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#include <cereal/types/vector.hpp>
#include <cereal/types/unordered_map.hpp>
#include <cereal/archives/binary.hpp>
#include "RapMapUtils.hpp"
#include "RapMapSAIndex.hpp"
#include "RapMapIndex.hpp"
#include "PairAlignmentFormatter.hpp"
#include "SingleAlignmentFormatter.hpp"
//#include "jellyfish/whole_sequence_parser.hpp"
#include "FastxParser.hpp"
#include "BooMap.hpp"
namespace rapmap {
namespace utils {
std::vector<std::string> tokenize(const std::string &s, char delim) {
std::stringstream ss(s);
std::string item;
std::vector<std::string> elems;
while (std::getline(ss, item, delim)) {
elems.push_back(item);
}
return elems;
}
// positions are stored in a packed format, where the highest
// 2-bits encode if this position refers to a new transcript
// and whether or not the k-mer from the hash matches this txp
// in the forward or rc direction.
void decodePosition(uint32_t p, int32_t& pOut, bool& newTxp, bool& isRC) {
uint32_t highBits = (p >> 30);
pOut = (p & 0x3fffffff);
newTxp = (highBits & 0x1);
isRC = (highBits & 0x2);
}
static constexpr int8_t rc_table[128] = {
78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, // 15
78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, // 31
78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, // 787
78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, // 63
78, 84, 78, 71, 78, 78, 78, 67, 78, 78, 78, 78, 78, 78, 78, 78, // 79
78, 78, 78, 78, 65, 65, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, // 95
78, 84, 78, 71, 78, 78, 78, 67, 78, 78, 78, 78, 78, 78, 78, 78, // 101
78, 78, 78, 78, 65, 65, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78 // 127
};
// Adapted from
// https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/blob/8c9933a1685e0ab50c7d8b7926c9068bc0c9d7d2/src/main.c#L36
void reverseRead(std::string& seq,
std::string& qual,
std::string& readWork,
std::string& qualWork) {
readWork.resize(seq.length(), 'A');
qualWork.resize(qual.length(), 'I');
int32_t end = seq.length()-1, start = 0;
//readWork[end] = '\0';
//qualWork[end] = '\0';
while (LIKELY(start < end)) {
readWork[start] = (char)rc_table[(int8_t)seq[end]];
readWork[end] = (char)rc_table[(int8_t)seq[start]];
qualWork[start] = qual[end];
qualWork[end] = qual[start];
++ start;
-- end;
}
// If odd # of bases, we still have to complement the middle
if (start == end) {
readWork[start] = (char)rc_table[(int8_t)seq[start]];
// but don't need to mess with quality
// qualWork[start] = qual[start];
}
//std::swap(seq, readWork);
//std::swap(qual, qualWork);
}
// Adapted from
// https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/blob/8c9933a1685e0ab50c7d8b7926c9068bc0c9d7d2/src/main.c#L36
// Don't modify the qual
void reverseRead(std::string& seq,
std::string& readWork) {
readWork.resize(seq.length(), 'A');
int32_t end = seq.length()-1, start = 0;
//readWork[end] = '\0';
//qualWork[end] = '\0';
while (LIKELY(start < end)) {
readWork[start] = (char)rc_table[(int8_t)seq[end]];
readWork[end] = (char)rc_table[(int8_t)seq[start]];
++ start;
-- end;
}
// If odd # of bases, we still have to complement the middle
if (start == end) {
readWork[start] = (char)rc_table[(int8_t)seq[start]];
// but don't need to mess with quality
// qualWork[start] = qual[start];
}
//std::swap(seq, readWork);
//std::swap(qual, qualWork);
}
template <typename ReadT, typename IndexT>
uint32_t writeAlignmentsToStream(
ReadT& r,
SingleAlignmentFormatter<IndexT>& formatter,
HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& hits,
fmt::MemoryWriter& sstream
) {
// Convenient variable name bindings
auto& txpNames = formatter.index->txpNames;
auto& txpLens = formatter.index->txpLens;
auto& readTemp = formatter.readTemp;
//auto& qualTemp = formatter.qualTemp;
auto& cigarStr = formatter.cigarStr;
uint16_t flags;
auto& readName = r.name;
#if defined(__DEBUG__) || defined(__TRACK_CORRECT__)
auto before = readName.find_first_of(':');
before = readName.find_first_of(':', before+1);
auto after = readName.find_first_of(':', before+1);
const auto& txpName = readName.substr(before+1, after-before-1);
#endif //__DEBUG__
// If the read name contains multiple space-separated parts, print
// only the first
size_t splitPos = readName.find(' ');
if (splitPos < readName.length()) {
readName[splitPos] = '\0';
}
std::string numHitFlag = fmt::format("NH:i:{}", hits.size());
uint32_t alnCtr{0};
bool haveRev{false};
for (auto& qa : hits) {
auto& transcriptName = txpNames[qa.tid];
// === SAM
rapmap::utils::getSamFlags(qa, flags);
if (alnCtr != 0) {
flags |= 0x900;
}
std::string* readSeq = &(r.seq);
//std::string* qstr = &(r.qual);
if (!qa.fwd) {
if (!haveRev) {
rapmap::utils::reverseRead(*readSeq, readTemp);
haveRev = true;
}
readSeq = &(readTemp);
//qstr = &(qualTemp);
}
rapmap::utils::adjustOverhang(qa.pos, qa.readLen, txpLens[qa.tid], cigarStr);
sstream << readName.c_str() << '\t' // QNAME
<< flags << '\t' // FLAGS
<< transcriptName << '\t' // RNAME
<< qa.pos + 1 << '\t' // POS (1-based)
<< 255 << '\t' // MAPQ
<< cigarStr.c_str() << '\t' // CIGAR
<< '*' << '\t' // MATE NAME
<< 0 << '\t' // MATE POS
<< qa.fragLen << '\t' // TLEN
<< *readSeq << '\t' // SEQ
<< "*\t" // QSTR
<< numHitFlag << '\n';
++alnCtr;
// === SAM
#if defined(__DEBUG__) || defined(__TRACK_CORRECT__)
if (txpNames[qa.tid] == txpName) { ++hctr.trueHits; }
#endif //__DEBUG__
}
return alnCtr;
}
// For reads paired *in sequencing*
template <typename ReadPairT, typename IndexT>
uint32_t writeAlignmentsToStream(
ReadPairT& r,
PairAlignmentFormatter<IndexT>& formatter,
HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream
) {
// Convenient variable name bindings
auto& txpNames = formatter.index->txpNames;
auto& txpLens = formatter.index->txpLens;
auto& read1Temp = formatter.read1Temp;
auto& read2Temp = formatter.read2Temp;
//auto& qual1Temp = formatter.qual1Temp;
//auto& qual2Temp = formatter.qual2Temp;
auto& cigarStr1 = formatter.cigarStr1;
auto& cigarStr2 = formatter.cigarStr2;
uint16_t flags1, flags2;
auto& readName = r.first.name;
// If the read name contains multiple space-separated parts,
// print only the first
size_t splitPos = readName.find(' ');
if (splitPos < readName.length()) {
readName[splitPos] = '\0';
} else {
splitPos = readName.length();
}
// trim /1 from the pe read
if (splitPos > 2 and readName[splitPos - 2] == '/') {
readName[splitPos - 2] = '\0';
}
auto& mateName = r.second.name;
// If the read name contains multiple space-separated parts,
// print only the first
splitPos = mateName.find(' ');
if (splitPos < mateName.length()) {
mateName[splitPos] = '\0';
} else {
splitPos = mateName.length();
}
// trim /2 from the pe read
if (splitPos > 2 and mateName[splitPos - 2] == '/') {
mateName[splitPos - 2] = '\0';
}
/*
// trim /1 and /2 from pe read names
if (readName.length() > 2 and
readName[readName.length() - 2] == '/') {
readName[readName.length() - 2] = '\0';
}
if (mateName.length() > 2 and
mateName[mateName.length() - 2] == '/') {
mateName[mateName.length() - 2] = '\0';
}
*/
std::string numHitFlag = fmt::format("NH:i:{}", jointHits.size());
uint32_t alnCtr{0};
uint32_t trueHitCtr{0};
QuasiAlignment* firstTrueHit{nullptr};
bool haveRev1{false};
bool haveRev2{false};
bool* haveRev = nullptr;
size_t i{0};
for (auto& qa : jointHits) {
++i;
auto& transcriptName = txpNames[qa.tid];
// === SAM
if (qa.isPaired) {
rapmap::utils::getSamFlags(qa, true, flags1, flags2);
if (alnCtr != 0) {
flags1 |= 0x100; flags2 |= 0x100;
}
auto txpLen = txpLens[qa.tid];
rapmap::utils::adjustOverhang(qa, txpLens[qa.tid], cigarStr1, cigarStr2);
// Reverse complement the read and reverse
// the quality string if we need to
std::string* readSeq1 = &(r.first.seq);
//std::string* qstr1 = &(r.first.qual);
if (!qa.fwd) {
if (!haveRev1) {
rapmap::utils::reverseRead(*readSeq1, read1Temp);
haveRev1 = true;
}
readSeq1 = &(read1Temp);
//qstr1 = &(qual1Temp);
}
std::string* readSeq2 = &(r.second.seq);
//std::string* qstr2 = &(r.second.qual);
if (!qa.mateIsFwd) {
if (!haveRev2) {
rapmap::utils::reverseRead(*readSeq2, read2Temp);
haveRev2 = true;
}
readSeq2 = &(read2Temp);
//qstr2 = &(qual2Temp);
}
// If the fragment overhangs the right end of the transcript
// adjust fragLen (overhanging the left end is already handled).
int32_t read1Pos = qa.pos;
int32_t read2Pos = qa.matePos;
const bool read1First{read1Pos < read2Pos};
const int32_t minPos = read1First ? read1Pos : read2Pos;
if (minPos + qa.fragLen > txpLen) { qa.fragLen = txpLen - minPos; }
// get the fragment length as a signed int
const int32_t fragLen = static_cast<int32_t>(qa.fragLen);
sstream << readName.c_str() << '\t' // QNAME
<< flags1 << '\t' // FLAGS
<< transcriptName << '\t' // RNAME
<< qa.pos + 1 << '\t' // POS (1-based)
<< 1 << '\t' // MAPQ
<< cigarStr1.c_str() << '\t' // CIGAR
<< '=' << '\t' // RNEXT
<< qa.matePos + 1 << '\t' // PNEXT
<< ((read1First) ? fragLen : -fragLen) << '\t' // TLEN
<< *readSeq1 << '\t' // SEQ
<< "*\t" // QUAL
<< numHitFlag << '\n';
sstream << mateName.c_str() << '\t' // QNAME
<< flags2 << '\t' // FLAGS
<< transcriptName << '\t' // RNAME
<< qa.matePos + 1 << '\t' // POS (1-based)
<< 1 << '\t' // MAPQ
<< cigarStr2.c_str() << '\t' // CIGAR
<< '=' << '\t' // RNEXT
<< qa.pos + 1 << '\t' // PNEXT
<< ((read1First) ? -fragLen : fragLen) << '\t' // TLEN
<< *readSeq2 << '\t' // SEQ
<< "*\t" // QUAL
<< numHitFlag << '\n';
} else {
rapmap::utils::getSamFlags(qa, true, flags1, flags2);
if (alnCtr != 0) {
flags1 |= 0x100; flags2 |= 0x100;
}
/*
else {
// If this is the first alignment for this read
// If the left end is mapped, set 0x100 on the right end
if (qa.mateStatus == MateStatus::PAIRED_END_LEFT) {
flags2 |= 0x100;
} else {
// Otherwise, set 0x100 on the left end
flags1 |= 0x100;
}
}
*/
std::string* readSeq{nullptr};
std::string* unalignedSeq{nullptr};
uint32_t flags, unalignedFlags;
//std::string* qstr{nullptr};
//std::string* unalignedQstr{nullptr};
std::string* alignedName{nullptr};
std::string* unalignedName{nullptr};
std::string* readTemp{nullptr};
//std::string* qualTemp{nullptr};
rapmap::utils::FixedWriter* cigarStr;
if (qa.mateStatus == MateStatus::PAIRED_END_LEFT) { // left read
alignedName = &readName;
unalignedName = &mateName;
readSeq = &(r.first.seq);
unalignedSeq = &(r.second.seq);
//qstr = &(r.first.qual);
//unalignedQstr = &(r.second.qual);
flags = flags1;
unalignedFlags = flags2;
cigarStr = &cigarStr1;
haveRev = &haveRev1;
readTemp = &read1Temp;
//qualTemp = &qual1Temp;
} else { // right read
alignedName = &mateName;
unalignedName = &readName;
readSeq = &(r.second.seq);
unalignedSeq = &(r.first.seq);
//qstr = &(r.second.qual);
//unalignedQstr = &(r.first.qual);
flags = flags2;
unalignedFlags = flags1;
cigarStr = &cigarStr2;
haveRev = &haveRev2;
readTemp = &read2Temp;
//qualTemp = &qual2Temp;
}
// Reverse complement the read and reverse
// the quality string if we need to
if (!qa.fwd) {
if (!(*haveRev)) {
rapmap::utils::reverseRead(*readSeq, *readTemp);
*haveRev = true;
}
readSeq = readTemp;
}
/*
if (!qa.fwd) {
rapmap::utils::reverseRead(*readSeq, *qstr,
read1Temp, qual1Temp);
}
*/
rapmap::utils::adjustOverhang(qa.pos, qa.readLen, txpLens[qa.tid], *cigarStr);
sstream << alignedName->c_str() << '\t' // QNAME
<< flags << '\t' // FLAGS
<< transcriptName << '\t' // RNAME
<< qa.pos + 1 << '\t' // POS (1-based)
<< 1 << '\t' // MAPQ
<< cigarStr->c_str() << '\t' // CIGAR
<< '=' << '\t' // RNEXT
<< qa.pos+1 << '\t' // PNEXT (only 1 read in templte)
<< 0 << '\t' // TLEN (spec says 0, not read len)
<< *readSeq << '\t' // SEQ
<< "*\t" // QUAL
<< numHitFlag << '\n';
// Output the info for the unaligned mate.
sstream << unalignedName->c_str() << '\t' // QNAME
<< unalignedFlags << '\t' // FLAGS
<< transcriptName << '\t' // RNAME (same as mate)
<< qa.pos + 1 << '\t' // POS (same as mate)
<< 0 << '\t' // MAPQ
<< unalignedSeq->length() << 'S' << '\t' // CIGAR
<< '=' << '\t' // RNEXT
<< qa.pos + 1 << '\t' // PNEXT (only 1 read in template)
<< 0 << '\t' // TLEN (spec says 0, not read len)
<< *unalignedSeq << '\t' // SEQ
<< "*\t" // QUAL
<< numHitFlag << '\n';
}
++alnCtr;
// == SAM
#if defined(__DEBUG__) || defined(__TRACK_CORRECT__)
if (transcriptName == trueTxpName) {
if (trueHitCtr == 0) {
++hctr.trueHits;
++trueHitCtr;
firstTrueHit = &qa;
} else {
++trueHitCtr;
std::cerr << "Found true hit " << trueHitCtr << " times!\n";
std::cerr << transcriptName << '\t' << firstTrueHit->pos
<< '\t' << firstTrueHit->fwd << '\t' << firstTrueHit->fragLen
<< '\t' << (firstTrueHit->isPaired ? "Paired" : "Orphan") << '\t';
printMateStatus(firstTrueHit->mateStatus);
std::cerr << '\n';
std::cerr << transcriptName << '\t' << qa.pos
<< '\t' << qa.fwd << '\t' << qa.fragLen
<< '\t' << (qa.isPaired ? "Paired" : "Orphan") << '\t';
printMateStatus(qa.mateStatus);
std::cerr << '\n';
}
}
#endif //__DEBUG__
}
return alnCtr;
}
// Is there a smarter way to do save / load here?
/*
template <typename Archive, typename MerT>
void save(Archive& archive, const MerT& mer) const {
auto key = mer.get_bits(0, 2*mer.k());
archive(key);
}
template <typename Archive>
void load(Archive& archive, const MerT& mer) {
mer.polyT();
uint64_t bits;
archive(bits);
auto k = mer.k();
mer.set_bits(0, 2*k, bits);
}
*/
}
}
using SAIndex32BitDense = RapMapSAIndex<int32_t,google::dense_hash_map<uint64_t, rapmap::utils::SAInterval<int32_t>,
rapmap::utils::KmerKeyHasher>>;
using SAIndex64BitDense = RapMapSAIndex<int64_t,google::dense_hash_map<uint64_t, rapmap::utils::SAInterval<int64_t>,
rapmap::utils::KmerKeyHasher>>;
using SAIndex32BitPerfect = RapMapSAIndex<int32_t, BooMap<uint64_t, rapmap::utils::SAInterval<int32_t>>>;
using SAIndex64BitPerfect = RapMapSAIndex<int64_t, BooMap<uint64_t, rapmap::utils::SAInterval<int64_t>>>;
// Explicit instantiations
// pair parser, 32-bit, dense hash
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadPair, SAIndex32BitDense*>(
fastx_parser::ReadPair& r,
PairAlignmentFormatter<SAIndex32BitDense*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream);
// pair parser, 64-bit, dense hash
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadPair, SAIndex64BitDense*>(
fastx_parser::ReadPair& r,
PairAlignmentFormatter<SAIndex64BitDense*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream);
// pair parser, 32-bit, perfect hash
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadPair, SAIndex32BitPerfect*>(
fastx_parser::ReadPair& r,
PairAlignmentFormatter<SAIndex32BitPerfect*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream);
// pair parser, 64-bit, perfect hash
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadPair, SAIndex64BitPerfect*>(
fastx_parser::ReadPair& r,
PairAlignmentFormatter<SAIndex64BitPerfect*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream);
// single parser, 32-bit, dense hash
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadSeq, SAIndex32BitDense*>(
fastx_parser::ReadSeq& r,
SingleAlignmentFormatter<SAIndex32BitDense*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream);
// single parser, 64-bit, dense hash
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadSeq, SAIndex64BitDense*>(
fastx_parser::ReadSeq& r,
SingleAlignmentFormatter<SAIndex64BitDense*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream);
// single parser, 32-bit, perfect hash
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadSeq, SAIndex32BitPerfect*>(
fastx_parser::ReadSeq& r,
SingleAlignmentFormatter<SAIndex32BitPerfect*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream);
// single parser, 64-bit, perfect hash
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadSeq, SAIndex64BitPerfect*>(
fastx_parser::ReadSeq& r,
SingleAlignmentFormatter<SAIndex64BitPerfect*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream);
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadPair, RapMapIndex*>(
fastx_parser::ReadPair& r,
PairAlignmentFormatter<RapMapIndex*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream
);
template uint32_t rapmap::utils::writeAlignmentsToStream<fastx_parser::ReadSeq, RapMapIndex*>(
fastx_parser::ReadSeq& r,
SingleAlignmentFormatter<RapMapIndex*>& formatter,
rapmap::utils::HitCounters& hctr,
std::vector<rapmap::utils::QuasiAlignment>& jointHits,
fmt::MemoryWriter& sstream
);
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