Package picard.flow
Class FlowBasedRead
java.lang.Object
picard.flow.FlowBasedRead
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionFlowBasedRead
(htsjdk.samtools.SAMRecord samRecord, String flowOrder, int maxHmer, FlowBasedArgumentCollection fbargs) Same as above but constructs from SAMRecord -
Method Summary
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Field Details
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MAX_CLASS
public static final int MAX_CLASS- See Also:
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MAX_CLASS_READ_GROUP_TAG
- See Also:
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Constructor Details
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FlowBasedRead
public FlowBasedRead(htsjdk.samtools.SAMRecord samRecord, String flowOrder, int maxHmer, FlowBasedArgumentCollection fbargs) Same as above but constructs from SAMRecord- Parameters:
samRecord
- record from SAM fileflowOrder
- flow order (single cycle)maxHmer
- maximal hmer to keep in the flow matrixfbargs
- arguments that control resoltion of the flow matrix
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Method Details
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getMaxHmer
public int getMaxHmer() -
getNFlows
public int getNFlows() -
isValid
public boolean isValid() -
getProb
public double getProb(int flow, int hmer) get a specific cell from the flow matrix. Each cell contains the probability for an hmer of the given length to appear the given position in the flow key- Parameters:
flow
- - position in the flow key (index into key[])hmer
- - length of the hmer- Returns:
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getKey
public int[] getKey() -
getReadName
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