TEST_F(HDFCCSReaderTEST, ReadCCSFromCCSH5) {
string fileName = ccsFile1;
HDFCCSReader<CCSSequence> reader;
reader.SetReadBasesFromCCS();
reader.InitializeDefaultIncludedFields();
ASSERT_EQ(reader.Initialize(fileName), 1);
ASSERT_EQ(reader.GetMovieName(),
"m130328_211423_ethan_c100499512550000001823070408081371_s1_p0");
CCSSequence seq;
for(int i=0; i < 1000; i++) {
reader.GetNext(seq);
}
reader.Close();
}
TEST(CcsTest, EndToEnd_Multiple)
{
// setup
const string movieName = "m131018_081703_42161_c100585152550000001823088404281404_s1_p0";
vector<string> baxFilenames;
baxFilenames.push_back(tests::Data_Dir + "/data/" + movieName + ".1.ccs.h5");
const string generatedBam = movieName + ".ccs.bam";
// run conversion
const int result = RunBax2Bam(baxFilenames, "--ccs");
EXPECT_EQ(0, result);
{ // ensure PBI exists
const BamFile generatedBamFile(generatedBam);
EXPECT_TRUE(generatedBamFile.PacBioIndexExists());
}
// open BAX reader on original data
HDFCCSReader<CCSSequence> baxReader;
baxReader.IncludeField("Basecall");
baxReader.IncludeField("QualityValue");
baxReader.IncludeField("DeletionQV");
baxReader.IncludeField("InsertionQV");
baxReader.IncludeField("SubstitutionQV");
string baxBasecallerVersion;
string baxBindingKit;
string baxSequencingKit;
// set magic bits
baxReader.SetReadBasesFromCCS();
const int initOk = baxReader.Initialize(baxFilenames.front());
EXPECT_EQ(1, initOk);
if (initOk == 1) {
if (baxReader.scanDataReader.fileHasScanData && baxReader.scanDataReader.initializedRunInfoGroup) {
if (baxReader.scanDataReader.runInfoGroup.ContainsAttribute("BindingKit")) {
HDFAtom<std::string> bkAtom;
if (bkAtom.Initialize(baxReader.scanDataReader.runInfoGroup, "BindingKit")) {
bkAtom.Read(baxBindingKit);
bkAtom.dataspace.close();
}
}
if (baxReader.scanDataReader.runInfoGroup.ContainsAttribute("SequencingKit")) {
HDFAtom<std::string> skAtom;
if (skAtom.Initialize(baxReader.scanDataReader.runInfoGroup, "SequencingKit")) {
skAtom.Read(baxSequencingKit);
skAtom.dataspace.close();
}
}
{
HDFGroup bcGroup;
if (baxReader.pulseDataGroup.ContainsObject("BaseCalls") &&
bcGroup.Initialize(baxReader.pulseDataGroup.group, "BaseCalls"))
{
HDFAtom<std::string> clAtom;
if (bcGroup.ContainsAttribute("ChangeListID") &&
clAtom.Initialize(bcGroup.group, "ChangeListID"))
{
clAtom.Read(baxBasecallerVersion);
clAtom.dataspace.close();
}
bcGroup.Close();
}
}
}
}
EXPECT_NO_THROW(
{
// open BAM file
BamFile bamFile(generatedBam);
// check BAM header information
const BamHeader& header = bamFile.Header();
EXPECT_EQ(string("1.5"), header.Version());
EXPECT_EQ(string("unknown"), header.SortOrder());
EXPECT_EQ(string("3.0.2"), header.PacBioBamVersion());
EXPECT_TRUE(header.Sequences().empty());
EXPECT_TRUE(header.Comments().empty());
ASSERT_FALSE(header.Programs().empty());
const vector<string> readGroupIds = header.ReadGroupIds();
ASSERT_FALSE(readGroupIds.empty());
const ReadGroupInfo& rg = header.ReadGroup(readGroupIds.front());
string rawId = movieName + "//CCS";
string md5Id;
MakeMD5(rawId, md5Id, 8);
EXPECT_EQ(md5Id, rg.Id());
EXPECT_EQ(string("PACBIO"), rg.Platform());
EXPECT_EQ(movieName, rg.MovieName());
EXPECT_TRUE(rg.SequencingCenter().empty());
EXPECT_TRUE(rg.Date().empty());
EXPECT_TRUE(rg.FlowOrder().empty());
EXPECT_TRUE(rg.KeySequence().empty());
EXPECT_TRUE(rg.Library().empty());
EXPECT_TRUE(rg.Programs().empty());
EXPECT_TRUE(rg.PredictedInsertSize().empty());
EXPECT_TRUE(rg.Sample().empty());
EXPECT_EQ("CCS", rg.ReadType());
EXPECT_EQ(baxBasecallerVersion, rg.BasecallerVersion());
EXPECT_EQ(baxBindingKit, rg.BindingKit());
EXPECT_EQ(baxSequencingKit, rg.SequencingKit());
EXPECT_EQ(75, std::stod(rg.FrameRateHz()));
EXPECT_EQ("dq", rg.BaseFeatureTag(BaseFeature::DELETION_QV));
EXPECT_EQ("iq", rg.BaseFeatureTag(BaseFeature::INSERTION_QV));
EXPECT_EQ("sq", rg.BaseFeatureTag(BaseFeature::SUBSTITUTION_QV));
EXPECT_FALSE(rg.HasBaseFeature(BaseFeature::DELETION_TAG));
EXPECT_FALSE(rg.HasBaseFeature(BaseFeature::IPD));
EXPECT_FALSE(rg.HasBaseFeature(BaseFeature::MERGE_QV));
EXPECT_FALSE(rg.HasBaseFeature(BaseFeature::SUBSTITUTION_TAG));
// compare 1st record from each file
CCSSequence baxRecord;
const UInt holeNumber = baxRecord.zmwData.holeNumber;
size_t numTested = 0;
EntireFileQuery entireFile(bamFile);
for (BamRecord& bamRecord : entireFile) {
while (baxReader.GetNext(baxRecord)) {
if (baxRecord.length > 0)
goto compare;
}
goto cleanup;
compare:
EXPECT_GT(baxRecord.length, 0U);
const BamRecordImpl& bamRecordImpl = bamRecord.Impl();
EXPECT_EQ(4680U,bamRecordImpl.Bin());
EXPECT_EQ(0, bamRecordImpl.InsertSize());
EXPECT_EQ(255, bamRecordImpl.MapQuality());
EXPECT_EQ(-1, bamRecordImpl.MatePosition());
EXPECT_EQ(-1, bamRecordImpl.MateReferenceId());
EXPECT_EQ(-1, bamRecordImpl.Position());
EXPECT_EQ(-1, bamRecordImpl.ReferenceId());
EXPECT_FALSE(bamRecordImpl.IsMapped());
const int holeNumber = baxRecord.zmwData.holeNumber;
const int numPasses = baxRecord.numPasses;
const string expectedName = baxRecord.GetName();
EXPECT_EQ(expectedName, bamRecordImpl.Name());
using PacBio::BAM::QualityValue;
using PacBio::BAM::QualityValues;
const DNALength length = baxRecord.length;
string expectedSequence;
expectedSequence.assign((const char*)baxRecord.seq, length);
QualityValues expectedQualities;
expectedQualities.assign((uint8_t*)baxRecord.qual.data, baxRecord.qual.data + length);
const string bamSequence = bamRecord.Sequence();
const QualityValues bamQualities = bamRecord.Qualities();
EXPECT_EQ(expectedSequence, bamSequence);
EXPECT_EQ(expectedQualities, bamQualities);
const QualityValues bamDeletionQVs = bamRecord.DeletionQV();
const QualityValues bamInsertionQVs = bamRecord.InsertionQV();
const QualityValues bamSubstitutionQVs = bamRecord.SubstitutionQV();
for (size_t i = 0; i < length; ++i) {
EXPECT_EQ((QualityValue)baxRecord.GetDeletionQV(i), bamDeletionQVs.at(i));
EXPECT_EQ((QualityValue)baxRecord.GetInsertionQV(i), bamInsertionQVs.at(i));
EXPECT_EQ((QualityValue)baxRecord.GetSubstitutionQV(i), bamSubstitutionQVs.at(i));
}
EXPECT_EQ(md5Id, bamRecord.ReadGroupId());
EXPECT_EQ(movieName, bamRecord.MovieName());
EXPECT_EQ(numPasses, bamRecord.NumPasses());
EXPECT_EQ(holeNumber, bamRecord.HoleNumber());
EXPECT_FALSE(bamRecord.HasLocalContextFlags());
EXPECT_FALSE(bamRecord.HasSignalToNoise());
numTested++;
}
cleanup:
EXPECT_GT(numTested, 1UL);
// cleanup
baxReader.Close();
RemoveFile(generatedBam);
RemoveFile(generatedBam + ".pbi");
}); // EXPECT_NO_THROW
