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#ifndef __ALIGNMENTCOMMON_H__
#define __ALIGNMENTCOMMON_H__
#include <atomic>
#include <memory>
#include <mutex>
// logger includes
#include "spdlog/spdlog.h"
extern "C" {
#include "io_lib/os.h"
#include "io_lib/scram.h"
#undef max
#undef min
}
struct UnpairedRead;
struct ReadPair;
class Transcript;
// Common functionalities to different alignment models
class AlignmentCommon {
public:
AlignmentCommon()
: burnedIn_(false)
{ }
bool burnedIn() { return burnedIn_; }
void burnedIn(bool burnedIn) { burnedIn_ = burnedIn; }
void setLogger(std::shared_ptr<spdlog::logger> logger) { logger_ = logger; }
bool hasLogger() { return (logger_) ? true : false; }
static bool hasIndel(ReadPair& hit);
static bool hasIndel(UnpairedRead& hit);
protected:
enum AlignmentModelChar {
ALN_A = 0,
ALN_C = 1,
ALN_G = 2,
ALN_T = 3,
ALN_DASH = 4,
ALN_SOFT_CLIP = 5,
ALN_HARD_CLIP = 6,
ALN_PAD = 7,
ALN_REF_SKIP = 8
};
static bool hasIndel(bam_seq_t* read);
static void setBasesFromCIGAROp_(enum cigar_op op, size_t& curRefBase, size_t& curReadBase);
static char opToChr(enum cigar_op op);
template<typename T>
static int32_t alnLen(const T& aln, const T& primary) {
const auto l = aln.readLen();
return l != 0 ? l : primary.readLen();
}
struct ErrorCount {
protected:
int32_t insertions_, deletions_, mismatches_, matches_;
int32_t sclips_, hclips_; // soft and hard clips
int32_t fclips_, bclips_; // clips at front and at back
friend AlignmentCommon;
public:
inline int32_t clips() const { return sclips_ + hclips_; }
// Indels + mismatches
inline int32_t ims() const { return insertions_ + deletions_ + mismatches_; }
// Should be equal to the length of the query sequence
inline int32_t length() const { return insertions_ + mismatches_ + matches_ + sclips_; }
void clear() {
insertions_ = deletions_ = mismatches_ = matches_ = sclips_ = hclips_ = fclips_ = bclips_ = 0;
}
inline int32_t insertions() const { return insertions_; }
inline int32_t deletions() const { return deletions_; }
inline int32_t mismatches() const { return mismatches_; }
inline int32_t matches() const { return matches_; }
inline int32_t sclips() const { return sclips_; }
inline int32_t hclips() const { return hclips_; }
inline int32_t fclips() const { return fclips_; }
inline int32_t bclips() const { return bclips_; }
bool computeErrorCount(bam_seq_t* read, bam_seq_t* primary, Transcript& ref,
const char* src);
};
bool computeErrorCount(bam_seq_t* read, bam_seq_t* primary, Transcript& ref,
ErrorCount& counts, const char* src);
std::shared_ptr<spdlog::logger> logger_;
std::atomic<bool> burnedIn_;
std::mutex throwMutex_;
};
#endif /* __ALIGNMENTCOMMON_H__ */
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