remove unused ReadRaw functions

shock-server/node/file/format/fasta/fasta.go

@@ -61,27 +61,6 @@ func (self *Reader) Read() (sequence *seq.Seq, err error) {
 	return
 }
 
-// Read a single sequence and return it or an error.
-func (self *Reader) ReadRaw(p []byte) (n int, err error) {
-	if self.r == nil {
-		self.r = bufio.NewReader(self.f)
-	}
-	p[n] = byte('>')
-	n = 1
-	for {
-		read, er := self.r.ReadBytes('>')
-		if len(read) > 1 {
-			copy(p[n:n+len(read)-1], read[0:len(read)-1])
-			n += len(read) - 1
-			break
-		} else if er != nil {
-			err = er
-			break
-		}
-	}
-	return
-}
-
 // Read a single sequence and return read offset for indexing.
 func (self *Reader) GetReadOffset() (n int, err error) {
 	if self.r == nil {

shock-server/node/file/format/fastq/fastq.go

@@ -17,7 +17,7 @@ import (
 )
 
 var (
-	Regex = regexp.MustCompile(`^[\n\r]*@[\S\t ]+[\n\r]+[A-Za-z\-]+[\n\r]+\+[\S\t ]*[\n\r]+\S*[\n\r]+`)
+	Regex = regexp.MustCompile(`^[\n\r]*@\S+[\S\t ]+[\n\r]+[A-Za-z\-]+[\n\r]+\+[\S\t ]*[\n\r]+\S*[\n\r]+`)
 )
 
 // Fastq sequence format reader type.
@@ -97,47 +97,6 @@ READ:
 	return
 }
 
-func (self *Reader) ReadRaw(p []byte) (n int, err error) {
-	if self.r == nil {
-		self.r = bufio.NewReader(self.f)
-	}
-	curr := 0
-	id, err := self.r.ReadBytes('\n')
-	if err != nil {
-		return 0, err
-	} else if !bytes.HasPrefix(id, []byte{'@'}) {
-		return 0, errors.New("Invalid format: id line does not start with @")
-	}
-	copy(p[curr:len(id)+curr], id)
-	curr += len(id)
-
-	seq, err := self.r.ReadBytes('\n')
-	if err != nil {
-		return 0, err
-	}
-	copy(p[curr:len(seq)+curr], seq)
-	curr += len(seq)
-
-	plus, err := self.r.ReadBytes('\n')
-	if err != nil {
-		return 0, err
-	} else if !bytes.HasPrefix(plus, []byte{'+'}) {
-		return 0, errors.New("Invalid format: plus line does not start with +")
-	}
-	copy(p[curr:len(plus)+curr], plus)
-	curr += len(plus)
-
-	qual, err := self.r.ReadBytes('\n')
-	if err != nil {
-		return 0, err
-	} else if len(seq) != len(qual) {
-		return 0, errors.New("Invalid format: length of sequence and quality lines do not match")
-	}
-	copy(p[curr:len(qual)+curr], qual)
-	n = curr + len(qual)
-	return
-}
-
 // Read a single sequence and return read offset for indexing.
 func (self *Reader) GetReadOffset() (n int, err error) {
 	if self.r == nil {

shock-server/node/file/format/multi/multi.go

@@ -71,16 +71,6 @@ func (r *Reader) Read() (*seq.Seq, error) {
 	return r.r.Read()
 }
 
-func (r *Reader) ReadRaw(p []byte) (n int, err error) {
-	if r.r == nil {
-		err := r.DetermineFormat()
-		if err != nil {
-			return 0, err
-		}
-	}
-	return r.r.ReadRaw(p)
-}
-
 func (r *Reader) GetReadOffset() (n int, err error) {
 	if r.r == nil {
 		err := r.DetermineFormat()

shock-server/node/file/format/sam/sam.go

@@ -78,25 +78,6 @@ func (self *Reader) Read() (sequence *seq.Seq, err error) {
 	return
 }
 
-// Read a single sequence and return it or an error. (used for making record index)
-func (self *Reader) ReadRaw(p []byte) (n int, err error) {
-	for {
-		read, er := self.r.ReadBytes('\n')
-		n += len(read)
-		if len(read) > 1 {
-			if read[0] == '@' {
-				continue
-			}
-			copy(p[0:len(read)], read[0:len(read)])
-			break
-		} else if er != nil {
-			err = er
-			break
-		}
-	}
-	return
-}
-
 // Read a single sequence and return read offset for indexing.
 func (self *Reader) GetReadOffset() (n int, err error) {
 	for {

shock-server/node/file/format/seq/seq.go

@@ -26,14 +26,12 @@ type ReadFormater interface {
 
 type Reader interface {
 	Read() (*Seq, error)
-	ReadRaw(p []byte) (int, error)
 	GetReadOffset() (int, error)
 	SeekChunk(int64) (int64, error)
 }
 
 type ReadRewinder interface {
 	Read() (*Seq, error)
-	ReadRaw(p []byte) (int, error)
 	GetReadOffset() (int, error)
 	SeekChunk(int64) (int64, error)
 	Rewind() error