C++ (Cpp) bam_record::read_no示例

static
void
getSingleReadSVCandidates(
    const ReadScannerOptions& opt,
    const ReadScannerDerivOptions& dopt,
    const bam_record& localRead,
    const SimpleAlignment& localAlign,
    const chromMap_t& chromToIndex,
    const reference_contig_segment& refSeq,
    std::vector<SVObservation>& candidates)
{
    using namespace illumina::common;

    const bool isRead2(localRead.is_paired() && (localRead.read_no() == 2));
    const FRAGSOURCE::index_t fragSource(isRead2 ? FRAGSOURCE::READ2 : FRAGSOURCE::READ1);

    // - process any large indels in the localRead:
    getSVCandidatesFromReadIndels(opt, dopt, localAlign, fragSource, candidates);
#ifdef DEBUG_SCANNER
    log_os << __FUNCTION__ << ": post-indels candidate_size: " << candidates.size() << "\n";
#endif

    // a read can provide SA split evidence or semi-aligned/soft-clip, but not both.
    // this prevents split reads from triggering spurious local assembles. It is
    // possible for a read to genuinely contain evidence of both, but this should
    // be very rare.
    if (localRead.isSASplit())
    {
        getSACandidatesFromRead(opt, dopt, localRead, localAlign, fragSource, chromToIndex,
                                candidates);
#ifdef DEBUG_SCANNER
        log_os << __FUNCTION__ << ": post-split read candidate_size: " << candidates.size() << "\n";
#endif
    }
    else
    {
        if (dopt.isSmallCandidates)
        {
            getSVCandidatesFromSemiAligned(opt, dopt, localRead, localAlign, fragSource, refSeq,
                                           candidates);
        }
#ifdef DEBUG_SCANNER
        log_os << __FUNCTION__ << ": post-semialigned candidate_size: " << candidates.size() << "\n";
#endif
    }
}

示例#2

显示文件

文件： SVCandidateSetData.cpp 项目： Illumina/manta

void
SVCandidateSetSequenceFragmentSampleGroup::
add(
    const bam_header_info& bamHeader,
    const bam_record& bamRead,
    const bool isExpectRepeat,
    const bool isSourcedFromGraphEdgeNode1,
    const bool isSubMapped)
{
    using namespace illumina::common;

#ifdef DEBUG_SVDATA
    log_os << "SVDataGroup adding: " << bamRead << "\n";
#endif

    SVCandidateSetSequenceFragment* fragPtr(getSequenceFragment(bamRead.qname()));
    if (nullptr == fragPtr) return;

    SVCandidateSetSequenceFragment& fragment(*fragPtr);

    SVCandidateSetRead* targetReadPtr(nullptr);
    if (2 == bamRead.read_no())
    {
        if (bamRead.isNonStrictSupplement())
        {
            fragment.read2Supplemental.emplace_back();
            targetReadPtr = (&(fragment.read2Supplemental.back()));
        }
        else
        {
            targetReadPtr = (&(fragment.read2));
        }
    }
    else
    {
        if (bamRead.isNonStrictSupplement())
        {
            fragment.read1Supplemental.emplace_back();
            targetReadPtr = (&(fragment.read1Supplemental.back()));
        }
        else
        {
            targetReadPtr = (&(fragment.read1));
        }
    }

    SVCandidateSetRead& targetRead(*targetReadPtr);
    if (targetRead.isSet())
    {
        if (isExpectRepeat) return;

        std::ostringstream oss;
        oss << "Unexpected alignment name collision. Source: '" << dataSourceName << "'\n"
            << "\tExisting read: ";
        summarizeAlignmentRecord(bamHeader, targetRead.bamrec, oss);
        oss << "\n"
            << "\tNew read: ";
        summarizeAlignmentRecord(bamHeader, bamRead, oss);
        oss << "\n";
        BOOST_THROW_EXCEPTION(GeneralException(oss.str()));
    }

    targetRead.bamrec = bamRead;
    targetRead.isSourcedFromGraphEdgeNode1 = isSourcedFromGraphEdgeNode1;
    targetRead.isSubMapped = isSubMapped;
    targetRead.readIndex = (isSubMapped ? _subMappedReadIndex : _mappedReadIndex);
}