static inline void PackUnsignedInt(char* buffer, unsigned int value);\r
// packs an unsigned short into the specified buffer\r
static inline void PackUnsignedShort(char* buffer, unsigned short value);\r
+ \r
// unpacks a buffer into a signed int\r
static inline signed int UnpackSignedInt(char* buffer);\r
- // unpacks a buffer into a unsigned int\r
+ // unpacks a buffer into an unsigned int\r
static inline unsigned int UnpackUnsignedInt(char* buffer);\r
- // unpacks a buffer into a unsigned short\r
+ // unpacks a buffer into a signed short\r
+ static inline signed short UnpackSignedShort(char* buffer);\r
+ // unpacks a buffer into an unsigned short\r
static inline unsigned short UnpackUnsignedShort(char* buffer);\r
+ // unpacks a buffer into a double\r
+ static inline double UnpackDouble(char* buffer);\r
+ // unpacks a buffer into a float\r
+ static inline float UnpackFloat(char* buffer); \r
+ \r
+ // unpacks a buffer into a signed int\r
+ static inline signed int UnpackSignedInt(const char* buffer);\r
+ // unpacks a buffer into an unsigned int\r
+ static inline unsigned int UnpackUnsignedInt(const char* buffer);\r
+ // unpacks a buffer into a signed short\r
+ static inline signed short UnpackSignedShort(const char* buffer);\r
+ // unpacks a buffer into an unsigned short\r
+ static inline unsigned short UnpackUnsignedShort(const char* buffer);\r
+ // unpacks a buffer into a double\r
+ static inline double UnpackDouble(const char* buffer);\r
+ // unpacks a buffer into a float\r
+ static inline float UnpackFloat(const char* buffer); \r
};\r
\r
// -------------------------------------------------------------\r
return un.value;\r
}\r
\r
+// 'unpacks' a buffer into a signed short\r
+inline\r
+signed short BgzfData::UnpackSignedShort(char* buffer) {\r
+ union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ return un.value;\r
+}\r
+\r
// 'unpacks' a buffer into an unsigned short\r
inline\r
unsigned short BgzfData::UnpackUnsignedShort(char* buffer) {\r
return un.value;\r
}\r
\r
+// 'unpacks' a buffer into a double\r
+inline\r
+double BgzfData::UnpackDouble(char* buffer) {\r
+ union { double value; unsigned char valueBuffer[sizeof(double)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ un.valueBuffer[2] = buffer[2];\r
+ un.valueBuffer[3] = buffer[3];\r
+ un.valueBuffer[4] = buffer[4];\r
+ un.valueBuffer[5] = buffer[5];\r
+ un.valueBuffer[6] = buffer[6];\r
+ un.valueBuffer[7] = buffer[7];\r
+ return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into a float\r
+inline\r
+float BgzfData::UnpackFloat(char* buffer) {\r
+ union { float value; unsigned char valueBuffer[sizeof(float)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ un.valueBuffer[2] = buffer[2];\r
+ un.valueBuffer[3] = buffer[3];\r
+ return un.value;\r
+}\r
+\r
+// ---------\r
+\r
+// 'unpacks' a buffer into a signed int\r
+inline\r
+signed int BgzfData::UnpackSignedInt(const char* buffer) {\r
+ union { signed int value; unsigned char valueBuffer[sizeof(signed int)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ un.valueBuffer[2] = buffer[2];\r
+ un.valueBuffer[3] = buffer[3];\r
+ return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into an unsigned int\r
+inline\r
+unsigned int BgzfData::UnpackUnsignedInt(const char* buffer) {\r
+ union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ un.valueBuffer[2] = buffer[2];\r
+ un.valueBuffer[3] = buffer[3];\r
+ return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into a signed short\r
+inline\r
+signed short BgzfData::UnpackSignedShort(const char* buffer) {\r
+ union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into an unsigned short\r
+inline\r
+unsigned short BgzfData::UnpackUnsignedShort(const char* buffer) {\r
+ union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into a double\r
+inline\r
+double BgzfData::UnpackDouble(const char* buffer) {\r
+ union { double value; unsigned char valueBuffer[sizeof(double)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ un.valueBuffer[2] = buffer[2];\r
+ un.valueBuffer[3] = buffer[3];\r
+ un.valueBuffer[4] = buffer[4];\r
+ un.valueBuffer[5] = buffer[5];\r
+ un.valueBuffer[6] = buffer[6];\r
+ un.valueBuffer[7] = buffer[7];\r
+ return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into a float\r
+inline\r
+float BgzfData::UnpackFloat(const char* buffer) {\r
+ union { float value; unsigned char valueBuffer[sizeof(float)]; } un;\r
+ un.value = 0;\r
+ un.valueBuffer[0] = buffer[0];\r
+ un.valueBuffer[1] = buffer[1];\r
+ un.valueBuffer[2] = buffer[2];\r
+ un.valueBuffer[3] = buffer[3];\r
+ return un.value;\r
+}\r
+\r
} // namespace BamTools\r
\r
#endif // BGZF_H\r
// ***************************************************************************
-// bamtools_sam.h (c) 2010 Derek Barnett, Erik Garrison
+// bamtools_sam.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 1 June 2010
+// Last modified: 2 June 2010
// ---------------------------------------------------------------------------
// Prints a BAM file in the text-based SAM format.
// ***************************************************************************
#include <cstdlib>
#include <iostream>
+#include <sstream>
#include <string>
#include "bamtools_sam.h"
#include "bamtools_options.h"
#include "BamReader.h"
+#include "BGZF.h"
using namespace std;
using namespace BamTools;
-RefVector references;
+static RefVector references;
// ---------------------------------------------
// print BamAlignment in SAM format
// tab-delimited
// <QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> [ <TAG>:<VTYPE>:<VALUE> [...] ]
- // ******************************* //
- // ** NOT FULLY IMPLEMENTED YET ** //
- //******************************** //
- //
- // Todo : build CIGAR string
- // build TAG string
- // there are some quirks, per the spec, regarding when to use '=' or not
- //
- // ******************************* //
-
- //
- // do validity check on RefID / MateRefID ??
- //
-
- // build CIGAR string
- string cigarString("CIGAR:NOT YET");
-
- // build TAG string
- string tagString("TAG:NOT YET");
-
- // print BamAlignment to stdout in SAM format
- cout << a.Name << '\t'
- << a.AlignmentFlag << '\t'
- << references[a.RefID].RefName << '\t'
- << a.Position << '\t'
- << a.MapQuality << '\t'
- << cigarString << '\t'
- << ( a.IsPaired() ? references[a.MateRefID].RefName : "*" ) << '\t'
- << ( a.IsPaired() ? a.MatePosition : 0 ) << '\t'
- << ( a.IsPaired() ? a.InsertSize : 0 ) << '\t'
- << a.QueryBases << '\t'
- << a.Qualities << '\t'
- << tagString << endl;
+ ostringstream sb("");
+
+ // write name & alignment flag
+ cout << a.Name << "\t" << a.AlignmentFlag << "\t";
+
+ // write reference name
+ if ( (a.RefID >= 0) && (a.RefID < (int)references.size()) ) cout << references[a.RefID].RefName << "\t";
+ else cout << "*\t";
+
+ // write position & map quality
+ cout << a.Position+1 << "\t" << a.MapQuality << "\t";
+
+ // write CIGAR
+ const vector<CigarOp>& cigarData = a.CigarData;
+ if ( cigarData.empty() ) cout << "*\t";
+ else {
+ vector<CigarOp>::const_iterator cigarIter = cigarData.begin();
+ vector<CigarOp>::const_iterator cigarEnd = cigarData.end();
+ for ( ; cigarIter != cigarEnd; ++cigarIter ) {
+ const CigarOp& op = (*cigarIter);
+ cout << op.Length << op.Type;
+ }
+ cout << "\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 ) cout << "=\t";
+ else cout << references[a.MateRefID].RefName << "\t";
+ cout << a.MatePosition+1 << "\t" << a.InsertSize << "\t";
+ }
+ else cout << "*\t0\t0\t";
+
+ // write sequence
+ if ( a.QueryBases.empty() ) cout << "*\t";
+ else cout << a.QueryBases << "\t";
+
+ // write qualities
+ if ( a.Qualities.empty() ) cout << "*";
+ else cout << 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
+ cout << "\t" << a.TagData.substr(index, 2) << ":";
+ index += 2;
+
+ // get data type
+ char type = a.TagData.at(index);
+ ++index;
+
+ switch (type) {
+ case('A') :
+ cout << "A:" << tagData[index];
+ ++index;
+ break;
+
+ case('C') :
+ cout << "i:" << atoi(&tagData[index]);
+ ++index;
+ break;
+
+ case('c') :
+ cout << "i:" << atoi(&tagData[index]);
+ ++index;
+ break;
+
+ case('S') :
+ cout << "i:" << BgzfData::UnpackUnsignedShort(&tagData[index]);
+ index += 2;
+ break;
+
+ case('s') :
+ cout << "i:" << BgzfData::UnpackSignedShort(&tagData[index]);
+ index += 2;
+ break;
+
+ case('I') :
+ cout << "i:" << BgzfData::UnpackUnsignedInt(&tagData[index]);
+ index += 4;
+ break;
+
+ case('i') :
+ cout << "i:" << BgzfData::UnpackSignedInt(&tagData[index]);
+ index += 4;
+ break;
+
+ case('f') :
+ cout << "f:" << BgzfData::UnpackFloat(&tagData[index]);
+ index += 4;
+ break;
+
+ case('d') :
+ cout << "d:" << BgzfData::UnpackDouble(&tagData[index]);
+ index += 8;
+ break;
+
+ case('Z') :
+ case('H') :
+ cout << type << ":";
+ while (tagData[index]) {
+ cout << tagData[index];
+ ++index;
+ }
+ ++index;
+ break;
+ }
+ }
+
+ // write stream to stdout
+ cout << sb.str() << endl;
}
// ---------------------------------------------
projects / bamtools.git / commitdiff