Class AlignedReadLayout
Stores a two dimensional visible layout of a multi-read alignment.

Defined in <seqan/store.h>
Signature struct AlignedReadLayout;

Interface Function Overview

Member Variable Overview

Interface Functions Detail

void layoutAlignment(layout, store);

Calculates a visible layout of aligned reads.


layout The resulting layout structure.
store The FragmentStore.

For each contig, thisf unction layouts all reads in rows from up to down reusing empty row spaces.

See Also

void printAlignment(stream, format, layout, store, contigID, posBegin, posEnd, lineBegin, lineEnd);

Prints a window of the visible layout of reads into a std::outstream.


stream The std::ostream to print to.
format The output format, e.g. Raw.
layout The AlignedReadLayout computed earlier in layoutAlignment.
store The FragmentStore that this layout belongs to.
contigID The id of the contig for the alignments to print.
posBegin The begin position of the window.
posEnd The end position of the window.
lineBegin The first line of the window.
lineEnd The end line of the window.

The window coordinates (beginPos, ...) may be chosen bigger than the lyaout is. The empty space is then filled with spaces.

Member Variables Detail

TContigRows AlignedReadLayout::contigRows

2D multi-read layout.

Stores for a contig and row the ids of aligned reads from left to right. contigRows[contigId][row] stores the alignId of all aligned reads from left to right assigned to the same row. row is the row of the alignment in the multiple sequence alignment and contigId the id of the reference contig.