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);
}
static
bool
isGoodShadow(
const bam_record& bamRead,
const std::string& lastQname)
{
#ifdef DEBUG_IS_SHADOW
static const std::string logtag("isGoodShadow");
#endif
if (! bamRead.is_paired()) return false;
if (bamRead.isNonStrictSupplement()) return false;
// sanity check that this is a shadow read:
if (!bamRead.is_unmapped()) return false;
if (bamRead.is_mate_unmapped()) return false;
static const unsigned minAvgQualShadow = 25;
if (get_avg_quality(bamRead) < minAvgQualShadow)
{
return false;
}
if (strcmp(bamRead.qname(),lastQname.c_str()) != 0)
{
// something went wrong here, shadows should have their singleton partner
// preceding them in the BAM file.
#ifdef DEBUG_IS_SHADOW
log_os << logtag << " ERROR: Shadow without matching singleton : " << bamRead.qname() << " vs " << lastQname << std::endl;
#endif
return false;
}
#ifdef DEBUG_IS_SHADOW
log_os << logtag << " Found shadow!\n";
<< logtag << " this mapq = " << ((unsigned int)bamRead.map_qual()) << std::endl;
/// 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
}
/// get SV candidates from shadow/singleton pairs
/// look for singletons, create candidateSV around conf. interval of shadow position
/// cache singletons? might be needed to remove poor quality shadows.
/// should be able to re-use code, follow soft-clipping example.
static
void
getSVCandidatesFromShadow(
const ReadScannerOptions& opt,
const SVLocusScanner::CachedReadGroupStats& rstats,
const bam_record& localRead,
const SimpleAlignment& localAlign,
const bam_record* remoteReadPtr,
TrackedCandidates& candidates)
{
using namespace SVEvidenceType;
static const index_t svSource(SHADOW);
static const bool isComplex(true);
pos_t singletonGenomePos(0);
int targetId(0);
if (NULL == remoteReadPtr)
{
if (!localRead.is_unmapped()) return;
// need to take care of this case
// need to rely on cached mapq and qname
return;
if (!isGoodShadow(localRead,lastMapq,lastQname,opt.minSingletonMapqGraph))
{
return;
}
singletonGenomePos = localAlign.pos;
targetId = localRead.target_id();
}
else
{
// have both reads, straightforward from here
const bam_record& remoteRead(*remoteReadPtr);
const SimpleAlignment remoteAlign(remoteRead);
if (localRead.is_mate_unmapped())
{
// remote read is shadow candidate
if (!isGoodShadow(remoteRead,localRead.map_qual(),localRead.qname(),opt.minSingletonMapqGraph))
{
return;
}
singletonGenomePos = localAlign.pos;
targetId = remoteRead.target_id();
}
else if (localRead.is_unmapped())
{
// local is shadow candidate
if (!isGoodShadow(localRead,remoteRead.map_qual(),remoteRead.qname(),opt.minSingletonMapqGraph))
{
return;
}
singletonGenomePos = remoteAlign.pos;
targetId = localRead.target_id();
}
else
{
// none unmapped, skip this one
return;
}
}
const pos_t properPairRangeOffset = static_cast<pos_t>(rstats.properPair.min + (rstats.properPair.max-rstats.properPair.min)/2);
const pos_t shadowGenomePos = singletonGenomePos + properPairRangeOffset;
candidates.push_back(GetSplitSVCandidate(opt,targetId,shadowGenomePos,shadowGenomePos, svSource, isComplex));
}
