global multiple sequence alignment with efficiently stored long gaps. More...

#include <alignment.hh>

Public Member Functions
	Alignment (size_t k)

void	printTextGraph (ostream &strm)

void	merge (Alignment other, const MsaSignature sig=NULL)

int	maxRange ()

int	numRows () const

int	numFilledRows () const

int	getCumFragLen () const

int	getMaxSeqIdLen () const

string	getSignature () const

int	numFitting (const MsaSignature *sig) const

void	shiftAliPositions (int offset)

void	pack ()

Public Attributes
int	aliLen

vector< AlignmentRow * >	rows

Friends
bool	mergeable (Alignment a1, Alignment a2, int maxGapLen, float mergeableFrac, bool strong)

ostream &	operator<< (ostream &strm, const Alignment &a)

Alignment *	mergeAliList (list< Alignment * > alis, const MsaSignature *sig)

void	capAliSize (list< Alignment * > &alis, int maxRange)

void	reduceOvlpRanges (list< Alignment * > &alis, size_t maxCov, float covPen)

int	medianChrStartEndDiff (Alignment a1, Alignment a2)

Detailed Description

global multiple sequence alignment with efficiently stored long gaps.

Generation of exon candidates

     1000      1010       1020      1030       1040      1050    chromosomal

chr21 |.........|..........|.........|..........|.........| positions ********* ************ in species 1 \ \ / / align chr21 *********----------—************---------— ment chr7 -—*****--------------—******************** | | \ a fragment \

chr7 |.........|..........|.........|..........|.........| chromosomal 2000 2010 2020 2030 2040 2050 positions in species 2 Here: Alignment a; a.aliLen = 46 a.rows[0].frags = ((1002, 0, 9), (1027, 23, 12)) a.rows[0].chrStart() = 1002 a.rows[0].chrEnd() = 1037

Coordinates are LEFT TO RIGHT, for reverse strand alignments, they refer to the REVERSE COMPLEMENT of the sequence.

Author: Mario Stanke

Friends And Related Symbol Documentation

◆ capAliSize

void capAliSize	(	list< Alignment * > &	alis,
		int	maxRange
	)

friend

For each alignment in the 'alis' list, if necessary, chunk it into piece alignments that have sequence ranges of size at most maxRange. The new alignments are added to the end. The maxRange limit can be violated in the untypical case that a single gapless fragment exceed this length threshold. The (recursively chosen) split point is before the largest gap in the interval [2/3*maxRange, maxRange].

The documentation for this class was generated from the following files:

include/alignment.hh
src/alignment.cc

Public Member Functions

Public Attributes

Friends

Detailed Description

Friends And Related Symbol Documentation

◆ capAliSize