yat
0.11.3pre
|
Classes and functions related to genomics and proteomics. More...
Classes | |
class | BamFile |
class | InBamFile |
class | OutBamFile |
class | BamHeader |
Wrapper around bam_header_t struct. More... | |
class | BamRead |
Class holding a bam query. More... | |
struct | BamLessPos |
struct | BamLessEnd |
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 |
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 | |
Classes and functions related to genomics and proteomics.
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 IteratorIterator
's reference
type must be convertible to BamReadVisitor
must have an operator()(BamRead, BamRead)
(or any const
or reference combination)
[first, last
) must be sorted or behaviour is undefined.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.