blob: e70e943877441c7c4b7ecffa3100994cde9ad4a4 [file] [log] [blame]
// Copyright 2016 Google Inc.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
syntax = "proto3";
package google.genomics.v1;
import "google/api/annotations.proto";
option cc_enable_arenas = true;
option go_package = "google.golang.org/genproto/googleapis/genomics/v1;genomics";
option java_multiple_files = true;
option java_outer_classname = "CigarProto";
option java_package = "com.google.genomics.v1";
// A single CIGAR operation.
message CigarUnit {
// Describes the different types of CIGAR alignment operations that exist.
// Used wherever CIGAR alignments are used.
enum Operation {
OPERATION_UNSPECIFIED = 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`.
ALIGNMENT_MATCH = 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`.
INSERT = 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`.
DELETE = 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`.
SKIP = 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.
CLIP_SOFT = 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`.
CLIP_HARD = 6;
// The pad operator indicates that there is padding in an alignment. This
// operator is equivalent to SAM's `P`.
PAD = 7;
// This operator indicates that this portion of the aligned sequence exactly
// matches the reference. This operator is equivalent to SAM's `=`.
SEQUENCE_MATCH = 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`.
SEQUENCE_MISMATCH = 9;
}
Operation operation = 1;
// The number of genomic bases that the operation runs for. Required.
int64 operation_length = 2;
// `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.
string reference_sequence = 3;
}