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. See Also layoutAlignment SeqAn - Sequence Analysis Library - www.seqan.de

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