IndexedFastaReader¶
#include <pbbam/IndexedFastaReader.h>
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class
PacBio::BAM::
IndexedFastaReader
¶ The IndexedFastaReader class provides random-access to FASTA file data.
Constructors & Related Methods
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IndexedFastaReader
()¶
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IndexedFastaReader
(const std::string &filename)¶
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IndexedFastaReader
(const IndexedFastaReader &src)¶
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IndexedFastaReader &
operator=
(const IndexedFastaReader &rhs)¶
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~IndexedFastaReader
()¶
Unnamed Group
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std::string
Subsequence
(const std::string &id, Position begin, Position end) const¶ Fetches FASTA sequence for desired interval.
name Sequence Access
- Return
- sequence string at desired interval
- Parameters
id
: reference sequence namebegin
: start positionend
: end position
- Exceptions
std::runtime_error
: on failure to fetch sequence
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std::string
Subsequence
(const GenomicInterval &interval) const¶ Fetches FASTA sequence for desired interval.
- Return
- sequence string at desired interval
- Parameters
interval
: desired interval
- Exceptions
std::runtime_error
: on failure to fetch sequence
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std::string
Subsequence
(const char *htslibRegion) const¶ Fetches FASTA sequence for desired interval.
- Return
- sequence string at desired interval
- Parameters
htslibRegion
: htslib/samtools-formatted REGION string representing the desired interval
- Exceptions
std::runtime_error
: on failure to fetch sequence
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std::string
ReferenceSubsequence
(const BamRecord &bamRecord, const Orientation orientation = Orientation::GENOMIC, const bool gapped = false, const bool exciseSoftClips = false) const¶ Fetches FASTA sequence corresponding to a BamRecord, oriented and gapped as requested.
For example, “native” orientation and “gapped” will return the reference sequence with gaps inserted, as would align against the read in “native” orientation.
- Return
- sequence string over the record’s interval
- Parameters
bamRecord
: input BamRecord to derive interval/CIGAR dataorientation
: orientation of outputgapped
: if true, gaps/padding will be inserted, per record’s CIGAR info.exciseSoftClips
: if true, any soft-clipped positions will be removed from query ends
- Exceptions
std::runtime_error
: on failure to fetch sequence
File Attributes
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bool
HasSequence
(const std::string &name) const¶ - Return
- true if FASTA file contains a sequence matching
name
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std::string
Name
(const size_t idx) const¶ - Return
- the names of the sequence at a specific index in the FASTA file
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std::vector<std::string>
Names
() const¶ - Return
- the names of all sequences stored in the FASTA file
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int
NumSequences
() const¶ - Return
- number of sequences stored in FASTA file
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int
SequenceLength
(const std::string &name) const¶ - Return
- length of FASTA sequence
- Exceptions
std::runtime_error
: if length could not be determined
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