bool BamTemplate::filterLowQualityFragments(const unsigned mapqThreshold)
{
bool ret = false;
unsigned alignmentScore = 0;
for (unsigned i = 0; getFragmentCount() > i; ++i)
{
FragmentMetadata &fragment = getFragmentMetadata(i);
if (mapqThreshold > fragment.getAlignmentScore())
{
fragment.cigarLength = 0;
fragment.cigarOffset = 0;
fragment.alignmentScore = 0;
const FragmentMetadata &mate = getFragmentMetadata((i+1) % getFragmentCount());
fragment.position = mate.position;
fragment.contigId = mate.contigId;
}
else if (fragment.isAligned())
{
ret = true;
}
// update the alignment score of the templates that didn't resolve into a proper pair
alignmentScore += fragment.alignmentScore;
}
setAlignmentScore(alignmentScore);
return ret;
}
std::string UUID_TrackFragmentReference::toPrettyString(uint32_t indent) {
std::stringstream r;
r << std::string(indent, ' ') << "[d4807ef2-ca39-4695-8e54-26cb9e46a79f] Track Fragment Reference (" << boxedSize() << ")" << std::endl;
r << std::string(indent + 1, ' ') << "Version: " << getVersion() << std::endl;
r << std::string(indent + 1, ' ') << "Fragments: " << getFragmentCount() << std::endl;
int j = getFragmentCount();
for (int i = 0; i < j; ++i) {
r << std::string(indent + 2, ' ') << "[" << i << "] Time = " << getTime(i) << ", Duration = " << getDuration(i) << std::endl;
}
return r.str();
}
