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#include "SoloFeature.h"
#include "BAMfunctions.h"
#include "SequenceFuns.h"
void SoloFeature::addBAMtags(char *&bam0, uint32 &size0, char *bam1)
{//add extra tags to the BAM record
uint64 iread = * ((uint64*) (bam0+size0));
iread = iread >> 32; //iRead was encoded in the upper 32 bitsls
string cb="-";
string umi="-";
if (readInfo[iread].cb+1 != 0)
cb = pSolo.cbWLstr[readInfo[iread].cb];
if (readInfo[iread].umi+1 != 0)
umi = convertNuclInt64toString(readInfo[iread].umi, pSolo.umiL);
memcpy(bam1, bam0, size0);
size0 += bamAttrArrayWrite(cb, "CB", bam1+size0);
size0 += bamAttrArrayWrite(umi, "UB", bam1+size0);
uint32 *bam1i = (uint32*) bam1;
bam1i[0] = size0-sizeof(uint32);
bam0=bam1;
};
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