/*! \brief Compute effect of soft and hard clipping on coordinates
* When offset is applied to either reference position or query position
* the origin of sequencing can be identified.
* @return offset of origin of sequencing from start or end
* @deprecated - Use cigar operation directly to avoid constructing multiple Cigar objects
*/
int getOriginOffset() const
{
assert(m_dataPtr);
// Now delegated to Cigar
const Strand & strand = getStrand();
if(strand == FORWARD) {
return getCigar().getOriginOffsetForward();
} else if(strand == REVERSE) {
return getCigar().getOriginOffsetReverse();
}
return 0; // Strand NA?
}
static uint64_t getReferenceLength(uint8_t const * D)
{
uint64_t reflen = 0;
uint32_t const ncigar = getNCigar(D);
uint8_t const * cigar = getCigar(D);
for ( uint32_t i = 0; i < ncigar; ++i, cigar+=4 )
{
uint32_t const v = getLEInteger(cigar,4);
uint8_t const op = v & ((1ull<<(4))-1);
switch ( op )
{
case 0: // M
case 2: // D
case 3: // N
case 7: // =
case 8: // X
reflen += (v >> 4) & ((1ull<<(32-4))-1);
break;
}
}
return reflen;
}
static uint64_t getLseqByCigar(uint8_t const * D)
{
uint64_t seqlen = 0;
uint64_t const ncigar = getNCigar(D);
uint8_t const * cigar = getCigar(D);
for ( uint32_t i = 0; i < ncigar; ++i, cigar+=4 )
{
uint32_t const v = getLEInteger(cigar,4);
uint8_t const op = v & ((1ull<<(4))-1);
// MIS=X
switch ( op )
{
case 0: // M
case 1: // I
case 4: // S
case 7: // =
case 8: // X
seqlen += (v >> 4) & ((1ull<<(32-4))-1);
break;
}
}
return seqlen;
}
static uint64_t getFrontClipping(uint8_t const * D)
{
uint32_t const ncigar = getNCigar(D);
uint8_t const * cigar = getCigar(D);
uint64_t frontclip = 0;
for ( uint32_t i = 0; i < ncigar; ++i, cigar+=4 )
{
uint32_t const v = getLEInteger(cigar,4);
uint8_t const op = v & ((1ull<<(4))-1);
if ( op == 4 /* S */ || op == 5 /* H */ )
frontclip += static_cast<int64_t>((v >> 4) & ((1ull<<(32-4))-1));
else
break;
}
static uint64_t getNumPreCigarBytes(uint8_t const * D)
{
return getCigar(D) - D;
}
static uint32_t getCigarField(uint8_t const * D, uint64_t const i) { return getLEInteger(getCigar(D)+4*i,4); }
