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

Classes
class	BamFile

class	InBamFile

class	OutBamFile

class	BamHeader
	Wrapper around bam_hdr_t struct. More...

class	BamPair

class	BamPairProxy

class	BamPairIterator

class	BamRead
	Class holding a bam query. More...

struct	BamLessPos

struct	BamLessEnd

struct	BamLessName

class	BamReadFilter
	Filter bam reads. More...

class	BamReadIterator
	class to iterate through a InBamFile More...

class	BamWriter

class	BamWriteIterator
	Output iterator for bam file. More...

class	Codon

struct	AminoAcidEqual
	Functor comparing if two Codons translate to the same amino acid. More...

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	Pileup

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)

Detailed Description

Classes and functions related to genomics and proteomics.

Function Documentation

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

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

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

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

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

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, but this function works also when building against libbam. In libbam the array was called bam_nt16_rev_table.

This is the inverse of function nt16_table.

Since: New in yat 0.13

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, but this function works also when building against libbam. In libbam the array was called bam_nt16_table.

This is the inverse of function nt16_str.

Since: New in yat 0.13

double theplu::yat::omic::phred ( double p )

Phred scaled probability is defined as $\textrm{Phred} = -10 \log_{10} (p)$

Returns: phred scaled probability

Since: New in yat 0.13

See Also: phred_inv

double theplu::yat::omic::phred_inv ( double x )

The inverse of Phred scaling is calculated as $10^{-x/10}$

Returns: inverse of Phred scaling

Since: New in yat 0.13

See Also: phred

Classes

Functions

Detailed Description

Function Documentation