source: trunk/test/bam_header.cc @ 3408

// $Id: bam_header.cc 3408 2015-04-16 00:22:24Z peter $
//
// Copyright (C) 2013, 2014 Peter Johansson
//
// This program is free software; you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation; either version 3 of the License, or
// (at your option) any later version.
//
// This program is distributed in the hope that it will be useful, but
// WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
// General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program. If not, see <http://www.gnu.org/licenses/>.

#include <config.h>

#include "Suite.h"

#ifdef YAT_HAVE_LIBBAM
#include "yat/omic/BamFile.h"
#include "yat/omic/BamHeader.h"
#endif

using namespace theplu::yat;

void test1(test::Suite& suite);

int main(int argc, char* argv[])
{
  test::Suite suite(argc, argv, true);
  try {
    test1(suite);
  }
  catch (std::runtime_error& e) {
    suite.err() << "what: " << e.what() << "\n";
    suite.add(false);
  }

  return suite.return_value();
}

void test1(test::Suite& suite)
{
#ifdef YAT_HAVE_LIBBAM
  using namespace omic;
  std::string file = "../../data/foo.sorted.bam";

  InBamFile bam_stream(file);
  BamHeader hdr = bam_stream.header();
  suite.out() << hdr.n_targets() << "\n";
  suite.add(hdr.n_targets()==84);
  suite.out() << hdr.target_name(0) << "\n";
  if (!suite.add(std::string("1")==hdr.target_name(0)))
    suite.err() << "error\n";
  int32_t tid = hdr.tid("1");
  suite.out() << "tid: " << tid << "\n";
  if (!suite.add(tid==0))
    suite.err() << "error\n";

  int begin, end;
  hdr.parse_region("GL000197.1", tid, begin, end);
  suite.out() << tid << " " << begin << " " << end << "\n";
  suite.add(tid==35);
  hdr.parse_region("GL000197.1:1000-2000", tid, begin, end);
  suite.out() << tid << " " << begin << " " << end << "\n";
  if (!suite.add(tid==35))
    suite.err() << "incorrect tid\n";
  if (!suite.add(begin==999))
    suite.err() << "incorrect begin\n";
  if (!suite.add(end==2000))
    suite.err() << "incorrect end\n";

  suite.out() << hdr.target_name(35) << "\n";
  if (!suite.add(std::string("GL000197.1")==hdr.target_name(35)))
    suite.err() << "error\n";
  suite.out() << hdr.target_length(0) << "\n";
  suite.add(hdr.target_length(0)==249250621);

  std::string str = hdr.text();
  std::string str1(str);
  str1 += "@PG\tID:prog\tVN:1.0\n";
  omic::BamHeader hdr2(hdr);
  hdr.text(str1);
  std::string str2 = hdr.text();
  if (str2.substr(0, str.size()) != str) {
    suite.add(false);
    suite.err() << "incorrect text:\n" << str2 << "\nexpected:\n"
                << str1 << "\n";
  }
  else if (str2 != str1) {
    suite.add(false);
    suite.err() << "error: line was not added to header\n";
  }
  if (hdr2.text() != str) {
    suite.add(false);
    suite.err() << "function text(1) affects copies\n";
  }

#endif
}