C++ (Cpp) BamRecordImpl Examples

Example #1

File: test_BamRecordBuilder.cpp Project: Debian/pbbam

static
void CheckRawData(const BamRecordImpl& bam)
{
    // ensure raw data (lengths at least) matches API-facing data

    const uint32_t expectedNameLength  = bam.Name().size() + 1;
    const uint32_t expectedNumCigarOps = bam.CigarData().size();
    const int32_t  expectedSeqLength   = bam.Sequence().length();
    const size_t   expectedTagsLength  = BamTagCodec::Encode(bam.Tags()).size();

    //  Name        CIGAR         Sequence       Quals      Tags
    // l_qname + (n_cigar * 4) + (l_qseq+1)/2 + l_qseq + << TAGS >>

    const int expectedTotalDataLength = expectedNameLength +
                                        (expectedNumCigarOps * 4) +
                                        (expectedSeqLength+1)/2 +
                                         expectedSeqLength +
                                         expectedTagsLength;

    EXPECT_TRUE((bool)bam.d_);
    EXPECT_EQ(expectedNameLength,      bam.d_->core.l_qname);
    EXPECT_EQ(expectedNumCigarOps,     bam.d_->core.n_cigar);
    EXPECT_EQ(expectedSeqLength,       bam.d_->core.l_qseq);
    EXPECT_EQ(expectedTotalDataLength, bam.d_->l_data);
}

Example #2

File: ccs.cpp Project: ylipacbio/pbccs

void WriteBamRecords(BamWriter& ccsBam, unique_ptr<PbiBuilder>& ccsPbi, Results& counts,
                     Results&& results)
{
    counts += results;

    for (const auto& ccs : results) {
        BamRecordImpl record;
        TagCollection tags;
        stringstream name;

        // some defaults values
        record.Bin(0)
        .InsertSize(0)
        .MapQuality(255)
        .MatePosition(-1)
        .MateReferenceId(-1)
        .Position(-1)
        .ReferenceId(-1)
        .Flag(0)
        .SetMapped(false);

        name << *(ccs.Id.MovieName) << '/' << ccs.Id.HoleNumber << "/ccs";

        vector<float> snr = {
            static_cast<float>(ccs.SignalToNoise.A), static_cast<float>(ccs.SignalToNoise.C),
            static_cast<float>(ccs.SignalToNoise.G), static_cast<float>(ccs.SignalToNoise.T)
        };

        tags["RG"] = MakeReadGroupId(*(ccs.Id.MovieName), "CCS");
        tags["zm"] = static_cast<int32_t>(ccs.Id.HoleNumber);
        tags["np"] = static_cast<int32_t>(ccs.NumPasses);
        tags["rq"] = static_cast<float>(ccs.PredictedAccuracy);
        tags["sn"] = snr;

        // TODO(lhepler) maybe remove one day
        tags["za"] = static_cast<float>(ccs.AvgZScore);
        vector<float> zScores;
        for (const double z : ccs.ZScores)
            zScores.emplace_back(static_cast<float>(z));
        tags["zs"] = zScores;
        tags["rs"] = ccs.StatusCounts;

#if DIAGNOSTICS
        if (ccs.Barcodes) {
            vector<uint16_t> bcs{ccs.Barcodes->first, ccs.Barcodes->second};
            tags["bc"] = bcs;
        }
        tags["ms"] = ccs.ElapsedMilliseconds;
        tags["mt"] = static_cast<int32_t>(ccs.MutationsTested);
        tags["ma"] = static_cast<int32_t>(ccs.MutationsApplied);
#endif

        record.Name(name.str()).SetSequenceAndQualities(ccs.Sequence, ccs.Qualities).Tags(tags);

        int64_t offset;
        ccsBam.Write(record, &offset);

        if (ccsPbi) ccsPbi->AddRecord(record, offset);
    }
    ccsBam.TryFlush();
}