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syntax = "proto3";

import "third_party/nucleus/protos/range.proto";

package nucleus.genomics.v1;

// This file contains information about a reference genome assembly. It
// currently only defines a message to represent a single contig, but can be
// extended to capture information about an entire assembly as well (e.g.
// all contigs present on an assembly, the species, build, etc.).

// This record type records information about a contig. This is used both in
// VCF header parsing and by GenomeReference objects for querying references.
// Due to its generality, this message is also used by the FastaReader to
// provide detailed information on the description line of a FASTA record even
// in cases where the record does not correspond to a reference genome contig.
message ContigInfo {
  // Required. The name of the contig. Canonically this is the first
  // non-whitespace-containing string after the > marker in a FASTA file.
  // For example, the line:
  //      >chr1 more info here
  // has a name of "chr1" and a description of "more info here"
  string name = 1;

  // Ideally this record is filled in as described above, but not all FASTA
  // readers capture the description information after the name. Since a
  // description is not required by the FASTA spec, we cannot distinguish cases
  // where a description was not present and where a parser ignored it.
  string description = 2;

  // The length of this contig in basepairs.
  int64 n_bases = 3;

  // Additional information used when reading and writing VCF headers. An
  // example map of key-value extra fields would transform an input line
  // containing 'assembly=B36,taxonomy=x,species="Homo sapiens"' to a map with
  // "assembly" -> "B36", "taxonomy" -> "x", "species" -> "Homo sapiens". We
  // never use this information internally, other than reading it in so we can
  // write the contig out again.
  map<string, string> extra = 5;

  // The position of this contig in the src_fasta file. The first contig would
  // have position 0.
  // TODO: rename to something more generic.
  int32 pos_in_fasta = 4;
}

// A full, or partial, sequence of bases from a contig in a reference genome.
message ReferenceSequence {
  // The location on the genome this sequence of bases comes from.
  Range region = 1;

  // The bases of this part of the reference genome.
  string bases = 2;
}