int main(int argc, char const ** argv)
{
if (argc < 2)
{
std::cerr << "USAGE: basic_seq_io_example FILENAME\n";
return 1;
}
seqan::SequenceStream seqStream(argv[1], seqan::SequenceStream::WRITE);
if (!isGood(seqStream))
{
std::cerr << "ERROR: Could not open the file.\n";
return 1;
}
seqan::StringSet<seqan::CharString> ids;
appendValue(ids, "seq1");
appendValue(ids, "seq2");
seqan::StringSet<seqan::Dna5String> seqs;
appendValue(seqs, "CGAT");
appendValue(seqs, "TTTT");
if (writeAll(seqStream, ids, seqs) != 0)
{
std::cerr << "ERROR: Could not write to file!\n";
return 1;
}
return 0;
}
bool QSslCertificatePrivate::parseExtension(const QByteArray &data, QSslCertificateExtension *extension)
{
bool ok;
bool critical = false;
QAsn1Element oidElem, valElem;
QDataStream seqStream(data);
// oid
if (!oidElem.read(seqStream) || oidElem.type() != QAsn1Element::ObjectIdentifierType)
return false;
const QByteArray oid = oidElem.toObjectId();
// critical and value
if (!valElem.read(seqStream))
return false;
if (valElem.type() == QAsn1Element::BooleanType) {
critical = valElem.toBool(&ok);
if (!ok || !valElem.read(seqStream))
return false;
}
if (valElem.type() != QAsn1Element::OctetStringType)
return false;
// interpret value
QAsn1Element val;
bool supported = true;
QVariant value;
if (oid == "1.3.6.1.5.5.7.1.1") {
// authorityInfoAccess
if (!val.read(valElem.value()) || val.type() != QAsn1Element::SequenceType)
return false;
QVariantMap result;
foreach (const QAsn1Element &el, val.toVector()) {
QVector<QAsn1Element> items = el.toVector();
if (items.size() != 2)
return false;
const QString key = QString::fromLatin1(items.at(0).toObjectName());
switch (items.at(1).type()) {
case QAsn1Element::Rfc822NameType:
case QAsn1Element::DnsNameType:
case QAsn1Element::UniformResourceIdentifierType:
result[key] = items.at(1).toString();
break;
}
}
value = result;
} else if (oid == "2.5.29.14") {
Alignment::Alignment(string filePath, string fileName) {
string filePathAndName = filePath + PATH_SEPERATOR + fileName;
/* open the file */
ifstream seqStream(filePathAndName.c_str());
if (!seqStream)
{
cerr << "Cannot open file \"" + fileName + "\"" << endl;
exit(1);
}
string linestring = "";
int line = 0;
string theSequence = "";
int taxonNum = 0;
matrix = NULL;
numTaxa = numChar = 0;
while( getline(seqStream, linestring).good() )
{
istringstream linestream(linestring);
int ch;
string word = "";
int wordNum = 0;
int siteNum = 0;
do
{
word = "";
linestream >> word;
wordNum++;
//cout << "word(" << wordNum << ") = " << word << endl;
if (line == 0)
{
/* read the number of taxa/chars from the first line */
int x;
istringstream buf(word);
buf >> x;
if (wordNum == 1)
numTaxa = x;
else
numChar = numSitePatterns = x;
if (numTaxa > 0 && numChar > 0 && matrix == NULL)
{
matrix = new int*[numTaxa];
matrix[0] = new int[numTaxa * numChar];
for (int i=1; i<numTaxa; i++)
matrix[i] = matrix[i-1] + numChar;
for (int i=0; i<numTaxa; i++)
for (int j=0; j<numChar; j++)
matrix[i][j] = 0;
patternCount = new int[numChar];
for (int i=0; i<numChar; i++)
patternCount[i] = 1;
compressedData = false;
}
}
else
{
if (wordNum == 1)
{
taxonNames.push_back(word);
taxonNum++;
}
else
{
for (int i=0; i<word.length(); i++)
{
char site = word.at(i);
matrix[taxonNum-1][siteNum++] = nucID(site);
}
}
}
} while ( (ch=linestream.get()) != EOF );
// NOTE: We probably do not need this bit of code.
if (line == 0)
{
/* the first line should contain the number of taxa and the sequence length */
istringstream buf(word);
//buf >> genomeSize;
}
else
{
for (int i=0; i<word.length(); i++)
{
char site = word.at(i);
if (tolower(site) == 'a' || tolower(site) == 'c' || tolower(site) == 'g' || tolower(site) == 't')
theSequence += tolower(site);
}
}
//cout << linestring << endl;
line++;
}
void indexTranscriptsSA(ParserT* parser,
std::string& outputDir,
std::mutex& iomutex) {
// Seed with a real random value, if available
std::random_device rd;
// Create a random uniform distribution
std::default_random_engine eng(rd());
std::uniform_int_distribution<> dis(0, 3);
uint32_t n{0};
uint32_t k = rapmap::utils::my_mer::k();
std::vector<std::string> transcriptNames;
std::vector<uint32_t> transcriptStarts;
//std::vector<uint32_t> positionIDs;
constexpr char bases[] = {'A', 'C', 'G', 'T'};
uint32_t polyAClipLength{10};
uint32_t numPolyAsClipped{0};
std::string polyA(polyAClipLength, 'A');
using TranscriptList = std::vector<uint32_t>;
using eager_iterator = MerMapT::array::eager_iterator;
using KmerBinT = uint64_t;
size_t numDistinctKmers{0};
size_t numKmers{0};
size_t currIndex{0};
std::cerr << "\n[Step 1 of 4] : counting k-mers\n";
//rsdic::RSDicBuilder rsdb;
std::vector<uint32_t> onePos; // Positions in the bit array where we should write a '1'
fmt::MemoryWriter txpSeqStream;
{
ScopedTimer timer;
while(true) {
typename ParserT::job j(*parser);
if(j.is_empty()) break;
for(size_t i = 0; i < j->nb_filled; ++i) { // For each sequence
std::string& readStr = j->data[i].seq;
readStr.erase(std::remove_if(readStr.begin(), readStr.end(),
[](const char a) -> bool {
return !(isprint(a));
}), readStr.end());
// Do Kallisto-esque clipping of polyA tails
if (readStr.size() > polyAClipLength and
readStr.substr(readStr.length() - polyAClipLength) == polyA) {
auto newEndPos = readStr.find_last_not_of("Aa");
// If it was all As
if (newEndPos == std::string::npos) {
readStr.resize(0);
} else {
readStr.resize(newEndPos + 1);
}
++numPolyAsClipped;
}
uint32_t readLen = readStr.size();
uint32_t txpIndex = n++;
// The name of the current transcript
transcriptNames.push_back(j->data[i].header);
// The position at which this transcript starts
transcriptStarts.push_back(currIndex);
bool firstBase{true};
rapmap::utils::my_mer mer;
mer.polyT();
for (size_t b = 0; b < readLen; ++b) {
readStr[b] = ::toupper(readStr[b]);
int c = jellyfish::mer_dna::code(readStr[b]);
// Replace non-ACGT bases with pseudo-random bases
if (jellyfish::mer_dna::not_dna(c)) {
char rbase = bases[dis(eng)];
c = jellyfish::mer_dna::code(rbase);
readStr[b] = rbase;
}
//positionIDs.push_back(txpIndex);
//rsdb.PushBack(0);
}
txpSeqStream << readStr;
txpSeqStream << '$';
//positionIDs.push_back(txpIndex);
//rsdb.PushBack(1);
currIndex += readLen + 1;
onePos.push_back(currIndex - 1);
}
if (n % 10000 == 0) {
std::cerr << "\r\rcounted k-mers for " << n << " transcripts";
}
}
}
std::cerr << "\n";
std::cerr << "Clipped poly-A tails from " << numPolyAsClipped << " transcripts\n";
// Put the concatenated text in a string
std::string concatText = txpSeqStream.str();
// And clear the stream
txpSeqStream.clear();
// Make our dense bit arrray
BIT_ARRAY* bitArray = bit_array_create(concatText.length());
for (auto p : onePos) {
bit_array_set_bit(bitArray, p);
}
/** SANITY CHECKS RELATED TO THE RANK structure **/
/*
uint64_t nextSetBit{0};
uint64_t offset{0};
auto numBits = bit_array_length(bitArray);
while (offset < numBits and bit_array_find_next_set_bit(bitArray, offset, &nextSetBit)) {
if (concatText[nextSetBit] != '$') {
std::cerr << "Bit # " << nextSetBit << " is set to 1, but the "
<< "corresponding character in the text is " << concatText[nextSetBit] << "\n";
}
offset = nextSetBit + 1;
}
if (bit_array_num_bits_set(bitArray) != onePos.size()) {
std::cerr << "ERROR: Bit array has " << bit_array_num_bits_set(bitArray)
<< " bits set, but this should be " << onePos.size() << "!\n";
std::exit(1);
}
rank9b bitmap(bitArray->words, bitArray->num_of_bits);
for (size_t i = 0; i < onePos.size() - 1; ++i) {
auto pos = onePos[i];
auto r = bitmap.rank(pos+1);
if (r != i+1) {
std::cerr << "rank should be " << i+1 << " but it's " << r << "\n";
std::cerr << "text is " << concatText[pos] < "\n\n";
std::cerr << "bit vector says " << (bit_array_get_bit(bitArray, pos) ? '1' : '0') << "\n";
}
}
std::ofstream rsStream(outputDir + "rsdSafe.bin", std::ios::binary);
{
ScopedTimer timer;
rsdic::RSDic rsd;
rsdb.Build(rsd);
rsd.Save(rsStream);
std::cerr << "done\n";
}
rsStream.close();
*/
/** END OF SANITY CHECK **/
onePos.clear();
onePos.shrink_to_fit();
std::string rsFileName = outputDir + "rsd.bin";
FILE* rsFile = fopen(rsFileName.c_str(), "w");
{
ScopedTimer timer;
std::cerr << "Building rank-select dictionary and saving to disk ";
bit_array_save(bitArray, rsFile);
std::cerr << "done\n";
}
fclose(rsFile);
bit_array_free(bitArray);
std::ofstream seqStream(outputDir + "txpInfo.bin", std::ios::binary);
{
ScopedTimer timer;
std::cerr << "Writing sequence data to file . . . ";
cereal::BinaryOutputArchive seqArchive(seqStream);
seqArchive(transcriptNames);
seqArchive(transcriptStarts);
//seqArchive(positionIDs);
seqArchive(concatText);
std::cerr << "done\n";
}
seqStream.close();
// clear stuff we no longer need
//positionIDs.clear();
//positionIDs.shrink_to_fit();
transcriptStarts.clear();
transcriptStarts.shrink_to_fit();
transcriptNames.clear();
transcriptNames.shrink_to_fit();
// done clearing
// Build the suffix array
size_t tlen = concatText.length();
std::vector<int> SA(tlen, 0);
std::ofstream saStream(outputDir + "sa.bin", std::ios::binary);
{
ScopedTimer timer;
std::cerr << "Building suffix array . . . ";
auto ret = sais(reinterpret_cast<unsigned char*>(
const_cast<char*>(concatText.c_str())),
SA.data(), tlen + 1);
if (ret == 0) {
std::cerr << "success\n";
{
ScopedTimer timer2;
std::cerr << "saving to disk . . . ";
cereal::BinaryOutputArchive saArchive(saStream);
saArchive(SA);
// don't actually need the LCP right now
// saArchive(LCP);
std::cerr << "done\n";
}
} else {
std::cerr << "FAILURE: return code from sais() was " << ret << "\n";
std::exit(1);
}
std::cerr << "done\n";
}
saStream.close();
// clear things we don't need
//LCP.clear();
// LCP.shrink_to_fit();
// done clearing
// Now, build the k-mer lookup table
/*
std::unordered_map<uint64_t,
rapmap::utils::SAInterval,
rapmap::utils::KmerKeyHasher> khash;
*/
google::dense_hash_map<uint64_t,
rapmap::utils::SAInterval,
rapmap::utils::KmerKeyHasher> khash;
khash.set_empty_key(std::numeric_limits<uint64_t>::max());
/*
concatText.erase(std::remove_if(concatText.begin(),
concatText.end(),
[] (const char a) -> bool { return !isprint(a); }),
concatText.end());
*/
// The start and stop of the current interval
uint32_t start = 0, stop = 0;
// An iterator to the beginning of the text
auto textB = concatText.begin();
auto textE = concatText.end();
// The current k-mer as a string
rapmap::utils::my_mer mer;
bool currentValid{false};
std::string currentKmer;
std::string nextKmer;
while (stop < tlen) {
// Check if the string starting at the
// current position is valid (i.e. doesn't contain $)
// and is <= k bases from the end of the string
nextKmer = concatText.substr(SA[stop], k);
if (nextKmer.length() == k and
nextKmer.find_first_of('$') == std::string::npos) {
// If this is a new k-mer, then hash the current k-mer
if (nextKmer != currentKmer) {
if (currentKmer.length() == k and
currentKmer.find_first_of('$') == std::string::npos) {
mer = rapmap::utils::my_mer(currentKmer);
auto bits = mer.get_bits(0, 2*k);
auto hashIt = khash.find(bits);
if (hashIt == khash.end()) {
if (start > 1) {
if (concatText.substr(SA[start-1], k) ==
concatText.substr(SA[start], k)) {
std::cerr << "T[SA["
<< start-1 << "]:" << k << "] = "
<< concatText.substr(SA[start-1], k)
<< " = T[SA[" << start << "]:" << k << "]\n";
std::cerr << "start = " << start << ", stop = " << stop << "\n";
std::cerr << "(1) THIS SHOULD NOT HAPPEN\n";
std::exit(1);
}
}
if (start == stop) {
std::cerr << "AHH (1) : Interval is empty! (start = " << start
<< ") = (stop = " << stop << ")\n";
}
if (start == stop) {
std::cerr << "AHH (2) : Interval is empty! (start = " << start
<< ") = (stop = " << stop << ")\n";
}
khash[bits] = {start, stop};
} else {
std::cerr << "\nERROR (1): trying to add same suffix "
<< currentKmer << " (len = "
<< currentKmer.length() << ") multiple times!\n";
auto prevInt = hashIt->second;
std::cerr << "existing interval is ["
<< prevInt.begin << ", " << prevInt.end << ")\n";
for (auto x = prevInt.begin; x < prevInt.end; ++x) {
auto suff = concatText.substr(SA[x], k);
for (auto c : suff) {
std::cerr << "*" << c << "*";
}
std::cerr << " (len = " << suff.length() <<")\n";
}
std::cerr << "new interval is ["
<< start << ", " << stop << ")\n";
for (auto x = start; x < stop; ++x) {
auto suff = concatText.substr(SA[x], k);
for (auto c : suff) {
std::cerr << "*" << c << "*";
}
std::cerr << "\n";
}
}
}
currentKmer = nextKmer;
start = stop;
}
} else {
// If this isn't a valid suffix (contains a $)
// If the previous interval was valid, put it
// in the hash.
if (currentKmer.length() == k and
currentKmer.find_first_of('$') == std::string::npos) {
mer = rapmap::utils::my_mer(currentKmer);
auto bits = mer.get_bits(0, 2*k);
auto hashIt = khash.find(bits);
if (hashIt == khash.end()) {
if (start > 2) {
if (concatText.substr(SA[start-1], k) ==
concatText.substr(SA[start], k)) {
std::cerr << "T[SA["
<< start-1 << "]:" << k << "] = "
<< concatText.substr(SA[start-1], k)
<< " = T[SA[" << start << "]:" << k << "]\n";
std::cerr << "start = " << start << ", stop = " << stop << "\n";
std::cerr << "(2) THIS SHOULD NOT HAPPEN\n";
std::exit(1);
}
}
khash[bits] = {start, stop};
} else {
std::cerr << "\nERROR (2): trying to add same suffix "
<< currentKmer << "multiple times!\n";
auto prevInt = hashIt->second;
std::cerr << "existing interval is ["
<< prevInt.begin << ", " << prevInt.end << ")\n";
for (auto x = prevInt.begin; x < prevInt.end; ++x) {
std::cerr << concatText.substr(SA[x], k) << "\n";
}
std::cerr << "new interval is ["
<< start << ", " << stop << ")\n";
for (auto x = start; x < stop; ++x) {
std::cerr << concatText.substr(SA[x], k) << "\n";
}
}
}
// The current interval is invalid and empty
currentKmer = nextKmer;
start = stop;
}
if (stop % 1000000 == 0) {
std::cerr << "\r\rprocessed " << stop << " positions";
}
// We always update the end position
++stop;
}
if (start < tlen) {
if (currentKmer.length() == k and
currentKmer.find_first_of('$') != std::string::npos) {
mer = rapmap::utils::my_mer(currentKmer);
khash[mer.get_bits(0, 2*k)] = {start, stop};
}
}
std::cerr << "\nkhash had " << khash.size() << " keys\n";
std::ofstream hashStream(outputDir + "hash.bin", std::ios::binary);
{
ScopedTimer timer;
std::cerr << "saving hash to disk . . . ";
cereal::BinaryOutputArchive hashArchive(hashStream);
hashArchive(k);
khash.serialize(google::dense_hash_map<uint64_t,
rapmap::utils::SAInterval,
rapmap::utils::KmerKeyHasher>::NopointerSerializer(), &hashStream);
//hashArchive(khash);
std::cerr << "done\n";
}
hashStream.close();
std::string indexVersion = "q0";
IndexHeader header(IndexType::QUASI, indexVersion, true, k);
// Finally (since everything presumably succeeded) write the header
std::ofstream headerStream(outputDir + "header.json");
{
cereal::JSONOutputArchive archive(headerStream);
archive(header);
}
headerStream.close();
}
bool RapMapSAIndex::load(const std::string& indDir) {
auto logger = spdlog::get("stderrLog");
size_t n{0};
// This part takes the longest, so do it in it's own asynchronous task
std::future<std::pair<bool, uint32_t>> loadingHash = std::async(std::launch::async, [this, logger, indDir]() -> std::pair<bool, uint32_t> {
this->khash.set_empty_key(std::numeric_limits<uint64_t>::max());
uint32_t k;
std::ifstream hashStream(indDir + "hash.bin");
{
logger->info("Loading Position Hash");
cereal::BinaryInputArchive hashArchive(hashStream);
hashArchive(k);
khash.unserialize(google::dense_hash_map<uint64_t,
rapmap::utils::SAInterval,
rapmap::utils::KmerKeyHasher>::NopointerSerializer(), &hashStream);
//hashArchive(khash);
}
hashStream.close();
return std::make_pair(true, k);
});
std::ifstream saStream(indDir + "sa.bin");
{
logger->info("Loading Suffix Array ");
cereal::BinaryInputArchive saArchive(saStream);
saArchive(SA);
//saArchive(LCP);
}
saStream.close();
std::ifstream seqStream(indDir + "txpInfo.bin");
{
logger->info("Loading Transcript Info ");
cereal::BinaryInputArchive seqArchive(seqStream);
seqArchive(txpNames);
seqArchive(txpOffsets);
//seqArchive(positionIDs);
seqArchive(seq);
}
seqStream.close();
/*
std::ifstream rsStream(indDir + "rsdSafe.bin", std::ios::binary);
{
logger->info("Loading Rank-Select Data");
rankDictSafe.Load(rsStream);
}
rsStream.close();
*/
std::string rsFileName = indDir + "rsd.bin";
FILE* rsFile = fopen(rsFileName.c_str(), "r");
{
logger->info("Loading Rank-Select Bit Array");
bitArray.reset(bit_array_create(0));
if (!bit_array_load(bitArray.get(), rsFile)) {
logger->error("Couldn't load bit array from {}!", rsFileName);
std::exit(1);
}
logger->info("There were {} set bits in the bit array", bit_array_num_bits_set(bitArray.get()));
rankDict.reset(new rank9b(bitArray->words, bitArray->num_of_bits));
}
fclose(rsFile);
{
logger->info("Computing transcript lengths");
txpLens.resize(txpOffsets.size());
if (txpOffsets.size() > 1) {
for(size_t i = 0; i < txpOffsets.size() - 1; ++i) {
auto nextOffset = txpOffsets[i+1];
auto currentOffset = txpOffsets[i];
txpLens[i] = (nextOffset - 1) - currentOffset;
}
}
// The last length is just the length of the suffix array - the last offset
txpLens[txpOffsets.size()-1] = (SA.size() - 1) - txpOffsets[txpOffsets.size() - 1];
}
logger->info("Waiting to finish loading hash");
loadingHash.wait();
auto hashLoadRes = loadingHash.get();
if (!hashLoadRes.first) {
logger->error("Failed to load hash!");
std::exit(1);
}
rapmap::utils::my_mer::k(hashLoadRes.second);
logger->info("Done loading index");
return true;
}