net.maizegenetics.dna.read

Class PERead

java.lang.Object

net.maizegenetics.dna.read.PERead

public class PERead
extends Object

Holding paired end read. Providing merging function

Author:

Fei Lu

Constructor Summary

Constructors

Constructor and Description
PERead(Read rf, Read rb)

Method Summary

Modifier and Type	Method and Description
Read	getBackwardRead() Return backward read
Read	getForwardRead() Return forward read
float	getOverlapIdentity() Return identity of overlap of PE
int	getOverlapLength() Return length of overlap of PE
Read	getPContig() Return Pcontig read Return null when there is no Pcontig
boolean	merge(boolean ifPrintAlignment)

Methods inherited from class java.lang.Object

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

Constructor Detail

PERead

public PERead(Read rf,
              Read rb)

Method Detail

merge

public boolean merge(boolean ifPrintAlignment)

getForwardRead

public Read getForwardRead()

Return forward read

Returns:

getBackwardRead

public Read getBackwardRead()

Return backward read

Returns:

getPContig

public Read getPContig()

Return Pcontig read Return null when there is no Pcontig

Returns:

getOverlapLength

public int getOverlapLength()

Return length of overlap of PE

Returns:

getOverlapIdentity

public float getOverlapIdentity()

Return identity of overlap of PE

Returns: