File: header.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 (588 lines) | stat: -rw-r--r-- 14,435 bytes parent folder | download
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
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
// 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

import (
	"bytes"
	"encoding/binary"
	"errors"
	"fmt"
	"io"
)

var (
	errDupReference     = errors.New("sam: duplicate reference name")
	errDupReadGroup     = errors.New("sam: duplicate read group name")
	errDupProgram       = errors.New("sam: duplicate program name")
	errUsedReference    = errors.New("sam: reference already used")
	errUsedReadGroup    = errors.New("sam: read group already used")
	errUsedProgram      = errors.New("sam: program already used")
	errInvalidReference = errors.New("sam: reference not owned by header")
	errInvalidReadGroup = errors.New("sam: read group not owned by header")
	errInvalidProgram   = errors.New("sam: program not owned by header")
	errBadLen           = errors.New("sam: reference length out of range")
)

// SortOrder indicates the sort order of a SAM or BAM file.
type SortOrder int

const (
	UnknownOrder SortOrder = iota
	Unsorted
	QueryName
	Coordinate
)

var (
	sortOrder = [...]string{
		UnknownOrder: "unknown",
		Unsorted:     "unsorted",
		QueryName:    "queryname",
		Coordinate:   "coordinate",
	}
	sortOrderMap = map[string]SortOrder{
		"unknown":    UnknownOrder,
		"unsorted":   Unsorted,
		"queryname":  QueryName,
		"coordinate": Coordinate,
	}
)

// String returns the string representation of a SortOrder.
func (so SortOrder) String() string {
	if so < Unsorted || so > Coordinate {
		return sortOrder[UnknownOrder]
	}
	return sortOrder[so]
}

// GroupOrder indicates the grouping order of a SAM or BAM file.
type GroupOrder int

const (
	GroupUnspecified GroupOrder = iota
	GroupNone
	GroupQuery
	GroupReference
)

var (
	groupOrder = [...]string{
		GroupUnspecified: "none",
		GroupNone:        "none",
		GroupQuery:       "query",
		GroupReference:   "reference",
	}
	groupOrderMap = map[string]GroupOrder{
		"none":      GroupNone,
		"query":     GroupQuery,
		"reference": GroupReference,
	}
)

// String returns the string representation of a GroupOrder.
func (g GroupOrder) String() string {
	if g < GroupNone || g > GroupReference {
		return groupOrder[GroupUnspecified]
	}
	return groupOrder[g]
}

type set map[string]int32

// Header is a SAM or BAM header.
type Header struct {
	Version    string
	SortOrder  SortOrder
	GroupOrder GroupOrder
	otherTags  []tagPair

	refs       []*Reference
	rgs        []*ReadGroup
	progs      []*Program
	seenRefs   set
	seenGroups set
	seenProgs  set

	Comments []string
}

type tagPair struct {
	tag   Tag
	value string
}

// NewHeader returns a new Header based on the given text and list
// of References. If there is a conflict between the text and the
// given References NewHeader will return a non-nil error.
func NewHeader(text []byte, r []*Reference) (*Header, error) {
	var err error
	bh := &Header{
		refs:       r,
		seenRefs:   set{},
		seenGroups: set{},
		seenProgs:  set{},
	}
	for i, r := range bh.refs {
		if r.owner != nil || r.id >= 0 {
			return nil, errUsedReference
		}
		r.owner = bh
		r.id = int32(i)
	}
	if text != nil {
		err = bh.UnmarshalText(text)
		if err != nil {
			return nil, err
		}
	}
	return bh, nil
}

// Tags applies the function fn to each of the tag-value pairs of the Header.
// The SO and GO tags are only used if they are set to the non-default values.
// The function fn must not add or delete tags held by the receiver during
// iteration.
func (bh *Header) Tags(fn func(t Tag, value string)) {
	if fn == nil {
		return
	}
	fn(versionTag, bh.Version)
	if bh.SortOrder != UnknownOrder {
		fn(sortOrderTag, bh.SortOrder.String())
	}
	if bh.GroupOrder != GroupNone {
		fn(groupOrderTag, bh.GroupOrder.String())
	}
	for _, tp := range bh.otherTags {
		fn(tp.tag, tp.value)
	}
}

// Get returns the string representation of the value associated with the
// given header line tag. If the tag is not present the empty string is returned.
func (bh *Header) Get(t Tag) string {
	switch t {
	case versionTag:
		return bh.Version
	case sortOrderTag:
		return bh.SortOrder.String()
	case groupOrderTag:
		return bh.GroupOrder.String()
	}
	for _, tp := range bh.otherTags {
		if t == tp.tag {
			return tp.value
		}
	}
	return ""
}

// Set sets the value associated with the given header line tag to the specified
// value. If value is the empty string and the tag may be absent, it is deleted
// or set to a meaningful default (SO:UnknownOrder and GO:GroupUnspecified),
// otherwise an error is returned.
func (bh *Header) Set(t Tag, value string) error {
	switch t {
	case versionTag:
		if value == "" {
			return errBadHeader
		}
		bh.Version = value
	case sortOrderTag:
		if value == "" {
			bh.SortOrder = UnknownOrder
			return nil
		}
		sortOrder, ok := sortOrderMap[value]
		if !ok {
			return errBadHeader
		}
		bh.SortOrder = sortOrder
	case groupOrderTag:
		if value == "" {
			bh.GroupOrder = GroupUnspecified
			return nil
		}
		groupOrder, ok := groupOrderMap[value]
		if !ok {
			return errBadHeader
		}
		bh.GroupOrder = groupOrder
	default:
		if value == "" {
			for i, tp := range bh.otherTags {
				if t == tp.tag {
					copy(bh.otherTags[i:], bh.otherTags[i+1:])
					bh.otherTags = bh.otherTags[:len(bh.otherTags)-1]
					return nil
				}
			}
		} else {
			for i, tp := range bh.otherTags {
				if t == tp.tag {
					bh.otherTags[i].value = value
					return nil
				}
			}
			bh.otherTags = append(bh.otherTags, tagPair{tag: t, value: value})
		}
	}
	return nil
}

// Clone returns a deep copy of the receiver.
func (bh *Header) Clone() *Header {
	c := &Header{
		Version:    bh.Version,
		SortOrder:  bh.SortOrder,
		GroupOrder: bh.GroupOrder,
		otherTags:  append([]tagPair(nil), bh.otherTags...),
		Comments:   append([]string(nil), bh.Comments...),
		seenRefs:   make(set, len(bh.seenRefs)),
		seenGroups: make(set, len(bh.seenGroups)),
		seenProgs:  make(set, len(bh.seenProgs)),
	}
	if len(bh.refs) != 0 {
		c.refs = make([]*Reference, len(bh.refs))
	}
	if len(bh.rgs) != 0 {
		c.rgs = make([]*ReadGroup, len(bh.rgs))
	}
	if len(bh.progs) != 0 {
		c.progs = make([]*Program, len(bh.progs))
	}

	for i, r := range bh.refs {
		if r == nil {
			continue
		}
		c.refs[i] = new(Reference)
		*c.refs[i] = *r
		c.refs[i].owner = c
	}
	for i, r := range bh.rgs {
		c.rgs[i] = new(ReadGroup)
		*c.rgs[i] = *r
		c.rgs[i].owner = c
	}
	for i, p := range bh.progs {
		c.progs[i] = new(Program)
		*c.progs[i] = *p
		c.progs[i].owner = c
	}
	for k, v := range bh.seenRefs {
		c.seenRefs[k] = v
	}
	for k, v := range bh.seenGroups {
		c.seenGroups[k] = v
	}
	for k, v := range bh.seenProgs {
		c.seenProgs[k] = v
	}

	return c
}

// MergeHeaders returns a new Header resulting from the merge of the
// source Headers, and a mapping between the references in the source
// and the References in the returned Header. Sort order is set to
// unknown and group order is set to none. If a single Header is passed
// to MergeHeaders, the mapping between source and destination headers,
// reflink, is returned as nil.
// The returned Header contains the read groups and programs of the
// first Header in src.
func MergeHeaders(src []*Header) (h *Header, reflinks [][]*Reference, err error) {
	switch len(src) {
	case 0:
		return nil, nil, nil
	case 1:
		return src[0], nil, nil
	}
	reflinks = make([][]*Reference, len(src))
	h = src[0].Clone()
	h.SortOrder = UnknownOrder
	h.GroupOrder = GroupUnspecified
	for i, add := range src {
		if i == 0 {
			reflinks[i] = h.refs
			continue
		}
		links := make([]*Reference, len(add.refs))
		for id, r := range add.refs {
			r = r.Clone()
			err := h.AddReference(r)
			if err != nil {
				return nil, nil, err
			}
			if r.owner != h {
				// r was not actually added, so use the ref
				// that h owns.
				for _, hr := range h.refs {
					if equalRefs(r, hr) {
						r = hr
						break
					}
				}
			}
			links[id] = r
		}
		reflinks[i] = links
	}

	return h, reflinks, nil
}

// MarshalText implements the encoding.TextMarshaler interface.
func (bh *Header) MarshalText() ([]byte, error) {
	var buf bytes.Buffer
	if bh.Version != "" {
		if bh.GroupOrder == GroupUnspecified {
			fmt.Fprintf(&buf, "@HD\tVN:%s\tSO:%s", bh.Version, bh.SortOrder)
		} else {
			fmt.Fprintf(&buf, "@HD\tVN:%s\tSO:%s\tGO:%s", bh.Version, bh.SortOrder, bh.GroupOrder)
		}
		for _, tp := range bh.otherTags {
			fmt.Fprintf(&buf, "\t%s:%s", tp.tag, tp.value)
		}
		buf.WriteByte('\n')
	}
	for _, r := range bh.refs {
		fmt.Fprintf(&buf, "%s\n", r)
	}
	for _, rg := range bh.rgs {
		fmt.Fprintf(&buf, "%s\n", rg)
	}
	for _, p := range bh.progs {
		fmt.Fprintf(&buf, "%s\n", p)
	}
	for _, co := range bh.Comments {
		fmt.Fprintf(&buf, "@CO\t%s\n", co)
	}
	return buf.Bytes(), nil
}

// MarshalBinary implements the encoding.BinaryMarshaler.
func (bh *Header) MarshalBinary() ([]byte, error) {
	b := &bytes.Buffer{}
	err := bh.EncodeBinary(b)
	if err != nil {
		return nil, err
	}
	return b.Bytes(), nil
}

// EncodeBinary writes a binary encoding of the Header to the given io.Writer.
// The format of the encoding is defined in the SAM specification, section 4.2.
func (bh *Header) EncodeBinary(w io.Writer) error {
	wb := &errWriter{w: w}

	binary.Write(wb, binary.LittleEndian, bamMagic)
	text, _ := bh.MarshalText()
	binary.Write(wb, binary.LittleEndian, int32(len(text)))
	wb.Write(text)
	binary.Write(wb, binary.LittleEndian, int32(len(bh.refs)))

	if !validInt32(len(bh.refs)) {
		return errors.New("sam: value out of range")
	}
	var name []byte
	for _, r := range bh.refs {
		name = append(name, []byte(r.name)...)
		name = append(name, 0)
		binary.Write(wb, binary.LittleEndian, int32(len(name)))
		wb.Write(name)
		name = name[:0]
		binary.Write(wb, binary.LittleEndian, r.lRef)
	}
	if wb.err != nil {
		return wb.err
	}

	return nil
}

type errWriter struct {
	w   io.Writer
	err error
}

func (w *errWriter) Write(p []byte) (int, error) {
	if w.err != nil {
		return 0, w.err
	}
	var n int
	n, w.err = w.w.Write(p)
	return n, w.err
}

// Validate checks r against the Header for record validity according to the
// SAM specification:
//
//  - a program auxiliary field must refer to a program listed in the header
//  - a read group auxiliary field must refer to a read group listed in the
//    header and these must agree on platform unit and library.
func (bh *Header) Validate(r *Record) error {
	rp := r.AuxFields.Get(programTag)
	found := false
	for _, hp := range bh.Progs() {
		if hp.UID() == rp.Value() {
			found = true
			break
		}
	}
	if !found && len(bh.Progs()) != 0 {
		return fmt.Errorf("sam: program uid not found: %v", rp.Value())
	}

	rg := r.AuxFields.Get(readGroupTag)
	found = false
	for _, hg := range bh.RGs() {
		if hg.Name() == rg.Value() {
			rPlatformUnit := r.AuxFields.Get(platformUnitTag).Value()
			if rPlatformUnit != hg.PlatformUnit() {
				return fmt.Errorf("sam: mismatched platform for read group %s: %v != %v", hg.Name(), rPlatformUnit, hg.platformUnit)
			}
			rLibrary := r.AuxFields.Get(libraryTag).Value()
			if rLibrary != hg.Library() {
				return fmt.Errorf("sam: mismatched library for read group %s: %v != %v", hg.Name(), rLibrary, hg.library)
			}
			found = true
			break
		}
	}
	if !found && len(bh.RGs()) != 0 {
		return fmt.Errorf("sam: read group not found: %v", rg.Value())
	}

	return nil
}

// Refs returns the Header's list of References. The returned slice
// should not be altered.
func (bh *Header) Refs() []*Reference {
	return bh.refs
}

// RGs returns the Header's list of ReadGroups. The returned slice
// should not be altered.
func (bh *Header) RGs() []*ReadGroup {
	return bh.rgs
}

// Progs returns the Header's list of Programs. The returned slice
// should not be altered.
func (bh *Header) Progs() []*Program {
	return bh.progs
}

// AddReference adds r to the Header.
func (bh *Header) AddReference(r *Reference) error {
	if dupID, dup := bh.seenRefs[r.name]; dup {
		er := bh.refs[dupID]
		if equalRefs(er, r) {
			return nil
		} else if !equalRefs(r, &Reference{id: -1, name: er.name, lRef: er.lRef}) {
			return errDupReference
		}
		if r.md5 == "" {
			r.md5 = er.md5
		}
		if r.assemID == "" {
			r.assemID = er.assemID
		}
		if r.species == "" {
			r.species = er.species
		}
		if r.uri == nil {
			r.uri = er.uri
		}
		bh.refs[dupID] = r
		return nil
	}
	if r.owner != nil || r.id >= 0 {
		return errUsedReference
	}
	r.owner = bh
	r.id = int32(len(bh.refs))
	bh.seenRefs[r.name] = r.id
	bh.refs = append(bh.refs, r)
	return nil
}

// RemoveReference removes r from the Header and makes it
// available to add to another Header.
func (bh *Header) RemoveReference(r *Reference) error {
	if r.id < 0 || int(r.id) >= len(bh.refs) || bh.refs[r.id] != r {
		return errInvalidReference
	}
	bh.refs = append(bh.refs[:r.id], bh.refs[r.id+1:]...)
	for i := range bh.refs[r.id:] {
		bh.refs[i+int(r.id)].id--
	}
	r.id = -1
	delete(bh.seenRefs, r.name)
	return nil
}

// AddReadGroup adds rg to the Header.
func (bh *Header) AddReadGroup(rg *ReadGroup) error {
	if _, ok := bh.seenGroups[rg.name]; ok {
		return errDupReadGroup
	}
	if rg.owner != nil || rg.id >= 0 {
		return errUsedReadGroup
	}
	rg.owner = bh
	rg.id = int32(len(bh.rgs))
	bh.seenGroups[rg.name] = rg.id
	bh.rgs = append(bh.rgs, rg)
	return nil
}

// RemoveReadGroup removes rg from the Header and makes it
// available to add to another Header.
func (bh *Header) RemoveReadGroup(rg *ReadGroup) error {
	if rg.id < 0 || int(rg.id) >= len(bh.refs) || bh.rgs[rg.id] != rg {
		return errInvalidReadGroup
	}
	bh.rgs = append(bh.rgs[:rg.id], bh.rgs[rg.id+1:]...)
	for i := range bh.rgs[rg.id:] {
		bh.rgs[i+int(rg.id)].id--
	}
	rg.id = -1
	delete(bh.seenGroups, rg.name)
	return nil
}

// AddProgram adds p to the Header.
func (bh *Header) AddProgram(p *Program) error {
	if _, ok := bh.seenProgs[p.uid]; ok {
		return errDupProgram
	}
	if p.owner != nil || p.id >= 0 {
		return errUsedProgram
	}
	p.owner = bh
	p.id = int32(len(bh.progs))
	bh.seenProgs[p.uid] = p.id
	bh.progs = append(bh.progs, p)
	return nil
}

// RemoveProgram removes p from the Header and makes it
// available to add to another Header.
func (bh *Header) RemoveProgram(p *Program) error {
	if p.id < 0 || int(p.id) >= len(bh.progs) || bh.progs[p.id] != p {
		return errInvalidProgram
	}
	bh.progs = append(bh.progs[:p.id], bh.progs[p.id+1:]...)
	for i := range bh.progs[p.id:] {
		bh.progs[i+int(p.id)].id--
	}
	p.id = -1
	delete(bh.seenProgs, p.uid)
	return nil
}