void getBamBlocks(const BamAlignment &bam, const RefVector &refs,
BedVec &blocks, bool breakOnDeletionOps) {
CHRPOS currPosition = bam.Position;
CHRPOS blockStart = bam.Position;
string chrom = refs.at(bam.RefID).RefName;
string name = bam.Name;
string strand = "+";
float score = bam.MapQuality;
if (bam.IsReverseStrand()) strand = "-";
vector<CigarOp>::const_iterator cigItr = bam.CigarData.begin();
vector<CigarOp>::const_iterator cigEnd = bam.CigarData.end();
for ( ; cigItr != cigEnd; ++cigItr ) {
if (cigItr->Type == 'M') {
currPosition += cigItr->Length;
blocks.push_back( Bed(chrom, blockStart, currPosition, name, score, strand) );
blockStart = currPosition;
}
else if (cigItr->Type == 'D') {
if (breakOnDeletionOps == false)
currPosition += cigItr->Length;
else {
currPosition += cigItr->Length;
blockStart = currPosition;
}
}
else if (cigItr->Type == 'N') {
currPosition += cigItr->Length;
blockStart = currPosition; }
else if (cigItr->Type == 'S' || cigItr->Type == 'H' || cigItr->Type == 'P' || cigItr->Type == 'I') {
// do nothing
}
else {
cerr << "Input error: invalid CIGAR type (" << cigItr->Type
<< ") for: " << bam.Name << endl;
exit(1);
}
}
}
, m_bed(bed)
{}
private:
std::string m_building;
std::string m_pointOfCare;
int m_floor;
int m_bed;
};
TEST_CASE("ctor of Location")
{
const Location loc(
Building("Central"),
PointOfCare("Intensive Care"),
Floor(3),
Bed(12));
}
namespace My
{
template<class T1, class T2>
struct MaxSize
{
static const int value = sizeof(T1) > sizeof(T2) ? sizeof(T1) : sizeof(T2);
};
}
typedef My::MaxSize<int, char> MaxIntChar;
typedef My::MaxSize<int, long long> MaxIntLongLong;
struct Max1
{
Bedroom::Bed Bedroom::
getBed()
{
return Bed(data_);
}
