/*
 * Copyright 2018 Google LLC.
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 *    this list of conditions and the following disclaimer.
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 * 2. Redistributions in binary form must reproduce the above copyright
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 * 3. Neither the name of the copyright holder nor the names of its
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 *    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
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#include "htslib/hts.h"

#include <errno.h>
#include <stdlib.h>
#include <string>

#include "tensorflow/core/platform/test.h"
#include "absl/strings/str_cat.h"
#include "htslib/hts_log.h"
#include "htslib/kstring.h"
#include "third_party/nucleus/io/hts_path.h"
#include "third_party/nucleus/platform/types.h"
#include "third_party/nucleus/testing/test_utils.h"
#include "third_party/nucleus/util/port.h"

using absl::StrCat;

namespace nucleus {

// This tests minimal htslib functionality.
TEST(FileTest, HtsOpen) {
  hts_set_log_level(HTS_LOG_TRACE);

  string path = GetTestData("test.fasta");
  errno = 0;
  htsFile* f = hts_open(path.c_str(), "rb");
  EXPECT_EQ(errno, 0);
  ASSERT_NE(f, nullptr);

  kstring_t str = {0, 0, nullptr};
  int n = hts_getline(f, '\n', &str);
  EXPECT_GT(n, 0);
  EXPECT_EQ(ks_len(&str), 5);
  EXPECT_EQ(ks_str(&str), string(">chrM"));
  free(str.s);

  int close_ok = hts_close(f);
  EXPECT_EQ(close_ok, 0);
}

}  // namespace nucleus
