
+tggcataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2209:18822:35652_CONS_SUB_SUB_CMP ali_length=92; seq_ab_match=92; tail_quality=37.0; reverse_match=tttgtctgcttaattgcg; seq_a_deletion=0; forward_match=tcacagacctgttattgc; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; merged_sample={'AN4-29_b': 1}; forward_score=72.0; score=366.357546614; seq_a_mismatch=0; forward_tag=atcagtca; seq_b_mismatch=0; start=gtaaa; experiment=australie; mid_quality=60.7898550725; avg_quality=57.7784810127; seq_a_single=33; score_norm=3.98214724581; reverse_score=72.0; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=158; reverse_tag=agcacagt; goodAli=Alignement; count=1; seq_length=100; status=full; mode=alignment; head_quality=37.0; position=11_07E; seq_b_single=33; 
+gtaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttggcataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:2212:12163:84900_CONS_SUB_SUB merged_sample={'AN4-36_b': 1, 'AN4-39_b': 1, 'AN4-12_b': 1, 'AW2-03_b': 1, 'ABR-42_a': 1, 'AN4-46_b': 1, 'AN4-23_b': 1, 'AN4-37_b': 1, 'AN5-23_b': 1, 'AN5-41_b': 1, 'AW1-18_a': 1, 'AN4-35_b': 1, 'AW2-35_b': 1, 'AW2-35_a': 1}; reverse_score=72.0; seq_b_insertion=0; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; count=14; seq_length=99; start=taaaa; experiment=australie; seq_a_insertion=0; mode=alignment; status=full; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; goodAli=Alignement; 
+taaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagagt
+tggcataactatttagcaggttaaggtctcgttcgttaa
+>HWI-D00393:103:C6KCUANXX:2:1210:8971:79507_CONS_SUB_SUB_CMP merged_sample={'AN5-41_b': 1, 'AW2-01_a': 3, 'AN5-25_b': 2, 'AW2-07_b': 4, 'AN5-23_b': 3, 'AW2-01_b': 1}; ali_length=92; seq_b_insertion=0; seq_b_deletion=0; status=full; seq_a_deletion=0; count=14; seq_length=100; start=ttaaa; experiment=australie; seq_a_insertion=0; mode=alignment; seq_length_ori=158; forward_primer=tcacagacctgttattgc; reverse_primer=tttgtctgsttaattscg; seq_a_single=33; seq_b_single=33; goodAli=Alignement; 
+ttaaaacttccgtcggctaatcgccgacagtccctctaagaagttgactaccaacgagag
+ttagcataactattcagtaggttaaggtctcgttcgttaa
--- a/pkg/obiformats/kseq/test.seq
+++ b/pkg/obiformats/kseq/test.seq
@@ -0,0 +1,12 @@
+>1 {"taxid" : 1234, "specie_name" : "Lupus lupus"}
+acgtacgtacgtagc
+>2 {"taxid" : 3243, "specie_name" : "Gallus gallus"} test
+acgatcgatc
+@3  {"taxid" : 3243, "specie_name" : "Gallus gallus"} test2
+cgctagcatagc
+cgatatgactta
+
+78wo82usd980
+d88fau
+
+238ud8
--- a/pkg/obiformats/ncbitaxdump/read.go
+++ b/pkg/obiformats/ncbitaxdump/read.go
@@ -0,0 +1,141 @@
+package ncbitaxdump
+
+import (
+	"bufio"
+	"encoding/csv"
+	"errors"
+	"fmt"
+	"io"
+	"log"
+	"os"
+	"path"
+	"strconv"
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obitax"
+)
+
+func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
+	file := csv.NewReader(reader)
+	file.Comma = '|'
+	file.Comment = '#'
+	file.TrimLeadingSpace = true
+	file.ReuseRecord = true
+
+	for record, err := file.Read(); err == nil; record, err = file.Read() {
+		taxid, _ := strconv.Atoi(strings.TrimSpace(record[0]))
+		parent, _ := strconv.Atoi(strings.TrimSpace(record[1]))
+		rank := strings.TrimSpace(record[2])
+
+		taxonomy.AddNewTaxa(taxid, parent, rank, true, true)
+	}
+
+	taxonomy.ReindexParent()
+}
+
+func loadNameTable(reader io.Reader, taxonomy *obitax.Taxonomy, onlysn bool) int {
+	// file := csv.NewReader(reader)
+	// file.Comma = '|'
+	// file.Comment = '#'
+	// file.TrimLeadingSpace = true
+	// file.ReuseRecord = true
+	// file.LazyQuotes = true
+	file := bufio.NewReader(reader)
+
+	n := 0
+
+	for line, prefix, err := file.ReadLine(); err == nil; line, prefix, err = file.ReadLine() {
+
+		if prefix {
+			return -1
+		}
+
+		record := strings.Split(string(line), "|")
+		taxid, _ := strconv.Atoi(strings.TrimSpace(record[0]))
+		name := strings.TrimSpace(record[1])
+		classname := strings.TrimSpace(record[3])
+
+		if !onlysn || classname == "scientific name" {
+			n++
+			taxonomy.AddNewName(taxid, &name, &classname)
+		}
+	}
+
+	return n
+}
+
+func loadMergedTable(reader io.Reader, taxonomy *obitax.Taxonomy) int {
+	file := csv.NewReader(reader)
+	file.Comma = '|'
+	file.Comment = '#'
+	file.TrimLeadingSpace = true
+	file.ReuseRecord = true
+
+	n := 0
+
+	for record, err := file.Read(); err == nil; record, err = file.Read() {
+		oldtaxid, _ := strconv.Atoi(strings.TrimSpace(record[0]))
+		newtaxid, _ := strconv.Atoi(strings.TrimSpace(record[1]))
+		n++
+		taxonomy.AddNewAlias(newtaxid, oldtaxid)
+	}
+
+	return n
+}
+
+func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
+
+	taxonomy := obitax.NewTaxonomy()
+
+	//
+	// Load the Taxonomy nodes
+	//
+
+	log.Printf("Loading Taxonomy nodes\n")
+
+	nodefile, err := os.Open(path.Join(directory, "nodes.dmp"))
+	if err != nil {
+		return nil, errors.New(fmt.Sprintf("Cannot open nodes file from '%s'",
+			directory))
+	}
+	defer nodefile.Close()
+
+	buffered := bufio.NewReader(nodefile)
+	loadNodeTable(buffered, taxonomy)
+	log.Printf("%d Taxonomy nodes read\n", taxonomy.Length())
+
+	//
+	// Load the Taxonomy nodes
+	//
+
+	log.Printf("Loading Taxon names\n")
+
+	namefile, nerr := os.Open(path.Join(directory, "names.dmp"))
+	if nerr != nil {
+		return nil, errors.New(fmt.Sprintf("Cannot open names file from '%s'",
+			directory))
+	}
+	defer namefile.Close()
+
+	n := loadNameTable(namefile, taxonomy, onlysn)
+	log.Printf("%d taxon names read\n", n)
+
+	//
+	// Load the merged taxa
+	//
+
+	log.Printf("Loading Merged taxa\n")
+
+	aliasfile, aerr := os.Open(path.Join(directory, "merged.dmp"))
+	if aerr != nil {
+		return nil, errors.New(fmt.Sprintf("Cannot open merged file from '%s'",
+			directory))
+	}
+	defer aliasfile.Close()
+
+	buffered = bufio.NewReader(aliasfile)
+	n = loadMergedTable(buffered, taxonomy)
+	log.Printf("%d merged taxa read\n", n)
+
+	return taxonomy, nil
+}
--- a/pkg/obiformats/options.go
+++ b/pkg/obiformats/options.go
@@ -0,0 +1,158 @@
+package obiformats
+
+import "git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+
+type __options__ struct {
+	fastseq_header_parser obiseq.SeqAnnotator
+	fastseq_header_writer func(obiseq.BioSequence) string
+	with_progress_bar     bool
+	buffer_size           int
+	batch_size            int
+	quality_shift         int
+	parallel_workers      int
+}
+
+type Options struct {
+	pointer *__options__
+}
+
+type WithOption func(Options)
+
+func MakeOptions(setters []WithOption) Options {
+	o := __options__{
+		fastseq_header_parser: ParseGuessedFastSeqHeader,
+		fastseq_header_writer: FormatFastSeqJsonHeader,
+		with_progress_bar:     false,
+		buffer_size:           2,
+		quality_shift:         33,
+		parallel_workers:      4,
+		batch_size:            5000,
+	}
+
+	opt := Options{&o}
+
+	for _, set := range setters {
+		set(opt)
+	}
+
+	return opt
+}
+
+func (opt Options) QualityShift() int {
+	return opt.pointer.quality_shift
+}
+
+func (opt Options) BufferSize() int {
+	return opt.pointer.buffer_size
+}
+
+func (opt Options) BatchSize() int {
+	return opt.pointer.batch_size
+}
+
+func (opt Options) ParallelWorkers() int {
+	return opt.pointer.parallel_workers
+}
+
+func (opt Options) ParseFastSeqHeader() obiseq.SeqAnnotator {
+	return opt.pointer.fastseq_header_parser
+}
+
+func (opt Options) FormatFastSeqHeader() func(obiseq.BioSequence) string {
+	return opt.pointer.fastseq_header_writer
+}
+
+func (opt Options) ProgressBar() bool {
+	return opt.pointer.with_progress_bar
+}
+
+func OptionsBufferSize(size int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.buffer_size = size
+	})
+
+	return f
+}
+
+// Allows to specify the ascii code corresponding to
+// a quality of 0 in fastq encoded quality scores.
+func OptionsQualityShift(shift int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.quality_shift = shift
+	})
+
+	return f
+}
+
+// Allows to specify a quality shift of 33, corresponding
+// to a FastQ file qualities encoded following Sanger
+// convention. This corresponds to Illumina produced FastQ
+// files.
+func OptionsQualitySanger() WithOption {
+	return OptionsQualityShift(33)
+}
+
+// Allows to specify a quality shift of 64, corresponding
+// to a FastQ file qualities encoded following the Solexa
+// convention.
+func OptionsQualitySolexa() WithOption {
+	return OptionsQualityShift(64)
+}
+
+func OptionsFastSeqHeaderParser(parser obiseq.SeqAnnotator) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.fastseq_header_parser = parser
+	})
+
+	return f
+}
+
+func OptionFastSeqDoNotParseHeader() WithOption {
+	return OptionsFastSeqHeaderParser(nil)
+}
+
+func OptionsFastSeqDefaultHeaderParser() WithOption {
+	return OptionsFastSeqHeaderParser(ParseGuessedFastSeqHeader)
+}
+
+// OptionsFastSeqHeaderFormat allows foor specifying the format
+// used to write FASTA and FASTQ sequence.
+func OptionsFastSeqHeaderFormat(format func(obiseq.BioSequence) string) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.fastseq_header_writer = format
+	})
+
+	return f
+}
+
+func OptionsParallelWorkers(nworkers int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.parallel_workers = nworkers
+	})
+
+	return f
+}
+
+func OptionsBatchSize(size int) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.batch_size = size
+	})
+
+	return f
+}
+
+func OptionsWithProgressBar() WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.with_progress_bar = true
+	})
+
+	return f
+}
+
+func OptionsWithoutProgressBar() WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.with_progress_bar = false
+	})
+
+	return f
+}
--- a/pkg/obiformats/universal_read.go
+++ b/pkg/obiformats/universal_read.go
@@ -0,0 +1,93 @@
+package obiformats
+
+import (
+	"bufio"
+	"compress/gzip"
+	"io"
+	"log"
+	"os"
+	"strings"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func GuessSeqFileType(firstline string) string {
+	switch {
+	case strings.HasPrefix(firstline, "#@ecopcr-v2"):
+		return "ecopcr"
+
+	case strings.HasPrefix(firstline, "#"):
+		return "ecopcr"
+
+	case strings.HasPrefix(firstline, ">"):
+		return "fasta"
+
+	case strings.HasPrefix(firstline, "@"):
+		return "fastq"
+
+	case strings.HasPrefix(firstline, "ID   "):
+		return "embl"
+
+	case strings.HasPrefix(firstline, "LOCUS       "):
+		return "genebank"
+
+	default:
+		return "unknown"
+	}
+}
+
+func ReadSequencesBatchFromFile(filename string, options ...WithOption) (obiseq.IBioSequenceBatch, error) {
+	var file *os.File
+	var reader io.Reader
+	var greader io.Reader
+	var err error
+
+	file, err = os.Open(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return obiseq.NilIBioSequenceBatch, err
+	}
+
+	reader = file
+
+	// Test if the flux is compressed by gzip
+	greader, err = gzip.NewReader(reader)
+	if err != nil {
+		file.Seek(0, 0)
+	} else {
+		log.Printf("File %s is gz compressed ", filename)
+		reader = greader
+	}
+
+	breader := bufio.NewReader(reader)
+
+	tag, _ := breader.Peek(30)
+
+	filetype := GuessSeqFileType(string(tag))
+	log.Printf("File guessed format : %s (tag: %s)",
+		filetype, (strings.Split(string(tag), "\n"))[0])
+	reader = breader
+
+	switch filetype {
+	case "fastq", "fasta":
+		file.Close()
+		is, _ := ReadFastSeqBatchFromFile(filename, options...)
+		return is, nil
+	case "ecopcr":
+		return ReadEcoPCRBatch(reader, options...), nil
+	case "embl":
+		return ReadEMBLBatch(reader, options...), nil
+	default:
+		log.Fatalf("File %s has guessed format %s which is not yet implemented",
+			filename, filetype)
+	}
+
+	return obiseq.NilIBioSequenceBatch, nil
+}
+
+func ReadSequencesFromFile(filename string, options ...WithOption) (obiseq.IBioSequence, error) {
+	ib, err := ReadSequencesBatchFromFile(filename, options...)
+	return ib.SortBatches().IBioSequence(), err
+
+}
--- a/pkg/obiformats/universal_write.go
+++ b/pkg/obiformats/universal_write.go
@@ -0,0 +1,79 @@
+package obiformats
+
+import (
+	"fmt"
+	"io"
+	"log"
+	"os"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func WriteSequences(iterator obiseq.IBioSequence,
+	file io.Writer,
+	options ...WithOption) error {
+
+	opts := MakeOptions(options)
+
+	header_format := opts.FormatFastSeqHeader()
+	quality := opts.QualityShift()
+
+	ok := iterator.Next()
+
+	if ok {
+		seq := iterator.Get()
+		if seq.HasQualities() {
+			fmt.Fprintln(file, FormatFastq(seq, quality, header_format))
+			WriteFastq(iterator, file, options...)
+		} else {
+			fmt.Fprintln(file, FormatFasta(seq, header_format))
+			WriteFasta(iterator, file, options...)
+		}
+	}
+
+	return nil
+}
+
+func WriteSequencesToFile(iterator obiseq.IBioSequence,
+	filename string,
+	options ...WithOption) error {
+
+	file, err := os.Create(filename)
+
+	if err != nil {
+		log.Fatalf("open file error: %v", err)
+		return err
+	}
+
+	return WriteSequences(iterator, file, options...)
+}
+
+func WriteSequencesToStdout(iterator obiseq.IBioSequence, options ...WithOption) error {
+	return WriteSequences(iterator, os.Stdout, options...)
+}
+
+// func WriteSequenceBatch(iterator obiseq.IBioSequenceBatch,
+// 	file io.Writer,
+// 	options ...WithOption) error {
+
+// 	opts := MakeOptions(options)
+
+// 	header_format := opts.FormatFastSeqHeader()
+// 	quality := opts.QualityShift()
+
+// 	ok := iterator.Next()
+
+// 	if ok {
+// 		batch := iterator.Get()
+// 		if batch.Slice()[0].HasQualities() {
+// 			file.Write()
+// 			fmt.Fprintln(file, FormatFastq(seq, quality, header_format))
+// 			WriteFastq(iterator, file, options...)
+// 		} else {
+// 			fmt.Fprintln(file, FormatFasta(seq, header_format))
+// 			WriteFasta(iterator, file, options...)
+// 		}
+// 	}
+
+// 	return nil
+// }