Class
AlignedReadLayoutStores a two dimensional visible layout of a multi-read alignment.
Stores a two dimensional visible layout of a multi-read alignment.
Defined in | <seqan/store.h> |
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Signature |
struct AlignedReadLayout;
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Interface Function Overview
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void layoutAlignment(layout, store);
Calculates a visible layout of aligned reads. -
void printAlignment(stream, layout, store, contigID, posBegin, posEnd, lineBegin, lineEnd);
Prints a window of the visible layout of reads into a std::outstream.
Member Variable Overview
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TContigRows AlignedReadLayout::contigRows
2D multi-read layout.
Interface Functions Detail
void layoutAlignment(layout, store);
Calculates a visible layout of aligned reads.
Parameters
layout
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The resulting layout structure. |
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store
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The FragmentStore. |
For each contig, thisf unction layouts all reads in rows from up to down reusing empty row spaces.
Data Races
Thread safety unknown!
See Also
void printAlignment(stream, layout, store, contigID, posBegin, posEnd, lineBegin, lineEnd);
Prints a window of the visible layout of reads into a std::outstream.
Parameters
stream
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The std::ostream to print to. |
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layout
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The AlignedReadLayout computed earlier in layoutAlignment. |
store
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The FragmentStore that this layout belongs to. |
contigID
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The id of the contig for the alignments to print. |
posBegin
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The begin position of the window. |
posEnd
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The end position of the window. |
lineBegin
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The first line of the window. |
lineEnd
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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.
Data Races
Thread safety unknown!
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.