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// Copyright ©2012 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.
// Package sam implements SAM file format reading and writing. The SAM format
// is described in the SAM specification.
//
// http://samtools.github.io/hts-specs/SAMv1.pdf
package sam
import (
"bufio"
"errors"
"io"
)
// Reader implements SAM format reading.
type Reader struct {
r *bufio.Reader
h *Header
seenRefs map[string]*Reference
}
// NewReader returns a new Reader, reading from the given io.Reader.
func NewReader(r io.Reader) (*Reader, error) {
h, _ := NewHeader(nil, nil)
sr := &Reader{
r: bufio.NewReader(r),
h: h,
}
var b []byte
p, err := sr.r.Peek(1)
if err != nil {
return nil, err
}
if p[0] != '@' {
sr.seenRefs = make(map[string]*Reference)
return sr, nil
}
for {
l, err := sr.r.ReadBytes('\n')
if err != nil {
return nil, io.ErrUnexpectedEOF
}
b = append(b, l...)
p, err := sr.r.Peek(1)
if err == io.EOF {
break
}
if err != nil {
return nil, err
}
if p[0] != '@' {
break
}
}
err = sr.h.UnmarshalText(b)
if err != nil {
return nil, err
}
return sr, nil
}
// Header returns the SAM Header held by the Reader.
func (r *Reader) Header() *Header {
return r.h
}
// Read returns the next sam.Record in the SAM stream.
func (r *Reader) Read() (*Record, error) {
b, err := r.r.ReadBytes('\n')
if err != nil {
return nil, err
}
b = b[:len(b)-1]
if b[len(b)-1] == '\r' {
b = b[:len(b)-1]
}
var rec Record
// Handle cases where a header was present.
if r.seenRefs == nil {
err = rec.UnmarshalSAM(r.h, b)
if err != nil {
return nil, err
}
return &rec, nil
}
// Handle cases where no SAM header is present.
err = rec.UnmarshalSAM(nil, b)
if err != nil {
return nil, err
}
if ref, ok := r.seenRefs[rec.Ref.Name()]; ok {
rec.Ref = ref
} else if rec.Ref != nil {
err = r.h.AddReference(rec.Ref)
if err != nil {
return nil, err
}
r.seenRefs[rec.Ref.Name()] = rec.Ref
} else {
r.seenRefs["*"] = nil
}
if ref, ok := r.seenRefs[rec.MateRef.Name()]; ok {
rec.MateRef = ref
} else if rec.MateRef != nil {
err = r.h.AddReference(rec.MateRef)
if err != nil {
return nil, err
}
r.seenRefs[rec.MateRef.Name()] = rec.MateRef
} else {
r.seenRefs["*"] = nil
}
return &rec, nil
}
// RecordReader wraps types that can read SAM Records.
type RecordReader interface {
Read() (*Record, error)
}
// Iterator wraps a Reader to provide a convenient loop interface for reading SAM/BAM data.
// Successive calls to the Next method will step through the features of the provided
// Reader. Iteration stops unrecoverably at EOF or the first error.
type Iterator struct {
r RecordReader
rec *Record
err error
}
// NewIterator returns a Iterator to read from r.
//
// i, err := NewIterator(r)
// if err != nil {
// return err
// }
// for i.Next() {
// fn(i.Record())
// }
// return i.Error()
//
func NewIterator(r RecordReader) *Iterator { return &Iterator{r: r} }
// Next advances the Iterator past the next record, which will then be available through
// the Record method. It returns false when the iteration stops, either by reaching the end of the
// input or an error. After Next returns false, the Error method will return any error that
// occurred during iteration, except that if it was io.EOF, Error will return nil.
func (i *Iterator) Next() bool {
if i.err != nil {
return false
}
i.rec, i.err = i.r.Read()
return i.err == nil
}
// Error returns the first non-EOF error that was encountered by the Iterator.
func (i *Iterator) Error() error {
if i.err == io.EOF {
return nil
}
return i.err
}
// Record returns the most recent record read by a call to Next.
func (i *Iterator) Record() *Record { return i.rec }
// Writer implements SAM format writing.
type Writer struct {
w io.Writer
flags int
}
// NewWriter returns a Writer to the given io.Writer using h for the SAM
// header. The format of flags for SAM lines can be FlagDecimal, FlagHex
// or FlagString.
func NewWriter(w io.Writer, h *Header, flags int) (*Writer, error) {
if flags < FlagDecimal || flags > FlagString {
return nil, errors.New("bam: flag format option out of range")
}
sw := &Writer{w: w, flags: flags}
text, _ := h.MarshalText()
_, err := w.Write(text)
if err != nil {
return nil, err
}
return sw, nil
}
// Write writes r to the SAM stream.
func (w *Writer) Write(r *Record) error {
b, err := r.MarshalSAM(w.flags)
if err != nil {
return err
}
b = append(b, '\n')
_, err = w.w.Write(b)
return err
}
const (
wordBits = 31
maxInt32 = int(int32(^uint32(0) >> 1))
minInt32 = -int(maxInt32) - 1
)
func validInt32(i int) bool { return minInt32 <= i && i <= maxInt32 }
func validLen(i int) bool { return 1 <= i && i <= 1<<wordBits-1 }
func validPos(i int) bool { return -1 <= i && i <= (1<<wordBits-1)-1 } // 0-based.
func validTmpltLen(i int) bool { return -(1<<wordBits) <= i && i <= 1<<wordBits-1 }
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