File: sam.go

package info (click to toggle)
golang-github-biogo-hts 1.1.0%2Bdfsg1-2
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 1,660 kB
  • sloc: makefile: 3
file content (221 lines) | stat: -rw-r--r-- 5,051 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
// 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 }