printAlignment

Function

printAlignment

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

printAlignment(stream, format, layout, store, contigId, posBegin, posEnd, lineBegin, lineEnd)

Include Headers

seqan/store.h

Parameters

stream	A C++ outstream, e.g. std::cout.
layout	A layout structure created by a previous call of layoutAlignment. Types: AlignedReadLayout
format	Output format. Types: Raw Remarks: This tag is used for subsequent calls of write for contig and read gaps data structures.
store	The fragment store. Types: FragmentStore
contigId	The contigId of the affected contig.
posBegin	Window begin position in gap-space.
posEnd	Window end position in gap-space.
lineBegin	Begin line of the window.
lineEnd	End line of the window.

Remarks

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