diff --git a/const.go b/const.go
index 0bd9b27..0b197b5 100644
--- a/const.go
+++ b/const.go
@@ -20,13 +20,14 @@ var conf config
 var region *Region
 
 const (
-	VERSION            = "0.0.2-beta"
+	VERSION            = "0.0.3-beta"
 	DefaultBaseQuality = 30
 )
 
 type config struct {
 	Config                 string  `goptions:"-c, --config, description='Config file'"`
 	Version                bool    `goptions:"-v, --version, description='Show version'"`
+	Mode                   bool    `goptions:"--fast, description='Usage fast mode with higher memory usage'"`
 	Debug                  bool    `goptions:"--debug, description='Show debug info'" long:"debug" description:"Config file"`
 	File                   string  `goptions:"-f, --file, description='The bam file to be analyzed'"`
 	Output                 string  `goptions:"-o, --output-file, description='The output statistics file'"`
diff --git a/fast.go b/fast.go
new file mode 100644
index 0000000..eb4308e
--- /dev/null
+++ b/fast.go
@@ -0,0 +1,152 @@
+package main
+
+import (
+	"github.com/biogo/hts/sam"
+	"github.com/golang-collections/collections/set"
+	"strings"
+	"sync"
+)
+
+func workerFast(
+	wg *sync.WaitGroup, refs chan *ChanChunk, w chan string,
+	omopolymericPositions, splicePositions, targetPositions map[string]*set.Set,
+	chrRefs map[string][]byte) {
+	defer wg.Done()
+
+	for {
+		ref, ok := <-refs
+		if !ok {
+			break
+		}
+
+		//chrRef, err := fetchFasta(ref.ToRegion())
+		//if err != nil {
+		//	sugar.Warnf("try to modify %s", ref)
+		//	chrRef, err = fetchFasta(ref.SwitchRegion())
+		//}
+		//if err != nil {
+		//	sugar.Fatal(err)
+		//}
+
+		chrRef, ok := chrRefs[ref.Ref]
+		if !ok {
+			sugar.Errorf("failed to get %s from reference", ref.Ref)
+			continue
+		}
+
+		iter, err := fetchBamFast(ref.Chunks)
+		if err != nil {
+			sugar.Fatal(err)
+		}
+
+		lastEnd := 0
+		total := 0
+		edits := make(map[int]*EditsInfo)
+		for iter.Next() {
+			record := NewRecord(iter.Record())
+
+			if lastEnd == 0 {
+				lastEnd = record.End
+			}
+
+			total++
+
+			if !filterReads(record) {
+				continue
+			}
+
+			start, index := 0, 0
+			for _, i := range record.Cigar {
+				if i.Type() == sam.CigarMatch {
+					for j := 1; j <= i.Len(); j++ {
+						at := index + j - 1
+
+						if at >= record.Seq.Length {
+							sugar.Errorf("%s - %d - %d - %d", record.Cigar, index, at, record.Seq.Length)
+							sugar.Fatal(record.SeqString())
+						}
+
+						genomic := start + record.Start
+
+						if _, ok := edits[genomic]; !ok {
+							edits[genomic] = NewEditsInfo(ref.Ref, chrRef[genomic-1], genomic)
+						}
+
+						edits[genomic].AddReads(record, at)
+						start++
+					}
+					index += i.Len()
+				} else if i.Type() != sam.CigarDeletion || i.Type() != sam.CigarHardClipped || i.Type() != sam.CigarInsertion {
+					start += i.Len()
+				}
+			}
+
+			if record.Start > lastEnd {
+				getColumn(edits, []map[string]*set.Set{omopolymericPositions, splicePositions}, targetPositions, w)
+
+				edits = make(map[int]*EditsInfo)
+				lastEnd = record.End
+			}
+		}
+
+		getColumn(edits, []map[string]*set.Set{omopolymericPositions, splicePositions}, targetPositions, w)
+	}
+
+	w <- "done"
+}
+
+func fastMode(
+	wg *sync.WaitGroup, w chan string,
+	omopolymericPositions, spicePositions, targetPositions map[string]*set.Set) {
+	var lock sync.Mutex
+	refs := make(chan *ChanChunk)
+
+	references, err := fetchBamRefsFast()
+	if err != nil {
+		sugar.Fatal(err)
+	}
+
+	sugar.Infof("load reference from %s", conf.Reference)
+	chrRefs := make(map[string][]byte)
+	for ref, _ := range references {
+		wg.Add(1)
+		go func(ref string, wg *sync.WaitGroup, lock *sync.Mutex) {
+			defer wg.Done()
+			temp, err := fetchFasta(&Region{Chrom: ref})
+			if err != nil {
+				sugar.Warnf("try to modify %s", ref)
+				if strings.HasPrefix(ref, "chr") {
+					temp, err = fetchFasta(&Region{Chrom: strings.ReplaceAll(ref, "chr", "")})
+				} else {
+					temp, err = fetchFasta(&Region{Chrom: "chr" + ref})
+				}
+			}
+			if err != nil {
+				sugar.Fatal(err)
+			}
+			lock.Lock()
+			chrRefs[ref] = temp
+			lock.Unlock()
+		}(ref, wg, &lock)
+	}
+
+	wg.Wait()
+
+	wg.Add(1)
+	go writer(w, wg)
+
+	for i := 0; i < conf.Process; i++ {
+		go workerFast(wg, refs, w, omopolymericPositions, spicePositions, targetPositions, chrRefs)
+		wg.Add(1)
+	}
+
+	for ref, chunks := range references {
+		sugar.Infof("read reads from %s", ref)
+		for _, c := range chunks {
+			sugar.Debug(c)
+			refs <- c
+		}
+	}
+
+	close(refs)
+}
diff --git a/go.mod b/go.mod
index 713d772..05b891b 100644
--- a/go.mod
+++ b/go.mod
@@ -5,11 +5,10 @@ go 1.14
 require (
 	github.com/biogo/biogo v1.0.2
 	github.com/biogo/hts v1.1.0
-	github.com/cheggaaa/pb v2.0.7+incompatible
-	github.com/cheggaaa/pb/v3 v3.0.4
 	github.com/golang-collections/collections v0.0.0-20130729185459-604e922904d3
 	github.com/mattn/go-colorable v0.1.7 // indirect
 	github.com/pkg/errors v0.8.1
+	github.com/schollz/progressbar/v3 v3.3.4
 	github.com/voxelbrain/goptions v0.0.0-20180630082107-58cddc247ea2
 	go.uber.org/zap v1.15.0
 	gopkg.in/VividCortex/ewma.v1 v1.1.1 // indirect
diff --git a/go.sum b/go.sum
index 0ccfa15..3496735 100644
--- a/go.sum
+++ b/go.sum
@@ -12,11 +12,6 @@ github.com/biogo/hts v1.1.0 h1:J6Na8+e+MYyEpV1B762GUvt4mhtPn3tnQQaxWyKo5rk=
 github.com/biogo/hts v1.1.0/go.mod h1:6C9MdMt9ALD5PsluK5n0B0svHOpmVse3UjQQx/cTgOw=
 github.com/biogo/store v0.0.0-20200104231603-2c6ad937eb83 h1:wQjRDdhQmyjOlYPJGS/FHKMA13hgT4anRXIWjHX84zU=
 github.com/biogo/store v0.0.0-20200104231603-2c6ad937eb83/go.mod h1:wdbXg77soR6ESRprAMEwAQDFtLT6EAGF5o1GRy0cB5k=
-github.com/cheggaaa/pb v1.0.28 h1:kWGpdAcSp3MxMU9CCHOwz/8V0kCHN4+9yQm2MzWuI98=
-github.com/cheggaaa/pb v2.0.7+incompatible h1:gLKifR1UkZ/kLkda5gC0K6c8g+jU2sINPtBeOiNlMhU=
-github.com/cheggaaa/pb v2.0.7+incompatible/go.mod h1:pQciLPpbU0oxA0h+VJYYLxO+XeDQb5pZijXscXHm81s=
-github.com/cheggaaa/pb/v3 v3.0.4 h1:QZEPYOj2ix6d5oEg63fbHmpolrnNiwjUsk+h74Yt4bM=
-github.com/cheggaaa/pb/v3 v3.0.4/go.mod h1:7rgWxLrAUcFMkvJuv09+DYi7mMUYi8nO9iOWcvGJPfw=
 github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/fatih/color v1.7.0 h1:DkWD4oS2D8LGGgTQ6IvwJJXSL5Vp2ffcQg58nFV38Ys=
@@ -25,6 +20,7 @@ github.com/go-gl/glfw/v3.3/glfw v0.0.0-20191125211704-12ad95a8df72/go.mod h1:tQ2
 github.com/golang-collections/collections v0.0.0-20130729185459-604e922904d3 h1:zN2lZNZRflqFyxVaTIU61KNKQ9C0055u9CAfpmqUvo4=
 github.com/golang-collections/collections v0.0.0-20130729185459-604e922904d3/go.mod h1:nPpo7qLxd6XL3hWJG/O60sR8ZKfMCiIoNap5GvD12KU=
 github.com/google/renameio v0.1.0/go.mod h1:KWCgfxg9yswjAJkECMjeO8J8rahYeXnNhOm40UhjYkI=
+github.com/k0kubun/go-ansi v0.0.0-20180517002512-3bf9e2903213/go.mod h1:vNUNkEQ1e29fT/6vq2aBdFsgNPmy8qMdSay1npru+Sw=
 github.com/kisielk/gotool v1.0.0/go.mod h1:XhKaO+MFFWcvkIS/tQcRk01m1F5IRFswLeQ+oQHNcck=
 github.com/kortschak/utter v0.0.0-20190412033250-50fe362e6560/go.mod h1:oDr41C7kH9wvAikWyFhr6UFr8R7nelpmCF5XR5rL7I8=
 github.com/kr/pretty v0.1.0/go.mod h1:dAy3ld7l9f0ibDNOQOHHMYYIIbhfbHSm3C4ZsoJORNo=
@@ -42,10 +38,17 @@ github.com/mattn/go-isatty v0.0.12 h1:wuysRhFDzyxgEmMf5xjvJ2M9dZoWAXNNr5LSBS7uHX
 github.com/mattn/go-isatty v0.0.12/go.mod h1:cbi8OIDigv2wuxKPP5vlRcQ1OAZbq2CE4Kysco4FUpU=
 github.com/mattn/go-runewidth v0.0.7 h1:Ei8KR0497xHyKJPAv59M1dkC+rOZCMBJ+t3fZ+twI54=
 github.com/mattn/go-runewidth v0.0.7/go.mod h1:H031xJmbD/WCDINGzjvQ9THkh0rPKHF+m2gUSrubnMI=
+github.com/mattn/go-runewidth v0.0.9 h1:Lm995f3rfxdpd6TSmuVCHVb/QhupuXlYr8sCI/QdE+0=
+github.com/mattn/go-runewidth v0.0.9/go.mod h1:H031xJmbD/WCDINGzjvQ9THkh0rPKHF+m2gUSrubnMI=
+github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db h1:62I3jR2EmQ4l5rM/4FEfDWcRD+abF5XlKShorW5LRoQ=
+github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db/go.mod h1:l0dey0ia/Uv7NcFFVbCLtqEBQbrT4OCwCSKTEv6enCw=
 github.com/pkg/errors v0.8.1 h1:iURUrRGxPUNPdy5/HRSm+Yj6okJ6UtLINN0Q9M4+h3I=
 github.com/pkg/errors v0.8.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
 github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
 github.com/rogpeppe/go-internal v1.3.0/go.mod h1:M8bDsm7K2OlrFYOpmOWEs/qY81heoFRclV5y23lUDJ4=
+github.com/schollz/progressbar v1.0.0 h1:gbyFReLHDkZo8mxy/dLWMr+Mpb1MokGJ1FqCiqacjZM=
+github.com/schollz/progressbar/v3 v3.3.4 h1:nMinx+JaEm/zJz4cEyClQeAw5rsYSB5th3xv+5lV6Vg=
+github.com/schollz/progressbar/v3 v3.3.4/go.mod h1:Rp5lZwpgtYmlvmGo1FyDwXMqagyRBQYSDwzlP9QDu84=
 github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
 github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
 github.com/stretchr/testify v1.4.0/go.mod h1:j7eGeouHqKxXV5pUuKE4zz7dFj8WfuZ+81PSLYec5m4=
@@ -82,6 +85,8 @@ golang.org/x/sys v0.0.0-20191128015809-6d18c012aee9/go.mod h1:h1NjWce9XRLGQEsW7w
 golang.org/x/sys v0.0.0-20200116001909-b77594299b42/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae h1:/WDfKMnPU+m5M4xB+6x4kaepxRw6jWvR5iDRdvjHgy8=
 golang.org/x/sys v0.0.0-20200223170610-d5e6a3e2c0ae/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
+golang.org/x/sys v0.0.0-20200615200032-f1bc736245b1 h1:ogLJMz+qpzav7lGMh10LMvAkM/fAoGlaiiHYiFYdm80=
+golang.org/x/sys v0.0.0-20200615200032-f1bc736245b1/go.mod h1:h1NjWce9XRLGQEsW7wpKNCjG9DtNlClVuFLEZdDNbEs=
 golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
 golang.org/x/tools v0.0.0-20190311212946-11955173bddd/go.mod h1:LCzVGOaR6xXOjkQ3onu1FJEFr0SW1gC7cKk1uF8kGRs=
 golang.org/x/tools v0.0.0-20190621195816-6e04913cbbac/go.mod h1:/rFqwRUd4F7ZHNgwSSTFct+R/Kf4OFW1sUzUTQQTgfc=
diff --git a/load.go b/load.go
index b56eb1d..0278ce8 100644
--- a/load.go
+++ b/load.go
@@ -9,6 +9,7 @@ import (
 	"regexp"
 	"strconv"
 	"strings"
+	"sync"
 
 	"github.com/biogo/biogo/alphabet"
 	"github.com/biogo/biogo/io/seqio"
@@ -17,15 +18,10 @@ import (
 	"github.com/biogo/hts/bam"
 	"github.com/biogo/hts/bgzf"
 	"github.com/biogo/hts/fai"
-	"github.com/cheggaaa/pb/v3"
+	"github.com/biogo/hts/sam"
 	"github.com/golang-collections/collections/set"
 	"github.com/pkg/errors"
-	"io"
-	"math"
-	"os"
-	"regexp"
-	"strconv"
-	"strings"
+	"github.com/schollz/progressbar/v3"
 )
 
 // loadBedFile is function that load bed files
@@ -47,12 +43,14 @@ func loadBedFile() (map[string]*set.Set, error) {
 	}
 	defer f.Close()
 
-	bar := pb.New64(stats.Size())
-	r := bar.NewProxyReader(f)
+	bar := progressbar.DefaultBytes(
+		stats.Size(),
+		"loading",
+	)
 
-	reader := bufio.NewReader(r)
+	reader := bufio.NewReader(f)
 	if strings.HasSuffix(conf.BedFile, ".gz") {
-		gr, err := gzip.NewReader(r)
+		gr, err := gzip.NewReader(f)
 		if err != nil {
 			return targetPosition, errors.Wrapf(err, "failed to open %s", conf.BedFile)
 		}
@@ -69,6 +67,8 @@ func loadBedFile() (map[string]*set.Set, error) {
 			}
 		}
 
+		bar.Add(len([]byte(line)))
+
 		fields := strings.Split(strings.TrimSpace(line), "\t")
 
 		chr := fields[0]
@@ -167,43 +167,75 @@ func createOmopolymericPositions() error {
 		return err
 	}
 
-	for _, chromosome := range chromosomes {
-		// fasta.Reader requires a known type template to fill
-		// with FASTA data. Here we use *linear.Seq.
-		template := linear.NewSeq(chromosome, nil, alphabet.DNAredundant)
-		r := fasta.NewReader(f, template)
-
-		// Make a seqio.Scanner to simplify iterating over a
-		// stream of data.
-		sc := seqio.NewScanner(r)
-
-		// Iterate through each sequence in a multifasta and examine the
-		// ID, description and sequence data.
-		for sc.Next() {
-			// Get the current sequence and type assert to *linear.Seq.
-			// While this is unnecessary here, it can be useful to have
-			// the concrete type.
-			s := sc.Seq().(*linear.Seq)
-
-			equals := 0
-			var last alphabet.Letter
-			for i, b := range s.Seq {
-				if b == last {
-					equals += 1
-				} else {
-					if equals >= conf.OmopolymericSpan {
-						positions = append(positions, &Omopolymeric{
-							Chromosome: chromosome, NegEquals: i - equals,
-							I: i, Equals: equals, Last: last,
-						})
+	chromChan := make(chan string)
+	outputChan := make(chan []*Omopolymeric)
+
+	var wg sync.WaitGroup
+	var lock sync.Mutex
+
+	for i := 0; i < maxInt(conf.Process, 1); i++ {
+		wg.Add(1)
+		go func(outputChan chan []*Omopolymeric, chromChan chan string, wg *sync.WaitGroup, lock *sync.Mutex) {
+			for {
+				chromosome, ok := <-chromChan
+				if !ok {
+					break
+				}
+				sugar.Debugf("Loading fasta of %s", chromosome)
+				tempPositions := make([]*Omopolymeric, 0, 0)
+				// fasta.Reader requires a known type template to fill
+				// with FASTA data. Here we use *linear.Seq.
+				template := linear.NewSeq(chromosome, nil, alphabet.DNAredundant)
+				r := fasta.NewReader(f, template)
+
+				// Make a seqio.Scanner to simplify iterating over a
+				// stream of data.
+				sc := seqio.NewScanner(r)
+
+				// Iterate through each sequence in a multifasta and examine the
+				// ID, description and sequence data.
+				for sc.Next() {
+					// Get the current sequence and type assert to *linear.Seq.
+					// While this is unnecessary here, it can be useful to have
+					// the concrete type.
+					s := sc.Seq().(*linear.Seq)
+
+					equals := 0
+					var last alphabet.Letter
+					for i, b := range s.Seq {
+						if b == last {
+							equals += 1
+						} else {
+							if equals >= conf.OmopolymericSpan {
+
+								tempPositions = append(tempPositions, &Omopolymeric{
+									Chromosome: chromosome, NegEquals: i - equals,
+									I: i, Equals: equals, Last: last,
+								})
+
+							}
+							equals = 1
+						}
+						last = b
 					}
-					equals = 1
 				}
-				last = b
+
+				lock.Lock()
+				positions = append(positions, tempPositions...)
+				lock.Unlock()
 			}
-		}
+
+			defer wg.Done()
+		}(outputChan, chromChan, &wg, &lock)
 	}
 
+	for _, chromosome := range chromosomes {
+		chromChan <- chromosome
+	}
+
+	close(chromChan)
+	wg.Wait()
+
 	sugar.Infof("%d total omopolymeric positions found.", len(positions))
 
 	sugar.Infof("Writing omopolymeric positions to file: %s.", conf.OmopolymericFile)
@@ -215,16 +247,24 @@ func createOmopolymericPositions() error {
 	defer f.Close()
 
 	writer := bufio.NewWriter(f)
+	defer writer.Flush()
 
 	if _, err := writer.WriteString("#" + strings.Join([]string{"Chromomosome", "Start", "End", "Length", "Symbol"}, "\t") + "\n"); err != nil {
 		return err
 	}
 
+	bar := progressbar.Default(int64(len(positions)), "writing")
+
 	for _, position := range positions {
-		if _, err := writer.WriteString(position.String() + "\n"); err != nil {
-			return err
+		data := position.String() + "\n"
+		bar.Add(1)
+		if _, err := writer.WriteString(data); err != nil {
+			sugar.Fatal(err)
+		} else {
+
 		}
 	}
+	bar.Finish()
 	return nil
 }
 
@@ -237,12 +277,22 @@ func loadOmopolymericPositions() (map[string]*set.Set, error) {
 
 	sugar.Infof("Loading omopolymeric positions from file %s", conf.OmopolymericFile)
 
+	stats, err := os.Stat(conf.OmopolymericFile)
+	if os.IsNotExist(err) {
+		return positions, errors.New(conf.OmopolymericFile + " not exists")
+	}
+
 	f, err := os.Open(conf.OmopolymericFile)
 	if err != nil {
 		return positions, errors.Wrapf(err, "failed to open %s", conf.OmopolymericFile)
 	}
 	defer f.Close()
 
+	bar := progressbar.DefaultBytes(
+		stats.Size(),
+		"loading",
+	)
+
 	r := bufio.NewReader(f)
 
 	total := 0
@@ -259,6 +309,7 @@ func loadOmopolymericPositions() (map[string]*set.Set, error) {
 		if strings.HasPrefix(line, "#") {
 			continue
 		}
+		bar.Add(len([]byte(line)))
 
 		fields := strings.Split(strings.TrimSpace(line), "\t")
 		if region.Chrom == "" || fields[0] == region.Chrom {
@@ -295,7 +346,9 @@ func loadOmopolymericPositions() (map[string]*set.Set, error) {
 		}
 	}
 
-	sugar.Infof("[%v] %d total omopolymeric positions found.", region, total)
+	bar.Finish()
+
+	sugar.Infof("%d total omopolymeric positions found.", total)
 	return positions, nil
 }
 
@@ -318,12 +371,14 @@ func loadSplicingPositions() (map[string]*set.Set, error) {
 	}
 	defer f.Close()
 
-	bar := pb.New64(stats.Size())
-	r := bar.NewProxyReader(f)
+	bar := progressbar.DefaultBytes(
+		stats.Size(),
+		"loading",
+	)
 
-	reader := bufio.NewReader(r)
+	reader := bufio.NewReader(f)
 	if strings.HasSuffix(conf.SplicingFile, ".gz") {
-		gr, err := gzip.NewReader(r)
+		gr, err := gzip.NewReader(f)
 		if err != nil {
 			return res, errors.Wrapf(err, "failed to open %s", conf.SplicingFile)
 		}
@@ -341,7 +396,7 @@ func loadSplicingPositions() (map[string]*set.Set, error) {
 				return res, err
 			}
 		}
-
+		bar.Add(len([]byte(line)))
 		lines := regexp.MustCompile("\\s+").Split(strings.TrimSpace(line), -1)
 		chrom := lines[0]
 
@@ -372,6 +427,8 @@ func loadSplicingPositions() (map[string]*set.Set, error) {
 		res[chrom] = temp
 	}
 
+	bar.Finish()
+
 	return res, nil
 }
 
@@ -458,8 +515,8 @@ func adjustRegion(regions []int, idx *bam.Index, ref *sam.Reference, bamReader *
 	return res, nil
 }
 
-func fetchBamRefs() ([]string, error) {
-	res := make([]string, 0, 0)
+func fetchBamRefsFast() (map[string][]*ChanChunk, error) {
+	res := make(map[string][]*ChanChunk)
 	ifh, err := os.Open(conf.File)
 	//Panic if something went wrong:
 	if err != nil {
@@ -512,6 +569,27 @@ func fetchBamRefs() ([]string, error) {
 	return res, nil
 }
 
+func fetchBamRefs() ([]string, error) {
+	res := make([]string, 0, 0)
+	ifh, err := os.Open(conf.File)
+	//Panic if something went wrong:
+	if err != nil {
+		return res, err
+	}
+
+	//Create a new BAM reader with maximum
+	//concurrency:
+	bamReader, err := bam.NewReader(ifh, 0)
+	if err != nil {
+		return res, err
+	}
+
+	for _, ref := range bamReader.Header().Refs() {
+		res = append(res, ref.Name())
+	}
+	return res, nil
+}
+
 func fetchFasta(region *Region) ([]byte, error) {
 	ifh, err := os.Open(conf.Reference)
 	if err != nil {
@@ -550,6 +628,54 @@ func fetchFasta(region *Region) ([]byte, error) {
 	return res, err
 }
 
+func fetchBamFast(region bgzf.Chunk) (*bam.Iterator, error) {
+	ifh, err := os.Open(conf.File)
+	//Panic if something went wrong:
+	if err != nil {
+		return nil, err
+	}
+
+	idxF, err := os.Open(conf.File + ".bai")
+	if err != nil {
+		return nil, err
+	}
+	defer idxF.Close()
+
+	idx, err := bam.ReadIndex(idxF)
+	if err != nil {
+		return nil, err
+	}
+
+	//Create a new BAM reader with maximum
+	//concurrency:
+	bamReader, err := bam.NewReader(ifh, 1)
+	if err != nil {
+		return nil, err
+	}
+
+	chunks := make([]bgzf.Chunk, 0, 0)
+
+	for _, ref := range bamReader.Header().Refs() {
+		if region.Chrom != "" && ref.Name() == region.Chrom {
+			if region.Start == 0 && region.End == 0 {
+				if stats, ok := idx.ReferenceStats(ref.ID()); ok {
+					chunks = append(chunks, stats.Chunk)
+				}
+			} else if region.Chrom != "" && region.Start > 0 && region.End > 0 {
+				if tempChunks, err := idx.Chunks(ref, region.Start, region.End); err != nil {
+					chunks = append(chunks, tempChunks...)
+				}
+			}
+		} else if region.Chrom == "" {
+			if stats, ok := idx.ReferenceStats(ref.ID()); ok {
+				chunks = append(chunks, stats.Chunk)
+			}
+		}
+	}
+
+	return bam.NewIterator(bamReader, chunks)
+}
+
 func fetchBam(region *Region) (*bam.Iterator, error) {
 	sugar.Infof("read reads from %s", region.String())
 	ifh, err := os.Open(conf.File)
diff --git a/main.go b/main.go
index 22a602c..79bac6c 100644
--- a/main.go
+++ b/main.go
@@ -7,8 +7,6 @@ import (
 	"strings"
 	"sync"
 
-	"github.com/biogo/hts/sam"
-	"github.com/golang-collections/collections/set"
 	"github.com/voxelbrain/goptions"
 )
 
@@ -73,93 +71,6 @@ func writer(w chan string, wg *sync.WaitGroup) {
 	wg.Done()
 }
 
-func worker(wg *sync.WaitGroup, refs chan *Region, w chan string, omopolymericPositions, splicePositions, targetPositions map[string]*set.Set) {
-	defer wg.Done()
-
-	for {
-		ref, ok := <-refs
-		if !ok {
-			break
-		}
-
-		//chrRef, err := fetchFasta(ref.ToRegion())
-		//if err != nil {
-		//	sugar.Warnf("try to modify %s", ref)
-		//	chrRef, err = fetchFasta(ref.SwitchRegion())
-		//}
-		//if err != nil {
-		//	sugar.Fatal(err)
-		//}
-
-		chrRef, ok := chrRefs[ref.Ref]
-		if !ok {
-			sugar.Errorf("failed to get %s from reference", ref.Ref)
-			continue
-		}
-
-		iter, err := fetchBam(ref)
-		if err != nil {
-			sugar.Fatal(err)
-		}
-
-		lastEnd := 0
-		total := 0
-		edits := make(map[int]*EditsInfo)
-		for iter.Next() {
-			record := NewRecord(iter.Record())
-
-			if lastEnd == 0 {
-				lastEnd = record.End
-			}
-
-			total++
-
-			if !filterReads(record) {
-				continue
-			}
-
-			start, index := 0, 0
-			for _, i := range record.Cigar {
-				if i.Type() == sam.CigarMatch {
-					for j := 1; j <= i.Len(); j++ {
-						at := index + j - 1
-
-						if at >= record.Seq.Length {
-							sugar.Errorf("%s - %d - %d - %d", record.Cigar, index, at, record.Seq.Length)
-							sugar.Fatal(record.SeqString())
-						}
-
-						genomic := start + record.Start
-
-						if _, ok := edits[genomic]; !ok {
-							edits[genomic] = NewEditsInfo(ref.Chrom, chrRef[genomic-1], genomic)
-						}
-
-						edits[genomic].AddReads(record, at)
-						start++
-					}
-					index += i.Len()
-				} else if i.Type() != sam.CigarDeletion || i.Type() != sam.CigarHardClipped || i.Type() != sam.CigarInsertion {
-					start += i.Len()
-				}
-			}
-
-			if record.Start > lastEnd {
-				getColumn(edits, []map[string]*set.Set{omopolymericPositions, splicePositions}, targetPositions, w)
-
-				edits = make(map[int]*EditsInfo)
-				lastEnd = record.End
-			}
-		}
-
-		getColumn(edits, []map[string]*set.Set{omopolymericPositions, splicePositions}, targetPositions, w)
-
-		sugar.Debugf("read %d reads from %s", total, ref)
-	}
-
-	w <- "done"
-}
-
 func main() {
 	conf = defaultConfig()
 	goptions.ParseAndFail(&conf)
@@ -214,58 +125,15 @@ func main() {
 	sugar.Infof("Narrowing REDItools to region %s", region.String())
 
 	var wg sync.WaitGroup
-	w := make(chan string)
-	refs := make(chan *ChanChunk)
-
-	references, err := fetchBamRefs()
-	if err != nil {
-		sugar.Fatal(err)
-	}
 
-	sugar.Infof("load reference from %s", conf.Reference)
-	chrRefs := make(map[string][]byte)
-	for ref, _ := range references {
-		wg.Add(1)
-		go func(ref string, wg *sync.WaitGroup, lock *sync.Mutex) {
-			defer wg.Done()
-			temp, err := fetchFasta(&Region{Chrom: ref})
-			if err != nil {
-				sugar.Warnf("try to modify %s", ref)
-				if strings.HasPrefix(ref, "chr") {
-					temp, err = fetchFasta(&Region{Chrom: strings.ReplaceAll(ref, "chr", "")})
-				} else {
-					temp, err = fetchFasta(&Region{Chrom: "chr" + ref})
-				}
-			}
-			if err != nil {
-				sugar.Fatal(err)
-			}
-			lock.Lock()
-			chrRefs[ref] = temp
-			lock.Unlock()
-		}(ref, &wg, &lock)
-	}
-
-	wg.Wait()
-
-	wg.Add(1)
-	go writer(w, &wg)
-	refs := make(chan *Region)
-
-	for i := 0; i < conf.Process; i++ {
-		go worker(&wg, refs, w, omopolymericPositions, spicePositions, targetPositions)
-		wg.Add(1)
-	}
+	w := make(chan string)
 
-	for ref, chunks := range references {
-		sugar.Infof("read reads from %s", ref)
-		for _, c := range chunks {
-			sugar.Debug(c)
-			refs <- c
-		}
+	if conf.Mode {
+		fastMode(&wg, w, omopolymericPositions, spicePositions, targetPositions)
+	} else {
+		slowMode(&wg, w, omopolymericPositions, spicePositions, targetPositions)
 	}
 
-	close(refs)
 	wg.Wait()
 
 	timer.Toc()
diff --git a/slow.go b/slow.go
new file mode 100644
index 0000000..e7449a7
--- /dev/null
+++ b/slow.go
@@ -0,0 +1,120 @@
+package main
+
+import (
+	"github.com/biogo/hts/sam"
+	"github.com/golang-collections/collections/set"
+	"strings"
+	"sync"
+)
+
+func worker(wg *sync.WaitGroup, refs chan *Region, w chan string, omopolymericPositions, splicePositions, targetPositions map[string]*set.Set) {
+	defer wg.Done()
+
+	for {
+		ref, ok := <-refs
+		if !ok {
+			break
+		}
+
+		chrRef, err := fetchFasta(ref)
+		if err != nil {
+			sugar.Warnf("try to modify %s", ref.Chrom)
+			if strings.HasPrefix(ref.Chrom, "chr") {
+				chrRef, err = fetchFasta(&Region{Chrom: strings.ReplaceAll(ref.Chrom, "chr", "")})
+			} else {
+				chrRef, err = fetchFasta(&Region{Chrom: "chr" + ref.Chrom})
+			}
+		}
+		if err != nil {
+			sugar.Fatal(err)
+		}
+
+		iter, err := fetchBam(ref)
+		if err != nil {
+			sugar.Fatal(err)
+		}
+
+		lastEnd := 0
+		total := 0
+		edits := make(map[int]*EditsInfo)
+		for iter.Next() {
+			record := NewRecord(iter.Record())
+
+			if lastEnd == 0 {
+				lastEnd = record.End
+			}
+
+			total++
+
+			if !filterReads(record) {
+				continue
+			}
+
+			start, index := 0, 0
+			for _, i := range record.Cigar {
+				if i.Type() == sam.CigarMatch {
+					for j := 1; j <= i.Len(); j++ {
+						at := index + j - 1
+
+						if at >= record.Seq.Length {
+							sugar.Errorf("%s - %d - %d - %d", record.Cigar, index, at, record.Seq.Length)
+							sugar.Fatal(record.SeqString())
+						}
+
+						// record.QueryPosition = append(record.QueryPosition, at)
+
+						genomic := start + record.Start
+
+						if _, ok := edits[genomic]; !ok {
+							edits[genomic] = NewEditsInfo(ref.Chrom, chrRef[genomic-1], genomic)
+						}
+
+						edits[genomic].AddReads(record, at)
+						start++
+					}
+					index += i.Len()
+				} else if i.Type() != sam.CigarDeletion || i.Type() != sam.CigarHardClipped || i.Type() != sam.CigarInsertion {
+					start += i.Len()
+				}
+			}
+
+			if record.Start > lastEnd {
+				getColumn(edits, []map[string]*set.Set{omopolymericPositions, splicePositions}, targetPositions, w)
+
+				edits = make(map[int]*EditsInfo)
+				lastEnd = record.End
+			}
+		}
+
+		getColumn(edits, []map[string]*set.Set{omopolymericPositions, splicePositions}, targetPositions, w)
+
+		sugar.Debugf("read %d reads from %s", total, ref)
+	}
+
+	w <- "done"
+}
+
+func slowMode(wg *sync.WaitGroup, w chan string,
+	omopolymericPositions, spicePositions, targetPositions map[string]*set.Set) {
+
+	wg.Add(1)
+	go writer(w, wg)
+	refs := make(chan *Region)
+
+	for i := 0; i < conf.Process; i++ {
+		go worker(wg, refs, w, omopolymericPositions, spicePositions, targetPositions)
+		wg.Add(1)
+	}
+
+	if region.Empty() {
+		if references, err := fetchBamRefs(); err == nil {
+			for _, r := range references {
+				refs <- &Region{Chrom: r}
+			}
+		}
+	} else {
+		refs <- region
+	}
+
+	close(refs)
+}
diff --git a/utils.go b/utils.go
index 70f3b70..72104bb 100644
--- a/utils.go
+++ b/utils.go
@@ -21,7 +21,6 @@ func withinInterval(i int) bool {
 	return region.Start <= i && i <= region.End
 }
 
-
 func prop(tot, va int) float64 {
 	if tot == 0 {
 		return 0.0
@@ -119,7 +118,7 @@ func getColumn(edits map[int]*EditsInfo, positions []map[string]*set.Set, target
 		if !ok {
 			continue
 		}
-		
+
 		if edit.Ref == byte('N') {
 			continue
 		}