[TAK-1730] Port from deprecated pbbam API

include/pbbam/BaiIndexedBamReader.h

@@ -6,7 +6,8 @@
 #include <pbbam/BaiIndexCache.h>
 #include <pbbam/BamFile.h>
 #include <pbbam/BamReader.h>
-#include <pbbam/GenomicInterval.h>
+
+#include <pbcopper/data/GenomicInterval.h>
 
 #include <htslib/sam.h>
 
@@ -56,8 +57,8 @@ class PBBAM_EXPORT BaiIndexedBamReader : public BamReader
     /// \throws std::runtime_error if either file (*.bam or *.bai) fails to open
     ///         for reading, or if the interval is invalid
     ///
-    BaiIndexedBamReader(const GenomicInterval& interval, std::string filename);
-    BaiIndexedBamReader(const GenomicInterval& interval, std::string filename,
+    BaiIndexedBamReader(const Data::GenomicInterval& interval, std::string filename);
+    BaiIndexedBamReader(const Data::GenomicInterval& interval, std::string filename,
                         const std::shared_ptr<BaiIndexCacheData>& index);
 
     /// \brief Constructs %BAM reader, bounded by a genomic interval.
@@ -70,8 +71,8 @@ class PBBAM_EXPORT BaiIndexedBamReader : public BamReader
     /// \throws std::runtime_error if either file (*.bam or *.bai) fails to open
     ///         for reading, or if the interval is invalid
     ///
-    BaiIndexedBamReader(const GenomicInterval& interval, BamFile bamFile);
-    BaiIndexedBamReader(const GenomicInterval& interval, BamFile bamFile,
+    BaiIndexedBamReader(const Data::GenomicInterval& interval, BamFile bamFile);
+    BaiIndexedBamReader(const Data::GenomicInterval& interval, BamFile bamFile,
                         const std::shared_ptr<BaiIndexCacheData>& index);
 
     /// \}
@@ -84,14 +85,14 @@ class PBBAM_EXPORT BaiIndexedBamReader : public BamReader
     const BamFile& File() const;
 
     /// \returns the current GenomicInterval in use by this reader
-    const GenomicInterval& Interval() const;
+    const Data::GenomicInterval& Interval() const;
 
     /// \brief Sets a new genomic interval on the reader.
     ///
     /// \param[in] interval
     /// \returns reference to this reader
     ///
-    BaiIndexedBamReader& Interval(const GenomicInterval& interval);
+    BaiIndexedBamReader& Interval(const Data::GenomicInterval& interval);
 
     /// \}
 

include/pbbam/BamRecord.h

@@ -3,25 +3,25 @@
 
 #include <pbbam/Config.h>
 
-#include <pbbam/Accuracy.h>
 #include <pbbam/BamHeader.h>
 #include <pbbam/BamRecordImpl.h>
 #include <pbbam/ClipType.h>
 #include <pbbam/FrameEncodingType.h>
-#include <pbbam/Frames.h>
-#include <pbbam/LocalContextFlags.h>
-#include <pbbam/Orientation.h>
 #include <pbbam/PulseBehavior.h>
 #include <pbbam/PulseExclusionReason.h>
-#include <pbbam/QualityValues.h>
 #include <pbbam/ReadGroupInfo.h>
 #include <pbbam/RecordType.h>
-#include <pbbam/Strand.h>
 #include <pbbam/ZmwType.h>
 #include <pbbam/virtual/VirtualRegionType.h>
 
+#include <pbcopper/data/Accuracy.h>
+#include <pbcopper/data/Frames.h>
+#include <pbcopper/data/LocalContextFlags.h>
 #include <pbcopper/data/MappedRead.h>
+#include <pbcopper/data/Orientation.h>
+#include <pbcopper/data/QualityValues.h>
 #include <pbcopper/data/Read.h>
+#include <pbcopper/data/Strand.h>
 #include <pbcopper/json/JSON.h>
 
 #include <memory>
@@ -846,8 +846,8 @@ class PBBAM_EXPORT BamRecord
     /// \param[in] orientation     Orientation of output.
     /// \returns PulseWidth as Frames object
     ///
-    Frames PulseWidthRaw(Orientation orientation = Orientation::NATIVE, bool aligned = false,
-                         bool exciseSoftClips = false) const;
+    Data::Frames PulseWidthRaw(Data::Orientation orientation = Data::Orientation::NATIVE,
+                               bool aligned = false, bool exciseSoftClips = false) const;
 
     /// \brief Fetches this record's reverse IPD values ("ri" tag).
     ///
@@ -1143,7 +1143,7 @@ class PBBAM_EXPORT BamRecord
     /// \param[in] labelQVs
     /// \returns reference to this record
     ///
-    BamRecord& LabelQV(const QualityValues& labelQVs);
+    BamRecord& LabelQV(const Data::QualityValues& labelQVs);
 
     /// \brief Sets this record's MergeQV values ("mq" tag).
     ///
@@ -1550,7 +1550,8 @@ class PBBAM_EXPORT BamRecord
 
     // sequence tags
     std::string FetchBasesRaw(BamRecordTag tag) const;
-    std::string FetchBases(BamRecordTag tag, Orientation orientation = Orientation::NATIVE,
+    std::string FetchBases(BamRecordTag tag,
+                           Data::Orientation orientation = Data::Orientation::NATIVE,
                            bool aligned = false, bool exciseSoftClips = false,
                            PulseBehavior pulseBehavior = PulseBehavior::ALL) const;
 

include/pbbam/BamRecordImpl.h

@@ -4,12 +4,13 @@
 #include <pbbam/Config.h>
 
 #include <pbbam/BamRecordTag.h>
-#include <pbbam/Cigar.h>
 #include <pbbam/Deleters.h>
-#include <pbbam/Position.h>
-#include <pbbam/QualityValues.h>
 #include <pbbam/TagCollection.h>
 
+#include <pbcopper/data/Cigar.h>
+#include <pbcopper/data/Position.h>
+#include <pbcopper/data/QualityValues.h>
+
 #include <htslib/sam.h>
 
 #include <map>
@@ -242,7 +243,7 @@ class PBBAM_EXPORT BamRecordImpl
 
     /// Sets the record's CIGAR data using a Cigar object
     ///
-    /// \param[in] cigar PacBio::BAM::Cigar object
+    /// \param[in] cigar PacBio::Data::Cigar object
     /// \returns reference to this record
     ///
     BamRecordImpl& CigarData(const Data::Cigar& cigar);

include/pbbam/BamRecordView.h

@@ -67,7 +67,7 @@ class PBBAM_EXPORT BamRecordView
     Data::QualityValues MergeQVs() const;
 
     /// \returns BamRecord::PulseMergeQV with this view's parameters applied
-    QualityValues PulseMergeQVs() const;
+    Data::QualityValues PulseMergeQVs() const;
 
     /// \returns BamRecord::Pkmean with this view's parameters applied
     std::vector<float> Pkmean() const;

include/pbbam/CompositeBamReader.h

@@ -10,9 +10,10 @@
 #include <pbbam/BamReader.h>
 #include <pbbam/BamRecord.h>
 #include <pbbam/DataSet.h>
-#include <pbbam/GenomicInterval.h>
 #include <pbbam/PbiIndexedBamReader.h>
 
+#include <pbcopper/data/GenomicInterval.h>
+
 #include <deque>
 #include <functional>
 #include <memory>
@@ -153,9 +154,9 @@ class PBBAM_EXPORT GenomicIntervalCompositeBamReader
     /// \throws std::runtime_error on failure to open/read underlying %BAM or
     ///         BAI files.
     ///
-    GenomicIntervalCompositeBamReader(const GenomicInterval& interval,
+    GenomicIntervalCompositeBamReader(const Data::GenomicInterval& interval,
                                       const std::vector<BamFile>& bamFiles);
-    GenomicIntervalCompositeBamReader(const GenomicInterval& interval,
+    GenomicIntervalCompositeBamReader(const Data::GenomicInterval& interval,
                                       const std::vector<BamFile>& bamFiles,
                                       const BaiIndexCache& cache);
 
@@ -168,8 +169,9 @@ class PBBAM_EXPORT GenomicIntervalCompositeBamReader
     /// \throws std::runtime_error on failure to open/read underlying %BAM or
     ///         BAI files.
     ///
-    GenomicIntervalCompositeBamReader(const GenomicInterval& interval, const DataSet& dataset);
-    GenomicIntervalCompositeBamReader(const GenomicInterval& interval, const DataSet& dataset,
+    GenomicIntervalCompositeBamReader(const Data::GenomicInterval& interval,
+                                      const DataSet& dataset);
+    GenomicIntervalCompositeBamReader(const Data::GenomicInterval& interval, const DataSet& dataset,
                                       const BaiIndexCache& cache);
 
     /// \}
@@ -182,17 +184,17 @@ class PBBAM_EXPORT GenomicIntervalCompositeBamReader
     ///
     /// \returns reference to this reader
     ///
-    GenomicIntervalCompositeBamReader& Interval(const GenomicInterval& interval);
+    GenomicIntervalCompositeBamReader& Interval(const Data::GenomicInterval& interval);
 
     /// \returns the current specified interval
     ///
-    const GenomicInterval& Interval() const;
+    const Data::GenomicInterval& Interval() const;
 
     /// \}
 
 private:
     BaiIndexCache indexCache_;
-    GenomicInterval interval_;
+    Data::GenomicInterval interval_;
 };
 
 /// \brief Provides read access to multipe %BAM files, limiting results to those

include/pbbam/DataSet.h

@@ -6,7 +6,8 @@
 #include <pbbam/BamFile.h>
 #include <pbbam/BamHeader.h>
 #include <pbbam/DataSetTypes.h>
-#include <pbbam/GenomicInterval.h>
+
+#include <pbcopper/data/GenomicInterval.h>
 
 #include <chrono>
 #include <iosfwd>
@@ -444,7 +445,7 @@ class PBBAM_EXPORT DataSet
     /// \throws std::runtime_error if DataSet contains invalid or non-sensical
     ///         filters, such as rname appearing twice, etc.
     ///
-    std::vector<GenomicInterval> GenomicIntervals() const;
+    std::vector<Data::GenomicInterval> GenomicIntervals() const;
 
     /// \}
 

include/pbbam/FastqSequence.h

@@ -4,7 +4,8 @@
 #include <pbbam/Config.h>
 
 #include <pbbam/FastaSequence.h>
-#include <pbbam/QualityValues.h>
+
+#include <pbcopper/data/QualityValues.h>
 
 #include <string>
 

include/pbbam/IndexedFastaReader.h

@@ -4,10 +4,10 @@
 #include <pbbam/Config.h>
 
 #include <pbbam/BamRecord.h>
-#include <pbbam/Orientation.h>
-#include <pbbam/Position.h>
 
 #include <pbcopper/data/GenomicInterval.h>
+#include <pbcopper/data/Orientation.h>
+#include <pbcopper/data/Position.h>
 
 #include <memory>
 #include <stdexcept>

include/pbbam/IndexedFastqReader.h

@@ -5,12 +5,12 @@
 
 #include <pbbam/BamRecord.h>
 #include <pbbam/FastqReader.h>
-#include <pbbam/Orientation.h>
-#include <pbbam/Position.h>
-#include <pbbam/QualityValues.h>
 #include <pbbam/internal/QueryBase.h>
 
 #include <pbcopper/data/GenomicInterval.h>
+#include <pbcopper/data/Orientation.h>
+#include <pbcopper/data/Position.h>
+#include <pbcopper/data/QualityValues.h>
 
 #include <memory>
 #include <stdexcept>

include/pbbam/PbiFilterTypes.h

@@ -170,7 +170,7 @@ class PbiAlignedStrandFilter
     /// \param[in] strand  strand value to compare on
     /// \param[in] cmp     compare type
     ///
-    PbiAlignedStrandFilter(Strand strand, Compare::Type cmp = Compare::EQUAL);
+    PbiAlignedStrandFilter(Data::Strand strand, Compare::Type cmp = Compare::EQUAL);
 };
 
 /// \brief The PbiBarcodeFilter class provides a PbiFilter-compatible filter on

include/pbbam/bed/BedReader.h

@@ -3,9 +3,10 @@
 
 #include <pbbam/Config.h>
 
-#include <pbbam/GenomicInterval.h>
 #include <pbbam/internal/QueryBase.h>
 
+#include <pbcopper/data/GenomicInterval.h>
+
 #include <memory>
 #include <string>
 #include <vector>

include/pbbam/internal/PbiFilterTypes.inl

@@ -83,7 +83,7 @@ bool FilterBase<T>::CompareSingleHelper(const T& lhs) const
 }
 
 template <>
-inline bool FilterBase<LocalContextFlags>::CompareSingleHelper(const LocalContextFlags& lhs) const
+inline bool FilterBase<Data::LocalContextFlags>::CompareSingleHelper(const Data::LocalContextFlags& lhs) const
 {
     switch (cmp_) {
         case Compare::EQUAL:
@@ -183,15 +183,15 @@ bool BasicDataFilterBase<T, field>::BasicDataFilterBase::Accepts(const PbiRawDat
 
 // this typedef exists purely so that the next method signature isn't 2 screen widths long
 using LocalContextFilter__ =
-    BasicDataFilterBase<LocalContextFlags, PbiFile::BasicField::CONTEXT_FLAG>;
+    BasicDataFilterBase<Data::LocalContextFlags, PbiFile::BasicField::CONTEXT_FLAG>;
 
 template <>
 inline bool LocalContextFilter__::BasicDataFilterBase::Accepts(const PbiRawData& idx,
                                                                const size_t row) const
 {
     const auto& basicData = idx.BasicData();
-    const auto rowFlags = static_cast<LocalContextFlags>(basicData.ctxtFlag_.at(row));
-    return FilterBase<LocalContextFlags>::CompareHelper(rowFlags);
+    const auto rowFlags = static_cast<Data::LocalContextFlags>(basicData.ctxtFlag_.at(row));
+    return FilterBase<Data::LocalContextFlags>::CompareHelper(rowFlags);
 }
 
 // BasicDataFilterBase
@@ -210,12 +210,12 @@ MappedDataFilterBase<T, field>::MappedDataFilterBase(std::vector<T> values, cons
 
 template <>
 inline bool
-MappedDataFilterBase<Strand, PbiFile::MappedField::STRAND>::MappedDataFilterBase::Accepts(
+MappedDataFilterBase<Data::Strand, PbiFile::MappedField::STRAND>::MappedDataFilterBase::Accepts(
     const PbiRawData& idx, const size_t row) const
 {
     const PbiRawMappedData& mappedData = idx.MappedData();
-    const Strand strand = (mappedData.revStrand_.at(row) == 1 ? Strand::REVERSE : Strand::FORWARD);
-    return FilterBase<Strand>::CompareHelper(strand);
+    const Data::Strand strand = (mappedData.revStrand_.at(row) == 1 ? Data::Strand::REVERSE : Data::Strand::FORWARD);
+    return FilterBase<Data::Strand>::CompareHelper(strand);
 }
 
 template <typename T, PbiFile::MappedField field>
@@ -278,8 +278,8 @@ inline PbiAlignedStartFilter::PbiAlignedStartFilter(const uint32_t position,
 
 // PbiAlignedStrandFilter
 
-inline PbiAlignedStrandFilter::PbiAlignedStrandFilter(const Strand strand, const Compare::Type cmp)
-    : internal::MappedDataFilterBase<Strand, PbiFile::MappedField::STRAND>{strand, cmp}
+inline PbiAlignedStrandFilter::PbiAlignedStrandFilter(const Data::Strand strand, const Compare::Type cmp)
+    : internal::MappedDataFilterBase<Data::Strand, PbiFile::MappedField::STRAND>{strand, cmp}
 {
     if (cmp != Compare::EQUAL && cmp != Compare::NOT_EQUAL) {
         throw std::runtime_error{
@@ -374,9 +374,9 @@ inline PbiIdentityFilter::PbiIdentityFilter(const float identity, const Compare:
 
 // PbiLocalContextFilter
 
-inline PbiLocalContextFilter::PbiLocalContextFilter(const LocalContextFlags& flags,
+inline PbiLocalContextFilter::PbiLocalContextFilter(const Data::LocalContextFlags& flags,
                                                     const Compare::Type cmp)
-    : internal::BasicDataFilterBase<LocalContextFlags, PbiFile::BasicField::CONTEXT_FLAG>{flags,
+    : internal::BasicDataFilterBase<Data::LocalContextFlags, PbiFile::BasicField::CONTEXT_FLAG>{flags,
                                                                                           cmp}
 {
 }
@@ -443,9 +443,9 @@ inline PbiQueryStartFilter::PbiQueryStartFilter(const int32_t position, const Co
 
 // PbiReadAccuracyFilter
 
-inline PbiReadAccuracyFilter::PbiReadAccuracyFilter(const Accuracy accuracy,
+inline PbiReadAccuracyFilter::PbiReadAccuracyFilter(const Data::Accuracy accuracy,
                                                     const Compare::Type cmp)
-    : internal::BasicDataFilterBase<Accuracy, PbiFile::BasicField::READ_QUALITY>{accuracy, cmp}
+    : internal::BasicDataFilterBase<Data::Accuracy, PbiFile::BasicField::READ_QUALITY>{accuracy, cmp}
 {
 }
 

include/pbbam/vcf/VcfVariant.h

@@ -3,9 +3,10 @@
 
 #include <pbbam/Config.h>
 
-#include <pbbam/Position.h>
 #include <pbbam/vcf/VcfHeaderTypes.h>
 
+#include <pbcopper/data/Position.h>
+
 #include <optional>
 #include <string>
 #include <unordered_map>

include/pbbam/virtual/VirtualRegion.h

@@ -3,9 +3,10 @@
 
 #include <pbbam/Config.h>
 
-#include <pbbam/LocalContextFlags.h>
 #include <pbbam/virtual/VirtualRegionType.h>
 
+#include <pbcopper/data/LocalContextFlags.h>
+
 namespace PacBio {
 namespace BAM {
 

src/BamRecord.cpp

@@ -2470,8 +2470,8 @@ BamRecord& BamRecord::StartFrame(const std::vector<uint32_t>& startFrame)
     return *this;
 }
 
-QualityValues BamRecord::SubstitutionQV(Data::Orientation orientation, bool aligned,
-                                        bool exciseSoftClips) const
+Data::QualityValues BamRecord::SubstitutionQV(Data::Orientation orientation, bool aligned,
+                                              bool exciseSoftClips) const
 {
     return FetchQualities(BamRecordTag::SUBSTITUTION_QV, orientation, aligned, exciseSoftClips);
 }