Fix the overflow issue in fragment length. Triggered in split-alignment mode.

#ifndef MAPPING_IN_MEMORY_H_

#define MAPPING_IN_MEMORY_H_

#include <stdint.h>

#include <string>

#include "utils.h"

namespace chromap {

// Regardless of mapping format, this struct can temporarily hold a mapping in

// memory for easily passing it into the several functions before pushing it

// to the result mapping vector. It never owns the read or the read qual. It

// owns the cigar before push the mapping to the vector. (For now, the cigar

// memory is released once a SAMMapping is created.) Since this struct is large,

// we should never create a huge vector of this struct.

struct MappingInMemory {

  uint32_t read_id = 0;

  int read_split_site = 0;

  int read_length = 0;

  uint32_t rid = 0;

  uint32_t ref_start_position = 0;

  uint32_t ref_end_position = 0;

  uint64_t barcode_key = 0;

  Strand strand = kPositive;

  bool is_unique = true;

  uint8_t mapq = 0;

  // It does NOT own read or read qual.

  const char *read_name = nullptr;

  const char *read_sequence = nullptr;

  const char *qual_sequence = nullptr;

  // SAM fields or tags.

  uint16_t SAM_flag = 0;

  uint32_t *cigar = nullptr;

  int n_cigar = 0;

  int NM = 0;

  std::string MD_tag;

  inline uint8_t GetStrand() const { return (strand == kPositive ? 1 : 0); }

  inline uint32_t GetFragmentStartPosition() const {

    return ref_start_position;

  }

  // TODO(Haowen): change this to alignment length.

  inline uint16_t GetFragmentLength() const {

    return ref_end_position - ref_start_position + 1;

  }

  inline uint16_t GetAlignmentLength() const {

    return ref_end_position - ref_start_position + 1;

  }

};

struct PairedEndMappingInMemory {

  MappingInMemory mapping_in_memory1;

  MappingInMemory mapping_in_memory2;

  uint8_t is_unique;

  uint8_t mapq;

  inline uint8_t GetStrand() const {

    return (mapping_in_memory1.strand == kPositive ? 1 : 0);

  }

  inline uint32_t GetReadId() const { return mapping_in_memory1.read_id; }

  inline uint64_t GetBarcode() const { return mapping_in_memory1.barcode_key; }

  inline uint32_t GetFragmentStartPosition() const {

    if (mapping_in_memory1.strand == kPositive) {

      return mapping_in_memory1.GetFragmentStartPosition();

    }

    return mapping_in_memory2.GetFragmentStartPosition();

  }

  inline int GetFragmentLength() const {

    if (mapping_in_memory1.strand == kPositive) {

      return mapping_in_memory2.ref_end_position -

             mapping_in_memory1.ref_start_position + 1;

    }

    return mapping_in_memory1.ref_end_position -

           mapping_in_memory2.ref_start_position + 1;

  }

  inline uint32_t GetPositiveAlignmentLength() const {

    if (mapping_in_memory1.strand == kPositive) {

      return mapping_in_memory1.GetAlignmentLength();

    }

    return mapping_in_memory2.GetAlignmentLength();

  }

  inline uint32_t GetNegativeAlignmentLength() const {

    if (mapping_in_memory1.strand == kNegative) {

      return mapping_in_memory1.GetAlignmentLength();

    }

    return mapping_in_memory2.GetAlignmentLength();

  }

};

}  // namespace chromap

#endif  // MAPPING_IN_MEMORY_H_