static void fillFrag(
::libmaus::bambam::BamAlignment const & p,
::libmaus::bambam::BamHeader const & header,
::libmaus::bambam::ReadEnds & RE
)
{
RE.libraryId = p.getLibraryId(header);
RE.read1Sequence = p.getRefIDChecked() + 1;
RE.read1Coordinate = p.getCoordinate() + 1;
RE.orientation = p.isReverse() ? ::libmaus::bambam::ReadEnds::R : ::libmaus::bambam::ReadEnds::F;
RE.read1IndexInFile = p.getRank();
RE.score = p.getScore();
if ( p.isPaired() && (!p.isMateUnmap()) )
RE.read2Sequence = p.getNextRefIDChecked() + 1;
char const * readname = p.getName();
char const * readnamee = readname + (p.getLReadName()-1);
int cnt[2] = { 0,0 };
for ( char const * c = readname; c != readnamee; ++c )
cnt [ (static_cast<int>(*c) - ':') == 0 ] ++;
bool const rnparseok = (cnt[1] == 4);
// parse tile, x, y
if ( rnparseok )
{
uint8_t const * sem[4];
uint8_t const ** psem = &sem[0];
for ( uint8_t const * c = reinterpret_cast<uint8_t const *>(readname); c != reinterpret_cast<uint8_t const *>(readnamee); ++c )
if ( *c == ':' )
*(psem++) = c+1;
uint8_t const * t = sem[1];
while ( D[*t] )
{
RE.tile *= 10;
RE.tile += *(t++)-'0';
}
RE.tile += 1;
t = sem[2];
while ( D[*t] )
{
RE.x *= 10;
RE.x += *(t++)-'0';
}
t = sem[3];
while ( D[*t] )
{
RE.y *= 10;
RE.y += *(t++)-'0';
}
}
int64_t const rg = p.getReadGroupId(header);
RE.readGroup = rg + 1;
}
