fn() reAlignPerform realignment using the Anson-Myers realignment.
Perform realignment using the Anson-Myers realignment.
Defined in | <seqan/consensus.h> |
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Signature |
void reAlign(fragStore, consensusScore, contigID, [realignmentMethod,] bandwidth, includeReference);
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Parameters
fragStore
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The FragmentStore with the alignment to realign. |
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consensusScore
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The Score to use for scoring alignments. |
contigID
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The integer id of the contig to realign. |
bandwidth
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The integer bandwidth to use for realignment. |
includeReference
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A bool flag that indicates whether to include the reference as a pseudo-read. |
Detailed Description
Deprecated.
Do not use this function but use the new function reAlignment instead.
If includeReference then the reference of the given contig will be used as a pseudo-read. In this case, the reference will be replaced by the consensus. When included as a pseudo-read, the alignment of the consensus relative to the original refernence can be used to call variants.
Data Races
Thread safety unknown!