// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 7 June 2010
// ---------------------------------------------------------------------------
// Converts between BAM and a number of other formats
// ***************************************************************************
#include <iostream>
+#include <sstream>
#include <string>
#include <vector>
#include "bamtools_convert.h"
-#include "bamtools_format.h"
+//#include "bamtools_format.h"
#include "bamtools_options.h"
+#include "BGZF.h"
#include "BamReader.h"
#include "BamMultiReader.h"
using namespace std;
using namespace BamTools;
+static RefVector references;
+
+namespace BamTools {
+
+ static const string FORMAT_FASTA = "fasta";
+ static const string FORMAT_FASTQ = "fastq";
+ static const string FORMAT_JSON = "json";
+ static const string FORMAT_SAM = "sam";
+
+ void PrintFASTA(ostream& out, const BamAlignment& a);
+ void PrintFASTQ(ostream& out, const BamAlignment& a);
+ void PrintJSON(ostream& out, const BamAlignment& a);
+ void PrintSAM(ostream& out, const BamAlignment& a);
+
+} // namespace BamTools
+
// ---------------------------------------------
// ConvertSettings implementation
int ConvertTool::Run(int argc, char* argv[]) {
+ bool convertedOk = true;
+
// parse command line arguments
Options::Parse(argc, argv, 1);
// open files
BamReader reader;
reader.Open(m_settings->InputFilename);
+ references = reader.GetReferenceData();
- // do conversion
+ // ----------------------------------------
+ // do conversion,depending on desired output format
+
+ // FASTA
+ if ( m_settings->Format == FORMAT_FASTA ) {
+ //cout << "Converting to FASTA" << endl;
+ }
+ // FASTQ
+ else if ( m_settings->Format == FORMAT_FASTQ) {
+ //cout << "Converting to FASTQ" << endl;
+ }
+ // JSON
+ else if ( m_settings->Format == FORMAT_JSON ) {
+ //cout << "Converting to JSON" << endl;
+ BamAlignment alignment;
+ while ( reader.GetNextAlignment(alignment) ) {
+ PrintJSON(cout, alignment);
+ }
+
+ }
+
+ // SAM
+ else if ( m_settings->Format == FORMAT_SAM ) {
+ BamAlignment alignment;
+ while ( reader.GetNextAlignment(alignment) ) {
+ PrintSAM(cout, alignment);
+ }
+ }
+ // uncrecognized format
+ else {
+ cerr << "Unrecognized format: " << m_settings->Format << endl;
+ cerr << "Please see help|README (?) for details on supported formats " << endl;
+ convertedOk = false;
+ }
+ // ------------------------
// clean up & exit
reader.Close();
- return 0;
-}
\ No newline at end of file
+ return (int)convertedOk;
+}
+
+// ----------------------------------------------------------
+// Conversion/output methods
+// ----------------------------------------------------------
+
+// print BamAlignment in FASTA format
+void BamTools::PrintFASTA(ostream& out, const BamAlignment& a) {
+
+}
+
+// print BamAlignment in FASTQ format
+void BamTools::PrintFASTQ(ostream& out, const BamAlignment& a) {
+
+}
+
+// print BamAlignment in JSON format
+void BamTools::PrintJSON(ostream& out, const BamAlignment& a) {
+
+ // tab-delimited
+ // <QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> [ <TAG>:<VTYPE>:<VALUE> [...] ]
+
+ // write name & alignment flag
+ out << "{\"name\":\"" << a.Name << "\",\"alignmentFlag\":\""
+ << a.AlignmentFlag << "\",";
+
+ // write reference name
+ if ( (a.RefID >= 0) && (a.RefID < (int)references.size()) ) out << "\"reference\":\"" << references[a.RefID].RefName << "\",";
+ //else out << "*\t";
+
+ // write position & map quality
+ out << "\"position\":" << a.Position+1 << ",\"mapQuality\":" << a.MapQuality << ",";
+
+ // write CIGAR
+ const vector<CigarOp>& cigarData = a.CigarData;
+ if ( !cigarData.empty() ) {
+ 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) out << ",";
+ out << "\"" << op.Length << op.Type << "\"";
+ }
+ out << "],";
+ }
+
+ // write mate reference name, mate position, & insert size
+ if ( a.IsPaired() && (a.MateRefID >= 0) && (a.MateRefID < (int)references.size()) ) {
+ out << "\"mate\":{"
+ << "\"reference\":\"" << references[a.MateRefID].RefName << "\","
+ << "\"position\":" << a.MatePosition+1
+ << ",\"insertSize\":" << a.InsertSize << "},";
+ }
+
+ // write sequence
+ if ( !a.QueryBases.empty() ) {
+ out << "\"queryBases\":\"" << a.QueryBases << "\",";
+ }
+
+ // write qualities
+ if ( !a.Qualities.empty() ) {
+ out << "\"qualities\":\"" << a.Qualities << "\",";
+ }
+
+ // write tag data
+ const char* tagData = a.TagData.c_str();
+ const size_t tagDataLength = a.TagData.length();
+ size_t index = 0;
+ if (index < tagDataLength) {
+
+ out << "\"tags\":{";
+
+ while ( index < tagDataLength ) {
+
+ if (index > 0)
+ out << ",";
+
+ // write tag name
+ out << "\"" << a.TagData.substr(index, 2) << "\":";
+ index += 2;
+
+ // get data type
+ char type = a.TagData.at(index);
+ ++index;
+
+ switch (type) {
+ case('A') :
+ out << "\"" << tagData[index] << "\"";
+ ++index;
+ break;
+
+ case('C') :
+ out << (int)tagData[index];
+ ++index;
+ break;
+
+ case('c') :
+ out << (int)tagData[index];
+ ++index;
+ break;
+
+ case('S') :
+ out << BgzfData::UnpackUnsignedShort(&tagData[index]);
+ index += 2;
+ break;
+
+ case('s') :
+ out << BgzfData::UnpackSignedShort(&tagData[index]);
+ index += 2;
+ break;
+
+ case('I') :
+ out << BgzfData::UnpackUnsignedInt(&tagData[index]);
+ index += 4;
+ break;
+
+ case('i') :
+ out << BgzfData::UnpackSignedInt(&tagData[index]);
+ index += 4;
+ break;
+
+ case('f') :
+ out << BgzfData::UnpackFloat(&tagData[index]);
+ index += 4;
+ break;
+
+ case('d') :
+ out << BgzfData::UnpackDouble(&tagData[index]);
+ index += 8;
+ break;
+
+ case('Z') :
+ case('H') :
+ out << "\"";
+ while (tagData[index]) {
+ out << tagData[index];
+ ++index;
+ }
+ out << "\"";
+ ++index;
+ break;
+ }
+
+ if ( tagData[index] == '\0') break;
+ }
+
+ out << "}";
+ }
+
+ out << "}" << endl;
+
+}
+
+// print BamAlignment in SAM format
+void BamTools::PrintSAM(ostream& out, const BamAlignment& a) {
+
+ // tab-delimited
+ // <QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> [ <TAG>:<VTYPE>:<VALUE> [...] ]
+
+ // write name & alignment flag
+ out << a.Name << "\t" << a.AlignmentFlag << "\t";
+
+ // write reference name
+ if ( (a.RefID >= 0) && (a.RefID < (int)references.size()) ) out << references[a.RefID].RefName << "\t";
+ else out << "*\t";
+
+ // write position & map quality
+ out << a.Position+1 << "\t" << a.MapQuality << "\t";
+
+ // write CIGAR
+ const vector<CigarOp>& cigarData = a.CigarData;
+ if ( cigarData.empty() ) 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);
+ out << op.Length << op.Type;
+ }
+ out << "\t";
+ }
+
+ // write mate reference name, mate position, & insert size
+ if ( a.IsPaired() && (a.MateRefID >= 0) && (a.MateRefID < (int)references.size()) ) {
+ if ( a.MateRefID == a.RefID ) out << "=\t";
+ else out << references[a.MateRefID].RefName << "\t";
+ out << a.MatePosition+1 << "\t" << a.InsertSize << "\t";
+ }
+ else out << "*\t0\t0\t";
+
+ // write sequence
+ if ( a.QueryBases.empty() ) out << "*\t";
+ else out << a.QueryBases << "\t";
+
+ // write qualities
+ if ( a.Qualities.empty() ) out << "*";
+ else 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
+ out << "\t" << a.TagData.substr(index, 2) << ":";
+ index += 2;
+
+ // get data type
+ char type = a.TagData.at(index);
+ ++index;
+
+ switch (type) {
+ case('A') :
+ out << "A:" << tagData[index];
+ ++index;
+ break;
+
+ case('C') :
+ out << "i:" << (int)tagData[index];
+ ++index;
+ break;
+
+ case('c') :
+ out << "i:" << (int)tagData[index];
+ ++index;
+ break;
+
+ case('S') :
+ out << "i:" << BgzfData::UnpackUnsignedShort(&tagData[index]);
+ index += 2;
+ break;
+
+ case('s') :
+ out << "i:" << BgzfData::UnpackSignedShort(&tagData[index]);
+ index += 2;
+ break;
+
+ case('I') :
+ out << "i:" << BgzfData::UnpackUnsignedInt(&tagData[index]);
+ index += 4;
+ break;
+
+ case('i') :
+ out << "i:" << BgzfData::UnpackSignedInt(&tagData[index]);
+ index += 4;
+ break;
+
+ case('f') :
+ out << "f:" << BgzfData::UnpackFloat(&tagData[index]);
+ index += 4;
+ break;
+
+ case('d') :
+ out << "d:" << BgzfData::UnpackDouble(&tagData[index]);
+ index += 8;
+ break;
+
+ case('Z') :
+ case('H') :
+ out << type << ":";
+ while (tagData[index]) {
+ out << tagData[index];
+ ++index;
+ }
+ ++index;
+ break;
+ }
+
+ if ( tagData[index] == '\0') break;
+ }
+
+ out << endl;
+}
projects / bamtools.git / blobdiff