//-------------------------------------------------------------------------
void XList::sortByElementNumber(String order){
// Get the number of sessions per speaker
LKVector spk(0,0);
for(unsigned long i=0;i<_vector.size();i++){
LKVector::type sps;
sps.idx = i;
sps.lk = _vector.getObject(i).getElementCount();
spk.addValue(sps);
}
// Sort Xlines of the temporary XList by element number
spk.descendingSort();
// Copy the current RefVector<XLine> into a temporary one
RefVector<XLine> tmpX;
for(unsigned long i=0;i<_vector.size();i++){
XLine *ll = new XLine(_vector.getObject(i));
tmpX.addObject(*ll);
}
// Remove all elements from the XList
_vector.deleteAllObjects();
// Fill the XList according to the number of elements
if(order == "descend"){
for(unsigned long i=0;i<tmpX.size();i++){
_vector.addObject(tmpX.getObject(spk[i].idx));
}
}
else if(order == "ascend"){
for(long i=tmpX.size()-1;i>=0;i--){
_vector.addObject(tmpX.getObject(spk[i].idx));
}
}
}
long get_ref_lengths(int id, RefVector ref) {
long length = 0;
for (size_t i = 0; i < (size_t) id && i < ref.size(); i++) {
length += (long) ref[i].RefLength + (long) Parameter::Instance()->max_dist;
}
return length;
}
GenomeFile::GenomeFile(const RefVector &genome) {
for (size_t i = 0; i < genome.size(); ++i) {
string chrom = genome[i].RefName;
int length = genome[i].RefLength;
_chromSizes[chrom] = length;
_chromList.push_back(chrom);
}
}
long Breakpoint::calc_pos(long pos, RefVector ref) {
size_t i = 0;
pos -= ref[i].RefLength;
while (i < ref.size() && pos >= 0) {
i++;
pos -= ref[i].RefLength;
}
return pos + ref[i].RefLength;
}
long fuck_off(long pos, RefVector ref, std::string &chr) {
size_t i = 0;
pos -= (ref[i].RefLength + Parameter::Instance()->max_dist);
while (i < ref.size() && pos >= 0) {
i++;
pos -= ((long) ref[i].RefLength + (long) Parameter::Instance()->max_dist);
}
chr = ref[i].RefName;
return pos + ref[i].RefLength + (long) Parameter::Instance()->max_dist;
}
std::string Breakpoint::get_chr(long pos, RefVector ref) {
// std::cout << "pos: " << pos << std::endl;
size_t id = 0;
while (id < ref.size() && pos >= 0) {
pos -= (long) ref[id].RefLength;
// std::cout << id << std::endl;
id++;
}
return ref[id - 1].RefName;
}
bool RandomTool::RandomToolPrivate::Run(void) {
// set to default stdin if no input files provided
if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
// add files in the filelist to the input file list
if ( m_settings->HasInputFilelist ) {
ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
if ( !filelist.is_open() ) {
cerr << "bamtools random ERROR: could not open input BAM file list... Aborting." << endl;
return false;
}
string line;
while ( getline(filelist, line) )
m_settings->InputFiles.push_back(line);
}
// open our reader
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
cerr << "bamtools random ERROR: could not open input BAM file(s)... Aborting." << endl;
return false;
}
// look up index files for all BAM files
reader.LocateIndexes();
// make sure index data is available
if ( !reader.HasIndexes() ) {
cerr << "bamtools random ERROR: could not load index data for all input BAM file(s)... Aborting." << endl;
reader.Close();
return false;
}
// get BamReader metadata
const string headerText = reader.GetHeaderText();
const RefVector references = reader.GetReferenceData();
if ( references.empty() ) {
cerr << "bamtools random ERROR: no reference data available... Aborting." << endl;
reader.Close();
return false;
}
// determine compression mode for BamWriter
bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
!m_settings->IsForceCompression );
BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;
// open BamWriter
BamWriter writer;
writer.SetCompressionMode(compressionMode);
if ( !writer.Open(m_settings->OutputFilename, headerText, references) ) {
cerr << "bamtools random ERROR: could not open " << m_settings->OutputFilename
<< " for writing... Aborting." << endl;
reader.Close();
return false;
}
// if user specified a REGION constraint, attempt to parse REGION string
BamRegion region;
if ( m_settings->HasRegion && !Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
cerr << "bamtools random ERROR: could not parse REGION: " << m_settings->Region << endl;
cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
<< endl;
reader.Close();
writer.Close();
return false;
}
// seed our random number generator
srand( time(NULL) );
// grab random alignments
BamAlignment al;
unsigned int i = 0;
while ( i < m_settings->AlignmentCount ) {
int randomRefId = 0;
int randomPosition = 0;
// use REGION constraints to select random refId & position
if ( m_settings->HasRegion ) {
// select a random refId
randomRefId = getRandomInt(region.LeftRefID, region.RightRefID);
// select a random position based on randomRefId
const int lowerBoundPosition = ( (randomRefId == region.LeftRefID)
? region.LeftPosition
: 0 );
const int upperBoundPosition = ( (randomRefId == region.RightRefID)
? region.RightPosition
: (references.at(randomRefId).RefLength - 1) );
randomPosition = getRandomInt(lowerBoundPosition, upperBoundPosition);
}
// otherwise select from all possible random refId & position
else {
// select random refId
randomRefId = getRandomInt(0, (int)references.size() - 1);
// select random position based on randomRefId
const int lowerBoundPosition = 0;
const int upperBoundPosition = references.at(randomRefId).RefLength - 1;
randomPosition = getRandomInt(lowerBoundPosition, upperBoundPosition);
}
// if jump & read successful, save first alignment that overlaps random refId & position
if ( reader.Jump(randomRefId, randomPosition) ) {
while ( reader.GetNextAlignmentCore(al) ) {
if ( al.RefID == randomRefId && al.Position >= randomPosition ) {
writer.SaveAlignment(al);
++i;
break;
}
}
}
}
// cleanup & exit
reader.Close();
writer.Close();
return true;
}
// this has been copied from bamtools utilities, since it isn't in the API. Original file is bamtools_utilities.cpp.
// Like the rest of Bamtools, it is under the BSD license.
bool Filter::ParseRegionString(const string& regionString, BamRegion& region)
{
// -------------------------------
// parse region string
// check first for empty string
if ( regionString.empty() )
return false;
// non-empty string, look for a colom
size_t foundFirstColon = regionString.find(':');
// store chrom strings, and numeric positions
string chrom;
int startPos;
int stopPos;
// no colon found
// going to use entire contents of requested chromosome
// just store entire region string as startChrom name
// use BamReader methods to check if its valid for current BAM file
if ( foundFirstColon == string::npos ) {
chrom = regionString;
startPos = 0;
stopPos = -1;
}
// colon found, so we at least have some sort of startPos requested
else {
// store start chrom from beginning to first colon
chrom = regionString.substr(0,foundFirstColon);
// look for ".." after the colon
size_t foundRangeDots = regionString.find("..", foundFirstColon+1);
// no dots found
// so we have a startPos but no range
// store contents before colon as startChrom, after as startPos
if ( foundRangeDots == string::npos ) {
startPos = atoi( regionString.substr(foundFirstColon+1).c_str() );
stopPos = -1;
}
// ".." found, so we have some sort of range selected
else {
// store startPos between first colon and range dots ".."
startPos = atoi( regionString.substr(foundFirstColon+1, foundRangeDots-foundFirstColon-1).c_str() );
// look for second colon
size_t foundSecondColon = regionString.find(':', foundRangeDots+1);
// no second colon found
// so we have a "standard" chrom:start..stop input format (on single chrom)
if ( foundSecondColon == string::npos ) {
stopPos = atoi( regionString.substr(foundRangeDots+2).c_str() );
} else {
return false;
}
}
}
// -------------------------------
// validate reference IDs & genomic positions
const RefVector references = getReferences();
int RefID = -1;
for(int i = 0; i < references.size(); i++) {
if(references[i].RefName == chrom)
RefID = i;
}
// if startRefID not found, return false
if ( RefID == -1 ) {
cerr << "Can't find chromosome'" << chrom << "'" << endl;
return false;
}
// startPos cannot be greater than or equal to reference length
const RefData& startReference = references.at(RefID);
if ( startPos >= startReference.RefLength ) {
cerr << "Start position (" << startPos << ") after end of the reference sequence (" << startReference.RefLength << ")" << endl;
return false;
}
// stopPosition cannot be larger than reference length
const RefData& stopReference = references.at(RefID);
if ( stopPos > stopReference.RefLength ) {
cerr << "Start position (" << stopPos << ") after end of the reference sequence (" << stopReference.RefLength << ")" << endl;
return false;
}
// if no stopPosition specified, set to reference end
if ( stopPos == -1 ) stopPos = stopReference.RefLength;
// -------------------------------
// set up Region struct & return
region.LeftRefID = RefID;
region.LeftPosition = startPos;
region.RightRefID = RefID;;
region.RightPosition = stopPos;
return true;
}
bool check(const PropertyFilter& filter, const BamAlignment& al) {
bool keepAlignment = true;
const PropertyMap& properties = filter.Properties;
PropertyMap::const_iterator propertyIter = properties.begin();
PropertyMap::const_iterator propertyEnd = properties.end();
for ( ; propertyIter != propertyEnd; ++propertyIter ) {
// check alignment data field depending on propertyName
const string& propertyName = (*propertyIter).first;
const PropertyFilterValue& valueFilter = (*propertyIter).second;
if ( propertyName == ALIGNMENTFLAG_PROPERTY ) keepAlignment &= valueFilter.check(al.AlignmentFlag);
else if ( propertyName == CIGAR_PROPERTY ) {
stringstream cigarSs;
const vector<CigarOp>& cigarData = al.CigarData;
if ( !cigarData.empty() ) {
vector<CigarOp>::const_iterator cigarBegin = cigarData.begin();
vector<CigarOp>::const_iterator cigarIter = cigarBegin;
vector<CigarOp>::const_iterator cigarEnd = cigarData.end();
for ( ; cigarIter != cigarEnd; ++cigarIter ) {
const CigarOp& op = (*cigarIter);
cigarSs << op.Length << op.Type;
}
keepAlignment &= valueFilter.check(cigarSs.str());
}
}
else if ( propertyName == INSERTSIZE_PROPERTY ) keepAlignment &= valueFilter.check(al.InsertSize);
else if ( propertyName == ISDUPLICATE_PROPERTY ) keepAlignment &= valueFilter.check(al.IsDuplicate());
else if ( propertyName == ISFAILEDQC_PROPERTY ) keepAlignment &= valueFilter.check(al.IsFailedQC());
else if ( propertyName == ISFIRSTMATE_PROPERTY ) keepAlignment &= valueFilter.check(al.IsFirstMate());
else if ( propertyName == ISMAPPED_PROPERTY ) keepAlignment &= valueFilter.check(al.IsMapped());
else if ( propertyName == ISMATEMAPPED_PROPERTY ) keepAlignment &= valueFilter.check(al.IsMateMapped());
else if ( propertyName == ISMATEREVERSESTRAND_PROPERTY ) keepAlignment &= valueFilter.check(al.IsMateReverseStrand());
else if ( propertyName == ISPAIRED_PROPERTY ) keepAlignment &= valueFilter.check(al.IsPaired());
else if ( propertyName == ISPRIMARYALIGNMENT_PROPERTY ) keepAlignment &= valueFilter.check(al.IsPrimaryAlignment());
else if ( propertyName == ISPROPERPAIR_PROPERTY ) keepAlignment &= valueFilter.check(al.IsProperPair());
else if ( propertyName == ISREVERSESTRAND_PROPERTY ) keepAlignment &= valueFilter.check(al.IsReverseStrand());
else if ( propertyName == ISSECONDMATE_PROPERTY ) keepAlignment &= valueFilter.check(al.IsSecondMate());
else if ( propertyName == ISSINGLETON_PROPERTY ) {
const bool isSingleton = al.IsPaired() && al.IsMapped() && !al.IsMateMapped();
keepAlignment &= valueFilter.check(isSingleton);
}
else if ( propertyName == MAPQUALITY_PROPERTY ) keepAlignment &= valueFilter.check(al.MapQuality);
else if ( propertyName == MATEPOSITION_PROPERTY ) keepAlignment &= ( al.IsPaired() && al.IsMateMapped() && valueFilter.check(al.MateRefID) );
else if ( propertyName == MATEREFERENCE_PROPERTY ) {
if ( !al.IsPaired() || !al.IsMateMapped() ) return false;
BAMTOOLS_ASSERT_MESSAGE( (al.MateRefID>=0 && (al.MateRefID<(int)filterToolReferences.size())), "Invalid MateRefID");
const string& refName = filterToolReferences.at(al.MateRefID).RefName;
keepAlignment &= valueFilter.check(refName);
}
else if ( propertyName == NAME_PROPERTY ) keepAlignment &= valueFilter.check(al.Name);
else if ( propertyName == POSITION_PROPERTY ) keepAlignment &= valueFilter.check(al.Position);
else if ( propertyName == QUERYBASES_PROPERTY ) keepAlignment &= valueFilter.check(al.QueryBases);
else if ( propertyName == REFERENCE_PROPERTY ) {
BAMTOOLS_ASSERT_MESSAGE( (al.RefID>=0 && (al.RefID<(int)filterToolReferences.size())), "Invalid RefID");
const string& refName = filterToolReferences.at(al.RefID).RefName;
keepAlignment &= valueFilter.check(refName);
}
else if ( propertyName == TAG_PROPERTY ) keepAlignment &= checkAlignmentTag(valueFilter, al);
else BAMTOOLS_ASSERT_UNREACHABLE;
// if alignment fails at ANY point, just quit and return false
if ( !keepAlignment ) return false;
}
BAMTOOLS_ASSERT_MESSAGE( keepAlignment, "Error in BamAlignmentChecker... keepAlignment should be true here");
return keepAlignment;
}
// ValidateReaders checks that all the readers point to BAM files representing
// alignments against the same set of reference sequences, and that the
// sequences are identically ordered. If these checks fail the operation of
// the multireader is undefined, so we force program exit.
bool BamMultiReaderPrivate::ValidateReaders() const
{
m_errorString.clear();
// skip if 0 or 1 readers opened
if (m_readers.empty() || (m_readers.size() == 1)) return true;
// retrieve first reader
const MergeItem& firstItem = m_readers.front();
const BamReader* firstReader = firstItem.Reader;
if (firstReader == 0) return false;
// retrieve first reader's header data
const SamHeader& firstReaderHeader = firstReader->GetHeader();
const std::string& firstReaderSortOrder = firstReaderHeader.SortOrder;
// retrieve first reader's reference data
const RefVector& firstReaderRefData = firstReader->GetReferenceData();
const int firstReaderRefCount = firstReader->GetReferenceCount();
const int firstReaderRefSize = firstReaderRefData.size();
// iterate over all readers
std::vector<MergeItem>::const_iterator readerIter = m_readers.begin();
std::vector<MergeItem>::const_iterator readerEnd = m_readers.end();
for (; readerIter != readerEnd; ++readerIter) {
const MergeItem& item = (*readerIter);
BamReader* reader = item.Reader;
if (reader == 0) continue;
// get current reader's header data
const SamHeader& currentReaderHeader = reader->GetHeader();
const std::string& currentReaderSortOrder = currentReaderHeader.SortOrder;
// check compatible sort order
if (currentReaderSortOrder != firstReaderSortOrder) {
const std::string message =
std::string("mismatched sort order in ") + reader->GetFilename() + ", expected " +
firstReaderSortOrder + ", but found " + currentReaderSortOrder;
SetErrorString("BamMultiReader::ValidateReaders", message);
return false;
}
// get current reader's reference data
const RefVector currentReaderRefData = reader->GetReferenceData();
const int currentReaderRefCount = reader->GetReferenceCount();
const int currentReaderRefSize = currentReaderRefData.size();
// init reference data iterators
RefVector::const_iterator firstRefIter = firstReaderRefData.begin();
RefVector::const_iterator firstRefEnd = firstReaderRefData.end();
RefVector::const_iterator currentRefIter = currentReaderRefData.begin();
// compare reference counts from BamReader ( & container size, in case of BR error)
if ((currentReaderRefCount != firstReaderRefCount) ||
(firstReaderRefSize != currentReaderRefSize)) {
std::stringstream s;
s << "mismatched reference count in " << reader->GetFilename() << ", expected "
<< firstReaderRefCount << ", but found " << currentReaderRefCount;
SetErrorString("BamMultiReader::ValidateReaders", s.str());
return false;
}
// this will be ok; we just checked above that we have identically-sized sets of references
// here we simply check if they are all, in fact, equal in content
while (firstRefIter != firstRefEnd) {
const RefData& firstRef = (*firstRefIter);
const RefData& currentRef = (*currentRefIter);
// compare reference name & length
if ((firstRef.RefName != currentRef.RefName) ||
(firstRef.RefLength != currentRef.RefLength)) {
std::stringstream s;
s << "mismatched references found in" << reader->GetFilename()
<< "expected: " << std::endl;
// print first reader's reference data
RefVector::const_iterator refIter = firstReaderRefData.begin();
RefVector::const_iterator refEnd = firstReaderRefData.end();
for (; refIter != refEnd; ++refIter) {
const RefData& entry = (*refIter);
std::stringstream s;
s << entry.RefName << ' ' << std::endl;
}
s << "but found: " << std::endl;
// print current reader's reference data
refIter = currentReaderRefData.begin();
refEnd = currentReaderRefData.end();
for (; refIter != refEnd; ++refIter) {
const RefData& entry = (*refIter);
s << entry.RefName << ' ' << entry.RefLength << std::endl;
}
SetErrorString("BamMultiReader::ValidateReaders", s.str());
return false;
}
// update iterators
++firstRefIter;
++currentRefIter;
}
}
// if we get here, everything checks out
return true;
}
