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);
}
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();
}