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/*
* inserts sequences into the SA and SAi indices
*/
#include "Genome.h"
#include "genomeScanFastaFiles.h"
#include "insertSeqSA.h"
#include "TimeFunctions.h"
void Genome::insertSequences()
{
if (pGe.gFastaFiles.at(0)!="-")
{
time_t rawtime;
time ( &rawtime );
P.inOut->logMain << timeMonthDayTime(rawtime) << " ..... inserting extra sequences into genome indexes" <<endl;
//move the junctions to free up space for seqs
// chrStart/Name/Length nChrReal include the extra sequences
// nGenome is the old, small genome size
uint sjdblen=nGenome-(chrStart.back()-genomeInsertL);//length of sjdb sequences
memmove(G+chrStart.back(),G+chrStart.back()-genomeInsertL,sjdblen);
memset(G+chrStart.back()-genomeInsertL, GENOME_spacingChar, genomeInsertL);//fill empty space with spacing characters
genomeScanFastaFiles(P, G+chrStart.back()-genomeInsertL, true, *this); //read the seqs from file(s) into the free space
uint64 nGenomeOld=nGenome;
nGenome=chrStart.back()+sjdblen;
//insert new sequences into the SA
insertSeqSA(SA, SAinsert, SAi, G, G+chrStart.back()-genomeInsertL, nGenomeOld-sjdblen, genomeInsertL, sjdblen, P, *this);
//insert new sequences into the SAi
//update P
//save the genome if necessary
};
};
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