void
SVScorePairRefProcessor::
processClearedRecord(
const bam_record& bamRead)
{
using namespace illumina::common;
assert(bamParams.isSet);
const pos_t refPos(bamRead.pos()-1);
if (! bamParams.interval.range.is_pos_intersect(refPos)) return;
const bool isLargeInsert(isLargeInsertSV(sv));
#ifdef DEBUG_MEGAPAIR
log_os << __FUNCTION__ << ": read: " << bamRead << "\n";
#endif
/// check if fragment is too big or too small:
const int templateSize(std::abs(bamRead.template_size()));
if (templateSize < bamParams.minFrag) return;
if (templateSize > bamParams.maxFrag) return;
// count only from the down stream reads
const bool isFirstBamRead(isFirstRead(bamRead));
// get fragment range:
pos_t fragBeginRefPos(refPos);
if (! isFirstBamRead)
{
fragBeginRefPos=bamRead.mate_pos()-1;
}
const pos_t fragEndRefPos(fragBeginRefPos+templateSize);
if (fragBeginRefPos > fragEndRefPos)
{
std::ostringstream oss;
oss << "ERROR: Failed to parse fragment range from bam record. Frag begin,end: " << fragBeginRefPos << " " << fragEndRefPos << " bamRecord: " << bamRead << "\n";
BOOST_THROW_EXCEPTION(LogicException(oss.str()));
}
{
const pos_t fragOverlap(std::min((1+svParams.centerPos-fragBeginRefPos), (fragEndRefPos-svParams.centerPos)));
#ifdef DEBUG_MEGAPAIR
log_os << __FUNCTION__ << ": frag begin/end/overlap: " << fragBeginRefPos << " " << fragEndRefPos << " " << fragOverlap << "\n";
#endif
if (fragOverlap < pairOpt.minFragSupport) return;
}
SVFragmentEvidence& fragment(evidence.getSampleEvidence(bamParams.bamIndex)[bamRead.qname()]);
static const bool isShadow(false);
SVFragmentEvidenceRead& evRead(fragment.getRead(bamRead.is_first()));
setReadEvidence(svParams.minMapQ, svParams.minTier2MapQ, bamRead, isShadow, evRead);
setAlleleFrag(*bamParams.fragDistroPtr, templateSize, fragment.ref.getBp(isBp1),isLargeInsert);
}
bool
isMateInsertionEvidenceCandidate(
const bam_record& bamRead,
const unsigned minMapq)
{
if (! bamRead.is_paired()) return false;
if (bamRead.isNonStrictSupplement()) return false;
if (bamRead.is_unmapped() || bamRead.is_mate_unmapped()) return false;
if (bamRead.map_qual() < minMapq) return false;
if (bamRead.target_id() < 0) return false;
if (bamRead.mate_target_id() < 0) return false;
if (bamRead.target_id() != bamRead.mate_target_id()) return true;
/// TODO: better candidate definition based on fragment size distro:
static const int minSize(10000);
return (std::abs(bamRead.pos()-bamRead.mate_pos()) >= minSize);
}