// print BamAlignment in FASTQ format
// N.B. - uses QueryBases NOT AlignedBases
void ConvertTool::ConvertToolPrivate::PrintFastq(const BamAlignment& a) {
// @BamAlignment.Name
// BamAlignment.QueryBases
// +
// BamAlignment.Qualities
//
// N.B. - QueryBases are reverse-complemented (& Qualities reversed) if aligned to reverse strand .
// Name is appended "/1" or "/2" if paired-end, to reflect which mate this entry is.
// handle paired-end alignments
string name = a.Name;
if ( a.IsPaired() )
name.append( (a.IsFirstMate() ? "/1" : "/2") );
// handle reverse strand alignment - bases & qualities
string qualities = a.Qualities;
string sequence = a.QueryBases;
if ( a.IsReverseStrand() ) {
Utilities::Reverse(qualities);
Utilities::ReverseComplement(sequence);
}
// write to output stream
m_out << "@" << name << endl
<< sequence << endl
<< "+" << endl
<< qualities << endl;
}
int DataStatisticsTool::Execute()
{
// iterate over reads in BAM file(s)
BamAlignment alignObj;
while(bamReader.GetNextAlignment(alignObj))
{
if (alignObj.IsDuplicate()) continue;
if (alignObj.IsFailedQC()) continue;
if (!alignObj.IsMapped()) continue;
if (!alignObj.IsPrimaryAlignment()) continue;
if (alignObj.IsPaired() && !alignObj.IsProperPair()) continue;
if (alignObj.IsPaired() && !alignObj.IsMateMapped()) continue;
if (!alignObj.HasTag("MD")) continue;
// // debug
// GenericBamAlignmentTools::printBamAlignmentCigar(alignObj);
// GenericBamAlignmentTools::printBamAlignmentMD(alignObj);
// shift InDel
GenericBamAlignmentTools::leftShiftInDel(alignObj);
// // debug
// GenericBamAlignmentTools::printBamAlignmentCigar(alignObj);
// GenericBamAlignmentTools::printBamAlignmentMD(alignObj);
// get the alignment sequences
string alignRead;
string alignGenome;
GenericBamAlignmentTools::getAlignmentSequences(alignObj, alignRead, alignGenome);
// update the statistics
statistics.update(alignRead, alignGenome);
}
// print to screen
cout << statistics << endl;
// statistics.printMatchMismatch();
// close BAM reader
bamReader.Close();
// close Fasta
genomeFasta.Close();
return 1;
}
// use current input alignment to update BAM file alignment stats
void StatsTool::StatsToolPrivate::ProcessAlignment(const BamAlignment& al) {
// increment total alignment counter
++numReads;
// check the paired-independent flags
if ( al.IsDuplicate() ) ++numDuplicates;
if ( al.IsFailedQC() ) ++numFailedQC;
if ( al.IsMapped() ) ++numMapped;
// check forward/reverse strand
if ( al.IsReverseStrand() )
++numReverseStrand;
else
++numForwardStrand;
// if alignment is paired-end
if ( al.IsPaired() ) {
// increment PE counter
++numPaired;
// increment first mate/second mate counters
if ( al.IsFirstMate() ) ++numFirstMate;
if ( al.IsSecondMate() ) ++numSecondMate;
// if alignment is mapped, check mate status
if ( al.IsMapped() ) {
// if mate mapped
if ( al.IsMateMapped() )
++numBothMatesMapped;
// else singleton
else
++numSingletons;
}
// check for explicit proper pair flag
if ( al.IsProperPair() ) ++numProperPair;
// store insert size for first mate
if ( settings->IsShowingInsertSizeSummary && al.IsFirstMate() && (al.InsertSize != 0) ) {
int insertSize = abs(al.InsertSize);
insertSizes.push_back( insertSize );
}
}
}
// print BamAlignment in SAM format
void ConvertTool::ConvertToolPrivate::PrintSam(const BamAlignment& a) {
// tab-delimited
// <QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> [ <TAG>:<VTYPE>:<VALUE> [...] ]
// write name & alignment flag
m_out << a.Name << "\t" << a.AlignmentFlag << "\t";
// write reference name
if ( (a.RefID >= 0) && (a.RefID < (int)m_references.size()) )
m_out << m_references[a.RefID].RefName << "\t";
else
m_out << "*\t";
// write position & map quality
m_out << a.Position+1 << "\t" << a.MapQuality << "\t";
// write CIGAR
const vector<CigarOp>& cigarData = a.CigarData;
if ( cigarData.empty() ) m_out << "*\t";
else {
vector<CigarOp>::const_iterator cigarIter = cigarData.begin();
vector<CigarOp>::const_iterator cigarEnd = cigarData.end();
for ( ; cigarIter != cigarEnd; ++cigarIter ) {
const CigarOp& op = (*cigarIter);
m_out << op.Length << op.Type;
}
m_out << "\t";
}
// write mate reference name, mate position, & insert size
if ( a.IsPaired() && (a.MateRefID >= 0) && (a.MateRefID < (int)m_references.size()) ) {
if ( a.MateRefID == a.RefID )
m_out << "=\t";
else
m_out << m_references[a.MateRefID].RefName << "\t";
m_out << a.MatePosition+1 << "\t" << a.InsertSize << "\t";
}
else
m_out << "*\t0\t0\t";
// write sequence
if ( a.QueryBases.empty() )
m_out << "*\t";
else
m_out << a.QueryBases << "\t";
// write qualities
if ( a.Qualities.empty() || (a.Qualities.at(0) == (char)0xFF) )
m_out << "*";
else
m_out << a.Qualities;
// write tag data
const char* tagData = a.TagData.c_str();
const size_t tagDataLength = a.TagData.length();
size_t index = 0;
while ( index < tagDataLength ) {
// write tag name
string tagName = a.TagData.substr(index, 2);
m_out << "\t" << tagName << ":";
index += 2;
// get data type
char type = a.TagData.at(index);
++index;
switch ( type ) {
case (Constants::BAM_TAG_TYPE_ASCII) :
m_out << "A:" << tagData[index];
++index;
break;
case (Constants::BAM_TAG_TYPE_INT8) :
case (Constants::BAM_TAG_TYPE_UINT8) :
m_out << "i:" << (int)tagData[index];
++index;
break;
case (Constants::BAM_TAG_TYPE_INT16) :
m_out << "i:" << BamTools::UnpackSignedShort(&tagData[index]);
index += sizeof(int16_t);
break;
case (Constants::BAM_TAG_TYPE_UINT16) :
m_out << "i:" << BamTools::UnpackUnsignedShort(&tagData[index]);
index += sizeof(uint16_t);
break;
case (Constants::BAM_TAG_TYPE_INT32) :
m_out << "i:" << BamTools::UnpackSignedInt(&tagData[index]);
index += sizeof(int32_t);
break;
case (Constants::BAM_TAG_TYPE_UINT32) :
m_out << "i:" << BamTools::UnpackUnsignedInt(&tagData[index]);
index += sizeof(uint32_t);
break;
case (Constants::BAM_TAG_TYPE_FLOAT) :
m_out << "f:" << BamTools::UnpackFloat(&tagData[index]);
index += sizeof(float);
break;
case (Constants::BAM_TAG_TYPE_HEX) :
case (Constants::BAM_TAG_TYPE_STRING) :
m_out << type << ":";
while (tagData[index]) {
m_out << tagData[index];
++index;
}
++index;
break;
}
if ( tagData[index] == '\0')
break;
}
m_out << endl;
}
// print BamAlignment in JSON format
void ConvertTool::ConvertToolPrivate::PrintJson(const BamAlignment& a) {
// write name & alignment flag
m_out << "{\"name\":\"" << a.Name << "\",\"alignmentFlag\":\"" << a.AlignmentFlag << "\",";
// write reference name
if ( (a.RefID >= 0) && (a.RefID < (int)m_references.size()) )
m_out << "\"reference\":\"" << m_references[a.RefID].RefName << "\",";
// write position & map quality
m_out << "\"position\":" << a.Position+1 << ",\"mapQuality\":" << a.MapQuality << ",";
// write CIGAR
const vector<CigarOp>& cigarData = a.CigarData;
if ( !cigarData.empty() ) {
m_out << "\"cigar\":[";
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);
if (cigarIter != cigarBegin)
m_out << ",";
m_out << "\"" << op.Length << op.Type << "\"";
}
m_out << "],";
}
// write mate reference name, mate position, & insert size
if ( a.IsPaired() && (a.MateRefID >= 0) && (a.MateRefID < (int)m_references.size()) ) {
m_out << "\"mate\":{"
<< "\"reference\":\"" << m_references[a.MateRefID].RefName << "\","
<< "\"position\":" << a.MatePosition+1
<< ",\"insertSize\":" << a.InsertSize << "},";
}
// write sequence
if ( !a.QueryBases.empty() )
m_out << "\"queryBases\":\"" << a.QueryBases << "\",";
// write qualities
if ( !a.Qualities.empty() && a.Qualities.at(0) != (char)0xFF ) {
string::const_iterator s = a.Qualities.begin();
m_out << "\"qualities\":[" << static_cast<short>(*s) - 33;
++s;
for ( ; s != a.Qualities.end(); ++s )
m_out << "," << static_cast<short>(*s) - 33;
m_out << "],";
}
// write alignment's source BAM file
m_out << "\"filename\":" << a.Filename << ",";
// write tag data
const char* tagData = a.TagData.c_str();
const size_t tagDataLength = a.TagData.length();
size_t index = 0;
if ( index < tagDataLength ) {
m_out << "\"tags\":{";
while ( index < tagDataLength ) {
if ( index > 0 )
m_out << ",";
// write tag name
m_out << "\"" << a.TagData.substr(index, 2) << "\":";
index += 2;
// get data type
char type = a.TagData.at(index);
++index;
switch ( type ) {
case (Constants::BAM_TAG_TYPE_ASCII) :
m_out << "\"" << tagData[index] << "\"";
++index;
break;
case (Constants::BAM_TAG_TYPE_INT8) :
case (Constants::BAM_TAG_TYPE_UINT8) :
m_out << (int)tagData[index];
++index;
break;
case (Constants::BAM_TAG_TYPE_INT16) :
m_out << BamTools::UnpackSignedShort(&tagData[index]);
index += sizeof(int16_t);
break;
case (Constants::BAM_TAG_TYPE_UINT16) :
m_out << BamTools::UnpackUnsignedShort(&tagData[index]);
index += sizeof(uint16_t);
break;
case (Constants::BAM_TAG_TYPE_INT32) :
m_out << BamTools::UnpackSignedInt(&tagData[index]);
index += sizeof(int32_t);
break;
case (Constants::BAM_TAG_TYPE_UINT32) :
m_out << BamTools::UnpackUnsignedInt(&tagData[index]);
index += sizeof(uint32_t);
break;
case (Constants::BAM_TAG_TYPE_FLOAT) :
m_out << BamTools::UnpackFloat(&tagData[index]);
index += sizeof(float);
break;
case (Constants::BAM_TAG_TYPE_HEX) :
case (Constants::BAM_TAG_TYPE_STRING) :
m_out << "\"";
while (tagData[index]) {
if (tagData[index] == '\"')
m_out << "\\\""; // escape for json
else
m_out << tagData[index];
++index;
}
m_out << "\"";
++index;
break;
}
if ( tagData[index] == '\0')
break;
}
m_out << "}";
}
m_out << "}" << endl;
}
int main (int argc, char *argv[]) {
int minBaseQuality = 0;
string usage=string(""+string(argv[0])+" [in BAM file] [in VCF file] [chr name] [deam out BAM] [not deam out BAM]"+
"\nThis program divides aligned single end reads into potentially deaminated\n"+
"\nreads and the puts the rest into another bam file if the deaminated positions are not called as the alternative base in the VCF.\n"+
"\nTip: if you do not need one of them, use /dev/null as your output\n"+
"arguments:\n"+
"\t"+"--bq [base qual] : Minimum base quality to flag a deaminated site (Default: "+stringify(minBaseQuality)+")\n"+
"\n");
if(argc == 1 ||
argc < 4 ||
(argc == 2 && (string(argv[0]) == "-h" || string(argv[0]) == "--help") )
){
cerr << "Usage "<<usage<<endl;
return 1;
}
for(int i=1;i<(argc-2);i++){
if(string(argv[i]) == "--bq"){
minBaseQuality=destringify<int>(argv[i+1]);
i++;
continue;
}
}
string bamfiletopen = string( argv[ argc-5 ] );
string vcffiletopen = string( argv[ argc-4 ] );
string chrname = string( argv[ argc-3 ] );
string deambam = string( argv[ argc-2 ] );
string nondeambam = string( argv[ argc-1 ] );
//dummy reader, will need to reposition anyway
VCFreader vcfr (vcffiletopen,
vcffiletopen+".tbi",
chrname,
1,
1,
0);
BamReader reader;
if ( !reader.Open(bamfiletopen) ) {
cerr << "Could not open input BAM file"<< bamfiletopen << endl;
return 1;
}
// if ( !reader.LocateIndex() ) {
// cerr << "The index for the BAM file cannot be located" << endl;
// return 1;
// }
// if ( !reader.HasIndex() ) {
// cerr << "The BAM file has not been indexed." << endl;
// return 1;
// }
//positioning the bam file
int refid=reader.GetReferenceID(chrname);
if(refid < 0){
cerr << "Cannot retrieve the reference ID for "<< chrname << endl;
return 1;
}
//cout<<"redif "<<refid<<endl;
//setting the BAM reader at that position
reader.SetRegion(refid,
0,
refid,
-1);
vector<RefData> testRefData=reader.GetReferenceData();
const SamHeader header = reader.GetHeader();
const RefVector references = reader.GetReferenceData();
BamWriter writerDeam;
if ( !writerDeam.Open(deambam, header, references) ) {
cerr << "Could not open output BAM file" << endl;
return 1;
}
BamWriter writerNoDeam;
if ( !writerNoDeam.Open(nondeambam, header, references) ) {
cerr << "Could not open output BAM file" << endl;
return 1;
}
unsigned int totalReads =0;
unsigned int deaminatedReads =0;
unsigned int ndeaminatedReads =0;
unsigned int skipped =0;
//iterating over the alignments for these regions
BamAlignment al;
int i;
while ( reader.GetNextAlignment(al) ) {
// cerr<<al.Name<<endl;
//skip unmapped
if(!al.IsMapped()){
skipped++;
continue;
}
//skip paired end !
if(al.IsPaired() ){
continue;
// cerr<<"Paired end not yet coded"<<endl;
// return 1;
}
string reconstructedReference = reconstructRef(&al);
char refeBase;
char readBase;
bool isDeaminated;
if(al.Qualities.size() != reconstructedReference.size()){
cerr<<"Quality line is not the same size as the reconstructed reference"<<endl;
return 1;
}
isDeaminated=false;
if(al.IsReverseStrand()){
//first base next to 3'
i = 0 ;
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
if( readBase == 'A' && int(al.Qualities[i]-offset) >= minBaseQuality){ //isDeaminated=true; }
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
transformRef(&refeBase,&readBase);
vcfr.repositionIterator(chrname,al.Position+1,al.Position+1);
while(vcfr.hasData()){
SimpleVCF * toprint=vcfr.getData();
// cout<<*toprint<<endl;
//skip deletions in the alt
if(toprint->getRef().length() != 1 )
continue;
if(toprint->getRef()[0] != refeBase){
cerr<<reconstructedReference<<endl;
cerr<<al.Position<<endl;
cerr<<numberOfDeletions(&al)<<endl;
cerr<<"Problem1 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
exit(1);
}
//if the VCF has a at least one G but no A
if( toprint->hasAtLeastOneG() &&
!toprint->hasAtLeastOneA() ){
isDeaminated=true;
}
}
}
//second base next to 3'
i = 1;
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//refeBase == 'G' &&
if( readBase == 'A' && int(al.Qualities[i]-offset) >= minBaseQuality){ //isDeaminated=true; }
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
transformRef(&refeBase,&readBase);
vcfr.repositionIterator(chrname,al.Position+2,al.Position+2);
while(vcfr.hasData()){
SimpleVCF * toprint=vcfr.getData();
// cout<<*toprint<<endl;
//skip deletions in the alt
if(toprint->getRef().length() != 1 )
continue;
if(toprint->getRef()[0] != refeBase){
cerr<<reconstructedReference<<endl;
cerr<<al.Position<<endl;
cerr<<numberOfDeletions(&al)<<endl;
cerr<<"Problem2 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
exit(1);
}
//if the VCF has at least one G but no A
// if(toprint->hasAtLeastOneG() &&
// toprint->getAlt().find("A") == string::npos){
if( toprint->hasAtLeastOneG() &&
!toprint->hasAtLeastOneA() ){
isDeaminated=true;
}
}
}
//last base next to 5'
i = (al.QueryBases.length()-1) ;
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//refeBase == 'G' &&
if( readBase == 'A' && int(al.Qualities[i]-offset) >= minBaseQuality){ //isDeaminated=true; }
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
transformRef(&refeBase,&readBase);
int lengthMatches=countMatchesRecons(reconstructedReference,0);
int positionJump = al.Position+lengthMatches+numberOfDeletions(&al);
vcfr.repositionIterator(chrname,positionJump,positionJump);
while(vcfr.hasData()){
SimpleVCF * toprint=vcfr.getData();
//skip deletions in the alt
if(toprint->getRef().length() != 1 )
continue;
if(toprint->getRef()[0] != refeBase){
cerr<<reconstructedReference<<endl;
cerr<<al.Position<<endl;
cerr<<lengthMatches<<endl;
cerr<<numberOfDeletions(&al)<<endl;
cerr<<positionJump<<endl;
cerr<<"Problem3 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
exit(1);
}
//if the VCF has at least one G but no A
if( toprint->hasAtLeastOneG() &&
!toprint->hasAtLeastOneA() ){
isDeaminated=true;
}
}
}
}else{
//first base next to 5'
i = 0;
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//refeBase == 'C'
if( readBase == 'T' && int(al.Qualities[i]-offset) >= minBaseQuality){
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
transformRef(&refeBase,&readBase);
vcfr.repositionIterator(chrname,al.Position+1,al.Position+1);
while(vcfr.hasData()){
SimpleVCF * toprint=vcfr.getData();
//cout<<*toprint<<endl;
//skip deletions in the alt
if(toprint->getRef().length() != 1 )
continue;
if(toprint->getRef()[0] != refeBase){
cerr<<reconstructedReference<<endl;
cerr<<al.Position<<endl;
cerr<<numberOfDeletions(&al)<<endl;
cerr<<"Problem4 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
exit(1);
}
//if the VCF has at least one C but no T
if( toprint->hasAtLeastOneC() &&
!toprint->hasAtLeastOneT() ){
isDeaminated=true;
}
}
//cout<<al.Position+
}
//second last base next to 3'
i = (al.QueryBases.length()-2);
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//refeBase == 'C' &&
if( readBase == 'T' && int(al.Qualities[i]-offset) >= minBaseQuality){
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
transformRef(&refeBase,&readBase);
int lengthMatches=countMatchesRecons(reconstructedReference,1);
int positionJump = al.Position+lengthMatches+numberOfDeletions(&al);
vcfr.repositionIterator(chrname,positionJump,positionJump);
while(vcfr.hasData()){
SimpleVCF * toprint=vcfr.getData();
//skip deletions in the alt
if(toprint->getRef().length() != 1 )
continue;
if(toprint->getRef()[0] != refeBase){
cerr<<reconstructedReference<<endl;
cerr<<al.Position<<endl;
cerr<<lengthMatches<<endl;
cerr<<numberOfDeletions(&al)<<endl;
cerr<<positionJump<<endl;
cerr<<"Problem5 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
exit(1);
}
if( toprint->hasAtLeastOneC() &&
!toprint->hasAtLeastOneT() ){
isDeaminated=true;
}
}
}
//last base next to 3'
i = (al.QueryBases.length()-1);
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//&& refeBase == 'C'
if( readBase == 'T' && int(al.Qualities[i]-offset) >= minBaseQuality){
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
transformRef(&refeBase,&readBase);
int lengthMatches=countMatchesRecons(reconstructedReference,0);
int positionJump = al.Position+lengthMatches+numberOfDeletions(&al);
vcfr.repositionIterator(chrname,positionJump,positionJump);
while(vcfr.hasData()){
SimpleVCF * toprint=vcfr.getData();
//skip deletions in the alt
if(toprint->getRef().length() != 1 )
continue;
if(toprint->getRef()[0] != refeBase){
cerr<<reconstructedReference<<endl;
cerr<<al.Position<<endl;
cerr<<lengthMatches<<endl;
cerr<<numberOfDeletions(&al)<<endl;
cerr<<positionJump<<endl;
cerr<<"Problem6 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
exit(1);
}
if( toprint->hasAtLeastOneC() &&
!toprint->hasAtLeastOneT() ){
isDeaminated=true;
}
}
}
}
totalReads++;
if(isDeaminated){
deaminatedReads++;
writerDeam.SaveAlignment(al);
}else{
ndeaminatedReads++;
writerNoDeam.SaveAlignment(al);
}
}//end for each read
reader.Close();
writerDeam.Close();
writerNoDeam.Close();
cerr<<"Program finished sucessfully, out of "<<totalReads<<" mapped reads (skipped: "<<skipped<<" reads) we flagged "<<deaminatedReads<<" as deaminated and "<<ndeaminatedReads<<" as not deaminated"<<endl;
return 0;
}
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;
}
int main (int argc, char *argv[]) {
if( (argc== 1) ||
(argc== 2 && string(argv[1]) == "-h") ||
(argc== 2 && string(argv[1]) == "-help") ||
(argc== 2 && string(argv[1]) == "--help") ){
cout<<"Usage:"<<endl;
cout<<""<<endl;
cout<<"plotQualScore input.bam"<<endl;
return 1;
}
string bamfiletopen = string(argv[1]);
BamReader reader;
if ( !reader.Open(bamfiletopen) ) {
cerr << "Could not open input BAM files." << endl;
return 1;
}
// if ( !reader.LocateIndex() ){
// cerr << "warning: cannot locate index for file " << bamfiletopen<<endl;
// //return 1;
// }
BamAlignment al;
BamAlignment al2;
bool unsurePEorSE=true;
bool pe=true;
int strLength=-1;
int vecLengthToUse=-1;
map<short,unsigned long> ** counterA = 0;
map<short,unsigned long> ** counterC = 0;
map<short,unsigned long> ** counterG = 0;
map<short,unsigned long> ** counterT = 0;
int lengthIndex1=0;
int lengthIndex2=0;
string seqInd1;
string seqInd2;
string qualInd1;
string qualInd2;
int offsetInd2;
while ( reader.GetNextAlignment(al) ) {
if(unsurePEorSE){
strLength=al.QueryBases.length();
if(al.IsPaired()){
pe=true;
vecLengthToUse=2*strLength;
}else{
pe=false;
vecLengthToUse=strLength;
}
string index1;
string index2;
if(al.HasTag("XI")){
al.GetTag("XI",index1);
vecLengthToUse+=index1.length();
lengthIndex1=index1.length();
}
if(al.HasTag("XJ")){
al.GetTag("XJ",index2);
vecLengthToUse+=index2.length();
lengthIndex2=index2.length();
}
counterA = new map<short,unsigned long> * [vecLengthToUse];
counterC = new map<short,unsigned long> * [vecLengthToUse];
counterG = new map<short,unsigned long> * [vecLengthToUse];
counterT = new map<short,unsigned long> * [vecLengthToUse];
for(int i=0;i<vecLengthToUse;i++){
counterA[i]=new map<short,unsigned long> ();
counterC[i]=new map<short,unsigned long> ();
counterG[i]=new map<short,unsigned long> ();
counterT[i]=new map<short,unsigned long> ();
for(short k=minQualScore;k<=maxQualScore;k++){
(*counterA[i])[k]=0;
(*counterC[i])[k]=0;
(*counterG[i])[k]=0;
(*counterT[i])[k]=0;
}
}
unsurePEorSE=false;
}else{
if(pe &&
!al.IsPaired()){
cerr << "Cannot have unpaired reads in PE mode" << endl;
return 1;
}
if(!pe &&
al.IsPaired()){
cerr << "Cannot have unpaired reads in SE mode" << endl;
return 1;
}
}
if(al.QueryBases.length() != al.Qualities.length()){
cerr << "Cannot have different lengths for sequence and quality" << endl;
return 1;
}
if(int(al.QueryBases.length()) != strLength){
cerr << "Cannot have different lengths for sequence and quality" << endl;
return 1;
}
if(pe){
if(al.IsFirstMate()){
reader.GetNextAlignment(al2);
if(al2.QueryBases.length() != al2.Qualities.length()){
cerr << "Cannot have different lengths for sequence and quality" << endl;
return 1;
}
}else{
cerr << "First read should be the first mate" << endl;
return 1;
}
}
//cycle
for(unsigned int i=0;i<al.QueryBases.length();i++){
short x=(short(al.Qualities[i])-qualOffset);
if(al.QueryBases[i] == 'A'){
(*counterA[i])[x]++;
}
if(al.QueryBases[i] == 'C'){
(*counterC[i])[x]++;
}
if(al.QueryBases[i] == 'G'){
(*counterG[i])[x]++;
}
if(al.QueryBases[i] == 'T'){
(*counterT[i])[x]++;
}
}
//The indices for al and al2 should hopefully be the same
if(lengthIndex1>0){
al.GetTag("XI",seqInd1);
al.GetTag("YI",qualInd1);
int j;
for(int i=0;i<lengthIndex1;i++){
j=i+al.QueryBases.length();
short x=(short(qualInd1[i])-qualOffset);
if(seqInd1[i] == 'A'){
(*counterA[j])[x]++;
}
if(seqInd1[i] == 'C'){
(*counterC[j])[x]++;
}
if(seqInd1[i] == 'G'){
(*counterG[j])[x]++;
}
if(seqInd1[i] == 'T'){
(*counterT[j])[x]++;
}
}
}
if(pe){
offsetInd2=al.QueryBases.length()+lengthIndex1+al2.QueryBases.length();
int j;
for(unsigned int i=0;i<al2.QueryBases.length();i++){
j=i+al.QueryBases.length()+lengthIndex1;
short x=(short(al2.Qualities[i])-qualOffset);
if(al2.QueryBases[i] == 'A'){
(*counterA[j])[x]++;
}
if(al2.QueryBases[i] == 'C'){
(*counterC[j])[x]++;
}
if(al2.QueryBases[i] == 'G'){
(*counterG[j])[x]++;
}
if(al2.QueryBases[i] == 'T'){
(*counterT[j])[x]++;
}
}
}else{
offsetInd2=al.QueryBases.length()+lengthIndex1;
}
//The indices for al and al2 should hopefully be the same
if(lengthIndex2>0){
al.GetTag("XJ",seqInd2);
al.GetTag("YJ",qualInd2);
int j;
for(int i=0;i<lengthIndex2;i++){
j=offsetInd2+i;
short x=(short(qualInd2[i])-qualOffset);
if(seqInd2[i] == 'A'){
(*counterA[j])[x]++;
}
if(seqInd2[i] == 'C'){
(*counterC[j])[x]++;
}
if(seqInd2[i] == 'G'){
(*counterG[j])[x]++;
}
if(seqInd2[i] == 'T'){
(*counterT[j])[x]++;
}
}
}
}
reader.Close();
cout<<"cycle\t"<<"nuc\t";
for(short k=minQualScore;k<maxQualScore;k++){
cout<<k<<"\t";
}
cout<<maxQualScore<<endl;
for(int i=0;i<vecLengthToUse;i++){
cout<<(i+1)<<"\t";
cout<<"A\t";
for(short k=minQualScore;k<maxQualScore;k++){
cout<<(*counterA[i])[k]<<"\t";
}
cout<<(*counterA[i])[maxQualScore]<<endl;
cout<<(i+1)<<"\t";
cout<<"C\t";
for(short k=minQualScore;k<maxQualScore;k++){
cout<<(*counterC[i])[k]<<"\t";
}
cout<<(*counterC[i])[maxQualScore]<<endl;
cout<<(i+1)<<"\t";
cout<<"G\t";
for(short k=minQualScore;k<maxQualScore;k++){
cout<<(*counterG[i])[k]<<"\t";
}
cout<<(*counterG[i])[maxQualScore]<<endl;
cout<<(i+1)<<"\t";
cout<<"T\t";
for(short k=minQualScore;k<maxQualScore;k++){
cout<<(*counterT[i])[k]<<"\t";
}
cout<<(*counterT[i])[maxQualScore]<<endl;
}
return 0;
}
int main (int argc, char *argv[]) {
int minBaseQuality = 0;
string usage=string(""+string(argv[0])+" [in BAM file] [in VCF file] [chr name] [deam out BAM] [not deam out BAM]"+
"\nThis program divides aligned single end reads into potentially deaminated\n"+
"\nreads and the puts the rest into another bam file if the deaminated positions are not called as the alternative base in the VCF.\n"+
"\nThis is like filterDeaminatedVCF but it loads the VCF before then labels the reads instead of doing it on the fly\n"+
"\nwhich is good if you have many reads in the bam file.\n"+
"\nTip: if you do not need one of them, use /dev/null as your output\n"+
"\narguments:\n"+
"\t"+"--bq [base qual] : Minimum base quality to flag a deaminated site (Default: "+stringify(minBaseQuality)+")\n"+
"\t"+"--1000g [vcf file] : VCF file from 1000g to get the putative A and T positions in modern humans (Default: "+vcf1000g+")\n"+
"\n");
if(argc == 1 ||
argc < 4 ||
(argc == 2 && (string(argv[0]) == "-h" || string(argv[0]) == "--help") )
){
cerr << "Usage "<<usage<<endl;
return 1;
}
for(int i=1;i<(argc-2);i++){
if(string(argv[i]) == "--bq"){
minBaseQuality=destringify<int>(argv[i+1]);
i++;
continue;
}
if(string(argv[i]) == "--1000g"){
vcf1000g=string(argv[i+1]);
i++;
continue;
}
}
unsigned int maxSizeChromosome=250000000;//larger than chr1 hg19
bool * hasCnoT;
bool * hasGnoA;
bool * thousandGenomesHasA;
bool * thousandGenomesHasT;
cerr<<"Trying to allocating memory"<<endl;
try{
hasCnoT = new bool[ maxSizeChromosome ];
hasGnoA = new bool[ maxSizeChromosome ];
thousandGenomesHasA = new bool[ maxSizeChromosome ];
thousandGenomesHasT = new bool[ maxSizeChromosome ];
}catch(bad_alloc& exc){
cerr<<"ERROR: allocating memory failed"<<endl;
return 1;
}
cerr<<"Success in allocating memory"<<endl;
for(unsigned int i = 0;i<maxSizeChromosome;i++){
hasCnoT[i]=false;
hasGnoA[i]=false;
thousandGenomesHasA[i]=false;
thousandGenomesHasT[i]=false;
}
string bamfiletopen = string( argv[ argc-5 ] );
string vcffiletopen = string( argv[ argc-4 ] );
string chrname = string( argv[ argc-3 ] );
string deambam = string( argv[ argc-2 ] );
string nondeambam = string( argv[ argc-1 ] );
cerr<<"Reading consensus VCF "<<vcffiletopen<<" ... "<<endl;
VCFreader vcfr (vcffiletopen,
// vcffiletopen+".tbi",
// chrname,
// 1,
// maxSizeChromosome,
0);
while(vcfr.hasData()){
SimpleVCF * toprint=vcfr.getData();
if(toprint->getRef().length() != 1 )
continue;
//if the VCF has a at least one G but no A
if( toprint->hasAtLeastOneG() &&
!toprint->hasAtLeastOneA() ){
hasGnoA[ toprint->getPosition() ] =true;
}
if( toprint->hasAtLeastOneC() &&
!toprint->hasAtLeastOneT() ){
hasCnoT[ toprint->getPosition() ] =true;
}
}
cerr<<"done reading VCF"<<endl;
cerr<<"Reading 1000g VCF :"<<vcf1000g<<" ..."<<endl;
string line1000g;
ifstream myFile1000g;
myFile1000g.open(vcf1000g.c_str(), ios::in);
if (myFile1000g.is_open()){
while ( getline (myFile1000g,line1000g)){
vector<string> fields=allTokens(line1000g,'\t');
//0 chr
//1 pos
//2 id
//3 ref
//4 alt
//check if same chr
if(fields[0] != chrname){
cerr <<"Error, wrong chromosome in 1000g file for line= "<<line1000g<<endl;
return 1;
}
//skip indels
if(fields[3].size() != 1 ||
fields[4].size() != 1 )
continue;
char ref=toupper(fields[3][0]);
char alt=toupper(fields[4][0]);
unsigned int pos=destringify<unsigned int>( fields[1] );
thousandGenomesHasA[ pos ] = ( (ref=='A') || (alt=='A') );
thousandGenomesHasT[ pos ] = ( (ref=='T') || (alt=='T') );
}
myFile1000g.close();
}else{
cerr <<"Unable to open file "<<vcf1000g<<endl;
return 1;
}
cerr<<"done reading 1000g VCF"<<endl;
BamReader reader;
if ( !reader.Open(bamfiletopen) ) {
cerr << "Could not open input BAM file"<< bamfiletopen << endl;
return 1;
}
//positioning the bam file
int refid=reader.GetReferenceID(chrname);
if(refid < 0){
cerr << "Cannot retrieve the reference ID for "<< chrname << endl;
return 1;
}
//cout<<"redif "<<refid<<endl;
//setting the BAM reader at that position
reader.SetRegion(refid,
0,
refid,
-1);
vector<RefData> testRefData=reader.GetReferenceData();
const SamHeader header = reader.GetHeader();
const RefVector references = reader.GetReferenceData();
BamWriter writerDeam;
if ( !writerDeam.Open(deambam, header, references) ) {
cerr << "Could not open output BAM file" << endl;
return 1;
}
BamWriter writerNoDeam;
if ( !writerNoDeam.Open(nondeambam, header, references) ) {
cerr << "Could not open output BAM file" << endl;
return 1;
}
unsigned int totalReads =0;
unsigned int deaminatedReads =0;
unsigned int ndeaminatedReads =0;
unsigned int skipped =0;
//iterating over the alignments for these regions
BamAlignment al;
int i;
while ( reader.GetNextAlignment(al) ) {
// cerr<<al.Name<<endl;
//skip unmapped
if(!al.IsMapped()){
skipped++;
continue;
}
//skip paired end !
if(al.IsPaired() ){
continue;
// cerr<<"Paired end not yet coded"<<endl;
// return 1;
}
string reconstructedReference = reconstructRef(&al);
char refeBase;
char readBase;
bool isDeaminated;
if(al.Qualities.size() != reconstructedReference.size()){
cerr<<"Quality line is not the same size as the reconstructed reference"<<endl;
return 1;
}
isDeaminated=false;
if(al.IsReverseStrand()){
//first base next to 3'
i = 0 ;
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
if( readBase == 'A' && int(al.Qualities[i]-offset) >= minBaseQuality){ //isDeaminated=true; }
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
if( hasGnoA[al.Position+1] &&
!thousandGenomesHasA[al.Position+1] )
isDeaminated=true;
// transformRef(&refeBase,&readBase);
// vcfr.repositionIterator(chrname,al.Position+1,al.Position+1);
// while(vcfr.hasData()){
// SimpleVCF * toprint=vcfr.getData();
// // cout<<*toprint<<endl;
// //skip deletions in the alt
// if(toprint->getRef().length() != 1 )
// continue;
// if(toprint->getRef()[0] != refeBase){
// cerr<<reconstructedReference<<endl;
// cerr<<al.Position<<endl;
// cerr<<numberOfDeletions(&al)<<endl;
// cerr<<"Problem1 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
// exit(1);
// }
// //if the VCF has a at least one G but no A
// if( toprint->hasAtLeastOneG() &&
// !toprint->hasAtLeastOneA() ){
// isDeaminated=true;
// }
// }
}
//second base next to 3'
i = 1;
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//refeBase == 'G' &&
if( readBase == 'A' && int(al.Qualities[i]-offset) >= minBaseQuality){ //isDeaminated=true; }
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
if( hasGnoA[al.Position+2] &&
!thousandGenomesHasA[al.Position+2] )
isDeaminated=true;
// transformRef(&refeBase,&readBase);
// vcfr.repositionIterator(chrname,al.Position+2,al.Position+2);
// while(vcfr.hasData()){
// SimpleVCF * toprint=vcfr.getData();
// // cout<<*toprint<<endl;
// //skip deletions in the alt
// if(toprint->getRef().length() != 1 )
// continue;
// if(toprint->getRef()[0] != refeBase){
// cerr<<reconstructedReference<<endl;
// cerr<<al.Position<<endl;
// cerr<<numberOfDeletions(&al)<<endl;
// cerr<<"Problem2 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
// exit(1);
// }
// //if the VCF has at least one G but no A
// // if(toprint->hasAtLeastOneG() &&
// // toprint->getAlt().find("A") == string::npos){
// if( toprint->hasAtLeastOneG() &&
// !toprint->hasAtLeastOneA() ){
// isDeaminated=true;
// }
// }
}
//last base next to 5'
i = (al.QueryBases.length()-1) ;
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//refeBase == 'G' &&
if( readBase == 'A' && int(al.Qualities[i]-offset) >= minBaseQuality){ //isDeaminated=true; }
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
transformRef(&refeBase,&readBase);
int lengthMatches=countMatchesRecons(reconstructedReference,0);
int positionJump = al.Position+lengthMatches+numberOfDeletions(&al);
if(hasGnoA[positionJump] &&
!thousandGenomesHasA[positionJump] )
isDeaminated=true;
// vcfr.repositionIterator(chrname,positionJump,positionJump);
// while(vcfr.hasData()){
// SimpleVCF * toprint=vcfr.getData();
// //skip deletions in the alt
// if(toprint->getRef().length() != 1 )
// continue;
// if(toprint->getRef()[0] != refeBase){
// cerr<<reconstructedReference<<endl;
// cerr<<al.Position<<endl;
// cerr<<lengthMatches<<endl;
// cerr<<numberOfDeletions(&al)<<endl;
// cerr<<positionJump<<endl;
// cerr<<"Problem3 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
// exit(1);
// }
// //if the VCF has at least one G but no A
// if( toprint->hasAtLeastOneG() &&
// !toprint->hasAtLeastOneA() ){
// isDeaminated=true;
// }
// }
}
}else{
//first base next to 5'
i = 0;
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//refeBase == 'C'
if( readBase == 'T' && int(al.Qualities[i]-offset) >= minBaseQuality){
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
// transformRef(&refeBase,&readBase);
if(hasCnoT[al.Position+1] &&
!thousandGenomesHasT[al.Position+1] )
isDeaminated=true;
// vcfr.repositionIterator(chrname,al.Position+1,al.Position+1);
// while(vcfr.hasData()){
// SimpleVCF * toprint=vcfr.getData();
// //cout<<*toprint<<endl;
// //skip deletions in the alt
// if(toprint->getRef().length() != 1 )
// continue;
// if(toprint->getRef()[0] != refeBase){
// cerr<<reconstructedReference<<endl;
// cerr<<al.Position<<endl;
// cerr<<numberOfDeletions(&al)<<endl;
// cerr<<"Problem4 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
// exit(1);
// }
// //if the VCF has at least one C but no T
// if( toprint->hasAtLeastOneC() &&
// !toprint->hasAtLeastOneT() ){
// isDeaminated=true;
// }
// }
//cout<<al.Position+
}
//second last base next to 3'
i = (al.QueryBases.length()-2);
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//refeBase == 'C' &&
if( readBase == 'T' && int(al.Qualities[i]-offset) >= minBaseQuality){
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
//transformRef(&refeBase,&readBase);
int lengthMatches=countMatchesRecons(reconstructedReference,1);
int positionJump = al.Position+lengthMatches+numberOfDeletions(&al);
if(hasCnoT[positionJump] &&
!thousandGenomesHasT[positionJump] )
isDeaminated=true;
// vcfr.repositionIterator(chrname,positionJump,positionJump);
// while(vcfr.hasData()){
// SimpleVCF * toprint=vcfr.getData();
// //skip deletions in the alt
// if(toprint->getRef().length() != 1 )
// continue;
// if(toprint->getRef()[0] != refeBase){
// cerr<<reconstructedReference<<endl;
// cerr<<al.Position<<endl;
// cerr<<lengthMatches<<endl;
// cerr<<numberOfDeletions(&al)<<endl;
// cerr<<positionJump<<endl;
// cerr<<"Problem5 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
// exit(1);
// }
// if( toprint->hasAtLeastOneC() &&
// !toprint->hasAtLeastOneT() ){
// isDeaminated=true;
// }
// }
}
//last base next to 3'
i = (al.QueryBases.length()-1);
refeBase=toupper(reconstructedReference[i]);
readBase=toupper( al.QueryBases[i]);
//&& refeBase == 'C'
if( readBase == 'T' && int(al.Qualities[i]-offset) >= minBaseQuality){
if( skipAlign(reconstructedReference,&al,&skipped) ){ continue; }
transformRef(&refeBase,&readBase);
int lengthMatches=countMatchesRecons(reconstructedReference,0);
int positionJump = al.Position+lengthMatches+numberOfDeletions(&al);
if(hasCnoT[positionJump] &&
!thousandGenomesHasT[positionJump] )
isDeaminated=true;
// vcfr.repositionIterator(chrname,positionJump,positionJump);
// while(vcfr.hasData()){
// SimpleVCF * toprint=vcfr.getData();
// //skip deletions in the alt
// if(toprint->getRef().length() != 1 )
// continue;
// if(toprint->getRef()[0] != refeBase){
// cerr<<reconstructedReference<<endl;
// cerr<<al.Position<<endl;
// cerr<<lengthMatches<<endl;
// cerr<<numberOfDeletions(&al)<<endl;
// cerr<<positionJump<<endl;
// cerr<<"Problem6 position "<<*toprint<<" does not have a "<<refeBase<<" as reference allele for read "<<al.Name<<endl;
// exit(1);
// }
// if( toprint->hasAtLeastOneC() &&
// !toprint->hasAtLeastOneT() ){
// isDeaminated=true;
// }
// }
}
}
totalReads++;
if(isDeaminated){
deaminatedReads++;
writerDeam.SaveAlignment(al);
}else{
ndeaminatedReads++;
writerNoDeam.SaveAlignment(al);
}
}//end for each read
reader.Close();
writerDeam.Close();
writerNoDeam.Close();
delete(hasCnoT);
delete(hasGnoA);
cerr<<"Program finished sucessfully, out of "<<totalReads<<" mapped reads (skipped: "<<skipped<<" reads) we flagged "<<deaminatedReads<<" as deaminated and "<<ndeaminatedReads<<" as not deaminated"<<endl;
return 0;
}
int main (int argc, char *argv[]) {
bool mapped =false;
bool unmapped=false;
const string usage=string(string(argv[0])+" [options] input.bam out.bam"+"\n\n"+
"This program takes a BAM file as input and produces\n"+
"another where the putative deaminated bases have\n"+
"have been cut\n"+
"\n"+
"Options:\n");
// "\t"+"-u , --unmapped" +"\n\t\t"+"For an unmapped bam file"+"\n"+
// "\t"+"-m , --mapped" +"\n\t\t"+"For an mapped bam file"+"\n");
if( (argc== 1) ||
(argc== 2 && string(argv[1]) == "-h") ||
(argc== 2 && string(argv[1]) == "-help") ||
(argc== 2 && string(argv[1]) == "--help") ){
cout<<"Usage:"<<endl;
cout<<usage<<endl;
cout<<""<<endl;
return 1;
}
// for(int i=1;i<(argc-1);i++){ //all but the last arg
// if(strcmp(argv[i],"-m") == 0 || strcmp(argv[i],"--mapped") == 0 ){
// mapped=true;
// continue;
// }
// if(strcmp(argv[i],"-u") == 0 || strcmp(argv[i],"--unmapped") == 0 ){
// unmapped=true;
// continue;
// }
// cerr<<"Unknown option "<<argv[i] <<" exiting"<<endl;
// return 1;
// }
if(argc != 3){
cerr<<"Error: Must specify the input and output BAM files";
return 1;
}
string inbamFile =argv[argc-2];
string outbamFile=argv[argc-1];
// if(!mapped && !unmapped){
// cerr << "Please specify whether you reads are mapped or unmapped" << endl;
// return 1;
// }
// if(mapped && unmapped){
// cerr << "Please specify either mapped or unmapped but not both" << endl;
// return 1;
// }
BamReader reader;
if ( !reader.Open(inbamFile) ) {
cerr << "Could not open input BAM files." << endl;
return 1;
}
vector<RefData> testRefData=reader.GetReferenceData();
const SamHeader header = reader.GetHeader();
const RefVector references = reader.GetReferenceData();
BamWriter writer;
if ( !writer.Open(outbamFile, header, references) ) {
cerr << "Could not open output BAM file" << endl;
return 1;
}
BamAlignment al;
// BamAlignment al2;
// bool al2Null=true;
while ( reader.GetNextAlignment(al) ) {
if(al.IsPaired() ){
if(al.IsFirstMate() ){ //5' end, need to check first base only
if(al.IsReverseStrand()){ //
if(!al.IsMapped()){
cerr << "Cannot have reverse complemented unmapped reads: " <<al.Name<< endl;
//return 1;
}
int indexToCheck;
//last
indexToCheck=al.QueryBases.length()-1;
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
//al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
al.QueryBases = al.QueryBases.substr(0,indexToCheck);
al.Qualities = al.Qualities.substr(0, indexToCheck);
}
}else{
int indexToCheck;
//first base
indexToCheck=0;
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
//al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
al.QueryBases = al.QueryBases.substr(indexToCheck+1);
al.Qualities = al.Qualities.substr(indexToCheck+1);
}
}
}else{ //3' end, need to check last two bases only
if( al.IsSecondMate() ){
if(al.IsReverseStrand()){ //
if(!al.IsMapped()){
cerr << "Cannot have reverse complemented unmapped reads: " <<al.Name<< endl;
//return 1;
}
int indexToCheck;
//second to last
indexToCheck=al.QueryBases.length()-2;
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
//al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
al.QueryBases = al.QueryBases.substr(0,indexToCheck);
al.Qualities = al.Qualities.substr(0, indexToCheck);
}else{
//last
indexToCheck=al.QueryBases.length()-1;
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
//al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
al.QueryBases = al.QueryBases.substr(0,indexToCheck);
al.Qualities = al.Qualities.substr(0, indexToCheck);
}
}
}else{
int indexToCheck;
//second base
indexToCheck=1;
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
//al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
al.QueryBases = al.QueryBases.substr(indexToCheck+1);
al.Qualities = al.Qualities.substr(indexToCheck+1);
}else{
//first base
indexToCheck=0;
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
//al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
al.QueryBases = al.QueryBases.substr(indexToCheck+1);
al.Qualities = al.Qualities.substr(indexToCheck+1);
}
}
}
}else{
cerr << "Wrong state" << endl;
return 1;
}
}
}//end of paired end
else{//we consider single reads to have been sequenced from 5' to 3'
if(al.IsReverseStrand()){ //need to consider
if(!al.IsMapped()){
cerr << "Cannot have reverse complemented unmapped reads: " <<al.Name<< endl;
//return 1;
}
int indexToCheck;
//second base
indexToCheck=1;
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
// al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
// cout<<"51 "<<al.QueryBases<<endl;
// cout<<"51 "<<al.Qualities<<endl;
al.QueryBases = al.QueryBases.substr(indexToCheck+1);
al.Qualities = al.Qualities.substr(indexToCheck+1);
// cout<<"52 "<<al.QueryBases<<endl;
// cout<<"52 "<<al.Qualities<<endl;
}else{
//first base
indexToCheck=0;
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
// al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
// cout<<"61 "<<al.QueryBases<<endl;
// cout<<"61 "<<al.Qualities<<endl;
al.QueryBases = al.QueryBases.substr(indexToCheck+1);
al.Qualities = al.Qualities.substr(indexToCheck+1);
// cout<<"62 "<<al.QueryBases<<endl;
// cout<<"62 "<<al.Qualities<<endl;
}
}
//last
indexToCheck=al.QueryBases.length()-1;
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
// al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
// cout<<"21 "<<al.QueryBases<<endl;
// cout<<"21 "<<al.Qualities<<endl;
al.QueryBases = al.QueryBases.substr(0,indexToCheck);
al.Qualities = al.Qualities.substr(0, indexToCheck);
// cout<<"22 "<<al.QueryBases<<endl;
// cout<<"22 "<<al.Qualities<<endl;
}
}else{
int indexToCheck;
//first base
indexToCheck=0;
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
// al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
// cout<<"11 "<<al.QueryBases<<endl;
// cout<<"11 "<<al.Qualities<<endl;
al.QueryBases = al.QueryBases.substr(indexToCheck+1);
al.Qualities = al.Qualities.substr(indexToCheck+1);
// cout<<"12 "<<al.QueryBases<<endl;
// cout<<"12 "<<al.Qualities<<endl;
}
//second to last
indexToCheck=al.QueryBases.length()-2;
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
// al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
// cout<<"31 "<<al.QueryBases<<endl;
// cout<<"31 "<<al.Qualities<<endl;
al.QueryBases = al.QueryBases.substr(0,indexToCheck);
al.Qualities = al.Qualities.substr(0, indexToCheck);
// cout<<"32 "<<al.QueryBases<<endl;
// cout<<"32 "<<al.Qualities<<endl;
}else{
//last
indexToCheck=al.QueryBases.length()-1;
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
// al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
// cout<<"41 "<<al.QueryBases<<endl;
// cout<<"41 "<<al.Qualities<<endl;
al.QueryBases = al.QueryBases.substr(0,indexToCheck);
al.Qualities = al.Qualities.substr(0, indexToCheck);
// cout<<"42 "<<al.QueryBases<<endl;
// cout<<"42 "<<al.Qualities<<endl;
}
}
}
}//end of single end
writer.SaveAlignment(al);
}// while ( reader.GetNextAlignment(al) ) {
reader.Close();
writer.Close();
return 0;
}
int main (int argc, char *argv[]) {
bool produceUnCompressedBAM=false;
bool verbose=false;
bool ancientDNA=false;
bool keepOrig=false;
string adapter_F=options_adapter_F_BAM;
string adapter_S=options_adapter_S_BAM;
string adapter_chimera=options_adapter_chimera_BAM;
string key="";
bool allowMissing=false;
int trimCutoff=1;
bool allowAligned=false;
bool printLog=false;
string logFileName;
BamReader reader;
BamWriter writer;
string bamFile;
string bamFileOUT="";
string key1;
string key2;
bool useDist=false;
double location=-1.0;
double scale =-1.0;
bool fastqFormat=false;
string fastqfile1 = "";
string fastqfile2 = "";
string fastqoutfile = "";
bool singleEndModeFQ=true;
const string usage=string(string(argv[0])+
" [options] BAMfile"+"\n"+
"\nThis program takes an unaligned BAM where mates are consecutive\nor fastq files and trims and merges reads\n"+
"\n\tYou can specify a unaligned bam file or one or two fastq :\n"+
"\t\t"+"-fq1" +"\t\t"+"First fastq"+"\n"+
"\t\t"+"-fq2" +"\t\t"+"Second fastq file (for paired-end)"+"\n"+
"\t\t"+"-fqo" +"\t\t"+"Output fastq prefix"+"\n\n"+
//"\t"+"-p , --PIPE"+"\n\t\t"+"Read BAM from and write it to PIPE"+"\n"+
"\t"+"-o , --outfile" +"\t\t"+"Output (BAM format)."+"\n"+
"\t"+"-u " +"\t\t"+"Produce uncompressed bam (good for pipe)"+"\n"+
// "\t"+" , --outprefix" +"\n\t\t"+"Prefix for output files (default '"+outprefix+"')."+"\n"+
//"\t"+" , --SAM" +"\n\t\t"+"Output SAM not BAM."+"\n"+
"\t"+"--aligned" +"\t\t"+"Allow reads to be aligned (default "+boolStringify(allowAligned)+")"+"\n"+
"\t"+"-v , --verbose" +"\t\t"+"Turn all messages on (default "+boolStringify(verbose)+")"+"\n"+
"\t"+"--log [log file]" +"\t"+"Print a tally of merged reads to this log file (default only to stderr)"+"\n"+
"\n\t"+"Paired End merging/Single Read trimming options"+"\n"+
"\t\t"+"You can specify either:"+"\n"+
"\t\t\t"+"--ancientdna"+"\t\t\t"+"ancient DNA (default "+boolStringify(ancientDNA)+")"+"\n"+
"\t\t"+" "+"\t\t\t\t"+"this allows for partial overlap"+"\n"+
"\n\t\t"+"or if you know your size length distribution:"+"\n"+
"\t\t\t"+"--loc"+"\t\t\t\t"+"Location for lognormal dist. (default none)"+"\n"+
"\t\t\t"+"--scale"+"\t\t\t\t"+"Scale for lognormal dist. (default none)"+"\n"+
// "\t\t\t\t\t\t\tGood for merging ancient DNA reads into a single sequence\n\n"
"\n\t\t"+"--keepOrig"+"\t\t\t\t"+"Write original reads if they are trimmed or merged (default "+boolStringify(keepOrig)+")"+"\n"+
"\t\t\t\t\t\t\tSuch reads will be marked as PCR duplicates\n\n"
"\t\t"+"-f , --adapterFirstRead" +"\t\t\t"+"Adapter that is observed after the forward read (def. Multiplex: "+options_adapter_F_BAM.substr(0,30)+")"+"\n"+
"\t\t"+"-s , --adapterSecondRead" +"\t\t"+"Adapter that is observed after the reverse read (def. Multiplex: "+options_adapter_S_BAM.substr(0,30)+")"+"\n"+
"\t\t"+"-c , --FirstReadChimeraFilter" +"\t\t"+"If the forward read looks like this sequence, the cluster is filtered out.\n\t\t\t\t\t\t\tProvide several sequences separated by comma (def. Multiplex: "+options_adapter_chimera_BAM.substr(0,30)+")"+"\n"+
"\t\t"+"-k , --key"+"\t\t\t\t"+"Key sequence with which each sequence starts. Comma separate for forward and reverse reads. (default '"+key+"')"+"\n"+
"\t\t"+"-i , --allowMissing"+"\t\t\t"+"Allow one base in one key to be missing or wrong. (default "+boolStringify(allowMissing)+")"+"\n"+
"\t\t"+"-t , --trimCutoff"+"\t\t\t"+"Lowest number of adapter bases to be observed for single Read trimming (default "+stringify(trimCutoff)+")");
if( (argc== 1) ||
(argc== 2 && string(argv[1]) == "-h") ||
(argc== 2 && string(argv[1]) == "-help") ||
(argc== 2 && string(argv[1]) == "--help") ){
cout<<"Usage:"<<endl;
cout<<""<<endl;
cout<<usage<<endl;
return 1;
}
for(int i=1;i<(argc-1);i++){ //all but the last arg
if(strcmp(argv[i],"-fq1") == 0 ){
fastqfile1=string(argv[i+1]);
fastqFormat=true;
i++;
continue;
}
if(strcmp(argv[i],"-fq2") == 0 ){
fastqfile2=string(argv[i+1]);
fastqFormat=true;
singleEndModeFQ=false;
i++;
continue;
}
if(strcmp(argv[i],"-fqo") == 0 ){
fastqoutfile=string(argv[i+1]);
fastqFormat=true;
i++;
continue;
}
if(strcmp(argv[i],"--log") == 0 ){
logFileName =string(argv[i+1]);
printLog=true;
i++;
continue;
}
if(strcmp(argv[i],"-p") == 0 || strcmp(argv[i],"--PIPE") == 0 ){
cerr<<"This version no longer works with pipe, exiting"<<endl;
return 1;
}
if(strcmp(argv[i],"-u") == 0 ){
produceUnCompressedBAM=true;
continue;
}
if(strcmp(argv[i],"--aligned") == 0 ){
allowAligned=true;
continue;
}
if(strcmp(argv[i],"-o") == 0 || strcmp(argv[i],"--outfile") == 0 ){
bamFileOUT =string(argv[i+1]);
i++;
continue;
}
if(strcmp(argv[i],"-v") == 0 || strcmp(argv[i],"--verbose") == 0 ){
verbose=true;
continue;
}
if(strcmp(argv[i],"--ancientdna") == 0 ){
ancientDNA=true;
continue;
}
if(strcmp(argv[i],"--keepOrig") == 0 ){
keepOrig=true;
continue;
}
if(strcmp(argv[i],"--loc") == 0 ){
location =destringify<double>(argv[i+1]);
i++;
continue;
}
if(strcmp(argv[i],"--scale") == 0 ){
scale =destringify<double>(argv[i+1]);
i++;
continue;
}
if(strcmp(argv[i],"-f") == 0 || strcmp(argv[i],"--adapterFirstRead") == 0 ){
adapter_F =string(argv[i+1]);
i++;
continue;
}
if(strcmp(argv[i],"-s") == 0 || strcmp(argv[i],"--adapterSecondRead") == 0 ){
adapter_S =string(argv[i+1]);
i++;
continue;
}
if(strcmp(argv[i],"-c") == 0 || strcmp(argv[i],"--FirstReadChimeraFilter") == 0 ){
adapter_chimera =string(argv[i+1]);
i++;
continue;
}
if(strcmp(argv[i],"-k") == 0 || strcmp(argv[i],"--keys") == 0 ){
key =string(argv[i+1]);
i++;
continue;
}
if(strcmp(argv[i],"-i") == 0 || strcmp(argv[i],"--allowMissing") == 0 ){
allowMissing=true;
continue;
}
if(strcmp(argv[i],"-t") == 0 || strcmp(argv[i],"--trimCutoff") == 0 ){
trimCutoff=atoi(argv[i+1]);
i++;
continue;
}
cerr<<"Unknown option "<<argv[i] <<" exiting"<<endl;
return 1;
}
bamFile=argv[argc-1];
if( (location != -1.0 && scale == -1.0) ||
(location == -1.0 && scale != -1.0) ){
cerr<<"Cannot specify --location without specifying --scale"<<endl;
return 1;
}
if( (location != -1.0 && scale != -1.0) ){
useDist=true;
if(ancientDNA){
cerr<<"Cannot specify --location/--scale and --ancientDNA"<<endl;
return 1;
}
}
MergeTrimReads mtr (adapter_F,adapter_S,adapter_chimera,
key1,key2,
trimCutoff,allowMissing,ancientDNA,location,scale,useDist);
fqwriters onereadgroup;
if(fastqFormat){
if( bamFileOUT != "" || produceUnCompressedBAM || allowAligned){
cerr<<"ERROR : Cannot specify options like -o, -u or --allowAligned for fastq"<<endl;
return 1;
}
if(fastqfile1 == ""){
cerr<<"ERROR : Must specify as least the first file for fastq"<<endl;
return 1;
}
FastQParser * fqp1;
FastQParser * fqp2;
if(singleEndModeFQ){
fqp1 = new FastQParser (fastqfile1);
string outdirs = fastqoutfile+".fq.gz";
string outdirsf = fastqoutfile+".fail.fq.gz";
onereadgroup.single.open(outdirs.c_str(), ios::out);
onereadgroup.singlef.open(outdirsf.c_str(), ios::out);
if(!onereadgroup.single.good()){ cerr<<"Cannot write to file "<<outdirs<<endl; return 1; }
if(!onereadgroup.singlef.good()){ cerr<<"Cannot write to file "<<outdirsf<<endl; return 1; }
}else{
fqp1 = new FastQParser (fastqfile1);
fqp2 = new FastQParser (fastqfile2);
string outdirs = fastqoutfile+".fq.gz";
string outdir1 = fastqoutfile+"_r1.fq.gz";
string outdir2 = fastqoutfile+"_r2.fq.gz";
string outdirsf = fastqoutfile+".fail.fq.gz";
string outdir1f = fastqoutfile+"_r1.fail.fq.gz";
string outdir2f = fastqoutfile+"_r2.fail.fq.gz";
onereadgroup.single.open(outdirs.c_str(), ios::out);
onereadgroup.pairr1.open(outdir1.c_str(), ios::out);
onereadgroup.pairr2.open(outdir2.c_str(), ios::out);
onereadgroup.singlef.open(outdirsf.c_str(), ios::out);
onereadgroup.pairr1f.open(outdir1f.c_str(), ios::out);
onereadgroup.pairr2f.open(outdir2f.c_str(), ios::out);
if(!onereadgroup.single.good()){ cerr<<"Cannot write to file "<<outdirs<<endl; return 1; }
if(!onereadgroup.pairr1.good()){ cerr<<"Cannot write to file "<<outdir1<<endl; return 1; }
if(!onereadgroup.pairr2.good()){ cerr<<"Cannot write to file "<<outdir2<<endl; return 1; }
if(!onereadgroup.singlef.good()){ cerr<<"Cannot write to file "<<outdirsf<<endl; return 1; }
if(!onereadgroup.pairr1f.good()){ cerr<<"Cannot write to file "<<outdir1f<<endl; return 1; }
if(!onereadgroup.pairr2f.good()){ cerr<<"Cannot write to file "<<outdir2f<<endl; return 1; }
}
unsigned int totalSeqs=0;
while(fqp1->hasData()){
FastQObj * fo1=fqp1->getData();
vector<string> def1=allTokens( *(fo1->getID()), ' ' );
string def1s=def1[0];
FastQObj * fo2;
string def2s;
string ext2s;
if(!singleEndModeFQ){
if(!fqp2->hasData()){
cerr << "ERROR: Discrepency between fastq files at record " << *(fo1->getID()) <<endl;
return 1;
}
fo2=fqp2->getData();
vector<string> def2=allTokens( *(fo2->getID()), ' ' );
def2s=def2[0];
if(strEndsWith(def1s,"/1")){
def1s=def1s.substr(0,def1s.size()-2);
}
if(strEndsWith(def2s,"/2")){
def2s=def2s.substr(0,def2s.size()-2);
}
if(strBeginsWith(def1s,"@")){
def1s=def1s.substr(1,def1s.size()-1);
}
if(strBeginsWith(def2s,"@")){
def2s=def2s.substr(1,def2s.size()-1);
}
if(def1s != def2s){
cerr << "ERROR: Discrepency between fastq files, different names " << *(fo1->getID()) <<" and "<< *(fo2->getID()) <<endl;
return 1;
}
merged result= mtr.process_PE(*(fo1->getSeq()),*(fo1->getQual()),
*(fo2->getSeq()),*(fo2->getQual()));
mtr.incrementCountall();
if(result.code != ' '){ //keys or chimeras
if(result.code == 'K'){
mtr.incrementCountfkey();
}else{
if(result.code == 'D'){
mtr.incrementCountchimera();
}else{
cerr << "leehom: Wrong return code =\""<<result.code<<"\""<<endl;
exit(1);
}
}
onereadgroup.pairr2f<<"@"<<def2s<<"/2" <<endl <<*(fo2->getSeq())<<endl<<"+"<<endl <<*(fo2->getQual())<<endl;
onereadgroup.pairr1f<<"@"<<def1s<<"/1" <<endl <<*(fo1->getSeq())<<endl<<"+"<<endl <<*(fo1->getQual())<<endl;
continue;
}else{
if(result.sequence != ""){ //new sequence
onereadgroup.single<<"@"<<def1s<<"" <<endl << result.sequence<<endl<<"+"<<endl <<result.quality<<endl;
if( result.sequence.length() > max(fo1->getSeq()->length(),fo2->getSeq()->length()) ){
mtr.incrementCountmergedoverlap();
}else{
mtr.incrementCountmerged();
}
}else{ //keep as is
mtr.incrementCountnothing();
onereadgroup.pairr2<<"@"<<def2s<<"/2" <<endl <<*(fo2->getSeq())<<endl<<"+"<<endl <<*(fo2->getQual())<<endl;
onereadgroup.pairr1<<"@"<<def1s<<"/1" <<endl <<*(fo1->getSeq())<<endl<<"+"<<endl <<*(fo1->getQual())<<endl;
}
}
}else{
merged result=mtr.process_SR(*(fo1->getSeq()),*(fo1->getQual()));
mtr.incrementCountall();
if(result.code != ' '){ //either chimera or missing key
if(result.code == 'K'){
mtr.incrementCountfkey();
}else{
if(result.code == 'D'){
mtr.incrementCountchimera();
}else{
cerr << "leehom: Wrong return code =\""<<result.code<<"\""<<endl;
exit(1);
}
}
onereadgroup.singlef<<""<<*(fo1->getID())<<"" <<endl << *(fo1->getSeq())<<endl<<"+"<<endl <<*(fo1->getQual())<<endl;
continue;
}
if(result.sequence != ""){ //new sequence
mtr.incrementCounttrimmed();
onereadgroup.single<<""<<*(fo1->getID())<<"" <<endl << result.sequence<<endl<<"+"<<endl <<result.quality<<endl;
}else{
mtr.incrementCountnothing();
onereadgroup.single<<""<<*(fo1->getID())<<"" <<endl << *(fo1->getSeq())<<endl<<"+"<<endl <<*(fo1->getQual())<<endl;
}
}
totalSeqs++;
}
delete fqp1;
if(!singleEndModeFQ){
delete fqp2;
}
if(singleEndModeFQ){
onereadgroup.single.close();
onereadgroup.singlef.close();
}else{
onereadgroup.single.close();
onereadgroup.pairr1.close();
onereadgroup.pairr2.close();
onereadgroup.singlef.close();
onereadgroup.pairr1f.close();
onereadgroup.pairr2f.close();
}
//fastq
}else{
//else BAM
// initMerge();
// set_adapter_sequences(adapter_F,
// adapter_S,
// adapter_chimera);
// set_options(trimCutoff,allowMissing,mergeoverlap);
if(key != ""){
size_t found=key.find(",");
if (found == string::npos){ //single end reads
key1=key;
key2="";
} else{ //paired-end
key1=key.substr(0,found);
key2=key.substr(found+1,key.length()-found+1);
}
}
if( bamFileOUT == "" ){
cerr<<"The output must be a be specified, exiting"<<endl;
return 1;
}
if ( !reader.Open(bamFile) ) {
cerr << "Could not open input BAM file "<<bamFile << endl;
return 1;
}
SamHeader header = reader.GetHeader();
string pID = "mergeTrimReadsBAM";
string pName = "mergeTrimReadsBAM";
string pCommandLine = "";
for(int i=0;i<(argc);i++){
pCommandLine += (string(argv[i])+" ");
}
putProgramInHeader(&header,pID,pName,pCommandLine,returnGitHubVersion(string(argv[0]),".."));
const RefVector references = reader.GetReferenceData();
//we will not call bgzip with full compression, good for piping into another program to
//lessen the load on the CPU
if(produceUnCompressedBAM)
writer.SetCompressionMode(BamWriter::Uncompressed);
if ( !writer.Open(bamFileOUT,header,references) ) {
cerr << "Could not open output BAM file "<<bamFileOUT << endl;
return 1;
}
SamHeader sh=reader.GetHeader();
//Up to the user to be sure that a sequence is followed by his mate
// if(!sh.HasSortOrder() ||
// sh.SortOrder != "queryname"){
// cerr << "Bamfile must be sorted by queryname" << endl;
// return 1;
// }
BamAlignment al;
BamAlignment al2;
bool al2Null=true;
while ( reader.GetNextAlignment(al) ) {
if(al.IsMapped() || al.HasTag("NM") || al.HasTag("MD") ){
if(!allowAligned){
cerr << "Reads should not be aligned" << endl;
return 1;
}else{
//should we remove tags ?
}
}
if(al.IsPaired() &&
al2Null ){
al2=al;
al2Null=false;
continue;
}else{
if(al.IsPaired() &&
!al2Null){
bool result = mtr.processPair(al,al2);
if( result ){//was merged
BamAlignment orig;
BamAlignment orig2;
if(keepOrig){
orig2 = al2;
orig = al;
}
writer.SaveAlignment(al);
if(keepOrig){
orig.SetIsDuplicate(true);
orig2.SetIsDuplicate(true);
writer.SaveAlignment(orig2);
writer.SaveAlignment(orig);
}
//the second record is empty
}else{
//keep the sequences as pairs
writer.SaveAlignment(al2);
writer.SaveAlignment(al);
}
//
// SINGLE END
//
}else{
BamAlignment orig;
if(keepOrig){
orig =al;
}
mtr.processSingle(al);
if(keepOrig){
//write duplicate
if(orig.QueryBases.length() != al.QueryBases.length()){
orig.SetIsDuplicate(true);
writer.SaveAlignment(orig);
}
}
writer.SaveAlignment(al);
} //end single end
al2Null=true;
}//second pair
} //while al
reader.Close();
writer.Close();
} //else BAM
cerr <<mtr.reportSingleLine()<<endl;
if(printLog){
ofstream fileLog;
fileLog.open(logFileName.c_str());
if (fileLog.is_open()){
fileLog <<mtr.reportMultipleLines() <<endl;
}else{
cerr << "Unable to print to file "<<logFileName<<endl;
}
fileLog.close();
}
return 0;
}
int main (int argc, char *argv[]) {
string usage=string(""+string(argv[0])+" [in BAM file]"+
"\nThis program reads a BAM file and computes the error rate for each cycle\n"+
// "\nreads and the puts the rest into another bam file.\n"+
// "\nTip: if you do not need one of them, use /dev/null as your output\n"+
// "arguments:\n"+
// "\t"+"--bq [base qual] : Minimum base quality to flag a deaminated site (Default: "+stringify(minBaseQuality)+")\n"+
"\n");
if(argc == 1 ||
(argc == 2 && (string(argv[0]) == "-h" || string(argv[0]) == "--help") )
){
cerr << "Usage "<<usage<<endl;
return 1;
}
// for(int i=1;i<(argc-2);i++){
// if(string(argv[i]) == "--bq"){
// minBaseQuality=destringify<int>(argv[i+1]);
// i++;
// continue;
// }
// }
string bamfiletopen = string( argv[ argc-1 ] );
// string deambam = string( argv[ argc-2 ] );
// string nondeambam = string( argv[ argc-1 ] );
BamReader reader;
if ( !reader.Open(bamfiletopen) ) {
cerr << "Could not open input BAM file"<< bamfiletopen << endl;
return 1;
}
//iterating over the alignments for these regions
BamAlignment al;
bool pairedEnd=false;
bool firstRead=true;
while ( reader.GetNextAlignment(al) ) {
if(firstRead){ //reads are either all paired end or single end, I don't allow a mix
numberOfCycles=al.QueryBases.size();
// cout<<"numberOfCycles "<<numberOfCycles<<endl;
if(al.IsPaired() ){
pairedEnd=true;
matches = vector<unsigned int> (2*numberOfCycles,0);
mismatches = vector<unsigned int> (2*numberOfCycles,0);
typesOfMismatches = vector< vector<unsigned int> >();
for(int i=0;i<12;i++)
typesOfMismatches.push_back( vector<unsigned int> (2*numberOfCycles,0) );
}else{
matches = vector<unsigned int> ( numberOfCycles,0);
mismatches = vector<unsigned int> ( numberOfCycles,0);
typesOfMismatches = vector< vector<unsigned int> >();
for(int i=0;i<12;i++)
typesOfMismatches.push_back( vector<unsigned int> ( numberOfCycles,0) );
}
firstRead=false;
}
if( ( pairedEnd && !al.IsPaired()) ||
( !pairedEnd && al.IsPaired()) ){
cerr<<"Read "<<al.Name<<" is wrong, cannot have a mixture of paired and unpaired read for this program"<<endl;
return 1;
}
//skip unmapped
if(!al.IsMapped())
continue;
if(numberOfCycles!=int(al.QueryBases.size())){
cerr<<"The length of read "<<al.Name<<" is wrong, should be "<<numberOfCycles<<"bp"<<endl;
return 1;
}
string reconstructedReference = reconstructRef(&al);
if(al.Qualities.size() != reconstructedReference.size()){
cerr<<"Quality line is not the same size as the reconstructed reference"<<endl;
return 1;
}
if( pairedEnd ){
if( al.IsFirstMate() ){ //start cycle 0
if( al.IsReverseStrand() ){
increaseCounters(al,reconstructedReference,numberOfCycles-1,-1); //start cycle numberOfCycles-1
}else{
increaseCounters(al,reconstructedReference,0 , 1); //start cycle 0
}
}else{
if( al.IsSecondMate() ){
if( al.IsReverseStrand() ){
increaseCounters(al,reconstructedReference,2*numberOfCycles-1,-1); //start cycle 2*numberOfCycles-1
}else{
increaseCounters(al,reconstructedReference,numberOfCycles , 1); //start cycle numberOfCycles
}
}else{
cerr<<"Reads "<<al.Name<<" must be either first or second mate"<<endl;
return 1;
}
}
}else{ //single end
if( al.IsReverseStrand() ){
increaseCounters(al,reconstructedReference,numberOfCycles-1,-1); //start cycle numberOfCycles-1
}else{
increaseCounters(al,reconstructedReference,0 , 1); //start cycle 0
}
}
}//end while each read
reader.Close();
cout<<"cycle\tmatches\tmismatches\tmismatches%\tA>C\tA>C%\tA>G\tA>G%\tA>T\tA>T%\tC>A\tC>A%\tC>G\tC>G%\tC>T\tC>T%\tG>A\tG>A%\tG>C\tG>C%\tG>T\tG>T%\tT>A\tT>A%\tT>C\tT>C%\tT>G\tT>G%"<<endl;
for(unsigned int i=0;i<matches.size();i++){
cout<<(i+1);
if( (matches[i]+mismatches[i]!=0) )
cout<<"\t"<<matches[i]<<"\t"<<mismatches[i]<<"\t"<< 100.0*(double(mismatches[i])/double(matches[i]+mismatches[i])) ;
else
cout<<"\t"<<matches[i]<<"\t"<<mismatches[i]<<"\tNA";
for(int j=0;j<12;j++){
cout<<"\t"<<typesOfMismatches[j][i];
if( (matches[i]+mismatches[i]!=0) )
cout<<"\t"<<100.0*double(typesOfMismatches[j][i])/double(matches[i]+mismatches[i]);
else
cout<<"\tNA";
}
cout<<endl;
}
return 0;
}
virtual void main()
{
//init
QTextStream out(stdout);
BamReader reader;
NGSHelper::openBAM(reader, getInfile("in"));
FastqOutfileStream out1(getOutfile("out1"), false);
FastqOutfileStream out2(getOutfile("out2"), false);
long long c_unpaired = 0;
long long c_paired = 0;
int max_cached = 0;
//iterate through reads
BamAlignment al;
QHash<QByteArray, BamAlignment> al_cache;
while (reader.GetNextAlignment(al))
{
//skip secondary alinments
if(!al.IsPrimaryAlignment()) continue;
//skip unpaired
if(!al.IsPaired())
{
++c_unpaired;
continue;
}
QByteArray name(al.Name.data()); //TODO use QByteArray::fromStdString (when upgraded to Qt5.4)
//store cached read when we encounter the mate
if (al_cache.contains(name))
{
BamAlignment mate = al_cache.take(name);
//out << name << " [AL] First: " << al.IsFirstMate() << " Reverse: " << al.IsReverseStrand() << " Seq: " << al.QueryBases.data() << endl;
//out << name << " [MA] First: " << mate.IsFirstMate() << " Reverse: " << mate.IsReverseStrand() << " Seq: " << mate.QueryBases.data() << endl;
if (al.IsFirstMate())
{
write(out1, al, al.IsReverseStrand());
write(out2, mate, mate.IsReverseStrand());
}
else
{
write(out1, mate, mate.IsReverseStrand());
write(out2, al, al.IsReverseStrand());
}
++c_paired;
}
//cache read for later retrieval
else
{
al_cache.insert(name, al);
}
max_cached = std::max(max_cached, al_cache.size());
}
reader.Close();
out1.close();
out2.close();
//write debug output
out << "Pair reads (written) : " << c_paired << endl;
out << "Unpaired reads (skipped) : " << c_unpaired << endl;
out << "Unmatched paired reads (skipped): " << al_cache.size() << endl;
out << endl;
out << "Maximum cached reads : " << max_cached << endl;
}
void BedGenomeCoverage::CoverageBam(string bamFile) {
ResetChromCoverage();
// open the BAM file
BamReader reader;
if (!reader.Open(bamFile)) {
cerr << "Failed to open BAM file " << bamFile << endl;
exit(1);
}
// get header & reference information
string header = reader.GetHeaderText();
RefVector refs = reader.GetReferenceData();
// load the BAM header references into a BEDTools "genome file"
_genome = new GenomeFile(refs);
// convert each aligned BAM entry to BED
// and compute coverage on B
BamAlignment bam;
while (reader.GetNextAlignment(bam)) {
// skip if the read is unaligned
if (bam.IsMapped() == false)
continue;
bool _isReverseStrand = bam.IsReverseStrand();
//changing second mate's strand to opposite
if( _dUTP && bam.IsPaired() && bam.IsMateMapped() && bam.IsSecondMate())
_isReverseStrand = !bam.IsReverseStrand();
// skip if we care about strands and the strand isn't what
// the user wanted
if ( (_filterByStrand == true) &&
((_requestedStrand == "-") != _isReverseStrand) )
continue;
// extract the chrom, start and end from the BAM alignment
string chrom(refs.at(bam.RefID).RefName);
CHRPOS start = bam.Position;
CHRPOS end = bam.GetEndPosition(false, false) - 1;
// are we on a new chromosome?
if ( chrom != _currChromName )
StartNewChrom(chrom);
if(_pair_chip_) {
// Skip if not a proper pair
if (bam.IsPaired() && (!bam.IsProperPair() or !bam.IsMateMapped()) )
continue;
// Skip if wrong coordinates
if( ( (bam.Position<bam.MatePosition) && bam.IsReverseStrand() ) ||
( (bam.MatePosition < bam.Position) && bam.IsMateReverseStrand() ) ) {
//chemically designed: left on positive strand, right on reverse one
continue;
}
/*if(_haveSize) {
if (bam.IsFirstMate() && bam.IsReverseStrand()) { //put fragmentSize in to the middle of pair end_fragment
int mid = bam.MatePosition+abs(bam.InsertSize)/2;
if(mid<_fragmentSize/2)
AddCoverage(0, mid+_fragmentSize/2);
else
AddCoverage(mid-_fragmentSize/2, mid+_fragmentSize/2);
}
else if (bam.IsFirstMate() && bam.IsMateReverseStrand()) { //put fragmentSize in to the middle of pair end_fragment
int mid = start+abs(bam.InsertSize)/2;
if(mid<_fragmentSize/2)
AddCoverage(0, mid+_fragmentSize/2);
else
AddCoverage(mid-_fragmentSize/2, mid+_fragmentSize/2);
}
} else */
if (bam.IsFirstMate() && bam.IsReverseStrand()) { //prolong to the mate to the left
AddCoverage(bam.MatePosition, end);
}
else if (bam.IsFirstMate() && bam.IsMateReverseStrand()) { //prolong to the mate to the right
AddCoverage(start, start + abs(bam.InsertSize) - 1);
}
} else if (_haveSize) {
if(bam.IsReverseStrand()) {
if(end<_fragmentSize) { //sometimes fragmentSize is bigger :(
AddCoverage(0, end);
} else {
AddCoverage(end + 1 - _fragmentSize, end );
}
} else {
AddCoverage(start,start+_fragmentSize - 1);
}
} else
// add coverage accordingly.
if (!_only_5p_end && !_only_3p_end) {
bedVector bedBlocks;
// we always want to split blocks when a D CIGAR op is found.
// if the user invokes -split, we want to also split on N ops.
if (_obeySplits) { // "D" true, "N" true
GetBamBlocks(bam, refs.at(bam.RefID).RefName, bedBlocks, true, true);
}
else { // "D" true, "N" false
GetBamBlocks(bam, refs.at(bam.RefID).RefName, bedBlocks, true, false);
}
AddBlockedCoverage(bedBlocks);
}
else if (_only_5p_end) {
CHRPOS pos = ( !bam.IsReverseStrand() ) ? start : end;
AddCoverage(pos,pos);
}
else if (_only_3p_end) {
CHRPOS pos = ( bam.IsReverseStrand() ) ? start : end;
AddCoverage(pos,pos);
}
}
// close the BAM
reader.Close();
// process the results of the last chromosome.
ReportChromCoverage(_currChromCoverage, _currChromSize,
_currChromName, _currChromDepthHist);
// report all empty chromsomes
PrintEmptyChromosomes();
// report the overall coverage if asked.
PrintFinalCoverage();
}
int main (int argc, char *argv[]) {
// bool mapped =false;
// bool unmapped=false;
int bpToDecrease5=1;
int bpToDecrease3=2;
const string usage=string(string(argv[0])+" [options] input.bam out.bam"+"\n\n"+
"\tThis program takes a BAM file as input and produces\n"+
"\tanother where the putative deaminated bases have\n"+
"\ta base quality score of "+intStringify(baseQualForDeam)+"\n"+
"\tgiven an "+intStringify(offset)+" offset \n"+
"\n"+
"\tOptions:\n"+
"\t\t"+"-n5" +"\t\t\t"+"Decrease the nth bases surrounding the 5' ends (Default:"+stringify(bpToDecrease5)+") "+"\n"+
"\t\t"+"-n3" +"\t\t\t"+"Decrease the nth bases surrounding the 3' ends (Default:"+stringify(bpToDecrease3)+") "+"\n"
);
// "\t"+"-u , --unmapped" +"\n\t\t"+"For an unmapped bam file"+"\n"+
// "\t"+"-m , --mapped" +"\n\t\t"+"For an mapped bam file"+"\n");
if( (argc== 1) ||
(argc== 2 && string(argv[1]) == "-h") ||
(argc== 2 && string(argv[1]) == "-help") ||
(argc== 2 && string(argv[1]) == "--help") ){
cout<<"Usage:"<<endl;
cout<<usage<<endl;
cout<<""<<endl;
return 1;
}
for(int i=1;i<(argc-2);i++){ //all but the last arg
if( string(argv[i]) == "-n5" ){
bpToDecrease5 = destringify<int>(argv[i+1]);
i++;
continue;
}
if( string(argv[i]) == "-n3" ){
bpToDecrease3 = destringify<int>(argv[i+1]);
i++;
continue;
}
cerr<<"Unknown option "<<argv[i] <<" exiting"<<endl;
return 1;
}
if(argc < 3){
cerr<<"Error: Must specify the input and output BAM files";
return 1;
}
string inbamFile =argv[argc-2];
string outbamFile=argv[argc-1];
if(inbamFile == outbamFile){
cerr<<"Input and output files are the same"<<endl;
return 1;
}
// if(!mapped && !unmapped){
// cerr << "Please specify whether you reads are mapped or unmapped" << endl;
// return 1;
// }
// if(mapped && unmapped){
// cerr << "Please specify either mapped or unmapped but not both" << endl;
// return 1;
// }
BamReader reader;
if ( !reader.Open(inbamFile) ) {
cerr << "Could not open input BAM files." << endl;
return 1;
}
vector<RefData> testRefData=reader.GetReferenceData();
SamHeader header = reader.GetHeader();
string pID = "decrQualDeaminated";
string pName = "decrQualDeaminated";
string pCommandLine = "";
for(int i=0;i<(argc);i++){
pCommandLine += (string(argv[i])+" ");
}
putProgramInHeader(&header,pID,pName,pCommandLine);
const RefVector references = reader.GetReferenceData();
BamWriter writer;
if ( !writer.Open(outbamFile, header, references) ) {
cerr << "Could not open output BAM file" << endl;
return 1;
}
BamAlignment al;
// BamAlignment al2;
// bool al2Null=true;
while ( reader.GetNextAlignment(al) ) {
if(al.IsPaired() ){
if(al.IsFirstMate() ){ //5' end, need to check first base only
if(al.IsReverseStrand()){ //
if(!al.IsMapped()){
cerr << "Cannot have reverse complemented unmapped reads :" <<al.Name<< endl;
//return 1;
}
int indexToCheck;
//5' of first mate reversed
indexToCheck=al.QueryBases.length()-1;
for(int i=0;i<bpToDecrease5;i++){
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
}
indexToCheck=max(indexToCheck-1,0);
}
}else{
int indexToCheck;
//5' of first mate
indexToCheck=0;
for(int i=0;i<bpToDecrease5;i++){ //first base
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
}
indexToCheck=min(indexToCheck+1,int(al.Qualities.size()));
}
}
}else{ //3' end, need to check last two bases only
if( al.IsSecondMate() ){
if(al.IsReverseStrand()){ //
if(!al.IsMapped()){
cerr << "Cannot have reverse complemented unmapped reads :" <<al.Name<< endl;
//return 1;
}
int indexToCheck;
//3' of second mate reversed
indexToCheck=al.QueryBases.length()-1;
for(int i=0;i<bpToDecrease3;i++){
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
}
indexToCheck=max(indexToCheck-1,0);
}
}else{
int indexToCheck;
//3' of second mate forward
indexToCheck=0;
for(int i=0;i<bpToDecrease3;i++){ //first base
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
}
indexToCheck=min(indexToCheck+1,int(al.Qualities.size()));
}
}
}else{
cerr << "Wrong state" << endl;
return 1;
}
}
}//end of paired end
else{//we consider single reads to have been sequenced from 5' to 3'
if(al.IsReverseStrand()){ //need to consider
if(!al.IsMapped()){
cerr << "Cannot have reverse complemented unmapped reads :" <<al.Name<< endl;
//return 1;
}
int indexToCheck;
//5' of single read reversed
indexToCheck=al.QueryBases.length()-1;
for(int i=0;i<bpToDecrease5;i++){
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
}
indexToCheck=max(indexToCheck-1,0);
}
//3' of single read reversed
indexToCheck=0;
for(int i=0;i<bpToDecrease3;i++){ //first base
if(toupper(al.QueryBases[indexToCheck]) == 'A'){
al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
}
indexToCheck=min(indexToCheck+1,int(al.Qualities.size()));
}
}else{
int indexToCheck;
//5' of single read
indexToCheck=0;
for(int i=0;i<bpToDecrease5;i++){ //first base
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
}
indexToCheck=min(indexToCheck+1,int(al.Qualities.size()));
}
//3' of single read
indexToCheck=al.QueryBases.length()-1;
for(int i=0;i<bpToDecrease3;i++){
if(toupper(al.QueryBases[indexToCheck]) == 'T'){
al.Qualities[indexToCheck]=char(offset+baseQualForDeam);
}
indexToCheck=max(indexToCheck-1,0);
}
}
}//end of single end
writer.SaveAlignment(al);
}// while ( reader.GetNextAlignment(al) ) {
reader.Close();
writer.Close();
cerr<<"Program terminated gracefully"<<endl;
return 0;
}
int main (int argc, char *argv[]) {
if(argc != 4){
cerr<<"This program strips the mapping information and cuts sequences"<<endl;
cerr<<"Usage "<<argv[0]<<" [bam file in] [bam file out] [distribution]"<<endl;
cerr<<"The distribution is one per line"<<endl;
return 1;
}
string bamfiletopen = string(argv[1]);
string bamfiletwrite = string(argv[2]);
string fileDist = string(argv[3]);
igzstream myFile;
string line;
vector<int> distToUse;
myFile.open(fileDist.c_str(), ios::in);
if (myFile.good()){
while ( getline (myFile,line)){
distToUse.push_back( destringify<int>(line) );
}
myFile.close();
}else{
cerr << "Unable to open file "<<fileDist<<endl;
return 1;
}
cerr<<"Read "<<distToUse.size()<<" data points "<<endl;
cerr<<"Reading "<<bamfiletopen<<" writing to "<<bamfiletwrite<<endl;
BamReader reader;
BamWriter writer;
if ( !reader.Open(bamfiletopen) ) {
cerr << "Could not open input BAM files." << endl;
return 1;
}
SamHeader myHeader=reader.GetHeader();
SamProgram sp;
string pID = "removeTagsMapping";
string pName = "removeTagsMapping";
string pCommandLine = "";
for(int i=0;i<(argc);i++){
pCommandLine += (string(argv[i])+" ");
}
putProgramInHeader(&myHeader,pID,pName,pCommandLine,returnGitHubVersion(string(argv[0]),"."));
//no @SQ
myHeader.Sequences.Clear();
vector< RefData > emptyRefVector;
if( !writer.Open(bamfiletwrite,myHeader,emptyRefVector ) ) {
cerr << "Could not open output BAM file "<<bamfiletwrite << endl;
return 1;
}
unsigned int readsTotal=0;
BamAlignment al;
while ( reader.GetNextAlignment(al) ) {
//deleting tag data
al.TagData="";
//reset the flag
// if(al.IsPaired()){
// if(al.IsFirstMate()){
// al.AlignmentFlag = flagFirstPair;
// }else{
// al.AlignmentFlag = flagSecondPair;
// }
// }else{
// }
if(al.IsPaired()){
if(al.IsFirstMate()){
al.Name = al.Name+"/1";
}else{
al.Name = al.Name+"/2";
}
}
al.AlignmentFlag = flagSingleReads;
//no ref or positon
al.RefID=-1;
al.MateRefID=-1;
al.Position=-1;
al.MatePosition=-1;
//no insert size
al.InsertSize=0;
//no cigar
al.CigarData.clear();
//no mapping quality
al.MapQuality=0;
int length = distToUse[ randomInt(0,distToUse.size()-1) ];
length = MIN( length, al.Length);
al.QueryBases = al.QueryBases.substr(0,length);
al.Qualities = al.Qualities.substr( 0,length);
writer.SaveAlignment(al);
readsTotal++;
}
reader.Close();
writer.Close();
cerr<<"Program "<<argv[0]<<" terminated gracefully, looked at "<<readsTotal<<endl;
return 0;
}
