BamRecordView¶
#include <pbbam/BamRecord.h>
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class
PacBio::BAM::
BamRecordView
¶ Provides a re-usable “view” onto a BamRecord.
This class acts a convenience wrapper for working with per-base BamRecord data. Most of these BamRecord methods take a list of parameters, to adjust how the underlying data are presented to client code. Often these parameters will be re-used for each BamRecord method call. Thus, to simplify such client code, a BamRecordView can be used to state those parameters once, and then simply request the desired fields.
Public Functions
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BamRecordView
(const BamRecord &record, const Orientation orientation, const bool aligned, const bool exciseSoftClips, const PulseBehavior pulseBehavior = PulseBehavior::ALL)¶ Constructs a view onto
record
using the supplied parameters.For frame or QV data, if
aligned
is true, a value of 0 (Accuracy or QualityValue) will be used at each inserted or padded base location.
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QualityValues
AltLabelQVs
() const¶ - Return
- BamRecord::AltLabelQV with this view’s parameters applied
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std::string
AltLabelTags
() const¶ - Return
- BamRecord::AltLabelTag with this view’s parameters applied
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QualityValues
DeletionQVs
() const¶ - Return
- BamRecord::DeletionQV with this view’s parameters applied
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std::string
DeletionTags
() const¶ - Return
- BamRecord::DeletionTag with this view’s parameters applied
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QualityValues
InsertionQVs
() const¶ - Return
- BamRecord::InsertionQV with this view’s parameters applied
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Frames
IPD
() const¶ - Return
- BamRecord::IPD with this view’s parameters applied
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QualityValues
LabelQVs
() const¶ - Return
- BamRecord::LabelQV with this view’s parameters applied
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QualityValues
MergeQVs
() const¶ - Return
- BamRecord::MergeQV with this view’s parameters applied
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QualityValues
PulseMergeQVs
() const¶ - Return
- BamRecord::PulseMergeQV with this view’s parameters applied
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std::vector<float>
Pkmean
() const¶ - Return
- BamRecord::Pkmean with this view’s parameters applied
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std::vector<float>
Pkmid
() const¶ - Return
- BamRecord::Pkmid with this view’s parameters applied
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std::vector<float>
Pkmean2
() const¶ - Return
- BamRecord::Pkmean2 with this view’s parameters applied
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std::vector<float>
Pkmid2
() const¶ - Return
- BamRecord::Pkmid2 with this view’s parameters applied
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Frames
PrebaseFrames
() const¶ - Return
- BamRecord::PreBaseFrames with this view’s parameters applied
-
Frames
PrePulseFrames
() const¶ - Return
- BamRecord::PrePulseFrames with this view’s parameters applied
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std::string
PulseCalls
() const¶ - Return
- BamRecord::PulseCalls with this view’s parameters applied
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Frames
PulseCallWidth
() const¶ - Return
- BamRecord::PulseCallWidth with this view’s parameters applied
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QualityValues
Qualities
() const¶ - Return
- BamRecord::Qualities with this view’s parameters applied
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std::string
Sequence
() const¶ - Return
- BamRecord::Sequence with this view’s parameters applied
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std::vector<uint32_t>
StartFrames
() const¶ - Return
- BamRecord::StartFrame with this view’s parameters applied
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QualityValues
SubstitutionQVs
() const¶ - Return
- BamRecord::SubstitutionQV with this view’s parameters applied
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std::string
SubstitutionTags
() const¶ - Return
- BamRecord::SubstitutionTag with this view’s parameters applied
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