// 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.
//
// 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.
//
// 3. Neither the name of the copyright holder nor the names of its
//    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"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
syntax = "proto3";

package nucleus.genomics.v1;

// This message represents a single BED record. See
// https://genome.ucsc.edu/FAQ/FAQformat.html#format1 for details.
message BedRecord {
  // The reference on which this variant occurs. Corresponds to "CHROM" in UCSC.
  string reference_name = 1;

  // The position at which this region occurs (0-based inclusive).
  int64 start = 2;

  // The position at which this region ends (0-based exclusive).
  int64 end = 3;

  // The name of the record.
  string name = 4;

  // As described in https://genome.ucsc.edu/FAQ/FAQformat.html#format1, score
  // should be an integer in [0, 1000]. However, many non-integer values are
  // seen in BED records in the wild, so we represent this as a double.
  double score = 5;

  enum Strand {
    // The strand is unspecified, unknown, or not meaningful.
    NO_STRAND = 0;
    FORWARD_STRAND = 1;
    REVERSE_STRAND = 2;
  }
  // The strand on the genome that the record is on.
  Strand strand = 6;

  // For visualization purposes, the position at which the feature starts to be
  // drawn thickly. In gene structures this corresponds to the start codon.
  // This is zero-based inclusive numbering, like the `start` field.
  int64 thick_start = 7;

  // For visualization purposes, the position at which the feature stops being
  // drawn thickly. In gene structures this corresponds to the stop codon.
  // This is zero-based exclusive numbering, like the `end` field.
  int64 thick_end = 8;

  // A comma-separated RGB value R,G,B for visualization.
  string item_rgb = 9;

  // The number of distinct blocks in the BED line (e.g. exon count in gene
  // structures).
  int32 block_count = 10;

  // Comma-separated list of block sizes. The number of items in the list should
  // be equal to `block_count`.
  string block_sizes = 11;

  // Comma-separated list of block start positions. The number of items in the
  // list should be equal to `block_count`.
  // This is zero-based inclusive numbering, like the `start` field.
  string block_starts = 12;
}

message BedHeader {
  // The number of fields in the BED file.
  int32 num_fields = 1;
}

///////////////////////////////////////////////////////////////////////////////
// I/O-related messages.
///////////////////////////////////////////////////////////////////////////////

// Options for reading BED files.
message BedReaderOptions {
  reserved 1;

  // Optional. The number of fields to read from the BED file. If this is unset,
  // or set to more fields than are present in the BED file, all fields are
  // read.
  int32 num_fields = 2;
}

// Options for writing BED files.
// Currently this is a placeholder message.
message BedWriterOptions {
}