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#ifndef DEF_BAMfunctions
#define DEF_BAMfunctions
#include "IncludeDefine.h"
#include SAMTOOLS_BGZF_H
#include SAMTOOLS_SAM_H
#include "ErrorWarning.h"
void outBAMwriteHeader (BGZF* fp, const string &samh, const vector <string> &chrn, const vector <uint> &chrl);
int bam_read1_fromArray(char *bamChar, bam1_t *b);
string bam_cigarString (bam1_t *b);
int reg2bin(int beg, int end);
int bamAttrArrayWrite(int32 attr, const char* tagName, char* attrArray );
int bamAttrArrayWrite(float attr, const char* tagName, char* attrArray );
int bamAttrArrayWrite(char attr, const char* tagName, char* attrArray );
int bamAttrArrayWrite(string &attr, const char* tagName, char* attrArray );
int bamAttrArrayWrite(const vector<char> &attr, const char* tagName, char* attrArray );
int bamAttrArrayWrite(const vector<int32> &attr, const char* tagName, char* attrArray );
int bamAttrArrayWriteSAMtags(string &attrStr, char *attrArray, Parameters &P);
template <class TintType>
TintType bamAttributeInt(const char *bamAux, const char *attrName) {//not tested!!!
const char *attrStart=strstr(bamAux,attrName);
if (attrStart==NULL) return (TintType) -1;
switch (attrStart[2]) {
case ('c'):
return (TintType) *(int8_t*)(attrStart+3);
case ('s'):
return (TintType) *(int16_t*)(attrStart+3);
case ('i'):
return (TintType) *(int32_t*)(attrStart+3);
case ('C'):
return (TintType) *(uint8_t*)(attrStart+3);
case ('S'):
return (TintType) *(uint16_t*)(attrStart+3);
case ('I'):
return (TintType) *(uint32_t*)(attrStart+3);
};
};
template <typename intType>
int bamAttrArrayWriteInt(intType xIn, const char* tagName, char* attrArray, Parameters &P) {//adapted from samtools
attrArray[0]=tagName[0];attrArray[1]=tagName[1];
#define ATTR_RECORD_INT(_intChar,_intType,_intValue) attrArray[2] = _intChar; *(_intType*)(attrArray+3) = (_intType) _intValue; return 3+sizeof(_intType)
int64 x = (int64) xIn;
if (x < 0) {
if (x >= -127) {
ATTR_RECORD_INT('c',int8_t,x);
} else if (x >= -32767) {
ATTR_RECORD_INT('s',int16_t,x);
} else {
ATTR_RECORD_INT('i',int32_t,x);
if (!(x>=-2147483647)) {
ostringstream errOut;
errOut <<"EXITING because of FATAL BUG: integer out of range for BAM conversion: "<< x <<"\n";
errOut <<"SOLUTION: contact Alex Dobin at dobin@cshl.edu\n";
exitWithError(errOut.str(), std::cerr, P.inOut->logMain, EXIT_CODE_BUG, P);
};
};
} else {
if (x <= 255) {
ATTR_RECORD_INT('C',uint8_t,x);
} else if (x <= 65535) {
ATTR_RECORD_INT('S',uint16_t,x);
} else {
ATTR_RECORD_INT('I',uint32_t,x);
if (!(x<=4294967295)) {
ostringstream errOut;
errOut <<"EXITING because of FATAL BUG: integer out of range for BAM conversion: "<< x <<"\n";
errOut <<"SOLUTION: contact Alex Dobin at dobin@cshl.edu\n";
exitWithError(errOut.str(), std::cerr, P.inOut->logMain, EXIT_CODE_BUG, P);
};
};
};
};
#endif
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