169 lines
7.8 KiB
Go
169 lines
7.8 KiB
Go
// Code generated by protoc-gen-go. DO NOT EDIT.
|
|
// source: google/genomics/v1/cigar.proto
|
|
|
|
package genomics
|
|
|
|
import proto "github.com/golang/protobuf/proto"
|
|
import fmt "fmt"
|
|
import math "math"
|
|
import _ "google.golang.org/genproto/googleapis/api/annotations"
|
|
|
|
// Reference imports to suppress errors if they are not otherwise used.
|
|
var _ = proto.Marshal
|
|
var _ = fmt.Errorf
|
|
var _ = math.Inf
|
|
|
|
// Describes the different types of CIGAR alignment operations that exist.
|
|
// Used wherever CIGAR alignments are used.
|
|
type CigarUnit_Operation int32
|
|
|
|
const (
|
|
CigarUnit_OPERATION_UNSPECIFIED CigarUnit_Operation = 0
|
|
// An alignment match indicates that a sequence can be aligned to the
|
|
// reference without evidence of an INDEL. Unlike the
|
|
// `SEQUENCE_MATCH` and `SEQUENCE_MISMATCH` operators,
|
|
// the `ALIGNMENT_MATCH` operator does not indicate whether the
|
|
// reference and read sequences are an exact match. This operator is
|
|
// equivalent to SAM's `M`.
|
|
CigarUnit_ALIGNMENT_MATCH CigarUnit_Operation = 1
|
|
// The insert operator indicates that the read contains evidence of bases
|
|
// being inserted into the reference. This operator is equivalent to SAM's
|
|
// `I`.
|
|
CigarUnit_INSERT CigarUnit_Operation = 2
|
|
// The delete operator indicates that the read contains evidence of bases
|
|
// being deleted from the reference. This operator is equivalent to SAM's
|
|
// `D`.
|
|
CigarUnit_DELETE CigarUnit_Operation = 3
|
|
// The skip operator indicates that this read skips a long segment of the
|
|
// reference, but the bases have not been deleted. This operator is commonly
|
|
// used when working with RNA-seq data, where reads may skip long segments
|
|
// of the reference between exons. This operator is equivalent to SAM's
|
|
// `N`.
|
|
CigarUnit_SKIP CigarUnit_Operation = 4
|
|
// The soft clip operator indicates that bases at the start/end of a read
|
|
// have not been considered during alignment. This may occur if the majority
|
|
// of a read maps, except for low quality bases at the start/end of a read.
|
|
// This operator is equivalent to SAM's `S`. Bases that are soft
|
|
// clipped will still be stored in the read.
|
|
CigarUnit_CLIP_SOFT CigarUnit_Operation = 5
|
|
// The hard clip operator indicates that bases at the start/end of a read
|
|
// have been omitted from this alignment. This may occur if this linear
|
|
// alignment is part of a chimeric alignment, or if the read has been
|
|
// trimmed (for example, during error correction or to trim poly-A tails for
|
|
// RNA-seq). This operator is equivalent to SAM's `H`.
|
|
CigarUnit_CLIP_HARD CigarUnit_Operation = 6
|
|
// The pad operator indicates that there is padding in an alignment. This
|
|
// operator is equivalent to SAM's `P`.
|
|
CigarUnit_PAD CigarUnit_Operation = 7
|
|
// This operator indicates that this portion of the aligned sequence exactly
|
|
// matches the reference. This operator is equivalent to SAM's `=`.
|
|
CigarUnit_SEQUENCE_MATCH CigarUnit_Operation = 8
|
|
// This operator indicates that this portion of the aligned sequence is an
|
|
// alignment match to the reference, but a sequence mismatch. This can
|
|
// indicate a SNP or a read error. This operator is equivalent to SAM's
|
|
// `X`.
|
|
CigarUnit_SEQUENCE_MISMATCH CigarUnit_Operation = 9
|
|
)
|
|
|
|
var CigarUnit_Operation_name = map[int32]string{
|
|
0: "OPERATION_UNSPECIFIED",
|
|
1: "ALIGNMENT_MATCH",
|
|
2: "INSERT",
|
|
3: "DELETE",
|
|
4: "SKIP",
|
|
5: "CLIP_SOFT",
|
|
6: "CLIP_HARD",
|
|
7: "PAD",
|
|
8: "SEQUENCE_MATCH",
|
|
9: "SEQUENCE_MISMATCH",
|
|
}
|
|
var CigarUnit_Operation_value = map[string]int32{
|
|
"OPERATION_UNSPECIFIED": 0,
|
|
"ALIGNMENT_MATCH": 1,
|
|
"INSERT": 2,
|
|
"DELETE": 3,
|
|
"SKIP": 4,
|
|
"CLIP_SOFT": 5,
|
|
"CLIP_HARD": 6,
|
|
"PAD": 7,
|
|
"SEQUENCE_MATCH": 8,
|
|
"SEQUENCE_MISMATCH": 9,
|
|
}
|
|
|
|
func (x CigarUnit_Operation) String() string {
|
|
return proto.EnumName(CigarUnit_Operation_name, int32(x))
|
|
}
|
|
func (CigarUnit_Operation) EnumDescriptor() ([]byte, []int) { return fileDescriptor1, []int{0, 0} }
|
|
|
|
// A single CIGAR operation.
|
|
type CigarUnit struct {
|
|
Operation CigarUnit_Operation `protobuf:"varint,1,opt,name=operation,enum=google.genomics.v1.CigarUnit_Operation" json:"operation,omitempty"`
|
|
// The number of genomic bases that the operation runs for. Required.
|
|
OperationLength int64 `protobuf:"varint,2,opt,name=operation_length,json=operationLength" json:"operation_length,omitempty"`
|
|
// `referenceSequence` is only used at mismatches
|
|
// (`SEQUENCE_MISMATCH`) and deletions (`DELETE`).
|
|
// Filling this field replaces SAM's MD tag. If the relevant information is
|
|
// not available, this field is unset.
|
|
ReferenceSequence string `protobuf:"bytes,3,opt,name=reference_sequence,json=referenceSequence" json:"reference_sequence,omitempty"`
|
|
}
|
|
|
|
func (m *CigarUnit) Reset() { *m = CigarUnit{} }
|
|
func (m *CigarUnit) String() string { return proto.CompactTextString(m) }
|
|
func (*CigarUnit) ProtoMessage() {}
|
|
func (*CigarUnit) Descriptor() ([]byte, []int) { return fileDescriptor1, []int{0} }
|
|
|
|
func (m *CigarUnit) GetOperation() CigarUnit_Operation {
|
|
if m != nil {
|
|
return m.Operation
|
|
}
|
|
return CigarUnit_OPERATION_UNSPECIFIED
|
|
}
|
|
|
|
func (m *CigarUnit) GetOperationLength() int64 {
|
|
if m != nil {
|
|
return m.OperationLength
|
|
}
|
|
return 0
|
|
}
|
|
|
|
func (m *CigarUnit) GetReferenceSequence() string {
|
|
if m != nil {
|
|
return m.ReferenceSequence
|
|
}
|
|
return ""
|
|
}
|
|
|
|
func init() {
|
|
proto.RegisterType((*CigarUnit)(nil), "google.genomics.v1.CigarUnit")
|
|
proto.RegisterEnum("google.genomics.v1.CigarUnit_Operation", CigarUnit_Operation_name, CigarUnit_Operation_value)
|
|
}
|
|
|
|
func init() { proto.RegisterFile("google/genomics/v1/cigar.proto", fileDescriptor1) }
|
|
|
|
var fileDescriptor1 = []byte{
|
|
// 367 bytes of a gzipped FileDescriptorProto
|
|
0x1f, 0x8b, 0x08, 0x00, 0x00, 0x00, 0x00, 0x00, 0x02, 0xff, 0x6c, 0x51, 0xcf, 0x0e, 0x93, 0x30,
|
|
0x1c, 0xb6, 0x63, 0x6e, 0xe3, 0x97, 0xb8, 0x75, 0x35, 0x33, 0xd3, 0x18, 0xb3, 0xec, 0xe2, 0x3c,
|
|
0x08, 0x99, 0xde, 0xf4, 0xc4, 0xa0, 0x73, 0x8d, 0x0c, 0x10, 0xd8, 0xc5, 0x0b, 0x41, 0x52, 0x91,
|
|
0x64, 0x6b, 0x11, 0x70, 0xaf, 0xe5, 0x1b, 0xf9, 0x1c, 0x1e, 0x0d, 0x30, 0x98, 0x89, 0xde, 0xbe,
|
|
0x7e, 0xff, 0x9a, 0xfc, 0x3e, 0x78, 0x91, 0x4a, 0x99, 0x9e, 0xb9, 0x9e, 0x72, 0x21, 0x2f, 0x59,
|
|
0x52, 0xea, 0xd7, 0xad, 0x9e, 0x64, 0x69, 0x5c, 0x68, 0x79, 0x21, 0x2b, 0x49, 0x48, 0xab, 0x6b,
|
|
0x9d, 0xae, 0x5d, 0xb7, 0xcf, 0x9e, 0xdf, 0x32, 0x71, 0x9e, 0xe9, 0xb1, 0x10, 0xb2, 0x8a, 0xab,
|
|
0x4c, 0x8a, 0xb2, 0x4d, 0xac, 0x7f, 0x0d, 0x40, 0x35, 0xeb, 0x86, 0x93, 0xc8, 0x2a, 0x42, 0x41,
|
|
0x95, 0x39, 0x2f, 0x1a, 0xc7, 0x12, 0xad, 0xd0, 0x66, 0xfa, 0xe6, 0xa5, 0xf6, 0x6f, 0xa7, 0xd6,
|
|
0x27, 0x34, 0xb7, 0xb3, 0xfb, 0xf7, 0x24, 0x79, 0x05, 0xb8, 0x7f, 0x44, 0x67, 0x2e, 0xd2, 0xea,
|
|
0xdb, 0x72, 0xb0, 0x42, 0x1b, 0xc5, 0x9f, 0xf5, 0xbc, 0xdd, 0xd0, 0xe4, 0x35, 0x90, 0x82, 0x7f,
|
|
0xe5, 0x05, 0x17, 0x09, 0x8f, 0x4a, 0xfe, 0xfd, 0x47, 0x0d, 0x96, 0xca, 0x0a, 0x6d, 0x54, 0x7f,
|
|
0xde, 0x2b, 0xc1, 0x4d, 0x58, 0xff, 0x44, 0xa0, 0xf6, 0x5f, 0x92, 0xa7, 0xb0, 0x70, 0x3d, 0xea,
|
|
0x1b, 0x21, 0x73, 0x9d, 0xe8, 0xe4, 0x04, 0x1e, 0x35, 0xd9, 0x9e, 0x51, 0x0b, 0x3f, 0x20, 0x8f,
|
|
0x61, 0x66, 0xd8, 0xec, 0x83, 0x73, 0xa4, 0x4e, 0x18, 0x1d, 0x8d, 0xd0, 0x3c, 0x60, 0x44, 0x00,
|
|
0x46, 0xcc, 0x09, 0xa8, 0x1f, 0xe2, 0x41, 0x8d, 0x2d, 0x6a, 0xd3, 0x90, 0x62, 0x85, 0x4c, 0x60,
|
|
0x18, 0x7c, 0x64, 0x1e, 0x1e, 0x92, 0x47, 0xa0, 0x9a, 0x36, 0xf3, 0xa2, 0xc0, 0xdd, 0x87, 0xf8,
|
|
0x61, 0xff, 0x3c, 0x18, 0xbe, 0x85, 0x47, 0x64, 0x0c, 0x8a, 0x67, 0x58, 0x78, 0x4c, 0x08, 0x4c,
|
|
0x03, 0xfa, 0xe9, 0x44, 0x1d, 0x93, 0xde, 0xca, 0x27, 0x64, 0x01, 0xf3, 0x3b, 0xc7, 0x82, 0x96,
|
|
0x56, 0x77, 0x1c, 0x9e, 0x24, 0xf2, 0xf2, 0x9f, 0x23, 0xee, 0xa0, 0xb9, 0xa2, 0x57, 0xcf, 0xe0,
|
|
0xa1, 0xcf, 0xef, 0x3a, 0x87, 0x3c, 0xc7, 0x22, 0xd5, 0x64, 0x91, 0xd6, 0x2b, 0x37, 0x23, 0xe9,
|
|
0xad, 0x14, 0xe7, 0x59, 0xf9, 0xf7, 0xf2, 0xef, 0x3b, 0xfc, 0x1b, 0xa1, 0x2f, 0xa3, 0xc6, 0xf9,
|
|
0xf6, 0x4f, 0x00, 0x00, 0x00, 0xff, 0xff, 0x98, 0xcc, 0xce, 0xde, 0x22, 0x02, 0x00, 0x00,
|
|
}
|