Package picard.flow

Class FlowBasedRead

java.lang.Object
picard.flow.FlowBasedRead

public class FlowBasedRead extends Object
  • Field Details

  • Constructor Details

    • 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 file
      flowOrder - flow order (single cycle)
      maxHmer - maximal hmer to keep in the flow matrix
      fbargs - arguments that control resoltion of the flow matrix
  • Method Details

    • 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:
    • getKey

      public int[] getKey()
    • getReadName

      public String getReadName()