void Contig::updateContig(BamAlignment b, int max_nsert, bool is_mp) {
readStatus read_status = computeReadType(b, max_nsert, is_mp);
uint32_t readLength = b.Length;
uint32_t iSize = abs(b.InsertSize);
uint32_t startRead = b.Position;
uint32_t endRead = startRead + readLength ; // position where reads ends
uint32_t startMateRead = b.MatePosition;
if (read_status == unmapped or read_status == lowQualty) {
return;
}
if (read_status != unmapped and read_status != lowQualty) { //if the read is aligned and is not duplicated or low quality use it in cov computation
updateCov(startRead, endRead, readCov); // update coverage
}
if (b.IsFirstMate() && read_status == pair_proper) {
int iSize = abs(b.InsertSize);
if(startRead < startMateRead) {
updateCov(startRead, startRead + iSize, insertCov);
} else {
updateCov(startMateRead, startMateRead + iSize, insertCov);
}
}
switch (read_status) {
case singleton:
updateCov(startRead, endRead, singCov);
break;
case pair_wrongChrs:
updateCov(startRead, endRead, mdcCov);
break;
case pair_wrongDistance:
updateCov(startRead, endRead, woCov); //
break;
case pair_wrongOrientation:
updateCov(startRead, endRead, woCov);
break;
case pair_proper:
updateCov(startRead, endRead, cmCov);
break;
default:
cout << read_status << " --> This should never be printed\n";
break;
}
}
void Contig::updateContig(bam1_t* b) {
const bam1_core_t* core = &b->core;
uint32_t* cigar = bam1_cigar(b);
int32_t alignmentLength = 0;
int32_t startRead=0;
int32_t endRead=0;
int32_t startPaired=0;
int32_t startInsert=0;
int32_t endInsert=0;
uint32_t iSize=0;
alignmentLength = bam_cigar2qlen(core,cigar);
//&& !(core->flag&BAM_FSECONDARY)
if (core->flag&BAM_FUNMAP) { // if read is unmapped discard
return;
} else if(!(core->flag&BAM_FUNMAP) && !(core->flag&BAM_FDUP) && !(core->flag&BAM_FQCFAIL)) { // if read has been mapped and it is not a DUPLICATE or a SECONDARY alignment
startRead = core->pos; // start position on the contig
endRead = startRead + alignmentLength ; // position where reads ends
updateCov(startRead, endRead, readCov); // update coverage
iSize = abs(core->isize);
if ((core->flag&BAM_FREAD1) //First in pair
&& !(core->flag&BAM_FMUNMAP) /*Mate is also mapped!*/
&& (core->tid == core->mtid) /*Mate on the same chromosome*/
) {
startPaired = core->mpos;
if(startRead < startPaired) {
iSize = (startPaired + core->l_qseq -1) - startRead; // insert size, I consider both reads of the same length
startInsert = startRead;
endInsert = startRead + iSize;
if (minInsert <= iSize && iSize <= maxInsert) { //useful to compute CE stats
//updateCov(startInsert,endInsert, insertCov); // update spanning coverage
//cout << startInsert << " " << startPaired << " " << endInsert << "\n";
}
if(!(core->flag&BAM_FREVERSE) && (core->flag&BAM_FMREVERSE) ) { //
//here reads are correctly oriented
if (minInsert <= iSize && iSize <= maxInsert) { //this is a right insert
updateCov(startRead, endRead, cmCov); // update good read coverage
updateCov(startInsert,endInsert, insertCov);
} else {
//pair is wrongly oriented
updateCov(startRead, endRead, woCov);
}
} else {
//pair is wrongly oriented
updateCov(startRead, endRead, woCov);
}
} else {
iSize = (startRead + alignmentLength - 1) - startPaired;
startInsert = startPaired;
endInsert = startInsert + iSize;
if (minInsert <= iSize && iSize <= maxInsert) { //useful to compute CE stats
//updateCov(startInsert,endInsert, insertCov); // update spanning coverage
//cout << startInsert << " " << startPaired << " " << endInsert << "\n";
}
if((core->flag&BAM_FREVERSE) && !(core->flag&BAM_FMREVERSE) ) { //
//here reads are correctly oriented
if (minInsert <= iSize && iSize <= maxInsert) { //this is a right insert
updateCov(startRead, endRead, cmCov); // update good read coverage
updateCov(startInsert,endInsert, insertCov);
} else {
//pair is wrongly oriented
updateCov(startRead, endRead, woCov);
}
} else {
updateCov(startRead, endRead, woCov);
}
}
} else if ((core->flag&BAM_FREAD2) //Second in pair
&& !(core->flag&BAM_FMUNMAP) /*Mate is also mapped!*/
&& (core->tid == core->mtid) /*Mate on the same chromosome*/
) {
startPaired = core->mpos;
if(startRead > startPaired) {
iSize = (startRead + alignmentLength -1) - startPaired;
if((core->flag&BAM_FREVERSE) && !(core->flag&BAM_FMREVERSE) ) { //
//here reads are correctly oriented
if (minInsert <= iSize && iSize <= maxInsert) { //this is a right insert, no need to update insert coverage
updateCov(startRead, endRead, cmCov); // update good read coverage
} else {
//pair is wrongly oriented
updateCov(startRead, endRead, woCov);
}
} else {
//pair is wrongly oriented
updateCov(startRead, endRead, woCov);
}
} else {
iSize = (startPaired + core->l_qseq -1) - startRead;
if(!(core->flag&BAM_FREVERSE) && (core->flag&BAM_FMREVERSE) ) { //
//here reads are correctly oriented
if (minInsert <= iSize && iSize <= maxInsert) { //this is a right insert, no need to update insert coverage
updateCov(startRead, endRead, cmCov); // update good read coverage
} else {
//pair is wrongly oriented
updateCov(startRead, endRead, woCov);
}
} else {
//pair is wrongly oriented
updateCov(startRead, endRead, woCov);
}
}
} else if (core->tid != core->mtid && !(core->flag&BAM_FMUNMAP)) {
//Count inter-chrom pairs
updateCov(startRead, endRead, mdcCov);
} else if(core->flag&BAM_FMUNMAP) {
// if mate read is unmapped
updateCov(startRead, endRead, singCov);
}
}
}
