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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
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
}
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