Bumping k8s dependencies to 1.13
This commit is contained in:
Cheng Xing
129
vendor/google.golang.org/genproto/googleapis/genomics/v1/readalignment.pb.go
generated
vendored
129
vendor/google.golang.org/genproto/googleapis/genomics/v1/readalignment.pb.go
generated
vendored
@@ -3,37 +3,68 @@
|
||||
|
||||
package genomics
|
||||
|
||||
import proto "github.com/golang/protobuf/proto"
|
||||
import fmt "fmt"
|
||||
import math "math"
|
||||
import _ "google.golang.org/genproto/googleapis/api/annotations"
|
||||
import google_protobuf3 "github.com/golang/protobuf/ptypes/struct"
|
||||
import (
|
||||
fmt "fmt"
|
||||
proto "github.com/golang/protobuf/proto"
|
||||
_struct "github.com/golang/protobuf/ptypes/struct"
|
||||
_ "google.golang.org/genproto/googleapis/api/annotations"
|
||||
math "math"
|
||||
)
|
||||
|
||||
// Reference imports to suppress errors if they are not otherwise used.
|
||||
var _ = proto.Marshal
|
||||
var _ = fmt.Errorf
|
||||
var _ = math.Inf
|
||||
|
||||
// This is a compile-time assertion to ensure that this generated file
|
||||
// is compatible with the proto package it is being compiled against.
|
||||
// A compilation error at this line likely means your copy of the
|
||||
// proto package needs to be updated.
|
||||
const _ = proto.ProtoPackageIsVersion2 // please upgrade the proto package
|
||||
|
||||
// A linear alignment can be represented by one CIGAR string. Describes the
|
||||
// mapped position and local alignment of the read to the reference.
|
||||
type LinearAlignment struct {
|
||||
// The position of this alignment.
|
||||
Position *Position `protobuf:"bytes,1,opt,name=position" json:"position,omitempty"`
|
||||
Position *Position `protobuf:"bytes,1,opt,name=position,proto3" json:"position,omitempty"`
|
||||
// The mapping quality of this alignment. Represents how likely
|
||||
// the read maps to this position as opposed to other locations.
|
||||
//
|
||||
// Specifically, this is -10 log10 Pr(mapping position is wrong), rounded to
|
||||
// the nearest integer.
|
||||
MappingQuality int32 `protobuf:"varint,2,opt,name=mapping_quality,json=mappingQuality" json:"mapping_quality,omitempty"`
|
||||
MappingQuality int32 `protobuf:"varint,2,opt,name=mapping_quality,json=mappingQuality,proto3" json:"mapping_quality,omitempty"`
|
||||
// Represents the local alignment of this sequence (alignment matches, indels,
|
||||
// etc) against the reference.
|
||||
Cigar []*CigarUnit `protobuf:"bytes,3,rep,name=cigar" json:"cigar,omitempty"`
|
||||
Cigar []*CigarUnit `protobuf:"bytes,3,rep,name=cigar,proto3" json:"cigar,omitempty"`
|
||||
XXX_NoUnkeyedLiteral struct{} `json:"-"`
|
||||
XXX_unrecognized []byte `json:"-"`
|
||||
XXX_sizecache int32 `json:"-"`
|
||||
}
|
||||
|
||||
func (m *LinearAlignment) Reset() { *m = LinearAlignment{} }
|
||||
func (m *LinearAlignment) String() string { return proto.CompactTextString(m) }
|
||||
func (*LinearAlignment) ProtoMessage() {}
|
||||
func (*LinearAlignment) Descriptor() ([]byte, []int) { return fileDescriptor6, []int{0} }
|
||||
func (m *LinearAlignment) Reset() { *m = LinearAlignment{} }
|
||||
func (m *LinearAlignment) String() string { return proto.CompactTextString(m) }
|
||||
func (*LinearAlignment) ProtoMessage() {}
|
||||
func (*LinearAlignment) Descriptor() ([]byte, []int) {
|
||||
return fileDescriptor_5882c5c7543d07e3, []int{0}
|
||||
}
|
||||
|
||||
func (m *LinearAlignment) XXX_Unmarshal(b []byte) error {
|
||||
return xxx_messageInfo_LinearAlignment.Unmarshal(m, b)
|
||||
}
|
||||
func (m *LinearAlignment) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
|
||||
return xxx_messageInfo_LinearAlignment.Marshal(b, m, deterministic)
|
||||
}
|
||||
func (m *LinearAlignment) XXX_Merge(src proto.Message) {
|
||||
xxx_messageInfo_LinearAlignment.Merge(m, src)
|
||||
}
|
||||
func (m *LinearAlignment) XXX_Size() int {
|
||||
return xxx_messageInfo_LinearAlignment.Size(m)
|
||||
}
|
||||
func (m *LinearAlignment) XXX_DiscardUnknown() {
|
||||
xxx_messageInfo_LinearAlignment.DiscardUnknown(m)
|
||||
}
|
||||
|
||||
var xxx_messageInfo_LinearAlignment proto.InternalMessageInfo
|
||||
|
||||
func (m *LinearAlignment) GetPosition() *Position {
|
||||
if m != nil {
|
||||
@@ -141,42 +172,42 @@ func (m *LinearAlignment) GetCigar() []*CigarUnit {
|
||||
type Read struct {
|
||||
// The server-generated read ID, unique across all reads. This is different
|
||||
// from the `fragmentName`.
|
||||
Id string `protobuf:"bytes,1,opt,name=id" json:"id,omitempty"`
|
||||
Id string `protobuf:"bytes,1,opt,name=id,proto3" json:"id,omitempty"`
|
||||
// The ID of the read group this read belongs to. A read belongs to exactly
|
||||
// one read group. This is a server-generated ID which is distinct from SAM's
|
||||
// RG tag (for that value, see
|
||||
// [ReadGroup.name][google.genomics.v1.ReadGroup.name]).
|
||||
ReadGroupId string `protobuf:"bytes,2,opt,name=read_group_id,json=readGroupId" json:"read_group_id,omitempty"`
|
||||
ReadGroupId string `protobuf:"bytes,2,opt,name=read_group_id,json=readGroupId,proto3" json:"read_group_id,omitempty"`
|
||||
// The ID of the read group set this read belongs to. A read belongs to
|
||||
// exactly one read group set.
|
||||
ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId" json:"read_group_set_id,omitempty"`
|
||||
ReadGroupSetId string `protobuf:"bytes,3,opt,name=read_group_set_id,json=readGroupSetId,proto3" json:"read_group_set_id,omitempty"`
|
||||
// The fragment name. Equivalent to QNAME (query template name) in SAM.
|
||||
FragmentName string `protobuf:"bytes,4,opt,name=fragment_name,json=fragmentName" json:"fragment_name,omitempty"`
|
||||
FragmentName string `protobuf:"bytes,4,opt,name=fragment_name,json=fragmentName,proto3" json:"fragment_name,omitempty"`
|
||||
// The orientation and the distance between reads from the fragment are
|
||||
// consistent with the sequencing protocol (SAM flag 0x2).
|
||||
ProperPlacement bool `protobuf:"varint,5,opt,name=proper_placement,json=properPlacement" json:"proper_placement,omitempty"`
|
||||
ProperPlacement bool `protobuf:"varint,5,opt,name=proper_placement,json=properPlacement,proto3" json:"proper_placement,omitempty"`
|
||||
// The fragment is a PCR or optical duplicate (SAM flag 0x400).
|
||||
DuplicateFragment bool `protobuf:"varint,6,opt,name=duplicate_fragment,json=duplicateFragment" json:"duplicate_fragment,omitempty"`
|
||||
DuplicateFragment bool `protobuf:"varint,6,opt,name=duplicate_fragment,json=duplicateFragment,proto3" json:"duplicate_fragment,omitempty"`
|
||||
// The observed length of the fragment, equivalent to TLEN in SAM.
|
||||
FragmentLength int32 `protobuf:"varint,7,opt,name=fragment_length,json=fragmentLength" json:"fragment_length,omitempty"`
|
||||
FragmentLength int32 `protobuf:"varint,7,opt,name=fragment_length,json=fragmentLength,proto3" json:"fragment_length,omitempty"`
|
||||
// The read number in sequencing. 0-based and less than numberReads. This
|
||||
// field replaces SAM flag 0x40 and 0x80.
|
||||
ReadNumber int32 `protobuf:"varint,8,opt,name=read_number,json=readNumber" json:"read_number,omitempty"`
|
||||
ReadNumber int32 `protobuf:"varint,8,opt,name=read_number,json=readNumber,proto3" json:"read_number,omitempty"`
|
||||
// The number of reads in the fragment (extension to SAM flag 0x1).
|
||||
NumberReads int32 `protobuf:"varint,9,opt,name=number_reads,json=numberReads" json:"number_reads,omitempty"`
|
||||
NumberReads int32 `protobuf:"varint,9,opt,name=number_reads,json=numberReads,proto3" json:"number_reads,omitempty"`
|
||||
// Whether this read did not pass filters, such as platform or vendor quality
|
||||
// controls (SAM flag 0x200).
|
||||
FailedVendorQualityChecks bool `protobuf:"varint,10,opt,name=failed_vendor_quality_checks,json=failedVendorQualityChecks" json:"failed_vendor_quality_checks,omitempty"`
|
||||
FailedVendorQualityChecks bool `protobuf:"varint,10,opt,name=failed_vendor_quality_checks,json=failedVendorQualityChecks,proto3" json:"failed_vendor_quality_checks,omitempty"`
|
||||
// The linear alignment for this alignment record. This field is null for
|
||||
// unmapped reads.
|
||||
Alignment *LinearAlignment `protobuf:"bytes,11,opt,name=alignment" json:"alignment,omitempty"`
|
||||
Alignment *LinearAlignment `protobuf:"bytes,11,opt,name=alignment,proto3" json:"alignment,omitempty"`
|
||||
// Whether this alignment is secondary. Equivalent to SAM flag 0x100.
|
||||
// A secondary alignment represents an alternative to the primary alignment
|
||||
// for this read. Aligners may return secondary alignments if a read can map
|
||||
// ambiguously to multiple coordinates in the genome. By convention, each read
|
||||
// has one and only one alignment where both `secondaryAlignment`
|
||||
// and `supplementaryAlignment` are false.
|
||||
SecondaryAlignment bool `protobuf:"varint,12,opt,name=secondary_alignment,json=secondaryAlignment" json:"secondary_alignment,omitempty"`
|
||||
SecondaryAlignment bool `protobuf:"varint,12,opt,name=secondary_alignment,json=secondaryAlignment,proto3" json:"secondary_alignment,omitempty"`
|
||||
// Whether this alignment is supplementary. Equivalent to SAM flag 0x800.
|
||||
// Supplementary alignments are used in the representation of a chimeric
|
||||
// alignment. In a chimeric alignment, a read is split into multiple
|
||||
@@ -188,7 +219,7 @@ type Read struct {
|
||||
// will be hard clipped. The `alignedSequence` and
|
||||
// `alignedQuality` fields in the alignment record will only
|
||||
// represent the bases for its respective linear alignment.
|
||||
SupplementaryAlignment bool `protobuf:"varint,13,opt,name=supplementary_alignment,json=supplementaryAlignment" json:"supplementary_alignment,omitempty"`
|
||||
SupplementaryAlignment bool `protobuf:"varint,13,opt,name=supplementary_alignment,json=supplementaryAlignment,proto3" json:"supplementary_alignment,omitempty"`
|
||||
// The bases of the read sequence contained in this alignment record,
|
||||
// **without CIGAR operations applied** (equivalent to SEQ in SAM).
|
||||
// `alignedSequence` and `alignedQuality` may be
|
||||
@@ -196,7 +227,7 @@ type Read struct {
|
||||
// alignment is part of a chimeric alignment, or if the read was trimmed. When
|
||||
// this occurs, the CIGAR for this read will begin/end with a hard clip
|
||||
// operator that will indicate the length of the excised sequence.
|
||||
AlignedSequence string `protobuf:"bytes,14,opt,name=aligned_sequence,json=alignedSequence" json:"aligned_sequence,omitempty"`
|
||||
AlignedSequence string `protobuf:"bytes,14,opt,name=aligned_sequence,json=alignedSequence,proto3" json:"aligned_sequence,omitempty"`
|
||||
// The quality of the read sequence contained in this alignment record
|
||||
// (equivalent to QUAL in SAM).
|
||||
// `alignedSequence` and `alignedQuality` may be shorter than the full read
|
||||
@@ -204,20 +235,43 @@ type Read struct {
|
||||
// chimeric alignment, or if the read was trimmed. When this occurs, the CIGAR
|
||||
// for this read will begin/end with a hard clip operator that will indicate
|
||||
// the length of the excised sequence.
|
||||
AlignedQuality []int32 `protobuf:"varint,15,rep,packed,name=aligned_quality,json=alignedQuality" json:"aligned_quality,omitempty"`
|
||||
AlignedQuality []int32 `protobuf:"varint,15,rep,packed,name=aligned_quality,json=alignedQuality,proto3" json:"aligned_quality,omitempty"`
|
||||
// The mapping of the primary alignment of the
|
||||
// `(readNumber+1)%numberReads` read in the fragment. It replaces
|
||||
// mate position and mate strand in SAM.
|
||||
NextMatePosition *Position `protobuf:"bytes,16,opt,name=next_mate_position,json=nextMatePosition" json:"next_mate_position,omitempty"`
|
||||
NextMatePosition *Position `protobuf:"bytes,16,opt,name=next_mate_position,json=nextMatePosition,proto3" json:"next_mate_position,omitempty"`
|
||||
// A map of additional read alignment information. This must be of the form
|
||||
// map<string, string[]> (string key mapping to a list of string values).
|
||||
Info map[string]*google_protobuf3.ListValue `protobuf:"bytes,17,rep,name=info" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key" protobuf_val:"bytes,2,opt,name=value"`
|
||||
Info map[string]*_struct.ListValue `protobuf:"bytes,17,rep,name=info,proto3" json:"info,omitempty" protobuf_key:"bytes,1,opt,name=key,proto3" protobuf_val:"bytes,2,opt,name=value,proto3"`
|
||||
XXX_NoUnkeyedLiteral struct{} `json:"-"`
|
||||
XXX_unrecognized []byte `json:"-"`
|
||||
XXX_sizecache int32 `json:"-"`
|
||||
}
|
||||
|
||||
func (m *Read) Reset() { *m = Read{} }
|
||||
func (m *Read) String() string { return proto.CompactTextString(m) }
|
||||
func (*Read) ProtoMessage() {}
|
||||
func (*Read) Descriptor() ([]byte, []int) { return fileDescriptor6, []int{1} }
|
||||
func (m *Read) Reset() { *m = Read{} }
|
||||
func (m *Read) String() string { return proto.CompactTextString(m) }
|
||||
func (*Read) ProtoMessage() {}
|
||||
func (*Read) Descriptor() ([]byte, []int) {
|
||||
return fileDescriptor_5882c5c7543d07e3, []int{1}
|
||||
}
|
||||
|
||||
func (m *Read) XXX_Unmarshal(b []byte) error {
|
||||
return xxx_messageInfo_Read.Unmarshal(m, b)
|
||||
}
|
||||
func (m *Read) XXX_Marshal(b []byte, deterministic bool) ([]byte, error) {
|
||||
return xxx_messageInfo_Read.Marshal(b, m, deterministic)
|
||||
}
|
||||
func (m *Read) XXX_Merge(src proto.Message) {
|
||||
xxx_messageInfo_Read.Merge(m, src)
|
||||
}
|
||||
func (m *Read) XXX_Size() int {
|
||||
return xxx_messageInfo_Read.Size(m)
|
||||
}
|
||||
func (m *Read) XXX_DiscardUnknown() {
|
||||
xxx_messageInfo_Read.DiscardUnknown(m)
|
||||
}
|
||||
|
||||
var xxx_messageInfo_Read proto.InternalMessageInfo
|
||||
|
||||
func (m *Read) GetId() string {
|
||||
if m != nil {
|
||||
@@ -331,7 +385,7 @@ func (m *Read) GetNextMatePosition() *Position {
|
||||
return nil
|
||||
}
|
||||
|
||||
func (m *Read) GetInfo() map[string]*google_protobuf3.ListValue {
|
||||
func (m *Read) GetInfo() map[string]*_struct.ListValue {
|
||||
if m != nil {
|
||||
return m.Info
|
||||
}
|
||||
@@ -341,11 +395,14 @@ func (m *Read) GetInfo() map[string]*google_protobuf3.ListValue {
|
||||
func init() {
|
||||
proto.RegisterType((*LinearAlignment)(nil), "google.genomics.v1.LinearAlignment")
|
||||
proto.RegisterType((*Read)(nil), "google.genomics.v1.Read")
|
||||
proto.RegisterMapType((map[string]*_struct.ListValue)(nil), "google.genomics.v1.Read.InfoEntry")
|
||||
}
|
||||
|
||||
func init() { proto.RegisterFile("google/genomics/v1/readalignment.proto", fileDescriptor6) }
|
||||
func init() {
|
||||
proto.RegisterFile("google/genomics/v1/readalignment.proto", fileDescriptor_5882c5c7543d07e3)
|
||||
}
|
||||
|
||||
var fileDescriptor6 = []byte{
|
||||
var fileDescriptor_5882c5c7543d07e3 = []byte{
|
||||
// 683 bytes of a gzipped FileDescriptorProto
|
||||
0x1f, 0x8b, 0x08, 0x00, 0x00, 0x00, 0x00, 0x00, 0x02, 0xff, 0x8c, 0x94, 0xcd, 0x4e, 0xdb, 0x4a,
|
||||
0x14, 0xc7, 0xe5, 0x84, 0x70, 0xc9, 0x09, 0x24, 0x61, 0xae, 0xc4, 0xf5, 0x8d, 0xb8, 0xb7, 0x21,
|
||||
|
||||
Reference in New Issue
Block a user