/*
 * 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.
 */

// Implementation of bed_writer.h
#include "third_party/nucleus/io/bed_writer.h"

#include <utility>

#include "absl/memory/memory.h"
#include "absl/strings/str_cat.h"
#include "third_party/nucleus/platform/types.h"
#include "third_party/nucleus/protos/bed.pb.h"
#include "third_party/nucleus/util/utils.h"
#include "tensorflow/core/lib/core/errors.h"
#include "tensorflow/core/lib/core/status.h"
#include "tensorflow/core/platform/logging.h"

namespace nucleus {

namespace tf = tensorflow;

// 256 KB write buffer.
constexpr int WRITER_BUFFER_SIZE = 256 * 1024;

// -----------------------------------------------------------------------------
//
// Writer for BED formats containing NGS reads.
//
// -----------------------------------------------------------------------------

StatusOr<std::unique_ptr<BedWriter>> BedWriter::ToFile(
    const string& bed_path, const nucleus::genomics::v1::BedHeader& header,
    const nucleus::genomics::v1::BedWriterOptions& options) {
  StatusOr<std::unique_ptr<TextWriter>> text_writer =
      TextWriter::ToFile(bed_path);
  TF_RETURN_IF_ERROR(text_writer.status());
  return absl::WrapUnique(
      new BedWriter(text_writer.ConsumeValueOrDie(), header, options));
}

BedWriter::BedWriter(std::unique_ptr<TextWriter> text_writer,
                     const nucleus::genomics::v1::BedHeader& header,
                     const nucleus::genomics::v1::BedWriterOptions& options)
    : header_(header),
      options_(options),
      text_writer_(std::move(text_writer)) {
}

BedWriter::~BedWriter() {
  if (text_writer_) {
    TF_CHECK_OK(Close());
  }
}

tf::Status BedWriter::Close() {
  if (!text_writer_)
    return tf::errors::FailedPrecondition(
        "Cannot close an already closed BedWriter");
  // Close the file pointer we have been writing to.
  tf::Status close_status = text_writer_->Close();
  text_writer_ = nullptr;
  return close_status;
}

tf::Status BedWriter::Write(const nucleus::genomics::v1::BedRecord& record) {
  if (!text_writer_)
    return tf::errors::FailedPrecondition("Cannot write to closed BED stream.");
  int numFields = header_.num_fields();
  string out = "";
  absl::StrAppend(&out,
                  record.reference_name(),
                  "\t", record.start(),
                  "\t", record.end());
  if (numFields > 3) absl::StrAppend(&out, "\t", record.name());
  if (numFields > 4) absl::StrAppend(&out, "\t", record.score());
  if (numFields > 5) {
    switch (record.strand()) {
      case nucleus::genomics::v1::BedRecord::FORWARD_STRAND:
        absl::StrAppend(&out, "\t+");
        break;
      case nucleus::genomics::v1::BedRecord::REVERSE_STRAND:
        absl::StrAppend(&out, "\t-");
        break;
      case nucleus::genomics::v1::BedRecord::NO_STRAND:
        absl::StrAppend(&out, "\t.");
        break;
      default:
        return tf::errors::Unknown("Unknown strand encoding in the BED proto.");
    }
  }
  if (numFields > 7)
    absl::StrAppend(&out,
                    "\t", record.thick_start(),
                    "\t", record.thick_end());
  if (numFields > 8) absl::StrAppend(&out, "\t", record.item_rgb());
  if (numFields == 12)
    absl::StrAppend(&out,
                    "\t", record.block_count(),
                    "\t", record.block_sizes(),
                    "\t", record.block_starts());
  absl::StrAppend(&out, "\n");
  TF_RETURN_IF_ERROR(text_writer_->Write(out));

  return tf::Status();
}

}  // namespace nucleus
