synced_variant_reader.h

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#ifndef gamgee__synced_variant_reader__guard
#define gamgee__synced_variant_reader__guard

#include "htslib/vcf.h"
#include "htslib/synced_bcf_reader.h"

#include "../exceptions.h"
#include "../utils/hts_memory.h"

#include <string>
#include <iostream>

using namespace std;

namespace gamgee {

template<class ITERATOR>
class SyncedVariantReader {
 public:

  SyncedVariantReader(const std::vector<std::string>& filenames, const std::string& interval_list) :
    m_synced_readers {utils::make_shared_synced_variant_reader(bcf_sr_init())}
  {
    auto success = 0;
    if (interval_list.empty()) {
      m_synced_readers->require_index = 1;
    }
    else {
      success = bcf_sr_set_regions(m_synced_readers.get(), interval_list.c_str(), 0);
      if (success != 0)
        throw HtslibException(success);
    }

    for (const auto& filename : filenames) {
      success = bcf_sr_add_reader(m_synced_readers.get(), filename.c_str());
      if (success != 1) {        // returns 1 on success to indicate 1 file added
        throw FileOpenException{filename};
      }
    }
  }

  SyncedVariantReader(SyncedVariantReader&& other) = default;
  SyncedVariantReader& operator=(SyncedVariantReader&& other) = default;

  SyncedVariantReader(const SyncedVariantReader&) = delete;
  SyncedVariantReader& operator=(const SyncedVariantReader&) = delete;

  ITERATOR begin() const {
    return ITERATOR{m_synced_readers};
  }

  ITERATOR end() const {
    return ITERATOR{};
  }

 private:
  std::shared_ptr<bcf_srs_t> m_synced_readers;          
};

}  // end namespace gamgee

#endif /* gamgee__synced_variant_reader__guard */