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#ifndef LEARNING_GENOMICS_DEEPVARIANT_REALIGNER_WINDOW_SELECTOR_H_
#define LEARNING_GENOMICS_DEEPVARIANT_REALIGNER_WINDOW_SELECTOR_H_

#include <vector>

#include "deepvariant/allelecounter.h"
#include "deepvariant/protos/realigner.pb.h"

namespace learning {
namespace genomics {
namespace deepvariant {

// Returns a vector of candidate counts for the realigner/window_selector.
//
// This algorithm assumes that the provided AlleleCounter object has had the
// reads we want to use to compute our candidate positions already added to it.
//
// We walk over the AlleleCounts in the AlleleCounter and increment our position
// counts for each non-REFERENCE allele we see as follows:
//
//  - SUBSTITITUION: at the substitution position only.
//  - DELETE: at positions within [position, position + length)
//  - INSERT and CLIP_SOFT: at positions within
//      [position - cigar_len, position + cigar_len)
//
// Returns:
//   A vector of counts. The value at offset [i] is the sum of candidate
//   positions across all alleles in AlleleCount that affected position i.
//   The i-th position in this vector corresponding to the i-th position in
//   allele_count->Interval(). So result[0] is the count for
//   allele_count->Interval().start().
std::vector<int> VariantReadsWindowSelectorCandidates(
    const AlleleCounter& allele_counter);

std::vector<float> AlleleCountLinearWindowSelectorCandidates(
    const AlleleCounter& allele_counter,
    const WindowSelectorModel::AlleleCountLinearModel& config);

}  // namespace deepvariant
}  // namespace genomics
}  // namespace learning

#endif  // LEARNING_GENOMICS_DEEPVARIANT_REALIGNER_WINDOW_SELECTOR_H_