theplu::yat::omic Namespace Reference

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
class	GenomicPosition
class	GFF
class	GFF2
class	GFF3
class	Pileup

Functions
template<class Iterator , class Visitor >
void	bam_pair_analyse (Iterator first, Iterator last, Visitor &visitor)
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.

Since

New in yat 0.13

template<class Iterator , class Visitor >

void theplu::yat::omic::bam_pair_analyse	(	Iterator	first,
		Iterator	last,
		Visitor &	visitor
	)

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 must be an Input 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

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

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

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

Returns

inverse of Phred scaling

Since

New in yat 0.13

See Also

phred