net.maizegenetics.pangenome.hapCalling

Class SAMMetricsPlugin.AlignmentSummary

net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary

Enclosing class:

SAMMetricsPlugin

public static class SAMMetricsPlugin.AlignmentSummary

data class containing summary of alignment statstics for one file: mappedReads: number of mapped reads unmappedReads: number of unmapped reads minEditDistances: list of the lowest edit distance for the alignments of each mapped read Instead of printing the entire editDistances list, toString() calculates and prints mean and median

Constructor Detail

AlignmentSummary

public AlignmentSummary(int mappedReads,
                        int unmappedReads,
                        @NotNull
                        java.util.List<java.lang.Integer> minEditDistances)

data class containing summary of alignment statstics for one file: mappedReads: number of mapped reads unmappedReads: number of unmapped reads minEditDistances: list of the lowest edit distance for the alignments of each mapped read Instead of printing the entire editDistances list, toString() calculates and prints mean and median

Method Detail

toString

@NotNull
public java.lang.String toString()

getMappedReads

public int getMappedReads()

getUnmappedReads

public int getUnmappedReads()

getMinEditDistances

@NotNull
public java.util.List<java.lang.Integer> getMinEditDistances()

component1

public int component1()

component2

public int component2()

component3

@NotNull
public java.util.List<java.lang.Integer> component3()

copy

@NotNull
public net.maizegenetics.pangenome.hapCalling.SAMMetricsPlugin.AlignmentSummary copy(int mappedReads,
                                                                                              int unmappedReads,
                                                                                              @NotNull
                                                                                              java.util.List<java.lang.Integer> minEditDistances)

data class containing summary of alignment statstics for one file: mappedReads: number of mapped reads unmappedReads: number of unmapped reads minEditDistances: list of the lowest edit distance for the alignments of each mapped read Instead of printing the entire editDistances list, toString() calculates and prints mean and median

hashCode

public int hashCode()

equals

public boolean equals(@Nullable
                      java.lang.Object p)