net.maizegenetics.pangenome.db_loading

Class AnchorDataPHG

java.lang.Object

net.maizegenetics.pangenome.db_loading.AnchorDataPHG

All Implemented Interfaces:

Comparable<AnchorDataPHG>

public class AnchorDataPHG
extends Object
implements Comparable<AnchorDataPHG>

THis class differs from AnchorData in WGS_whatever as it includes more fields to match what is stored in PHGSchema's anchor_haplotypes. Specifically it includes ave_allele_depth and additional_data May 26, 2017: Class updated to include gene_start and gene_end These values needed when trimming anchors. The stored anchors have sequence of merged genes whose GFF start/end positions overlapped with 1000bp flanking on each end. THis 1000bp may be less is the distance between 2 genes is less than 2000bps.

Author:

lcj34

Constructor Summary

Constructors

Constructor and Description
AnchorDataPHG(com.google.common.collect.Range<net.maizegenetics.dna.map.Position> interval, com.google.common.collect.Range<net.maizegenetics.dna.map.Position> gene, String gvcf, byte[] variants, String sequence, boolean isAnchor)

Method Summary

Modifier and Type	Method and Description
int	compareTo(AnchorDataPHG other)
static String	createSHA1Hash(String seq)
boolean	equals(Object obj)
com.google.common.collect.Range<net.maizegenetics.dna.map.Position>	geneCoordinates()
String	gvcf()
int	hashCode()
com.google.common.collect.Range<net.maizegenetics.dna.map.Position>	intervalCoordinates()
boolean	isAnchor()
String	seqHash()
int	seqLen()
String	sequence()
byte[]	variants()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AnchorDataPHG

public AnchorDataPHG(com.google.common.collect.Range<net.maizegenetics.dna.map.Position> interval,
                     com.google.common.collect.Range<net.maizegenetics.dna.map.Position> gene,
                     String gvcf,
                     byte[] variants,
                     String sequence,
                     boolean isAnchor)

Method Detail

createSHA1Hash

public static String createSHA1Hash(String seq)

intervalCoordinates

public com.google.common.collect.Range<net.maizegenetics.dna.map.Position> intervalCoordinates()

geneCoordinates

public com.google.common.collect.Range<net.maizegenetics.dna.map.Position> geneCoordinates()

gvcf

public String gvcf()

variants

public byte[] variants()

sequence

public String sequence()

seqLen

public int seqLen()

seqHash

public String seqHash()

isAnchor

public boolean isAnchor()

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

compareTo

public int compareTo(AnchorDataPHG other)

Specified by:

compareTo in interface Comparable<AnchorDataPHG>