bool ConvertTool::ConvertToolPrivate::Run(void) {
// ------------------------------------
// initialize conversion input/output
// set to default input if none provided
if ( !m_settings->HasInput )
m_settings->InputFiles.push_back(Options::StandardIn());
// open input files
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
cerr << "bamtools convert ERROR: could not open input BAM file(s)... Aborting." << endl;
return false;
}
// if input is not stdin & a region is provided, look for index files
if ( m_settings->HasInput && m_settings->HasRegion ) {
if ( !reader.LocateIndexes() ) {
cerr << "bamtools convert ERROR: could not locate index file(s)... Aborting." << endl;
return false;
}
}
// retrieve reference data
m_references = reader.GetReferenceData();
// set region if specified
BamRegion region;
if ( m_settings->HasRegion ) {
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
if ( reader.HasIndexes() ) {
if ( !reader.SetRegion(region) ) {
cerr << "bamtools convert ERROR: set region failed. Check that REGION describes a valid range" << endl;
reader.Close();
return false;
}
}
} else {
cerr << "bamtools convert 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();
return false;
}
}
// if output file given
ofstream outFile;
if ( m_settings->HasOutput ) {
// open output file stream
outFile.open(m_settings->OutputFilename.c_str());
if ( !outFile ) {
cerr << "bamtools convert ERROR: could not open " << m_settings->OutputFilename
<< " for output" << endl;
return false;
}
// set m_out to file's streambuf
m_out.rdbuf(outFile.rdbuf());
}
// -------------------------------------
// do conversion based on format
bool convertedOk = true;
// pileup is special case
// conversion not done per alignment, like the other formats
if ( m_settings->Format == FORMAT_PILEUP )
convertedOk = RunPileupConversion(&reader);
// all other formats
else {
bool formatError = false;
// set function pointer to proper conversion method
void (BamTools::ConvertTool::ConvertToolPrivate::*pFunction)(const BamAlignment&) = 0;
if ( m_settings->Format == FORMAT_BED ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintBed;
else if ( m_settings->Format == FORMAT_FASTA ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintFasta;
else if ( m_settings->Format == FORMAT_FASTQ ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintFastq;
else if ( m_settings->Format == FORMAT_JSON ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintJson;
else if ( m_settings->Format == FORMAT_SAM ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintSam;
else if ( m_settings->Format == FORMAT_YAML ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintYaml;
else {
cerr << "bamtools convert ERROR: unrecognized format: " << m_settings->Format << endl;
cerr << "Please see documentation for list of supported formats " << endl;
formatError = true;
convertedOk = false;
}
// if format selected ok
if ( !formatError ) {
// if SAM format & not omitting header, print SAM header first
if ( (m_settings->Format == FORMAT_SAM) && !m_settings->IsOmittingSamHeader )
m_out << reader.GetHeaderText();
// iterate through file, doing conversion
BamAlignment a;
while ( reader.GetNextAlignment(a) )
(this->*pFunction)(a);
// set flag for successful conversion
convertedOk = true;
}
}
// ------------------------
// clean up & exit
reader.Close();
if ( m_settings->HasOutput )
outFile.close();
return convertedOk;
}
int CountTool::Run(int argc, char* argv[]) {
// parse command line arguments
Options::Parse(argc, argv, 1);
// if no '-in' args supplied, default to stdin
if ( !m_settings->HasInput )
m_settings->InputFiles.push_back(Options::StandardIn());
// open reader without index
BamMultiReader reader;
if (!reader.Open(m_settings->InputFiles, false, true)) {
cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
return 1;
}
// alignment counter
BamAlignment al;
int alignmentCount(0);
// if no region specified, count entire file
if ( !m_settings->HasRegion ) {
while ( reader.GetNextAlignmentCore(al) )
++alignmentCount;
}
// otherwise attempt to use region as constraint
else {
// if region string parses OK
BamRegion region;
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
// attempt to re-open reader with index files
reader.Close();
bool openedOK = reader.Open(m_settings->InputFiles, true, true );
// if error
if ( !openedOK ) {
cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
return 1;
}
// if index data available, we can use SetRegion
if ( reader.IsIndexLoaded() ) {
// attempt to use SetRegion(), if failed report error
if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
reader.Close();
return 1;
}
// everything checks out, just iterate through specified region, counting alignments
while ( reader.GetNextAlignmentCore(al) )
++alignmentCount;
}
// no index data available, we have to iterate through until we
// find overlapping alignments
else {
while( reader.GetNextAlignmentCore(al) ) {
if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
(al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
{
++alignmentCount;
}
}
}
}
// error parsing REGION string
else {
cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
reader.Close();
return 1;
}
}
// print results
cout << alignmentCount << endl;
// clean & exit
reader.Close();
return 0;
}
int main (int argc, char * argv[])
{
vector<string> inputFilenames;
string combinedOutFilename, alignmentsOutFilename;
try
{
TCLAP::CmdLine cmd("Program description", ' ', VERSION);
TCLAP::ValueArg<string> combinedOutputArg("o", "out",
"Combined output filename (BAM format)", true, "", "combined.bam", cmd);
TCLAP::ValueArg<int> minInsertArg("n", "min-insert",
"Minimum insert size", false, DEFAULT_MIN_GAP, "min insert size", cmd);
TCLAP::ValueArg<int> maxInsertArg("x", "max-insert",
"Maximum insert size", false, DEFAULT_MAX_GAP, "max insert size", cmd);
TCLAP::MultiArg<string> inputArgs("b", "bam",
"Input BAM file", true,
"input.bam", cmd);
cmd.parse(argc, argv);
combinedOutFilename = combinedOutputArg.getValue();
MIN_GAP = minInsertArg.getValue();
MAX_GAP = maxInsertArg.getValue();
inputFilenames = inputArgs.getValue();
} catch (TCLAP::ArgException &e) {
cerr << "Error: " << e.error() << " " << e.argId() << endl;
}
// TODO require that alignments are sorted by name
BamMultiReader reader;
reader.Open(inputFilenames);
if (!ValidOut.Open(combinedOutFilename, reader.GetHeader(),
reader.GetReferenceData()))
{
cerr << ValidOut.GetErrorString() << endl;
return 1;
}
string current, prev;
char mateID;
Group group;
set<string> references;
Alignment a;
while (reader.GetNextAlignment(a))
{
parseID(a.Name, current, mateID);
if (current.compare(prev) && prev.size() > 0)
{
processGroup(group, references);
group.clear();
references.clear();
}
references.insert(a.RefName);
GroupKey key;
key.refID = a.RefName;
key.mateID = mateID;
key.rev = a.IsReverseStrand();
group.insert( std::make_pair( key, a ) );
prev = current;
}
processGroup(group, references);
}
bool ConvertTool::ConvertToolPrivate::Run(void) {
// ------------------------------------
// initialize conversion input/output
// set to default input if none provided
if ( !m_settings->HasInput )
m_settings->InputFiles.push_back(Options::StandardIn());
// open input files
BamMultiReader reader;
if ( !m_settings->HasInput ) { // don't attempt to open index for stdin
if ( !reader.Open(m_settings->InputFiles, false) ) {
cerr << "Could not open input files" << endl;
return false;
}
} else {
if ( !reader.Open(m_settings->InputFiles, true) ) {
if ( !reader.Open(m_settings->InputFiles, false) ) {
cerr << "Could not open input files" << endl;
return false;
} else {
cerr << "Opened reader without index file, jumping is disabled." << endl;
}
}
}
m_references = reader.GetReferenceData();
// set region if specified
BamRegion region;
if ( m_settings->HasRegion ) {
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
if ( !reader.SetRegion(region) ) {
cerr << "Could not set BamReader region to REGION: " << m_settings->Region << endl;
return false;
}
} else {
cerr << "Could not parse REGION: " << m_settings->Region << endl;
return false;
}
}
// if output file given
ofstream outFile;
if ( m_settings->HasOutput ) {
// open output file stream
outFile.open(m_settings->OutputFilename.c_str());
if ( !outFile ) {
cerr << "Could not open " << m_settings->OutputFilename << " for output" << endl;
return false;
}
// set m_out to file's streambuf
m_out.rdbuf(outFile.rdbuf());
}
// -------------------------------------
// do conversion based on format
bool convertedOk = true;
// pileup is special case
// conversion not done per alignment, like the other formats
if ( m_settings->Format == FORMAT_PILEUP )
convertedOk = RunPileupConversion(&reader);
// all other formats
else {
bool formatError = false;
// set function pointer to proper conversion method
void (BamTools::ConvertTool::ConvertToolPrivate::*pFunction)(const BamAlignment&) = 0;
if ( m_settings->Format == FORMAT_BED ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintBed;
else if ( m_settings->Format == FORMAT_BEDGRAPH ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintBedGraph;
else if ( m_settings->Format == FORMAT_FASTA ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintFasta;
else if ( m_settings->Format == FORMAT_FASTQ ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintFastq;
else if ( m_settings->Format == FORMAT_JSON ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintJson;
else if ( m_settings->Format == FORMAT_SAM ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintSam;
else if ( m_settings->Format == FORMAT_WIGGLE ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintWiggle;
else if ( m_settings->Format == FORMAT_YAML ) pFunction = &BamTools::ConvertTool::ConvertToolPrivate::PrintYaml;
else {
cerr << "Unrecognized format: " << m_settings->Format << endl;
cerr << "Please see help|README (?) for details on supported formats " << endl;
formatError = true;
convertedOk = false;
}
// if format selected ok
if ( !formatError ) {
// if SAM format & not omitting header, print SAM header first
if ( (m_settings->Format == FORMAT_SAM) && !m_settings->IsOmittingSamHeader )
m_out << reader.GetHeaderText();
// iterate through file, doing conversion
BamAlignment a;
while ( reader.GetNextAlignment(a) )
(this->*pFunction)(a);
// set flag for successful conversion
convertedOk = true;
}
}
// ------------------------
// clean up & exit
reader.Close();
if ( m_settings->HasOutput ) outFile.close();
return convertedOk;
}
int main ( int argc, char *argv[] ) {
struct parameters *param = 0;
param = interface(param, argc, argv);
//bam input and generate index if not yet
//-------------------------------------------------------------------------------------------------------+
// BAM input (file or filenames?) |
//-------------------------------------------------------------------------------------------------------+
char *fof = param->mapping_f;
FILE *IN=NULL;
char linefof[5000];
int filecount=0;
vector <string> fnames;
if (strchr(fof,' ')!=NULL) {
char *ptr;
ptr=strtok(fof," ");
while (ptr!=NULL) {
fnames.push_back(ptr);
filecount++;
ptr=strtok(NULL," ");
}
} else {
IN=fopen(fof,"rt");
if (IN!=NULL) {
long linecount=0;
while (fgets(linefof,5000-1,IN)!=NULL) {
linecount++;
if (linefof[0]!='#' && linefof[0]!='\n') {
char *ptr=strchr(linefof,'\n');
if (ptr!=NULL && ptr[0]=='\n') {
ptr[0]='\0';
}
FILE *dummy=NULL;
dummy=fopen(linefof,"rt");
if (dummy!=NULL) { // seems to be a file of filenames...
fclose(dummy);
fnames.push_back(linefof);
filecount++;
} else if (filecount==0 || linecount>=1000-1) { // seems to be a single file
fnames.push_back(fof);
filecount++;
break;
}
}
}
fclose(IN);
}
} //file or file name decided and stored in vector "fnames"
cerr << "the input mapping files are:" << endl;
vector <string>::iterator fit = fnames.begin();
for(; fit != fnames.end(); fit++) {
cerr << *fit << endl;
}
//-------------------------------------------------------------------------------------------------------+
// end of file or filenames |
//-------------------------------------------------------------------------------------------------------+
// open the BAM file(s)
BamMultiReader reader;
reader.Open(fnames);
// get header & reference information
string header = reader.GetHeaderText();
RefVector refs = reader.GetReferenceData();
// attempt to open BamWriter
BamWriter writer;
string outputBam = param->writer;
if ( outputBam != "" ) {
if ( !writer.Open(param->writer, header, refs) ) {
cerr << "Could not open output BAM file" << endl;
exit(0);
}
}
BamAlignment bam;
while (reader.GetNextAlignment(bam)) { //change RG
string rg = "RG";
string rgType = "Z";
string rgValue = "1";
bam.EditTag(rg,rgType,rgValue);
writer.SaveAlignment(bam);
} // read a bam
return 0;
} //main
bool FilterTool::FilterToolPrivate::Run(void) {
// set to default input if none 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 filter ERROR: could not open input BAM file list... Aborting." << endl;
return false;
}
string line;
while ( getline(filelist, line) )
m_settings->InputFiles.push_back(line);
}
// initialize defined properties & user-specified filters
// quit if failed
if ( !SetupFilters() )
return false;
// open reader without index
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
cerr << "bamtools filter ERROR: could not open input files for reading." << endl;
return false;
}
// retrieve reader header & reference data
const string headerText = reader.GetHeaderText();
filterToolReferences = reader.GetReferenceData();
// 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, filterToolReferences) ) {
cerr << "bamtools filter ERROR: could not open " << m_settings->OutputFilename << " for writing." << endl;
reader.Close();
return false;
}
// if no region specified, filter entire file
BamAlignment al;
if ( !m_settings->HasRegion ) {
while ( reader.GetNextAlignment(al) ) {
if ( CheckAlignment(al) )
writer.SaveAlignment(al);
}
}
// otherwise attempt to use region as constraint
else {
// if region string parses OK
BamRegion region;
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
// attempt to find index files
reader.LocateIndexes();
// if index data available for all BAM files, we can use SetRegion
if ( reader.HasIndexes() ) {
// attempt to use SetRegion(), if failed report error
if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
cerr << "bamtools filter ERROR: set region failed. Check that REGION describes a valid range" << endl;
reader.Close();
return false;
}
// everything checks out, just iterate through specified region, filtering alignments
while ( reader.GetNextAlignment(al) )
if ( CheckAlignment(al) )
writer.SaveAlignment(al);
}
// no index data available, we have to iterate through until we
// find overlapping alignments
else {
while ( reader.GetNextAlignment(al) ) {
if ( (al.RefID >= region.LeftRefID) && ((al.Position + al.Length) >= region.LeftPosition) &&
(al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
{
if ( CheckAlignment(al) )
writer.SaveAlignment(al);
}
}
}
}
// error parsing REGION string
else {
cerr << "bamtools filter 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();
return false;
}
}
// clean up & exit
reader.Close();
writer.Close();
return true;
}
int CropBamTool::CropBam()
{
// open bam files
BamMultiReader bamReader;
bamReader.Open(bamFiles);
// the dictionary of chromosomes
RefVector genome = bamReader.GetReferenceData();
// get the scanning window
vector<tuple<int,int,int>> windows;
int numWindows = GenericRegionTools::toScanWindow(genome, regionStrings, windows);
unordered_set<string> readpool;
// temporary struct for sequence object
typedef struct {
string name;
int head_soft_clip;
int tail_soft_clip;
string seq;
string qual;
}cropbam_seq_t;
// temporary struct for unique seqs
map<string,list<cropbam_seq_t>> uniqueSeqPool;
// lambda expression for output
auto Output = [this](cropbam_seq_t &a){
if (this->outFormat=="fasta"){
cout << ">" << a.name << "\t"
<< "head_soft_clip=" << a.head_soft_clip << "\t"
<< "tail_soft_clip=" << a.tail_soft_clip << "\t"
<< endl
<< a.seq << endl;
}
if (this->outFormat=="fastq"){
cout << "@" << a.name << "\t"
<< "head_soft_clip=" << a.head_soft_clip << "\t"
<< "tail_soft_clip=" << a.tail_soft_clip << "\t"
<< endl
<< a.seq << endl;
cout << "+" << endl
<< a.qual << endl;
}
};
// loop over windows
omp_set_dynamic(0);
omp_set_num_threads(numThreads);
#pragma omp parallel for shared(genome)
for (int i=0; i<numWindows; i++)
{
clock_t tStart = clock();
bamReader.Open(bamFiles);
int wId = get<0>(windows[i]);
int wLp = get<1>(windows[i]);
int wRp = get<2>(windows[i]);
if (verbose>=1) Verbose("process the window " + genome[wId].RefName + ":" + to_string(wLp+1) + "-" + to_string(wRp));
// rewind the bam reader
bamReader.Rewind();
// set the region
bamReader.SetRegion(wId, wLp, wId, wRp);
int numReads = 0;
// retrieve the alignment
BamAlignment aln;
while (bamReader.GetNextAlignment(aln))
{
// skip the alignment if it doesn't overlap the window
if (aln.Position>=wRp || aln.GetEndPosition()<=wLp)
continue;
// skip the invalid alignment
if (!isValidAlignment(aln, readLenThres, mapQualThres, alnFlagMarker))
continue;
// skip the alignment harboring too many mismatches
if (!GenericBamAlignmentTools::validReadIdentity(aln, 1-alnIdenThres))
continue;
stringstream keyss;
keyss << GenericBamAlignmentTools::getBamAlignmentName(aln) << "-"
<< wId << "-" << wLp << "-" << wRp;
string key = keyss.str();
auto ptr = readpool.find(key);
if (ptr!=readpool.end())
continue;
readpool.emplace(key);
// get the partial read
string readSegment, readQualSegment, genomeSegment;
GenericBamAlignmentTools::getLocalAlignment(aln, wLp, wRp-wLp, readSegment, readQualSegment, genomeSegment);
// add soft clip
int hsc=0;
auto ptr0 = aln.CigarData.begin();
if (aln.Position>=wLp && (ptr0->Type=='S' || ptr0->Type=='H'))
{
stringstream headClipSeq, headClipQual;
for (int i=0; i<ptr0->Length; i++)
{
headClipSeq << aln.QueryBases[i];
headClipQual << aln.Qualities[i];
}
if (keepClip)
{
readSegment=headClipSeq.str()+readSegment;
readQualSegment=headClipQual.str()+readQualSegment;
}
hsc += ptr0->Length;
}
int tsc=0;
auto ptr1 = aln.CigarData.rbegin();
if (aln.GetEndPosition()<wRp && (ptr1->Type=='S' || ptr1->Type=='H'))
{
string ss="", qs="";
auto str=aln.QueryBases.rbegin();
auto qtr=aln.Qualities.rbegin();
for (int i=0; i<ptr1->Length; i++,str++,qtr++)
{
ss=(*str)+ss;
qs=(*qtr)+qs;
}
if (keepClip)
{
readSegment=readSegment+ss;
readQualSegment=readQualSegment+qs;
}
tsc += ptr1->Length;
}
if (readSegment.length()>=segmentLenThres)
{
cropbam_seq_t a;
a.name = GenericBamAlignmentTools::getBamAlignmentName(aln);
a.head_soft_clip = hsc;
a.tail_soft_clip = tsc;
a.seq = readSegment;
a.qual = readQualSegment;
if (uniqueSeqPool.count(a.seq)==0)
uniqueSeqPool[a.seq] = list<cropbam_seq_t>(1,a);
else
uniqueSeqPool[a.seq].emplace_back(a);
// if (outFormat=="fasta"){
// cout << ">" << GenericBamAlignmentTools::getBamAlignmentName(aln) << "\t"
// << "head_soft_clip=" << hsc << "\t"
// << "tail_soft_clip=" << tsc << "\t"
// << endl
// << readSegment << endl;
// }
// if (outFormat=="fastq"){
// cout << "@" << GenericBamAlignmentTools::getBamAlignmentName(aln) << "\t"
// << "head_soft_clip=" << hsc << "\t"
// << "tail_soft_clip=" << tsc << "\t"
// << endl
// << readSegment << endl;
// cout << "+" << endl
// << readQualSegment << endl;
// }
numReads++;
}
}
numReads = 0;
if (useUnique){
ofstream of;
of.open(outFreq);
for (auto a : uniqueSeqPool){
if (a.second.size()>=thresFreq){
Output(*a.second.begin());
of << a.second.begin()->name << "\t" << a.second.size() << endl;
numReads ++;
}
}
of.close();
}else{
for (auto a : uniqueSeqPool){
for (auto b : a.second){
Output(b);
numReads ++;
}
}
}
clock_t tEnd = clock();
if (verbose>=1) Verbose("retrieve " + to_string(numReads) + " reads");
if (verbose>=1) Verbose("time elapsed " + to_string((double)(tEnd-tStart)/CLOCKS_PER_SEC) + " seconds");
}
return 0;
}
int bbctools_create( BbcUtils::OptParser &optParser ) {
const vector<string> cmdArgs = optParser.getArgs();
// remove .bbc extension from bbc file root, if present
string bbcfileRoot = optParser.getOptValue( "bbc" );
int i = bbcfileRoot.size() - 4;
if( i > 0 && bbcfileRoot.substr(i,4) == ".bbc" ) {
bbcfileRoot = bbcfileRoot.substr(0,i);
}
bool f_bci = optParser.getOptBoolean("index");
bool f_cbc = optParser.getOptBoolean("coarse");
string targetRegions = optParser.getOptValue("regions");
string annotationFields = optParser.getOptValue( "annotationFields");
vector<string> auxRegionSplit = BbcUtils::mapToPairList(annotationFields);
string sumstatsFile = optParser.getOptValue("sumStats");
string covstatsFile = optParser.getOptValue("covStats");
string readOrigFile = optParser.getOptValue("readOrigin");
string readType = optParser.getOptValue("readType");
string covDepths = optParser.getOptValue("covDepths","-");
double minPcCov = optParser.getOptNumber("minPcCov");
int32_t primerLength = optParser.getOptInteger( "primerLength", (readType == "AmpliSeq" ? 30 : 0) );
int32_t maxE2eEndGap = optParser.getOptInteger( "e2eGap", (readType == "AmpliSeq" ? 2 : 0) );
bool autoCreateBamIndex = optParser.getOptBoolean("autoCreateBamIndex");
bool samdepth = optParser.getOptBoolean("samdepth");
int32_t filterQuality = optParser.getOptInteger("minMAPQ");
int32_t minAlignLength = optParser.getOptInteger("minAlignLength");
bool filterDuplicates = optParser.getOptBoolean("noDups");
bool filterUnique = optParser.getOptBoolean("unique");
uint32_t skipFlag = filterDuplicates ? 0x704 : 0x304;
uint16_t minMapQuality = filterUnique ? 1 : filterQuality;
bool onlyOnTargetReads = optParser.getOptBoolean("onTargetReads");
bool onlyOnTargetBases = optParser.getOptBoolean("onTargetBases");
// possible future options
bool invertOnTarget = false;
// check basic valid argument values and combinations
int numOuts = !bbcfileRoot.empty() + !covstatsFile.empty() + !sumstatsFile.empty() + !readOrigFile.empty();
int numPipes = (bbcfileRoot == "-") + (covstatsFile == "-") + (sumstatsFile == "-") + (readOrigFile == "-");
if( numOuts == 0 && !f_bci && !f_cbc ) {
bbcfileRoot = "-"; // default if no other output specified
} else if( numPipes > 1 ) {
cerr << "Error: bbctools create: Only one file output (--covStats, --sumStats, --readOrigin or --bbc) may be piped to STDOUT." << endl;
return -1;
} else if( samdepth && numOuts ) {
cerr << "Error: bbctools create: --samdepth (-s) option may only be used without other output options." << endl;
return -1;
}
// check if single argument is a BBC file and leave open for reading if so
BbcView bbcView;
bool haveBbcFile = cmdArgs.size() == 1 && bbcView.Open( cmdArgs[0], true );
bbcView.SelectPrintStream( samdepth ? "SAMDEPTH" : "BBCVIEW" );
// check distinction between default and explicit no target regions - only for BBC input
bool explicitNoTargetRegions = false;
if( targetRegions == "-" ) {
explicitNoTargetRegions = haveBbcFile;
targetRegions = "";
}
if( targetRegions.empty() ) {
if( onlyOnTargetBases && explicitNoTargetRegions && !invertOnTarget ) {
cerr << "Warning: bbctools create --onTargetBases (-b) option with --regions '-' produces no coverage." << endl;
} else if( onlyOnTargetReads ) {
cerr << "Error: bbctools create --onTargetReads (-r) option requires a --regions file." << endl;
return -1;
}
}
// check for legal BBC create options
if( f_bci || f_cbc ) {
if( (bbcfileRoot.empty() || bbcfileRoot == "-") && !haveBbcFile ) {
string opt = f_bci ? "--index (-i)" : "--coarse (-c)";
cerr << "Error: bbctools create "+opt+" option requires the --bbc (-B) option or a BBC source file." << endl;
return -1;
}
}
BamMultiReader bamReader;
if( haveBbcFile ) {
// warn for options that do not work with BBC input
if( filterQuality > 0 || filterDuplicates || filterUnique || minAlignLength ) {
cerr << "Warning: SAM flag, alignment length and MAPQ filters ignored for BBC source file." << endl;
}
if( samdepth ) {
cerr << "Error: --samdepth option is not supported for BBC source files." << endl;
return -1;
}
if( !readOrigFile.empty() ) {
cerr << "Error: --readOrigin option is not supported for BBC source files." << endl;
return -1;
}
} else {
// check / open for multiple BAM file inputs
if ( !bamReader.Open(cmdArgs) ) {
if( cmdArgs.size() == 1 ) cerr << "ERROR: Could not read input BAM file:";
else cerr << "ERROR: Could not read all input BAM files:";
// get and clean up bamtools error msg
string errMsg = bamReader.GetErrorString();
size_t i = errMsg.find_first_of('\n');
if( i != string::npos ) errMsg = errMsg.substr(i+1);
i = errMsg.find("::");
if( i != string::npos ) {
i = errMsg.find(": ");
if( i != string::npos ) errMsg = errMsg.substr(i+1);
}
errMsg = BbcUtils::stringTrim(errMsg);
errMsg[0] = toupper(errMsg[0]);
cerr << endl << errMsg << "." << endl;
return 1;
}
}
// grab reference list from either input source
const RefVector &references = haveBbcFile ? bbcView.GetReferenceData() : bamReader.GetReferenceData();
if( !references.size() ) {
// Issue would already been detected if input was BBC file
cerr << "ERROR: " << (cmdArgs.size() > 1 ? "One or more " : "");
cerr << "BAM file contains unaligned reads (no references).\n";
return 1;
}
// check/set up target regions input regions/region statistics output
RegionCoverage *regions = NULL;
string covstatsStaticFields;
bool trackRegionBaseCov = !covDepths.empty();
if( covstatsFile.empty() ) {
trackRegionBaseCov = false;
if( !annotationFields.empty() ) {
cerr << "Warning: --annotationFields (A) option ignored without --covStats (-C) option." << endl;
}
if( !covDepths.empty() && covDepths != "-" ) {
cerr << "Warning: --covDepths (-D) option ignored without --covStats (-C) option." << endl;
}
if( !readType.empty() ) {
cerr << "Warning: --readType (-T) option ignored without --covStats (-C) option." << endl;
}
// read regions for input only and/or creating sumStats
if( !targetRegions.empty() || explicitNoTargetRegions || !sumstatsFile.empty() ) {
regions = new RegionCoverage(references);
}
} else if( readType == "trgreads" || readType == "amplicon" || readType == "AmpliSeq" ) {
if( haveBbcFile ) {
cerr << "Creation of read coverage requires BAM file input." << endl;
return -1;
}
AmpliconRegionStatistics *ampRegionStats = new AmpliconRegionStatistics(references);
ampRegionStats->SetGenericReads( readType == "trgreads" );
ampRegionStats->SetSigFacCoverage( minPcCov/100 );
ampRegionStats->SetMaxUpstreamPrimerStart( primerLength );
ampRegionStats->SetMaxE2eEndDistance( maxE2eEndGap );
covstatsStaticFields = "overlaps,";
covstatsStaticFields += (minPcCov > 0) ? "fwd_cov,rev_cov" : "fwd_e2e,rev_e2e";
covstatsStaticFields += ",total_reads,fwd_reads,rev_reads";
regions = ampRegionStats;
} else if( readType == "trgbases" ) {
if( haveBbcFile && targetRegions.empty() && !explicitNoTargetRegions ) {
cerr << "Warning: Assuming reference contigs for base coverage targets (=> option --regions -)" << endl;
}
RegionStatistics *regionStats = new RegionStatistics(references);
covstatsStaticFields = "covered,uncov_5p,uncov_3p,ave_basereads,fwd_basereads,rev_basereads";
trackRegionBaseCov = true;
regions = regionStats;
} else if( readType == "covdepth" || readType.empty() ) {
// output (sorted) targets file with only covDepth stats (if any)
regions = new RegionCoverage(references);
} else {
cerr << "Unknown read type '" << readType << "'" << endl;
return -1;
}
// Load the input regions or default to whole reference contig targets
if( regions ) {
regions->SetCovAtDepths( covDepths == "-" ? "20,100,500" : covDepths );
if( targetRegions.empty() ) {
regions->SetWholeContigTargets();
// set contigs as explicit regions means all reads will seen as on-target
// for consistency these are inverted (for input from BBC)
invertOnTarget = true;
} else {
string auxFieldIdx = auxRegionSplit.size() ? auxRegionSplit[0] : "";
string errMsg = regions->Load( targetRegions, "BED", auxFieldIdx );
if( !errMsg.empty() ) {
cerr << "ERROR: " + errMsg + "\n";
return 1;
}
}
if( onlyOnTargetReads && haveBbcFile ) {
cerr << "Error: bbctools create --onTargetReads option is not supported for BBC source file." << endl;
return -1;
}
}
//
// Perform all bbctools create utilities
//
BbcCreate *bbcCreate = NULL;
if( !bbcfileRoot.empty() && (bbcfileRoot != "-" || !haveBbcFile) ) {
bbcCreate = new BbcCreate(references);
if( bbcfileRoot != "-" && !bbcCreate->Open(bbcfileRoot+".bbc") ) {
return 1;
}
bbcCreate->SetNoOffTargetPositions(onlyOnTargetBases);
}
bbcView.SetNoOffTargetPositions(onlyOnTargetBases);
// Stream input to output creators
if( haveBbcFile ) {
// BBC reader and driver via BbcView object
if( bbcfileRoot != "-" || !covstatsFile.empty() ) {
// disable BbcView text stream if using for file creation
bbcView.SelectPrintStream("NONE");
}
// process input BBC for just new BBC and target coverage (defer BCI/CBC)
bbcView.SetBbcCreate(bbcCreate);
bbcView.SetRegionCoverage(regions);
// explicitNoTargetRegions intended for explicitly removing on-target coverage
bbcView.SetInvertOnTarget(explicitNoTargetRegions ^ invertOnTarget);
if( bbcCreate || regions || bbcfileRoot == "-" ) {
bbcView.ReadAll();
}
} else {
// Test read tracking option for file write
TrackReads *readTracker = NULL;
try {
if( !readOrigFile.empty() )
readTracker = new TrackReads( readOrigFile, regions );
} catch( std::runtime_error & ) {
cerr << "ERROR: Unable to write to read tracking file " << readOrigFile << endl;
return 1;
}
// BAM reader, BaseCoverage driver, dispatching to BbcCreate and BbcView objects
BaseCoverage baseCov(references);
baseCov.SetRegionCoverage(regions);
baseCov.SetBbcCreate(bbcCreate);
baseCov.SetInvertOnTarget(invertOnTarget);
if( bbcfileRoot == "-" ) {
baseCov.SetBbcView(&bbcView);
}
// Certain options require that all reads are processed, invalidating other performance options
bool trackAllReads = !sumstatsFile.empty() || readTracker;
// Implicit set of onlyOnTargetReads for performance when only these reads are required
bool useBaseCov = (bbcfileRoot == "-" || bbcCreate);
if( !targetRegions.empty() && !trackAllReads ) {
onlyOnTargetReads |= onlyOnTargetBases;
if( samdepth || !useBaseCov ) onlyOnTargetReads = true;
}
useBaseCov |= trackRegionBaseCov;
// do not allow jumping if sumStats option is used - need to count all reads
bool bamReaderSetRegions = (s_useBamReaderJump && !trackAllReads);
int trgContig = 0, trgSrtPos = 0, trgEndPos = 0;
int minJumpLen = s_initialMinJumpLen;
int maxReadLen = s_initialMaxReadLen;
if( onlyOnTargetReads ) {
// load/create BAM index files for targeted reading
// Note: BamIndex::BAMTOOLS format performed very badly and cannot use mixed with BTI/BAI files
if( bamReaderSetRegions && !bamReader.LocateIndexes() ) {
string plural( cmdArgs.size() > 1 ? "s" : "" );
if( autoCreateBamIndex ) {
cerr << "Warning: Did not locate BAM index (BAI) file" << plural << ", creating bamtools version..." << endl;
// to avoid bug use new instance of BamMultiReader
BamMultiReader bamReader2;
if( !bamReader2.Open(cmdArgs) || !bamReader2.CreateIndexes() ) {
cerr << "WARNING: Failed to create BAM index file" << plural << "." << endl;
bamReaderSetRegions = false;
} else {
if( cmdArgs.size() == 1 ) {
cerr << "Successfully created BAM index file: " << BbcUtils::fileName(cmdArgs[0]) << ".bai" << endl;
} else {
cerr << "Successfully created BAM index files." << endl;
}
// re-locate indexes with first reader - could not seem to locate BTI files created!
if( !bamReader.LocateIndexes() ) {
cerr << "WARNING: Failed to locate BAM index file" << plural << " just created!" << endl;
bamReaderSetRegions = false;
}
}
} else {
cerr << "Warning: BAM index file" << plural << " not located for targeted BAM access." << endl;
bamReaderSetRegions = false;
}
}
// cancel region filtering if there are no regions to iterate (unexpected)
if( !regions->GetNextRegion( trgContig, trgSrtPos, trgEndPos ) ) {
onlyOnTargetReads = bamReaderSetRegions = false;
}
if( bamReaderSetRegions ) {
bamReader.Jump( trgContig, trgSrtPos-maxReadLen );
}
}
BamAlignment aln;
while( bamReader.GetNextAlignmentCore(aln) ) {
// appears to be an undocumented behavior here
if( aln.RefID < 0 ) continue;
// skip filtered reads by flag, length or mapping quality
if( aln.AlignmentFlag & skipFlag ) continue;
if( aln.MapQuality < minMapQuality ) continue;
int32_t endPos = aln.GetEndPosition();
if( minAlignLength > 0 ) {
if( endPos - aln.Position < minAlignLength ) continue;
}
// screen for on-target reads
if( onlyOnTargetReads ) {
// find next region overlapping or beyond of current read
bool moreRegions = true;
bool setRegion = false;
while( aln.RefID > trgContig || (aln.RefID == trgContig && aln.Position > trgEndPos) ) {
if( !regions->GetNextRegion( trgContig, trgSrtPos, trgEndPos ) ) {
moreRegions = false;
break;
}
setRegion = bamReaderSetRegions;
}
if( !moreRegions ) {
// prevent further on-target checks and exit early if not using sumStats
onlyOnTargetReads = false;
if( trackAllReads ) {
// force tracking of off-target reads
regions->TrackReadsOnRegion(aln,endPos);
if( readTracker ) readTracker->Write(aln,endPos);
continue;
}
break;
}
if( setRegion ) {
// track max read length for future index jumps - just in case long reads ever used
if( endPos - aln.Position > maxReadLen ) {
maxReadLen = endPos - aln.Position;
if( maxReadLen > minJumpLen ) minJumpLen = maxReadLen;
}
if( aln.RefID != trgContig || trgSrtPos - aln.Position > minJumpLen ) {
bamReader.Jump( trgContig, trgSrtPos-maxReadLen );
}
}
if( aln.RefID < trgContig || endPos < trgSrtPos ) {
// force tracking of off-target reads
if( trackAllReads ) {
regions->TrackReadsOnRegion(aln,endPos);
if( readTracker ) readTracker->Write(aln,endPos);
}
continue; // current is before next target region - fetch the next within bounds
}
}
// record base coverage and region coverage statistics
if( useBaseCov ) {
endPos = baseCov.AddAlignment(aln,endPos);
if( endPos <= 0 ) {
if( endPos == 0 ) continue; // read was silently ignored
cerr << "ERROR: BAM file is not correctly sorted vs. reference." << endl;
return 1;
}
}
// record read coverage and region coverage statistics
if( regions ) {
regions->TrackReadsOnRegion(aln,endPos);
}
if( readTracker ) {
readTracker->Write(aln,endPos);
}
}
// flush and close objects associated with output
baseCov.Flush();
}
// Output in-memory region stats file and ensure BBC file is closed
if( regions ) {
// build output fields title string
string outFields = "contig_id,contig_srt,contig_end";
if( !auxRegionSplit.empty() ) outFields += "," + auxRegionSplit[1];
if( !covstatsStaticFields.empty() ) outFields += "," + covstatsStaticFields;
regions->Write( covstatsFile, outFields );
if( !sumstatsFile.empty() ) {
regions->WriteSummary( sumstatsFile, invertOnTarget );
}
delete regions;
}
delete bbcCreate;
// Complete remaining file creation options using a BBC file input
// NOTE: Using BbbCreate for this would require code duplication and concurrent file output streaming
if( f_bci || f_cbc ) {
// Check BBC file source
if( haveBbcFile ) {
bbcfileRoot = cmdArgs[0];
int i = bbcfileRoot.size() - 4;
if( i > 0 && bbcfileRoot.substr(i,4) == ".bbc" ) {
bbcfileRoot = bbcfileRoot.substr(0,i);
}
} else if( !bbcView.Open( bbcfileRoot+".bbc", true ) ) {
cerr << "ERROR: Unexpected failure to read new BBC file '"+bbcfileRoot+".bam'" << endl;
return 1;
}
if( f_bci ) {
BbcIndex indexer( bbcfileRoot+".bci" );
if( !bbcView.CreateIndex(indexer) ) {
cerr << "ERROR: Failed to create index file '" << bbcfileRoot << ".bci'" << endl;
return 1;
}
}
if( f_cbc ) {
// CBC generation can use BCI file but is no faster since whole BBC file is read
BbcCoarse cbcWriter( bbcfileRoot+".cbc" );
if( !bbcView.CreateCbc(cbcWriter) ) {
cerr << "ERROR: Failed to create coarse base coverage file '" << bbcfileRoot << ".cbc'" << endl;
return 1;
}
}
}
return 0;
}
bool MergeTool::MergeToolPrivate::Run(void) {
// set to default input if none provided
if ( !m_settings->HasInputBamFilename )
m_settings->InputFiles.push_back(Options::StandardIn());
// opens the BAM files (by default without checking for indexes)
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
cerr << "bamtools merge ERROR: could not open input BAM file(s)... Aborting." << endl;
return false;
}
// retrieve header & reference dictionary info
std::string mergedHeader = reader.GetHeaderText();
RefVector references = reader.GetReferenceData();
// 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, mergedHeader, references) ) {
cerr << "bamtools merge ERROR: could not open "
<< m_settings->OutputFilename << " for writing." << endl;
reader.Close();
return false;
}
// if no region specified, store entire contents of file(s)
if ( !m_settings->HasRegion ) {
BamAlignment al;
while ( reader.GetNextAlignmentCore(al) )
writer.SaveAlignment(al);
}
// otherwise attempt to use region as constraint
else {
// if region string parses OK
BamRegion region;
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
// attempt to find index files
reader.LocateIndexes();
// if index data available for all BAM files, we can use SetRegion
if ( reader.HasIndexes() ) {
// attempt to use SetRegion(), if failed report error
if ( !reader.SetRegion(region.LeftRefID,
region.LeftPosition,
region.RightRefID,
region.RightPosition) )
{
cerr << "bamtools merge ERROR: set region failed. Check that REGION describes a valid range"
<< endl;
reader.Close();
return false;
}
// everything checks out, just iterate through specified region, storing alignments
BamAlignment al;
while ( reader.GetNextAlignmentCore(al) )
writer.SaveAlignment(al);
}
// no index data available, we have to iterate through until we
// find overlapping alignments
else {
BamAlignment al;
while ( reader.GetNextAlignmentCore(al) ) {
if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
(al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
{
writer.SaveAlignment(al);
}
}
}
}
// error parsing REGION string
else {
cerr << "bamtools merge 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;
}
}
// clean & exit
reader.Close();
writer.Close();
return true;
}
int main ( int argc, char *argv[] ) {
struct parameters *param = 0;
param = interface(param, argc, argv);
//region file input (the region file should be sorted as the same way as the bam file)
ifstream region_f;
region_f.open(param->region_f, ios_base::in); // the region file is opened
//bam input and generate index if not yet
//-------------------------------------------------------------------------------------------------------+
// BAM input (file or filenames?) |
//-------------------------------------------------------------------------------------------------------+
char *fof = param->mapping_f;
FILE *IN=NULL;
char linefof[5000];
int filecount=0;
vector <string> fnames;
if (strchr(fof,' ')!=NULL) {
char *ptr;
ptr=strtok(fof," ");
while (ptr!=NULL) {
fnames.push_back(ptr);
filecount++;
ptr=strtok(NULL," ");
}
} else {
IN=fopen(fof,"rt");
if (IN!=NULL) {
long linecount=0;
while (fgets(linefof,5000-1,IN)!=NULL) {
linecount++;
if (linefof[0]!='#' && linefof[0]!='\n') {
char *ptr=strchr(linefof,'\n');
if (ptr!=NULL && ptr[0]=='\n') {
ptr[0]='\0';
}
FILE *dummy=NULL;
dummy=fopen(linefof,"rt");
if (dummy!=NULL) { // seems to be a file of filenames...
fclose(dummy);
fnames.push_back(linefof);
filecount++;
} else if (filecount==0 || linecount>=1000-1) { // seems to be a single file
fnames.push_back(fof);
filecount++;
break;
}
}
}
fclose(IN);
}
} //file or file name decided and stored in vector "fnames"
cerr << "the input mapping files are:" << endl;
vector <string>::iterator fit = fnames.begin();
for(; fit != fnames.end(); fit++) {
cerr << *fit << endl;
}
//-------------------------------------------------------------------------------------------------------+
// end of file or filenames |
//-------------------------------------------------------------------------------------------------------+
// open the BAM file(s)
BamMultiReader reader;
reader.Open(fnames);
// get header & reference information
string header = reader.GetHeaderText();
RefVector refs = reader.GetReferenceData();
if ( ! reader.LocateIndexes() ) // opens any existing index files that match our BAM files
reader.CreateIndexes(); // creates index files for BAM files that still lack one
// locus bias
struct lb empty_profile = {0,0,0,0};
vector <struct lb> locus_b(1000, empty_profile);
// output locus bias file
string locus_bias_set = param->lbias;
ofstream locus_bias;
if ( locus_bias_set != "" ) {
locus_bias.open(param->lbias);
if ( !locus_bias ) {
cerr << "can not open locus_bias file.\n";
exit(0);
}
}
//should decide which chromosome
string line;
string old_chr = "SRP";
string type = param->type;
//whether do some position-level pile-up stuff
bool posc = false;
ofstream posc_f;
ofstream chrmap_f;
string poscset = param->posc;
if ( poscset != "" ) {
posc = true;
posc_f.open(param->posc);
chrmap_f.open(param->chrmap);
}
bool noChr;
if ( param->nochr == 1 ){
noChr = true;
} else {
noChr = false;
}
//regions for the input of region file
deque <struct region> regions;
getline(region_f, line); //get the first line
eatline(line,regions,noChr);
deque <struct region>::iterator it = regions.begin();
while ( it->chr != old_chr ) {
old_chr = it->chr; // set the current chr as old chr
int chr_id = reader.GetReferenceID(it->chr);
if ( chr_id == -1 ) { //reference not found
for (; it != regions.end() && it->chr == old_chr; ) {
gene_processing(*it,locus_b); // print the old region info
it = regions.erase(it); // erase the current region
}
while ( regions.empty() ) {
getline(region_f, line);
if ( region_f.eof() ){
cerr << "finished: end of region file, zone 0" << endl;
break;
}
eatline(line, regions,noChr);
it = regions.begin();
if (it->chr == old_chr){
gene_processing(*it,locus_b);
regions.clear();
continue;
}
}
continue;
}
int chr_len = refs.at(chr_id).RefLength;
if ( !reader.SetRegion(chr_id, 1, chr_id, chr_len) ) // here set region
{
cerr << "bamtools count ERROR: Jump region failed " << it->chr << endl;
reader.Close();
exit(1);
}
//pile-up pos stats
set <string> fragment;
map <string, unsigned int> pileup;
bool isposPileup = false;
unsigned int old_start = 0;
unsigned int total_tags = 0;
unsigned int total_pos = 0;
unsigned int pileup_pos = 0;
BamAlignment bam;
while (reader.GetNextAlignment(bam)) {
if ( bam.IsMapped() == false ) continue; // skip unaligned reads
unsigned int unique;
bam.GetTag("NH", unique);
if (param->unique == 1) {
if (unique != 1) { // skipe uniquelly mapped reads
continue;
}
}
if (read_length == 0){
read_length = bam.Length;
}
//cout << bam.Name << endl;
string chrom = refs.at(bam.RefID).RefName;
string strand = "+";
if (bam.IsReverseStrand()) strand = "-";
unsigned int alignmentStart = bam.Position+1;
unsigned int mateStart;
if (type == "p") mateStart = bam.MatePosition+1;
unsigned int alignmentEnd = bam.GetEndPosition();
unsigned int cigarEnd;
vector <int> blockLengths;
vector <int> blockStarts;
blockStarts.push_back(0);
ParseCigar(bam.CigarData, blockStarts, blockLengths, cigarEnd);
// position check for unique mapped reads (because is paired-end reads, shoule base on fragment level for paired end reads)
if (posc == true && unique == 1) {
if (type == "p" && fragment.count(bam.Name) > 0)
fragment.erase(bam.Name);
else {
total_tags++;
if (type == "p"){
fragment.insert(bam.Name);
}
string alignSum;
if (type == "p") {
alignSum = int2str(alignmentStart) + "\t" + int2str(mateStart) + "\t.\t" + strand;
} else {
alignSum = int2str(alignmentStart) + "\t" + int2str(alignmentEnd) + "\t.\t" + strand;
}
if ( alignmentStart != old_start ) {
isposPileup = false;
map <string, unsigned int>::iterator pit = pileup.begin();
for (; pit != pileup.end(); pit++) {
posc_f << chrom << "\truping\tpileup\t" << pit->first << "\t.\t" << "Pileup=" << pit->second << endl; //print pileup
}
pileup.clear(); //clear pileup set
pileup.insert( pair <string, unsigned int> (alignSum, 1) ); //insert the new read
total_pos++;
}
else if ( alignmentStart == old_start ) { // same starts
if ( pileup.count(alignSum) > 0 ) { // pileup
if ( pileup[alignSum] == 1 && isposPileup == false ) {
pileup_pos++; isposPileup = true;
}
pileup[alignSum]++;
}
else {
pileup.insert( pair <string, unsigned int> (alignSum, 1) );
}
} //same starts
} //new fragment
old_start = alignmentStart;
} // do pos check
float incre = 1.;
if (blockStarts.size() > 1) incre = 0.5; // incre half for junction reads
incre /= static_cast < float >(unique); // for multi aligned reads
deque <struct region>::iterator iter = regions.begin();
if ( iter->start > alignmentEnd ) continue; // skip reads not overlapping with the first region
while ( iter->chr == old_chr && iter->start <= alignmentEnd && iter != regions.end() ) {
if (iter->end < alignmentStart) { // the region end is beyond the alignmentStart
gene_processing(*iter,locus_b); // processing
iter = regions.erase(iter); // this region should be removed
if ( regions.empty() ) {
getline(region_f, line); // get a line of region file
if ( ! region_f.eof() ) {
eatline(line, regions, noChr); // eat a line and put it into the duque
iter = regions.begin();
}
else { // it's reaching the end of the region file
cerr << "finished: end of region file, zone 3" << endl;
break;
}
}
continue;
}
if (iter->end >= alignmentStart && iter->start <= alignmentEnd) { //overlapping, should take action
vector <int>::iterator cigit = blockStarts.begin();
for (; cigit != blockStarts.end(); cigit++) {
unsigned int current_start = *cigit + alignmentStart;
int current_pos = current_start - (iter->start);
//cout << iter->chr << "\t" << iter->start << "\t" << iter->end << "\t" << current_start << endl;
if ( (iter->tags).count(current_pos) > 0 ) {
(iter->tags)[current_pos] += incre;
}
else
(iter->tags).insert( pair<int, float>(current_pos, incre) );
}
} // overlapping take action!
if ( (iter+1) != regions.end() )
iter++; // if this region is not the last element in the deque
else { // the last element
getline(region_f, line); // get a line of region file
if ( ! region_f.eof() ){
eatline(line, regions, noChr); // eat a line and put it into the duque
iter = regions.end();
iter--;
}
else { //it's reaching the end of the region file
cerr << "finished: end of region file, zone 4" << endl;
break;
}
}
} //while
} // read a bam
// print chr map
if (posc == true) {
chrmap_f << old_chr << "\t" << total_tags << "\t" << total_pos << "\t" << pileup_pos << endl;
}
//somehow to loop back
it = regions.begin(); //reset to begin
for (; it != regions.end() && it->chr == old_chr; ) {
gene_processing(*it,locus_b); // print the old region info
it = regions.erase(it); // erase the current region
}
while ( regions.empty() ) {
getline(region_f, line);
if ( region_f.eof() ){
cerr << "finished: end of region file, zone 5" << endl;
//print locus bias
for (unsigned int l = 0; l < 1000; l++){
locus_bias << l << "\t" << locus_b[l].ps << "\t" << locus_b[l].hs << "\t" << locus_b[l].pe << "\t" << locus_b[l].he << endl;
}
exit(0);
}
eatline(line, regions, noChr);
it = regions.begin();
if (it->chr == old_chr){
gene_processing(*it, locus_b);
regions.clear();
continue;
}
}
} // region chr != old chr
regions.clear();
reader.Close();
region_f.close();
return 0;
} //main
int FileReader::runInternal()
{
ogeNameThread("am_FileReader");
if(!format_specified)
format = deduceFileFormat();
if(format == FORMAT_BAM)
{
BamMultiReader reader;
if(!reader.Open(filenames)) {
cerr << "Error opening BAM files." << endl;
reader.Close();
return -1;
}
header = reader.GetHeader();
references = reader.GetReferenceData();
open = true;
BamAlignment * al;
while(true)
{
if(load_string_data)
al = reader.GetNextAlignment();
else
al = reader.GetNextAlignmentCore();
if(!al)
break;
putOutputAlignment(al);
}
reader.Close();
} else if(format == FORMAT_SAM) {
vector<SamReader> readers;
SamHeader first_header;
// before doing any reading, open the files to
// verify they are the right format, etc.
for(int i = 0; i < filenames.size(); i++) {
SamReader reader;
if(!reader.Open(filenames[i])) {
cerr << "Error opening SAM file: " << filenames[i] << endl;
return -1;
}
if(filenames.size() > 1 && i == 0)
first_header = header;
// TODO: We can probably find a better way to deal with multiple SAM file headers,
// but for now we should disallow different headers to avoid issues.
if(i > 0 && header.ToString() != first_header.ToString())
cerr << "Warning! SAM input files have different headers." << endl;
reader.Close();
}
for(int i = 0; i < filenames.size(); i++) {
SamReader reader;
if(!reader.Open(filenames[i])) {
cerr << "Error opening SAM file: " << filenames[i] << endl;
return -1;
}
header = reader.GetHeader();
references = reader.GetReferenceData();
open = true;
if(filenames.size() > 1 && i == 0)
first_header = header;
BamAlignment * al = NULL;
while(true)
{
al = reader.GetNextAlignment();
if(NULL == al)
break;
putOutputAlignment(al);
}
reader.Close();
}
} else {
cerr << "FileReader couldn't detect file format. Aborting." << endl;
exit(-1);
return -1;
}
return 0;
}
int MergeTool::Run(int argc, char* argv[]) {
// parse command line arguments
Options::Parse(argc, argv, 1);
// set to default input if none provided
if ( !m_settings->HasInputBamFilename )
m_settings->InputFiles.push_back(Options::StandardIn());
// opens the BAM files (by default without checking for indexes)
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles, false, true) ) {
cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
return 1;
}
// retrieve header & reference dictionary info
std::string mergedHeader = reader.GetHeaderText();
RefVector references = reader.GetReferenceData();
// open writer
BamWriter writer;
bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
if ( !writer.Open(m_settings->OutputFilename, mergedHeader, references, writeUncompressed) ) {
cerr << "ERROR: Could not open BAM file " << m_settings->OutputFilename << " for writing... Aborting." << endl;
reader.Close();
return 1;
}
// if no region specified, store entire contents of file(s)
if ( !m_settings->HasRegion ) {
BamAlignment al;
while ( reader.GetNextAlignmentCore(al) )
writer.SaveAlignment(al);
}
// otherwise attempt to use region as constraint
else {
// if region string parses OK
BamRegion region;
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
// attempt to re-open reader with index files
reader.Close();
bool openedOK = reader.Open(m_settings->InputFiles, true, true );
// if error
if ( !openedOK ) {
cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
return 1;
}
// if index data available, we can use SetRegion
if ( reader.IsIndexLoaded() ) {
// attempt to use SetRegion(), if failed report error
if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
reader.Close();
return 1;
}
// everything checks out, just iterate through specified region, storing alignments
BamAlignment al;
while ( reader.GetNextAlignmentCore(al) )
writer.SaveAlignment(al);
}
// no index data available, we have to iterate through until we
// find overlapping alignments
else {
BamAlignment al;
while ( reader.GetNextAlignmentCore(al) ) {
if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
(al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
{
writer.SaveAlignment(al);
}
}
}
}
// error parsing REGION string
else {
cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
reader.Close();
writer.Close();
return 1;
}
}
// clean & exit
reader.Close();
writer.Close();
return 0;
}