theplu::yat::omic Namespace Reference

Classes and functions related to genomics and proteomics. More...

Classes
struct	AminoAcidEqual
	Functor comparing if two Codons translate to the same amino acid. More...
class	BamFile
class	BamHeader
	Wrapper around bam_hdr_t struct. More...
struct	BamLessEnd
struct	BamLessName
struct	BamLessPos
class	BamPair
class	BamPairBuffer
class	BamPairIterator
class	BamPairIterator2
class	BamPairProxy
class	BamRead
	Class holding a bam query. More...
class	BamReadFilter
	Filter bam reads. More...
class	BamReadIterator
	class to iterate through a InBamFile More...
class	BamRegion
class	BamWriteIterator
	Output iterator for bam file. More...
class	BamWriter
class	Codon
class	DNA
struct	DnaComplementer
	Functor that calculates genomic complement. More...
class	Fasta
	wrapper class around struct faidx_t in libhts More...
class	GenomicPosition
class	GFF
class	GFF2
class	GFF3
class	InBamFile
class	OutBamFile
class	Pileup
class	VCF
class	VcfCompare
class	VcfFile
class	VcfHeader
class	VcfIterator

Functions
template<typename InputIterator , typename OutputIterator >
void	dna_complement (InputIterator begin, InputIterator end, OutputIterator out)
template<typename BidirectionalIterator >
void	dna_reverse_complement (BidirectionalIterator begin, BidirectionalIterator end)
template<typename BidirectionalIterator , typename OutputIterator >
void	dna_reverse_complement_copy (BidirectionalIterator begin, BidirectionalIterator end, OutputIterator out)
const unsigned char	nt16_table (char)
const char	nt16_str (uint8_t)
template<typename RandomAccessIterator >
double	alignment_score (const BamRead &bam, RandomAccessIterator ref, double mismatch, double gap=0.0, double open_gap=0.0)
unsigned short	chr2int (const std::string &str)
	transform a string to unsigned short chromosome number More...
double	phred (double p)
double	phred_inv (double x)
bool	is_indel (const VCF &)
bool	is_snv (const VCF &)
bool	is_dnv (const VCF &)
bool	is_mnv (const VCF &)

Detailed Description

Classes and functions related to genomics and proteomics.

Function Documentation

alignment_score()

template<typename RandomAccessIterator >

double theplu::yat::omic::alignment_score	(	const BamRead &	bam,
		RandomAccessIterator	ref,
		double	mismatch,
		double	gap = 0.0,
		double	open_gap = 0.0
	)

Calculate alignment score based on bam's cigar and sequence and the reference as in [ref, ref + bam.end()-bam.pos()).

For indels the score is calculated as open_gap + len * gap. For mismatches the score is calculated -mismatch. For matches the score is unity.

For cigar element BAM_CMATCH the sequence and reference is used to differentiate match from mismatch.

Type Requirments:

• RandomAccessIterator is a Readable Iterator
• RandomAccessIterator is a Random Access Traversal Iterator
• value_type is equality compareable with char

Since

New in yat 0.13

chr2int()

unsigned short theplu::yat::omic::chr2int

(

const std::string &

str

)

transform a string to unsigned short chromosome number

If str starts with 'chr' that prefix is stripped away before translating the string to chromosome number. Function translates "X" to 23, "Y" to 24, and "M" or "MT" to 25. For other inputs utility::convert is used to transform the input to an unsigned short.

Returns

chromosome number

Since

New in yat 0.7

dna_complement()

template<typename InputIterator , typename OutputIterator >

void theplu::yat::omic::dna_complement	(	InputIterator	begin,
		InputIterator	end,
		OutputIterator	out
	)

bam_pair_analyse performs an operation on bam read pairs as defined by visitor. The function iterates over sorted input range of reads; if read is first read, it is cached for later use; if read is second read and mate is present in cache, visitor operates on pair, i.e., Visitor (mate, read) is called.

Type Requirements:

• Iterator is a Readable Iterator
• Iterator is a Single Pass Iterator
• Iterator 's reference type must be convertible to BamRead
• Visitor must have an operator()(BamRead, BamRead) (or any const or reference combination)

Note

Input range [first, last ) must be sorted or behaviour is undefined.

Since

New in yat 0.10 Function that transforms a sequence of chars to its genomic complement (see DnaComplementer). Sequence can be transformed in-place, i.e., begin and out can point to the same element.

Type Requirements:

• InputIterator is Readable Iterator
• InputIterator models Single Pass Iterator
• value type of InputIterator is convertible to char
• OutputIterator models Incrementable Iterator
• OutputIterator is a Writable Iterator
• char must be convertible to value type of OutputIterator

Since

New in yat 0.14

dna_reverse_complement()

template<typename BidirectionalIterator >

void theplu::yat::omic::dna_reverse_complement	(	BidirectionalIterator	begin,
		BidirectionalIterator	end
	)

Function that transforms a sequence of chars to its genomic reverse complement, i.e., it transforms the sequence using DnaComplementer and reverse the sequence.

Type Requirements:

• BidirectionalIterator is Bidirectional Iterator
• BidirectionalIterator is Writable Iterator
• value type of BidirectionalIterator is convertible to char
• char must be convertible to value type of BidirectionalIterator

See also

dna_complement

dna_reverse_complement_copy

Since

New in yat 0.14

dna_reverse_complement_copy()

template<typename BidirectionalIterator , typename OutputIterator >

void theplu::yat::omic::dna_reverse_complement_copy	(	BidirectionalIterator	begin,
		BidirectionalIterator	end,
		OutputIterator	out
	)

Function that transforms a sequence of chars to its genomic reverse complement, i.e., it transforms the sequence using DnaComplementer and reverse the sequence.

Type Requirements:

• BidirectionalIterator is Readable Iterator
• BidirectionalIterator is Bidirectional Traversal Iterator
• value type of BidirectionalIterator is convertible to char
• char must be convertible to value type of BidirectionalIterator

Type Requirements:

• InputIterator is Readable Iterator
• InputIterator models Single Pass Iterator
• value type of InputIterator is convertible to char
• OutputIterator models Incrementable Iterator
• OutputIterator is a Writable Iterator
• char must be convertible to value type of OutputIterator

See also

dna_complement

dna_reverse_complement

Note

If input range and output range overlap, behaviour is undefined.

Since

New in yat 0.14

is_dnv()

bool theplu::yat::omic::is_dnv

(

const VCF &

)

Returns

true if at least one variant is a double-nucleotide variant (DNV), i.e., ref is 2bp and at least one alt allele is 2bp.

Note

ALT being an angle-bracketed ID string is ignored

is_indel()

bool theplu::yat::omic::is_indel

(

const VCF &

)

Returns

true if at least one variant is an indel, i.e., if at least one alt allele is not the same size as ref.

Note

ALT being an angle-bracketed ID string is ignored

is_mnv()

bool theplu::yat::omic::is_mnv

(

const VCF &

)

Returns

true if at least one variant is a multi-nucleotide variant (MNV), i.e., ref is >2bp and at least one alt allele is same length as ref.

Note

ALT being an angle-bracketed ID string is ignored

is_snv()

bool theplu::yat::omic::is_snv

(

const VCF &

)

Returns

true if at least one variant is a single-nucleotide variant (SNV), i.e., ref is 1bp and at least one alt allele is 1bp (but not '*').

Note

ALT being an angle-bracketed ID string is ignored

nt16_str()

const char theplu::yat::omic::nt16_str

(

uint8_t

)

Convert a 4-bit encoded nucleotide to a character.

This is the same functionality that is provided in HTSLIB's global array seq_nt16_str.

This is the inverse of function nt16_table.

Since

New in yat 0.13

nt16_table()

const unsigned char theplu::yat::omic::nt16_table

(

char

)

Convert nucleotide character to 4-bit encoding. The result is encoded as 1/2/4/8 for A/C/G/T or combinations of these bits.

This is the same functionality that is provided in HTSLIB's global array seq_nt16_table.

This is the inverse of function nt16_str.

Since

New in yat 0.13

phred()

double theplu::yat::omic::phred

(

double

p

)

Phred scaled probability is defined as

Returns

phred scaled probability

Since

New in yat 0.13

See also

phred_inv

phred_inv()

double theplu::yat::omic::phred_inv

(

double

x

)

The inverse of Phred scaling is calculated as

Returns

inverse of Phred scaling

Since

New in yat 0.13

See also

phred