// 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;
}