// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 22 July 2010
+// Last modified: 16 September 2010
// ---------------------------------------------------------------------------
// Converts between BAM and a number of other formats
// ***************************************************************************
#include <sstream>
#include <string>
#include <vector>
-
#include "bamtools_convert.h"
+#include "bamtools_fasta.h"
#include "bamtools_options.h"
-#include "bamtools_pileup.h"
+#include "bamtools_pileup_engine.h"
#include "bamtools_utilities.h"
#include "BGZF.h"
-#include "BamReader.h"
#include "BamMultiReader.h"
-
using namespace std;
using namespace BamTools;
namespace BamTools {
-
- // format names
+
+ // ---------------------------------------------
+ // ConvertTool constants
+
+ // supported conversion format command-line names
static const string FORMAT_BED = "bed";
static const string FORMAT_BEDGRAPH = "bedgraph";
static const string FORMAT_FASTA = "fasta";
// other constants
static const unsigned int FASTA_LINE_MAX = 50;
-} // namespace BamTools
-
-struct ConvertTool::ConvertToolPrivate {
-
- // ctor & dtor
- public:
- ConvertToolPrivate(ConvertTool::ConvertSettings* settings);
- ~ConvertToolPrivate(void);
+ // ---------------------------------------------
+ // ConvertPileupFormatVisitor declaration
- // interface
- public:
- bool Run(void);
+ class ConvertPileupFormatVisitor : public PileupVisitor {
+
+ // ctor & dtor
+ public:
+ ConvertPileupFormatVisitor(const RefVector& references,
+ const string& fastaFilename,
+ const bool isPrintingMapQualities,
+ ostream* out);
+ ~ConvertPileupFormatVisitor(void);
+
+ // PileupVisitor interface implementation
+ public:
+// void Visit(const int& refId, const int& position, const vector<BamAlignment>& alignments);
+
+ void Visit(const PileupPosition& pileupData);
+
+ // data members
+ private:
+ Fasta m_fasta;
+ bool m_hasFasta;
+ bool m_isPrintingMapQualities;
+ ostream* m_out;
+ RefVector m_references;
+ };
- // internal methods
- private:
- void PrintBed(const BamAlignment& a);
- void PrintBedGraph(const BamAlignment& a);
- void PrintFasta(const BamAlignment& a);
- void PrintFastq(const BamAlignment& a);
- void PrintJson(const BamAlignment& a);
- void PrintSam(const BamAlignment& a);
- void PrintWiggle(const BamAlignment& a);
-
- // data members
- private:
- ConvertTool::ConvertSettings* m_settings;
- RefVector m_references;
- ostream m_out;
-};
-
+} // namespace BamTools
+
// ---------------------------------------------
// ConvertSettings implementation
, IsOmittingSamHeader(false)
, IsPrintingPileupMapQualities(false)
, OutputFilename(Options::StandardOut())
+ , FastaFilename("")
{ }
-};
+};
// ---------------------------------------------
-// ConvertTool implementation
-
-ConvertTool::ConvertTool(void)
- : AbstractTool()
- , m_settings(new ConvertSettings)
- , m_impl(0)
-{
- // set program details
- Options::SetProgramInfo("bamtools convert", "converts BAM to a number of other formats", "-format <FORMAT> [-in <filename> -in <filename> ...] [-out <filename>] [other options]");
-
- // set up options
- OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
- Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
- Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
- Options::AddValueOption("-format", "FORMAT", "the output file format - see README for recognized formats", "", m_settings->HasFormat, m_settings->Format, IO_Opts);
-
- OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
- Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for better performance, and is read automatically if it exists as <filename>.bai. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
-
- OptionGroup* PileupOpts = Options::CreateOptionGroup("Pileup Options");
- Options::AddValueOption("-fasta", "FASTA filename", "FASTA reference file", "", m_settings->HasFastaFilename, m_settings->FastaFilename, PileupOpts, "");
- Options::AddOption("-mapqual", "print the mapping qualities", m_settings->IsPrintingPileupMapQualities, PileupOpts);
-
- OptionGroup* SamOpts = Options::CreateOptionGroup("SAM Options");
- Options::AddOption("-noheader", "omit the SAM header from output", m_settings->IsOmittingSamHeader, SamOpts);
-}
-
-ConvertTool::~ConvertTool(void) {
- delete m_settings;
- m_settings = 0;
-
- delete m_impl;
- m_impl = 0;
-}
-
-int ConvertTool::Help(void) {
- Options::DisplayHelp();
- return 0;
-}
-
-int ConvertTool::Run(int argc, char* argv[]) {
+// ConvertToolPrivate implementation
- // parse command line arguments
- Options::Parse(argc, argv, 1);
-
- // run internal ConvertTool implementation, return success/fail
- m_impl = new ConvertToolPrivate(m_settings);
+struct ConvertTool::ConvertToolPrivate {
+
+ // ctor & dtor
+ public:
+ ConvertToolPrivate(ConvertTool::ConvertSettings* settings);
+ ~ConvertToolPrivate(void);
- if ( m_impl->Run() )
- return 0;
- else
- return 1;
-}
-
-// ---------------------------------------------
-// ConvertToolPrivate implementation
+ // interface
+ public:
+ bool Run(void);
+
+ // internal methods
+ private:
+ void PrintBed(const BamAlignment& a);
+ void PrintBedGraph(const BamAlignment& a);
+ void PrintFasta(const BamAlignment& a);
+ void PrintFastq(const BamAlignment& a);
+ void PrintJson(const BamAlignment& a);
+ void PrintSam(const BamAlignment& a);
+ void PrintWiggle(const BamAlignment& a);
+
+ // special case - uses the PileupEngine
+ bool RunPileupConversion(BamMultiReader* reader);
+
+ // data members
+ private:
+ ConvertTool::ConvertSettings* m_settings;
+ RefVector m_references;
+ ostream m_out;
+};
ConvertTool::ConvertToolPrivate::ConvertToolPrivate(ConvertTool::ConvertSettings* settings)
: m_settings(settings)
bool ConvertTool::ConvertToolPrivate::Run(void) {
- bool convertedOk = true;
-
// ------------------------------------
// initialize conversion input/output
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;
+ 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;
}
}
m_out.rdbuf(outFile.rdbuf());
}
- // ------------------------
+ // -------------------------------------
+ // do conversion based on format
+
+ bool convertedOk = true;
+
// pileup is special case
- if ( m_settings->Format == FORMAT_PILEUP ) {
-
- // initialize pileup input/output
- Pileup pileup(&reader, &m_out);
-
- // ---------------------------
- // configure pileup settings
-
- if ( m_settings->HasRegion )
- pileup.SetRegion(region);
-
- if ( m_settings->HasFastaFilename )
- pileup.SetFastaFilename(m_settings->FastaFilename);
-
- pileup.SetIsPrintingMapQualities( m_settings->IsPrintingPileupMapQualities );
-
- // run pileup
- convertedOk = pileup.Run();
- }
+ // conversion not done per alignment, like the other formats
+ if ( m_settings->Format == FORMAT_PILEUP )
+ convertedOk = RunPileupConversion(&reader);
- // -------------------------------------
- // else determine 'simpler' format type
+ // 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;
convertedOk = false;
}
- // if SAM format & not omitting header, print SAM header
- if ( (m_settings->Format == FORMAT_SAM) && !m_settings->IsOmittingSamHeader ) {
- string headerText = reader.GetHeaderText();
- m_out << headerText;
- }
-
- // ------------------------
- // do conversion
+ // 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);
- }
+ 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;
// Conversion/output methods
// ----------------------------------------------------------
-void ConvertTool::ConvertToolPrivate::PrintBed(const BamAlignment& a) {
+void ConvertTool::ConvertToolPrivate::PrintBed(const BamAlignment& a) {
// tab-delimited, 0-based half-open
// (e.g. a 50-base read aligned to pos 10 could have BED coordinates (10, 60) instead of BAM coordinates (10, 59) )
}
m_out << "}" << endl;
-
}
// print BamAlignment in SAM format
void ConvertTool::ConvertToolPrivate::PrintWiggle(const BamAlignment& a) {
;
}
+
+bool ConvertTool::ConvertToolPrivate::RunPileupConversion(BamMultiReader* reader) {
+
+ // check for valid BamMultiReader
+ if ( reader == 0 ) return false;
+
+ // set up our pileup format 'visitor'
+ ConvertPileupFormatVisitor* v = new ConvertPileupFormatVisitor(m_references,
+ m_settings->FastaFilename,
+ m_settings->IsPrintingPileupMapQualities,
+ &m_out);
+
+ // set up PileupEngine
+ PileupEngine pileup;
+ pileup.AddVisitor(v);
+
+ // iterate through data
+ BamAlignment al;
+ while ( reader->GetNextAlignment(al) )
+ pileup.AddAlignment(al);
+ pileup.Flush();
+
+ // clean up
+ delete v;
+ v = 0;
+
+ // return success
+ return true;
+}
+
+// ---------------------------------------------
+// ConvertTool implementation
+
+ConvertTool::ConvertTool(void)
+ : AbstractTool()
+ , m_settings(new ConvertSettings)
+ , m_impl(0)
+{
+ // set program details
+ Options::SetProgramInfo("bamtools convert", "converts BAM to a number of other formats", "-format <FORMAT> [-in <filename> -in <filename> ...] [-out <filename>] [other options]");
+
+ // set up options
+ OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+ Options::AddValueOption("-format", "FORMAT", "the output file format - see README for recognized formats", "", m_settings->HasFormat, m_settings->Format, IO_Opts);
+
+ OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
+ Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for better performance, and is read automatically if it exists as <filename>.bai. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
+
+ OptionGroup* PileupOpts = Options::CreateOptionGroup("Pileup Options");
+ Options::AddValueOption("-fasta", "FASTA filename", "FASTA reference file", "", m_settings->HasFastaFilename, m_settings->FastaFilename, PileupOpts, "");
+ Options::AddOption("-mapqual", "print the mapping qualities", m_settings->IsPrintingPileupMapQualities, PileupOpts);
+
+ OptionGroup* SamOpts = Options::CreateOptionGroup("SAM Options");
+ Options::AddOption("-noheader", "omit the SAM header from output", m_settings->IsOmittingSamHeader, SamOpts);
+}
+
+ConvertTool::~ConvertTool(void) {
+ delete m_settings;
+ m_settings = 0;
+
+ delete m_impl;
+ m_impl = 0;
+}
+
+int ConvertTool::Help(void) {
+ Options::DisplayHelp();
+ return 0;
+}
+
+int ConvertTool::Run(int argc, char* argv[]) {
+
+ // parse command line arguments
+ Options::Parse(argc, argv, 1);
+
+ // run internal ConvertTool implementation, return success/fail
+ m_impl = new ConvertToolPrivate(m_settings);
+
+ if ( m_impl->Run() )
+ return 0;
+ else
+ return 1;
+}
+
+// ---------------------------------------------
+// ConvertPileupFormatVisitor implementation
+
+ConvertPileupFormatVisitor::ConvertPileupFormatVisitor(const RefVector& references,
+ const string& fastaFilename,
+ const bool isPrintingMapQualities,
+ ostream* out)
+ : PileupVisitor()
+ , m_hasFasta(false)
+ , m_isPrintingMapQualities(isPrintingMapQualities)
+ , m_out(out)
+ , m_references(references)
+{
+ // set up Fasta reader if file is provided
+ if ( !fastaFilename.empty() ) {
+
+ // check for FASTA index
+ string indexFilename = "";
+ if ( Utilities::FileExists(fastaFilename + ".fai") )
+ indexFilename = fastaFilename + ".fai";
+
+ // open FASTA file
+ if ( m_fasta.Open(fastaFilename, indexFilename) )
+ m_hasFasta = true;
+ }
+}
+
+ConvertPileupFormatVisitor::~ConvertPileupFormatVisitor(void) {
+ // be sure to close Fasta reader
+ if ( m_hasFasta ) {
+ m_fasta.Close();
+ m_hasFasta = false;
+ }
+}
+
+void ConvertPileupFormatVisitor::Visit(const PileupPosition& pileupData ) {
+
+ // skip if no alignments at this position
+ if ( pileupData.PileupAlignments.empty() ) return;
+
+ // retrieve reference name
+ const string& referenceName = m_references[pileupData.RefId].RefName;
+ const int& position = pileupData.Position;
+
+ // retrieve reference base from FASTA file, if one provided; otherwise default to 'N'
+ char referenceBase('N');
+ if ( m_hasFasta && (pileupData.Position < m_references[pileupData.RefId].RefLength) ) {
+ if ( !m_fasta.GetBase(pileupData.RefId, pileupData.Position, referenceBase ) ) {
+ cerr << "Pileup error : Could not read reference base from FASTA file" << endl;
+ return;
+ }
+ }
+
+ // get count of alleles at this position
+ const int numberAlleles = pileupData.PileupAlignments.size();
+
+ // -----------------------------------------------------------
+ // build strings based on alleles at this positionInAlignment
+
+ stringstream bases("");
+ stringstream baseQualities("");
+ stringstream mapQualities("");
+
+ // iterate over alignments at this pileup position
+ vector<PileupAlignment>::const_iterator pileupIter = pileupData.PileupAlignments.begin();
+ vector<PileupAlignment>::const_iterator pileupEnd = pileupData.PileupAlignments.end();
+ for ( ; pileupIter != pileupEnd; ++pileupIter ) {
+ const PileupAlignment pa = (*pileupIter);
+ const BamAlignment& ba = pa.Alignment;
+
+ // if beginning of read segment
+ if ( pa.IsSegmentBegin )
+ bases << '^' << ( ((int)ba.MapQuality > 93) ? (char)126 : (char)((int)ba.MapQuality+33) );
+
+ // if current base is not a DELETION
+ if ( !pa.IsCurrentDeletion ) {
+
+ // get base at current position
+ char base = ba.QueryBases.at(pa.PositionInAlignment);
+
+ // if base matches reference
+ if ( base == '=' ||
+ toupper(base) == toupper(referenceBase) ||
+ tolower(base) == tolower(referenceBase) )
+ {
+ base = (ba.IsReverseStrand() ? ',' : '.' );
+ }
+
+ // mismatches reference
+ else base = (ba.IsReverseStrand() ? tolower(base) : toupper(base) );
+
+ // store base
+ bases << base;
+
+ // if next position contains insertion
+ if ( pa.IsNextInsertion ) {
+ bases << '+' << pa.InsertionLength;
+ for (int i = 1; i <= pa.InsertionLength; ++i) {
+ char insertedBase = (char)ba.QueryBases.at(pa.PositionInAlignment + i);
+ bases << (ba.IsReverseStrand() ? (char)tolower(insertedBase) : (char)toupper(insertedBase) );
+ }
+ }
+
+ // if next position contains DELETION
+ else if ( pa.IsNextDeletion ) {
+ bases << '-' << pa.DeletionLength;
+ for (int i = 1; i <= pa.DeletionLength; ++i) {
+ char deletedBase('N');
+ if ( m_hasFasta && (pileupData.Position+i < m_references[pileupData.RefId].RefLength) ) {
+ if ( !m_fasta.GetBase(pileupData.RefId, pileupData.Position+i, deletedBase ) ) {
+ cerr << "Pileup error : Could not read reference base from FASTA file" << endl;
+ return;
+ }
+ }
+ bases << (ba.IsReverseStrand() ? (char)tolower(deletedBase) : (char)toupper(deletedBase) );
+ }
+ }
+ }
+
+ // otherwise, DELETION
+ else bases << '*';
+
+ // if end of read segment
+ if ( pa.IsSegmentEnd ) bases << '$';
+
+ // store current base quality
+ baseQualities << ba.Qualities.at(pa.PositionInAlignment);
+
+ // save alignment map quality if desired
+ if ( m_isPrintingMapQualities )
+ mapQualities << ( ((int)ba.MapQuality > 93) ? (char)126 : (char)((int)ba.MapQuality+33) );
+ }
+
+ // ----------------------
+ // print results
+
+ // tab-delimited
+ // <refName> <1-based pos> <refBase> <numberAlleles> <bases> <qualities> [mapQuals]
+
+ const string TAB = "\t";
+ *m_out << referenceName << TAB
+ << position + 1 << TAB
+ << referenceBase << TAB
+ << numberAlleles << TAB
+ << bases.str() << TAB
+ << baseQualities.str() << TAB
+ << mapQualities.str() << endl;
+}
projects / bamtools.git / blobdiff