org.broadinstitute.hellbender.tools.spark.sv.utils

Class SVFastqUtils.FastqRead

java.lang.Object

org.broadinstitute.hellbender.tools.spark.sv.utils.SVFastqUtils.FastqRead

All Implemented Interfaces:

org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembler.BasesAndQuals

Enclosing class:

SVFastqUtils

public static final class SVFastqUtils.FastqRead
extends java.lang.Object
implements org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembler.BasesAndQuals

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SVFastqUtils.FastqRead.Serializer

Constructor Summary

Constructors

Constructor and Description
FastqRead(GATKRead read)
FastqRead(GATKRead read, boolean includeMappingLocation)

Method Summary

Modifier and Type	Method and Description
byte[]	getBases() returns bases with values like 'A', 'C', 'G', and 'T'
java.lang.String	getDescription()
java.lang.String	getHeader() Returns the header line of this Fastq read starting with '@' followed by the read id and description separated by tab characters.
java.lang.String	getId()
SVFastqUtils.Mapping	getMapping()
java.lang.String	getName()
byte[]	getQuals() returns phred-scaled quals with no bias

Methods inherited from class java.lang.Object

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

Constructor Detail

FastqRead

public FastqRead(GATKRead read)

FastqRead

public FastqRead(GATKRead read,
                 boolean includeMappingLocation)

Method Detail

getHeader

public java.lang.String getHeader()

Returns the header line of this Fastq read starting with '@' followed by the read id and description separated by tab characters.

Returns:

never null.

getId

public java.lang.String getId()

getName

public java.lang.String getName()

getDescription

public java.lang.String getDescription()

getMapping

public SVFastqUtils.Mapping getMapping()

getBases

public byte[] getBases()

returns bases with values like 'A', 'C', 'G', and 'T'

Specified by:

getBases in interface org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembler.BasesAndQuals

getQuals

public byte[] getQuals()

returns phred-scaled quals with no bias

Specified by:

getQuals in interface org.broadinstitute.hellbender.utils.fermi.FermiLiteAssembler.BasesAndQuals