shore::alignment_helper Class Reference

Alignment string utilities. More...

Public Member Functions
size_t	extract_ref (const std::string &alignment, std::string &ref)
	Extract the sequence of the reference ([L*]/[F*] bases are ignored!). More...
size_t	extract_qry (const std::string &alignment, std::string &qry, const bool include_softclipped=false)
	Extract the sequence of the query. More...
void	extract_seq (const std::string &alignment, std::string &ref, std::string &qry, const bool include_softclipped=false)
	Combines extract_ref() & extract_qry().
size_t	calc_size_of_qry (const std::string &alignment, const bool include_softclipped=false)
	Calculates the size of the query sequence.
size_t	calc_size_on_ref (const std::string &alignment)
	Calculates the length of the range on the reference sequence.
int	calc_editdistance (const std::string &alignment)
	Calculates the edit distance from an alignment string.
std::pair< int, int >	calc_indels (const std::string &alignment)
	Calculates the number of insertions and deletions from an alignment string.
int	move_start_by_qrybases (std::string &alignment, int nbases)
	Remove/add a number of query bases at the left side of an alignment string. More...
int	move_start_by_refbases (std::string &alignment, int nbases)
	Remove/add a number of reference bases at the left side of an alignment string. More...
int	move_end_by_qrybases (std::string &alignment, int nbases)
	Remove/add a number of query bases at the right side of an alignment string. More...
int	move_end_by_refbases (std::string &alignment, int nbases)
	Remove/add a number of reference bases at the right side of an alignment string. More...
void	rebuild (std::string &alignment)
	Rebuild an alignment string in the most compact representation.
void	invert (std::string &alignment)
	Swap query and reference sequence.
void	revcomp (std::string &alignment)
	Reverse complement an alignment string.
void	paste (std::string &alignment, const std::string &other, int distance=0, bool inv=false, bool forcefrag=true, bool nomove=false)
	Join alignment strings adding a given distance. More...
void	cigar (const std::string &alignment, std::string &cigar, const char sep=0)
	Append CIGAR string for the alignment string somewhere. More...
size_t	calc_size_on_ref (const shore::alignment &a)
	Calculates the length of the alignment on the reference sequence.
long	calc_end_excl (const shore::alignment &a)
	Calculates the exclusive end position on the reference.
shore::refseq_coor	calc_end_coor_excl (const shore::alignment &a)
	Calculates the exclusive end position on the reference.
void	resize (shore::alignment &f, const size_t newsize)
	Appends or removes bases at the query's 3' end.

Static Public Member Functions
static std::string	compose (alignment_tokenizer &ref, alignment_tokenizer &qry)
	Put two alignments on top of each other.

Detailed Description

Alignment string utilities.

Member Function Documentation

void shore::alignment_helper::cigar	(	const std::string &	alignment,
		std::string &	cigar,
		const char	sep = 0
	)

Append CIGAR string for the alignment string somewhere.

Parameters

[in]	alignment	Alignment string.
[out]	cigar	CIGAR string.
	sep	Optional separator for cigar items.

size_t shore::alignment_helper::extract_qry	(	const std::string &	alignment,
		std::string &	qry,
		const bool	include_softclipped = false
	)

Extract the sequence of the query.

(never reverse complemented, strand is unknown anyway).

Returns

Same as calc_size_on_ref()

size_t shore::alignment_helper::extract_ref	(	const std::string &	alignment,
		std::string &	ref
	)

Extract the sequence of the reference ([L*]/[F*] bases are ignored!).

Returns

Same as calc_size_of_qry()

int shore::alignment_helper::move_end_by_qrybases	(	std::string &	alignment,
		int	nbases
	)

Remove/add a number of query bases at the right side of an alignment string.

Returns

The number of bases the alignment end has moved to the right on the reference sequence.

int shore::alignment_helper::move_end_by_refbases	(	std::string &	alignment,
		int	nbases
	)

Remove/add a number of reference bases at the right side of an alignment string.

Returns

The number of bases that were added at the end of the query.

int shore::alignment_helper::move_start_by_qrybases	(	std::string &	alignment,
		int	nbases
	)

Remove/add a number of query bases at the left side of an alignment string.

Returns

The number of bases the alignment has moved to the right on the reference sequence.

int shore::alignment_helper::move_start_by_refbases	(	std::string &	alignment,
		int	nbases
	)

Remove/add a number of reference bases at the left side of an alignment string.

Returns

The number of bases that were removed at the start of the query.

void shore::alignment_helper::paste	(	std::string &	alignment,
		const std::string &	other,
		int	distance = 0,
		bool	inv = false,
		bool	forcefrag = true,
		bool	nomove = false
	)

Join alignment strings adding a given distance.

Parameters

alignment	String being modified.
other	String to append.
distance	Distance between the alignments (may be negative).
inv	Indicate the alignments had different directions (use [f.. instead of [F..).
forcefrag	Insert [F0] token if distance <= 0.
nomove	For overlapping strings (distance < 0), insert [F-N] instead of truncating the string.

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The documentation for this class was generated from the following file:

• shore/datatype/alignment_string_ops.hpp