net.maizegenetics.pangenome.pipelineTests

Class SimpleGVCFReader

java.lang.Object

net.maizegenetics.pangenome.pipelineTests.SimpleGVCFReader

public class SimpleGVCFReader
extends Object

Created by edbuckler on 6/22/17.

Constructor Summary

Constructors

Constructor and Description
SimpleGVCFReader(String gvcfFileName, String refGenomeFile, int maxRowsToProcess, int minDepth)

Method Summary

Modifier and Type	Method and Description
String	genotype(int chromosome, int positionInChromosome)
String	genotype(net.maizegenetics.dna.map.Position position)
com.google.common.collect.RangeMap<net.maizegenetics.util.Tuple<Integer,Integer>,String>	getSubMap(com.google.common.collect.Range<net.maizegenetics.util.Tuple<Integer,Integer>> subRange)
boolean	inReferenceRange(int chromosome, int positionInChromosome)
boolean	inReferenceRange(net.maizegenetics.dna.map.Position position)
String	reference(int chromosome, int positionInChromosome)
String	reference(net.maizegenetics.dna.map.Position position)

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SimpleGVCFReader

public SimpleGVCFReader(String gvcfFileName,
                        String refGenomeFile,
                        int maxRowsToProcess,
                        int minDepth)

Method Detail

genotype

public String genotype(net.maizegenetics.dna.map.Position position)

genotype

public String genotype(int chromosome,
                       int positionInChromosome)

inReferenceRange

public boolean inReferenceRange(net.maizegenetics.dna.map.Position position)

inReferenceRange

public boolean inReferenceRange(int chromosome,
                                int positionInChromosome)

reference

public String reference(net.maizegenetics.dna.map.Position position)

reference

public String reference(int chromosome,
                        int positionInChromosome)

getSubMap

public com.google.common.collect.RangeMap<net.maizegenetics.util.Tuple<Integer,Integer>,String> getSubMap(com.google.common.collect.Range<net.maizegenetics.util.Tuple<Integer,Integer>> subRange)