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#ifndef READ_PAIR
#define READ_PAIR
#include "StadenUtils.hpp"
#include "SalmonMath.hpp"
#include "LibraryFormat.hpp"
#include "SalmonUtils.hpp"
#include "RapMapUtils.hpp"
#include "spdlog/fmt/fmt.h"
struct ReadPair {
bam_seq_t* read1 = nullptr;
bam_seq_t* read2 = nullptr;
salmon::utils::OrphanStatus orphanStatus;
double logProb;
LibraryFormat libFmt{ReadType::PAIRED_END, ReadOrientation::NONE, ReadStrandedness::U};
ReadPair():
read1(staden::utils::bam_init()),
read2(staden::utils::bam_init()),
orphanStatus(salmon::utils::OrphanStatus::Paired),
logProb(salmon::math::LOG_0) {}
ReadPair(bam_seq_t* r1, bam_seq_t* r2, salmon::utils::OrphanStatus os, double lp,
LibraryFormat lf) :
read1(r1), read2(r2), orphanStatus(os), logProb(lp),
libFmt(lf){}
ReadPair(ReadPair&& other) {
orphanStatus = other.orphanStatus;
logProb = other.logProb;
std::swap(read1, other.read1);
std::swap(read2, other.read2);
libFmt = other.libFmt;
}
ReadPair& operator=(ReadPair&& other) {
orphanStatus = other.orphanStatus;
logProb = other.logProb;
std::swap(read1, other.read1);
std::swap(read2, other.read2);
libFmt = other.libFmt;
return *this;
}
ReadPair(ReadPair& other) = default;
ReadPair& operator=(ReadPair& other) = default;
ReadPair* clone() {
return new ReadPair(bam_dup(read1), bam_dup(read2), orphanStatus, logProb, libFmt);
}
~ReadPair() {
staden::utils::bam_destroy(read1);
staden::utils::bam_destroy(read2);
}
inline LibraryFormat& libFormat() { return libFmt; }
inline bool isPaired() const { return (orphanStatus == salmon::utils::OrphanStatus::Paired); }
inline bool isLeftOrphan() const { return (orphanStatus == salmon::utils::OrphanStatus::LeftOrphan); }
inline bool isRightOrphan() const { return (orphanStatus == salmon::utils::OrphanStatus::RightOrphan); }
inline bam_seq_t* get5PrimeRead() {
return (isPaired() or isLeftOrphan()) ? read1 : nullptr;
}
inline rapmap::utils::MateStatus mateStatus() const {
if (isPaired()) {
return rapmap::utils::MateStatus::PAIRED_END_PAIRED;
} else if (isLeftOrphan()) {
return rapmap::utils::MateStatus::PAIRED_END_LEFT;
} else if (isRightOrphan()) {
return rapmap::utils::MateStatus::PAIRED_END_RIGHT;
}
std::cerr << "ReadPair.hpp : mateStatus() --- should not get here ";
std::cerr << "this may be a bug. Please report it\n";
return rapmap::utils::MateStatus::PAIRED_END_PAIRED;
}
inline int32_t pos() const { return left(); }
inline bool fwd() const { return !bam_strand(read1); }
/**
* returns 0 on success, -1 on failure.
*/
int writeToFile(scram_fd* fp) {
int r1 = scram_put_seq(fp, read1);
if (r1 == 0 and isPaired()) {
return scram_put_seq(fp, read2);
} else {
return r1;
}
}
inline char* getName() const {
return bam_name(read1);
}
inline uint32_t getNameLength() {
uint32_t l = bam_name_len(read1);
char* r = getName();
if ( l > 2 and r[l-2] == '/') {
return l-2;
}
return l;//bam_name_len(read1);
}
// from the leftmost end of the 5' read to the rightmost
// end of the 3' read (can be less than the length of a single read)
inline uint32_t fragLengthPedantic(uint32_t txpLen) const {
if (!isPaired()) { return 0; }
bool fw1 = !bam_strand(read1);
bool fw2 = !bam_strand(read2);
if (fw1 != fw2) {
int32_t p1 = fw1 ? bam_pos(read1) : bam_pos(read2);
p1 = (p1 < 0) ? 0 : p1;
p1 = (p1 > txpLen) ? txpLen : p1;
int32_t p2 = fw1 ? bam_pos(read2) + bam_seq_len(read2) : bam_pos(read1) + bam_seq_len(read1);
p2 = (p2 < 0) ? 0 : p2;
p2 = (p2 > txpLen) ? txpLen : p2;
return (p1 > p2) ? p1 - p2 : p2 - p1;
}
return 0;
}
inline uint32_t fragLen() const {
if (!isPaired()) { return 0; }
auto leftmost1 = bam_pos(read1);
auto leftmost2 = bam_pos(read2);
// The length of the mapped read that is "rightmost" w.r.t. the forward strand.
auto rightmostLen = (leftmost1 < leftmost2) ? bam_seq_len(read2) : bam_seq_len(read1);
return std::abs(leftmost1 - leftmost2) + rightmostLen;
//return std::abs(read1->core.isize) + std::abs(read1->core.l_qseq) + std::abs(read2->core.l_qseq);
}
inline bool isRight() const { return isPaired() ? false : (isRightOrphan() ? true : false) ; }
inline bool isLeft() const { return isPaired() ? false : (isLeftOrphan() ? true : false); }
inline int32_t left() const {
if (isPaired()) {
return std::min(bam_pos(read1), bam_pos(read2));
} else {
return bam_pos(read1);
}
}
inline int32_t right() const {
if (isPaired()) {
return std::max(bam_pos(read1) + bam_seq_len(read1),
bam_pos(read2) + bam_seq_len(read2));
} else {
return bam_pos(read1) + bam_seq_len(read1);
}
}
inline ReadType fragType() const { return ReadType::PAIRED_END; }
inline int32_t transcriptID() const { return bam_ref(read1); }
inline double logQualProb() {
return salmon::math::LOG_1;
/*
double q1 = bam_map_qual(read1);
double q2 = bam_map_qual(read2);
double logP1 = (q1 == 255) ? salmon::math::LOG_1 : std::log(std::pow(10.0, -q1 * 0.1));
double logP2 = (q2 == 255) ? salmon::math::LOG_1 : std::log(std::pow(10.0, -q2 * 0.1));
return logP1 + logP2;
*/
}
};
#endif //READ_PAIR
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