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#include <alignment/format/SAMHeaderPrinter.hpp>
#include <cassert>
const std::string SAMVERSION("1.5");
const std::string PBBAMVERSION("3.0.1");
const std::string PACBIOPL("PACBIO");
std::vector<SAMHeaderItem> MakeSAMHeaderItems(const std::string& fromString)
{
std::vector<SAMHeaderItem> items;
std::vector<std::string> vs;
Splice(fromString, ";", vs);
std::vector<std::string>::iterator it;
for (it = vs.begin(); it != vs.end(); it++) {
items.push_back(SAMHeaderItem(*it));
}
return items;
}
// SAMHeaderItem
SAMHeaderItem::SAMHeaderItem(const std::string& fromString)
{
std::size_t pos = fromString.find("=");
if (pos != std::string::npos) {
_key = fromString.substr(0, pos);
_val = fromString.substr(pos + 1);
}
}
std::string SAMHeaderItem::ToString()
{
std::stringstream ss;
if (_key != "") ss << _key << "=" << _val;
return ss.str();
}
// SAMHeaderTag
SAMHeaderTag::SAMHeaderTag(const std::string& fromString)
{
size_t pos = fromString.find(":");
if (pos != std::string::npos) {
_tagName = fromString.substr(0, pos);
std::string tagValue = fromString.substr(pos + 1);
if (tagValue.find("=") != std::string::npos) {
AddItems(tagValue);
} else {
_tagValue = tagValue;
}
} else {
std::cout << "Unable to parse SAM/BAM header" << fromString << std::endl;
std::exit(EXIT_FAILURE);
}
}
std::string SAMHeaderTag::ToString()
{
std::stringstream ss;
if (_tagName != "") {
ss << _tagName << ":";
if (_tagValue != "") {
ss << _tagValue;
} else {
std::vector<SAMHeaderItem>::iterator it;
for (it = _tagItems.begin(); it != _tagItems.end(); it++) {
if (it != _tagItems.begin() and (*it).ToString() != "") {
ss << ";";
}
ss << (*it).ToString();
}
}
}
return ss.str();
}
std::string SAMHeaderTag::TagName() const { return _tagName; }
void SAMHeaderTag::AddItem(SAMHeaderItem& item) { _tagItems.push_back(item); }
void SAMHeaderTag::AddItem(const std::string& fromString)
{
_tagItems.push_back(SAMHeaderItem(fromString));
}
void SAMHeaderTag::AddItems(const std::string& fromString)
{
// SAM Header Items: key=value;key=value
std::vector<SAMHeaderItem> items = MakeSAMHeaderItems(fromString);
_tagItems.insert(_tagItems.begin(), items.begin(), items.end());
}
// SAMHeaderGroup
SAMHeaderGroup::SAMHeaderGroup(const std::string& fromString)
{
if (fromString == "" || fromString[0] != '@') return;
std::vector<std::string> vs;
Splice(fromString.substr(1), "\t", vs);
if (vs.size() >= 1) {
std::vector<std::string>::iterator it = vs.begin();
_groupName = (*it);
it++;
for (; it != vs.end(); it++) {
_tags.push_back(SAMHeaderTag(*it));
}
}
}
std::string SAMHeaderGroup::ToString()
{
std::stringstream ss;
ss << "@" << _groupName;
SAMHeaderTags::iterator it;
for (it = _tags.begin(); it != _tags.end(); it++) {
ss << "\t" << (*it).ToString();
}
return ss.str();
}
std::ostream& operator<<(std::ostream& os, SAMHeaderGroup& g) { return os << g.ToString(); }
/// returns true if this SAMHeaderGroup contains a tag tagName.
bool SAMHeaderGroup::HasTag(std::string tagName)
{
for (SAMHeaderTags::iterator it = _tags.begin(); it != _tags.end(); it++) {
if ((*it).TagName() == tagName) {
return true;
}
}
return false;
}
/// returns value of a tag if it exists, otherwise, return an empty string.
std::string SAMHeaderGroup::Tag(const std::string& tagName)
{
for (SAMHeaderTags::iterator it = _tags.begin(); it != _tags.end(); it++) {
if ((*it).TagName() == tagName) {
return (*it).ToString();
}
}
return "";
}
// SAMHeaderGroupWithID
std::string SAMHeaderGroupWithID::ID() const { return _id; }
SAMHeaderGroupWithID::SAMHeaderGroupWithID(const std::string& fromString)
: SAMHeaderGroup(fromString)
{
assert(HasTag("ID"));
if (not HasTag("ID")) {
assert("ERROR! SAM Header read/program group must has ID tag." == 0);
}
_id = Tag("ID");
}
// SAMHeaderRG
SAMHeaderRG::SAMHeaderRG(const std::string& id, const std::string& pl, const std::string& pu,
const std::vector<SAMHeaderItem>& dsItems)
{
_groupName = "RG";
_id = id;
_tags.push_back(SAMHeaderTag("ID", id));
_tags.push_back(SAMHeaderTag("PU", pu));
_tags.push_back(SAMHeaderTag("PL", pl));
_tags.push_back(SAMHeaderTag("DS", dsItems));
}
SAMHeaderRG::SAMHeaderRG(const std::string& fromString) : SAMHeaderGroupWithID(fromString)
{
if (_groupName != "RG") {
assert("ERROR! SAM Header read group should start with @RG" == 0);
}
}
// SAMHeaderPG
SAMHeaderPG::SAMHeaderPG(const std::string& id, const std::string& progName,
const std::string& progVersion, const std::string& commandLine)
{
_groupName = "PG";
_id = id;
_tags.push_back(SAMHeaderTag("ID", id));
_tags.push_back(SAMHeaderTag("PN", progName));
_tags.push_back(SAMHeaderTag("VN", progVersion));
_tags.push_back(SAMHeaderTag("CL", commandLine));
}
SAMHeaderPG::SAMHeaderPG(const std::string& fromString) : SAMHeaderGroupWithID(fromString)
{
if (_groupName != "PG") {
assert("ERROR! SAM Header program group must start with @PG" == 0);
}
}
// SAMHeaderSQ
SAMHeaderSQ::SAMHeaderSQ(const std::string& sn, const DNALength& ln, const std::string& md5)
: SAMHeaderSQ(sn, std::to_string(ln), md5)
{
}
SAMHeaderSQ::SAMHeaderSQ(const std::string& sn, const std::string& ln, const std::string& md5)
: SAMHeaderGroup()
{
_groupName = "SQ";
_tags.push_back(SAMHeaderTag("SN", sn));
_tags.push_back(SAMHeaderTag("LN", ln));
_tags.push_back(SAMHeaderTag("M5", md5));
}
SAMHeaderSQ::SAMHeaderSQ(const std::string& fromString) : SAMHeaderGroup(fromString)
{
if (_groupName != "SQ") {
assert("ERROR! SAM Header soring order must start with @SO" == 0);
}
}
// SAMHeaderPrinter
std::string SAMHeaderPrinter::ToString()
{
std::stringstream ss;
ss << _hd.ToString() << _sqs.ToString() << _rgs.ToString() << _pgs.ToString()
<< _cos.ToString();
return ss.str();
}
/*
/// Add a SAM Header @RG entry, including the following tags:
/// ID (identifier), PL (platform), PU (platform unit),
/// DS (description, which may have many items)
SAMHeaderPrinter & SAMHeaderPrinter::AddRG(std::string & id, std::string & pl, std::string & pu, std::string & ds) {
_rgs.Add(SAMHeaderRG(id, pl, pu, ds));
return *this;
}*/
/// Add a SAM Header @RG entry from string, which may contain arbitary tags.
SAMHeaderPrinter& SAMHeaderPrinter::AddRG(const std::string& fromString)
{
_rgs.Add(SAMHeaderRG(fromString));
return *this;
}
/// Add a SAM Header @PG entry, including the following tags:
/// ID, progName, progVersion, commandLine. @PG must have unique ID.
SAMHeaderPrinter& SAMHeaderPrinter::AddPG(std::string& id, std::string& progName,
std::string& progVersion, std::string& commandLine)
{
_pgs.Add(SAMHeaderPG(id, progName, progVersion, commandLine));
return *this;
}
/// Add a SAM Header @PG entry from string, which may contain arbitary tags.
SAMHeaderPrinter& SAMHeaderPrinter::AddPG(const std::string& fromString)
{
_pgs.Add(SAMHeaderPG(fromString));
return *this;
}
/// Add a SAM Header @CO entry from string.
SAMHeaderPrinter& SAMHeaderPrinter::AddCO(const std::string& fromString)
{
_cos.Add(fromString);
return *this;
}
/// \returns SAMHeaderGroup @HD
SAMHeaderGroup SAMHeaderPrinter::MakeHD(const std::string& sortingOrder)
{
std::stringstream ss;
ss << "@HD"
<< "\t"
<< "VN:" << SAMVERSION << "\t"
<< "SO:" << sortingOrder << "\t"
<< "pb:" << PBBAMVERSION << std::endl;
return SAMHeaderGroup(ss.str());
}
/// \returns SAMHeaderSQs, SAM Header @SQ groups
SAMHeaderSQs SAMHeaderPrinter::MakeSQs(SequenceIndexDatabase<FASTASequence>& seqdb)
{
SAMHeaderSQs sqs;
for (int i = 0; i < seqdb.nSeqPos - 1; i++) {
std::string md5 = "";
if (static_cast<int>(seqdb.md5.size()) == seqdb.nSeqPos - 1) {
md5 = seqdb.md5[i];
}
std::string seqName;
seqdb.GetName(i, seqName);
sqs.Add(SAMHeaderSQ(seqName, seqdb.GetLengthOfSeq(i), md5));
}
return sqs;
}
SAMHeaderPrinter::SAMHeaderPrinter(const std::string& sortingOrder,
SequenceIndexDatabase<FASTASequence>& seqdb,
const std::vector<std::string>& readsFiles,
const ReadType::ReadTypeEnum& readType,
const SupplementalQVList& samQVs, const std::string& progName,
const std::string& progVersion, const std::string& commandLine)
: _sortingOrder(sortingOrder), _readsFiles(readsFiles), _seqdb(seqdb)
{
if (readsFiles.size() == 0) {
assert("Must specify input reads files" == 0);
}
// all read types supported, no check needed.
// Determine fileType based on extension of the first read file.
std::string rf = readsFiles[0];
BaseSequenceIO::DetermineFileTypeByExtension(rf, fileType);
// Make @HD, @SQ, @RG
_hd = MakeHD(sortingOrder);
_sqs = MakeSQs(seqdb);
_rgs = MakeRGs(readsFiles, readType, samQVs);
// Make PGs and COs
_pgs = MakePGs(readsFiles, progName, progVersion, commandLine);
_cos = MakeCOs(readsFiles);
}
/// \param[in] readsFiles - incoming reads files in BAM or other formats
/// \param[in] readType - read type, must be either SUBREAD or CCS or UNKNOWN
/// \param[in] samQVs - SupplementalQVList, an object that handles which
/// QVs to print in SAM/BAM file.
SAMHeaderRGs SAMHeaderPrinter::MakeRGs(const std::vector<std::string>& readsFiles,
const ReadType::ReadTypeEnum& readType,
const SupplementalQVList& samQVs)
{
SAMHeaderRGs rgs;
if (fileType != FileType::PBBAM and fileType != FileType::PBDATASET) {
ReaderAgglomerate* reader = new ReaderAgglomerate();
assert(reader != nullptr);
std::vector<std::string>::const_iterator rfit;
for (rfit = readsFiles.begin(); rfit != readsFiles.end(); rfit++) {
std::string rf(*rfit);
reader->SetReadFileName(rf);
reader->SetReadType(readType);
reader->Initialize();
// Get movie name from ReaderAgglomerate
std::string movieName;
reader->GetMovieName(movieName);
std::string bindingKit, sequencingKit, baseCallerVersion;
reader->GetChemistryTriple(bindingKit, sequencingKit, baseCallerVersion);
reader->Close();
std::vector<SAMHeaderItem> dsItems;
dsItems.push_back(SAMHeaderItem("READTYPE", ReadType::ToString(readType)));
dsItems.push_back(SAMHeaderItem("BINDINGKIT", bindingKit));
dsItems.push_back(SAMHeaderItem("SEQUENCINGKIT", sequencingKit));
dsItems.push_back(SAMHeaderItem("BASECALLERVERSION", baseCallerVersion));
// Add QVs, e.g., InsertionQV=iq;DeletionQV=dq;...
if (samQVs.useqv) {
for (int i = 0; i < samQVs.nTags; i++) {
if (samQVs.useqv & (1 << i)) {
dsItems.push_back(SAMHeaderItem(samQVs.qvNames[i], samQVs.qvTags[i]));
}
}
}
rgs.Add(SAMHeaderRG(reader->readGroupId, PACBIOPL, movieName, dsItems));
}
delete reader;
} else {
#ifdef USE_PBBAM
if (fileType == FileType::PBDATASET or fileType == FileType::PBBAM) {
// use + operator to merge headers
bool first = true;
PacBio::BAM::BamHeader mergedHeader;
//
// First stage : merge headers - loop thru all file headers and create a merged header
//
for (auto xmlfn : readsFiles) {
for (auto bamFile : PacBio::BAM::DataSet(xmlfn).BamFiles()) {
if (first) {
mergedHeader = bamFile.Header(); // assign first header to mergedHeader
first = false;
} else
mergedHeader +=
bamFile.Header(); // add subsequent headers and to mergedHeader
}
}
//
// Second stage : Loop thru all read groups, must modify ReadType if POLYMERASE
//
for (PacBio::BAM::ReadGroupInfo rg : mergedHeader.ReadGroups()) {
if (readType == ReadType::POLYMERASE) {
rg.ReadType("POLYMERASE");
rg.Id(rg.MovieName(), rg.ReadType());
}
rgs.Add(SAMHeaderRG(rg.ToSam()));
}
}
#else
REQUEST_PBBAM_ERROR();
#endif
}
return rgs;
}
SAMHeaderPGs SAMHeaderPrinter::MakePGs(const std::vector<std::string>& readsFiles,
const std::string& progName, const std::string& progVersion,
const std::string& commandLine)
{
PB_UNUSED(readsFiles);
SAMHeaderPGs pgs;
// program id, unique identifier for @PG lines;
int prog_id = 1;
if (fileType != FileType::PBBAM) {
// Reads files are not in BAM format, no other @PG lines.
} else {
#ifdef USE_PBBAM
// Reads files are in BAM format, keep all @PG lines from Bam files.
// TODO: use Derek's API to merge bamHeaders from different files when
// it is in place. Use the following code for now.
std::vector<std::string>::const_iterator rfit;
for (rfit = readsFiles.begin(); rfit != readsFiles.end(); rfit++) {
PacBio::BAM::BamFile bamFile(*rfit);
PacBio::BAM::BamHeader bamHeader = bamFile.Header();
std::vector<PacBio::BAM::ProgramInfo> progs = bamHeader.Programs();
std::vector<PacBio::BAM::ProgramInfo>::iterator it;
for (it = progs.begin(); it != progs.end(); it++) {
pgs.Add(SAMHeaderPG((*it).ToSam()));
prog_id++; // Increase prog_id;
}
}
#else
REQUEST_PBBAM_ERROR();
#endif
}
pgs.Add(SAMHeaderPG(std::to_string(prog_id), progName, progVersion, commandLine));
return pgs;
}
SAMHeaderCOs SAMHeaderPrinter::MakeCOs(const std::vector<std::string>& readsFiles)
{
PB_UNUSED(readsFiles);
SAMHeaderCOs cos;
if (fileType == FileType::PBBAM) {
#ifdef USE_PBBAM
// Reads files are in BAM format, keep all @CO lines from Bam files.
std::vector<std::string>::const_iterator rfit;
for (rfit = readsFiles.begin(); rfit != readsFiles.end(); rfit++) {
PacBio::BAM::BamFile bamFile(*rfit);
PacBio::BAM::BamHeader bamHeader = bamFile.Header();
cos.Append(bamHeader.Comments());
}
#else
REQUEST_PBBAM_ERROR();
#endif
} // reads files are not in BAM format, no comments.
return cos;
}
#ifdef USE_PBBAM
PacBio::BAM::BamHeader SAMHeaderPrinter::ToBamHeader()
{
std::string headerStr = ToString();
return PacBio::BAM::BamHeader(headerStr);
}
#endif
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