// Copyright 2018 Google LLC.

//

// Redistribution and use in source and binary forms, with or without

// modification, are permitted provided that the following conditions

// are met:

//

// 1. Redistributions of source code must retain the above copyright notice,

//    this list of conditions and the following disclaimer.

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// 2. Redistributions in binary form must reproduce the above copyright

//    notice, this list of conditions and the following disclaimer in the

//    documentation and/or other materials provided with the distribution.

//

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//    contributors may be used to endorse or promote products derived from this

//    software without specific prior written permission.

//

// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"

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// POSSIBILITY OF SUCH DAMAGE.

syntax = "proto3";

package nucleus.genomics.v1;

// This message represents a single FASTQ record.

message FastqRecord {

  // The first line of a FASTQ record begins with '@' and is followed by a

  // sequence identifier (up to the first whitespace character) and then an

  // optional description. This line is parsed into its constituent id and

  // description.

  // The sequence identifier.

  string id = 1;

  // Optional. The description provided in the header line.

  string description = 2;

  // The raw sequence letters.

  string sequence = 3;

  // The quality values for the sequence. Its length must be the same as the

  // sequence length, and is encoded in ASCII. The meaning of each base quality

  // may vary: it is usually a Phred-scaled score

  // (-10 * log_10(Pr{call is incorrect})) but differs for some older versions

  // of FASTQs.

  string quality = 4;

}

message FastqReaderOptions {

  reserved 1;

  // If true, simply drop invalid records. Otherwise, raise an error on invalid

  // records.

  bool skip_invalid_records = 2;

}

// Options for writing FASTQ files.

// Currently this is a placeholder message but could be used to support

// different choices on output like whether the pad line should include the

// header or not.

message FastqWriterOptions {

}