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);
}
/// get SV candidates from SA-tag split-read alignment
static
SVObservation
GetSplitSACandidate(
const ReadScannerDerivOptions& dopt,
const bam_record& localRead,
const SimpleAlignment& localAlign,
const SimpleAlignment& remoteAlign,
const FRAGSOURCE::index_t fragSource)
{
using namespace SVEvidenceType;
static const index_t svSource(SPLIT_ALIGN);
SVObservation sv;
sv.evtype = svSource;
sv.fragSource = fragSource;
SVBreakend& localBreakend(sv.bp1);
SVBreakend& remoteBreakend(sv.bp2);
// use single-side evidence, have to read the supp read to get the
// reverse edge. this protects against double-count:
localBreakend.lowresEvidence.add(svSource);
updateSABreakend(dopt, localAlign, localBreakend);
updateSABreakend(dopt, remoteAlign, remoteBreakend);
// If the local (bp1) alignment is split downstream (on the right side) then this read goes from bp1 -> bp2.
// If it is a forward read (e.g. read1 on + strand), this means it's a forward read for this event.
const bool isSplitDownstream(isSplitOpenDownstream(localAlign.path));
const bool isReadFw = (localRead.is_first() == localRead.is_fwd_strand());
if (dopt.isStranded)
{
if (isReadFw == isSplitDownstream)
{
sv.fwReads += 1;
}
else
{
sv.rvReads += 1;
}
}
return sv;
}
/// get SV candidates from anomalous read pairs
static
void
getSVCandidatesFromPair(
const ReadScannerOptions& opt,
const ReadScannerDerivOptions& dopt,
const SVLocusScanner::CachedReadGroupStats& rstats,
const bam_record& localRead,
const SimpleAlignment& localAlign,
const bam_record* remoteReadPtr,
std::vector<SVObservation>& candidates)
{
if (! localRead.is_paired()) return;
// don't count paired end evidence from SA-split reads twice:
if (localRead.isNonStrictSupplement()) return;
if (localRead.is_unmapped() || localRead.is_mate_unmapped()) return;
// special case typically used for RNA-Seq analysis:
if (opt.isIgnoreAnomProperPair && localRead.is_proper_pair()) return;
// abstract remote alignment to SimpleAlignment object:
const bool isRemote(nullptr != remoteReadPtr);
const SimpleAlignment remoteAlign(isRemote ? getAlignment(*remoteReadPtr) : getFakeMateAlignment(localRead));
AlignmentPairAnalyzer pairInspector(opt, dopt, rstats);
pairInspector.reset(localAlign, remoteAlign, isRemote, localRead.is_first());
if (! pairInspector.computeLargeEventRegionScale()) return;
candidates.emplace_back();
pairInspector.getSVObservation(candidates.back());
#ifdef DEBUG_SCANNER
log_os << __FUNCTION__ << " evaluating pair sv for inclusion: " << candidates.back() << "\n";
#endif
}