AlignmentPrinter

#include <pbbam/AlignmentPrinter.h>
class PacBio::BAM::AlignmentPrinter

The AlignmentPrinter class “pretty-prints” an alignment with respect to its associated reference sequence.

Example output: 

Read        : singleInsertion2
Reference   : lambda_NEB3011

Read-length : 49
Concordance : 0.96

5210 : GGCTGCAGTGTACAGCGGTCAGGAGGCC-ATTGATGCCGG : 5249
       |||||||| ||||||||||||||||||| |||||||||||
   0 : GGCTGCAG-GTACAGCGGTCAGGAGGCCAATTGATGCCGG :   39

5249 : ACTGGCTGAT : 5259
       ||||||||||
  39 : ACTGGCTGAT :   49

Constructors & Related Methods

AlignmentPrinter(const IndexedFastaReader &ifr)

Constructs the alignment printer with an associated FASTA file reader.

Parameters
  • ifr: FASTA reader
Exceptions
  • std::runtime_error: if FASTA file cannot be opened for reading.

AlignmentPrinter()
AlignmentPrinter(const AlignmentPrinter&)
AlignmentPrinter(AlignmentPrinter&&)
AlignmentPrinter &operator=(const AlignmentPrinter&)
AlignmentPrinter &operator=(AlignmentPrinter&&)
~AlignmentPrinter()

Printing

std::string Print(const BamRecord &record, const Orientation orientation = Orientation::GENOMIC)

Pretty-prints an aligned BamRecord to std::string.

Note
The current implementation includes ANSI escape sequences for coloring terminal output. Future versions of this method will likely make this optional.
Return
formatted string containing the alignment and summary information