theplu::yat::omic Namespace Reference

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

Classes
class	BamFile
class	InBamFile
class	OutBamFile
class	BamHeader
class	BamRead
	Class holding a bam query. More...
struct	BamLessPos
struct	BamLessEnd
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

Functions
template<class Iterator , class Visitor >
void	bam_pair_analyse (Iterator first, Iterator last, Visitor &visitor)
unsigned short	chr2int (const std::string &str)
	transform a string to unsigned short chromosome number

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Detailed Description

Classes and functions related to genomics and proteomics.

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Function Documentation

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