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200 lines
8.9 KiB
Go
200 lines
8.9 KiB
Go
// Code generated by protoc-gen-go. DO NOT EDIT.
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// source: google/genomics/v1/cigar.proto
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package genomics // import "google.golang.org/genproto/googleapis/genomics/v1"
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import proto "github.com/golang/protobuf/proto"
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import fmt "fmt"
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import math "math"
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import _ "google.golang.org/genproto/googleapis/api/annotations"
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// Reference imports to suppress errors if they are not otherwise used.
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var _ = proto.Marshal
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var _ = fmt.Errorf
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var _ = math.Inf
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// This is a compile-time assertion to ensure that this generated file
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// is compatible with the proto package it is being compiled against.
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// A compilation error at this line likely means your copy of the
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// proto package needs to be updated.
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const _ = proto.ProtoPackageIsVersion2 // please upgrade the proto package
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// Describes the different types of CIGAR alignment operations that exist.
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// Used wherever CIGAR alignments are used.
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type CigarUnit_Operation int32
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const (
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CigarUnit_OPERATION_UNSPECIFIED CigarUnit_Operation = 0
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// An alignment match indicates that a sequence can be aligned to the
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// reference without evidence of an INDEL. Unlike the
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// `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
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// the `ALIGNMENT_MATCH` operator does not indicate whether the
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// reference and read sequences are an exact match. This operator is
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// equivalent to SAM's `M`.
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CigarUnit_ALIGNMENT_MATCH CigarUnit_Operation = 1
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// The insert operator indicates that the read contains evidence of bases
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// being inserted into the reference. This operator is equivalent to SAM's
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// `I`.
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CigarUnit_INSERT CigarUnit_Operation = 2
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// The delete operator indicates that the read contains evidence of bases
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// being deleted from the reference. This operator is equivalent to SAM's
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// `D`.
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CigarUnit_DELETE CigarUnit_Operation = 3
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// The skip operator indicates that this read skips a long segment of the
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// reference, but the bases have not been deleted. This operator is commonly
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// used when working with RNA-seq data, where reads may skip long segments
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// of the reference between exons. This operator is equivalent to SAM's
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// `N`.
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CigarUnit_SKIP CigarUnit_Operation = 4
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// The soft clip operator indicates that bases at the start/end of a read
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// have not been considered during alignment. This may occur if the majority
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// of a read maps, except for low quality bases at the start/end of a read.
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// This operator is equivalent to SAM's `S`. Bases that are soft
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// clipped will still be stored in the read.
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CigarUnit_CLIP_SOFT CigarUnit_Operation = 5
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// The hard clip operator indicates that bases at the start/end of a read
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// have been omitted from this alignment. This may occur if this linear
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// alignment is part of a chimeric alignment, or if the read has been
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// trimmed (for example, during error correction or to trim poly-A tails for
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// RNA-seq). This operator is equivalent to SAM's `H`.
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CigarUnit_CLIP_HARD CigarUnit_Operation = 6
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// The pad operator indicates that there is padding in an alignment. This
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// operator is equivalent to SAM's `P`.
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CigarUnit_PAD CigarUnit_Operation = 7
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// This operator indicates that this portion of the aligned sequence exactly
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// matches the reference. This operator is equivalent to SAM's `=`.
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CigarUnit_SEQUENCE_MATCH CigarUnit_Operation = 8
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// This operator indicates that this portion of the aligned sequence is an
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// alignment match to the reference, but a sequence mismatch. This can
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// indicate a SNP or a read error. This operator is equivalent to SAM's
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// `X`.
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CigarUnit_SEQUENCE_MISMATCH CigarUnit_Operation = 9
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)
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var CigarUnit_Operation_name = map[int32]string{
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0: "OPERATION_UNSPECIFIED",
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1: "ALIGNMENT_MATCH",
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2: "INSERT",
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3: "DELETE",
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4: "SKIP",
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5: "CLIP_SOFT",
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6: "CLIP_HARD",
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7: "PAD",
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8: "SEQUENCE_MATCH",
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9: "SEQUENCE_MISMATCH",
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}
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var CigarUnit_Operation_value = map[string]int32{
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"OPERATION_UNSPECIFIED": 0,
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"ALIGNMENT_MATCH": 1,
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"INSERT": 2,
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"DELETE": 3,
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"SKIP": 4,
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"CLIP_SOFT": 5,
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"CLIP_HARD": 6,
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"PAD": 7,
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"SEQUENCE_MATCH": 8,
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"SEQUENCE_MISMATCH": 9,
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}
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func (x CigarUnit_Operation) String() string {
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return proto.EnumName(CigarUnit_Operation_name, int32(x))
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}
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func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) {
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return fileDescriptor_cigar_6b0f6bba324393a8, []int{0, 0}
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}
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// A single CIGAR operation.
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type CigarUnit struct {
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Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,proto3,enum=google.genomics.v1.CigarUnit_Operation" json:"operation,omitempty"`
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// The number of genomic bases that the operation runs for. Required.
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OperationLength int64 `protobuf:"varint,2,opt,name=operation_length,json=operationLength,proto3" json:"operation_length,omitempty"`
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// `referenceSequence` is only used at mismatches
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// (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
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// Filling this field replaces SAM's MD tag. If the relevant information is
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// not available, this field is unset.
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ReferenceSequence string `protobuf:"bytes,3,opt,name=reference_sequence,json=referenceSequence,proto3" json:"reference_sequence,omitempty"`
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XXX_NoUnkeyedLiteral struct{} `json:"-"`
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XXX_unrecognized []byte `json:"-"`
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XXX_sizecache int32 `json:"-"`
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}
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func (m *CigarUnit) Reset() { *m = CigarUnit{} }
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func (m *CigarUnit) String() string { return proto.CompactTextString(m) }
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func (*CigarUnit) ProtoMessage() {}
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func (*CigarUnit) Descriptor() ([]byte, []int) {
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return fileDescriptor_cigar_6b0f6bba324393a8, []int{0}
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}
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func (m *CigarUnit) XXX_Unmarshal(b []byte) error {
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return xxx_messageInfo_CigarUnit.Unmarshal(m, b)
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}
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func (m *CigarUnit) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
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return xxx_messageInfo_CigarUnit.Marshal(b, m, deterministic)
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}
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func (dst *CigarUnit) XXX_Merge(src proto.Message) {
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xxx_messageInfo_CigarUnit.Merge(dst, src)
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}
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func (m *CigarUnit) XXX_Size() int {
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return xxx_messageInfo_CigarUnit.Size(m)
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}
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func (m *CigarUnit) XXX_DiscardUnknown() {
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xxx_messageInfo_CigarUnit.DiscardUnknown(m)
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}
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var xxx_messageInfo_CigarUnit proto.InternalMessageInfo
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func (m *CigarUnit) GetOperation() CigarUnit_Operation {
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if m != nil {
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return m.Operation
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}
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return CigarUnit_OPERATION_UNSPECIFIED
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}
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func (m *CigarUnit) GetOperationLength() int64 {
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if m != nil {
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return m.OperationLength
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}
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return 0
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}
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func (m *CigarUnit) GetReferenceSequence() string {
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if m != nil {
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return m.ReferenceSequence
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}
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return ""
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}
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func init() {
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proto.RegisterType((*CigarUnit)(nil), "google.genomics.v1.CigarUnit")
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proto.RegisterEnum("google.genomics.v1.CigarUnit_Operation", CigarUnit_Operation_name, CigarUnit_Operation_value)
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}
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func init() {
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proto.RegisterFile("google/genomics/v1/cigar.proto", fileDescriptor_cigar_6b0f6bba324393a8)
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}
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var fileDescriptor_cigar_6b0f6bba324393a8 = []byte{
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// 367 bytes of a gzipped FileDescriptorProto
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}
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