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

Class SVFastqUtils.Mapping

java.lang.Object

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

All Implemented Interfaces:

htsjdk.samtools.util.Locatable

Enclosing class:

SVFastqUtils

public static final class SVFastqUtils.Mapping
extends java.lang.Object
implements htsjdk.samtools.util.Locatable

Constructor Summary

Constructors

Constructor and Description
Mapping(GATKRead read)
Mapping(java.lang.String str)

Method Summary

Modifier and Type	Method and Description
java.util.List<AlignmentInterval>	getAllIntervals()
htsjdk.samtools.Cigar	getCigar() Returns the cigar of the primary interval, or the empty cigar if unmapped.
java.lang.String	getContig() Returns the contig as per the primary interval, or null if unmapped.
int	getEnd() Returns the primary interval end position, or SAMRecord.NO_ALIGNMENT_START if unmapped.
AlignmentInterval	getPrimaryInterval()
int	getStart() Returns the primary interval start position, or SAMRecord.NO_ALIGNMENT_START if unmapped.
java.util.List<AlignmentInterval>	getSupplementaryIntervals()
boolean	isForwardStrand()
boolean	isMapped()
java.lang.String	toString() Generates the mapping string as it would be included in the Fastq read header.
static java.lang.String	toString(GATKRead read) Generates the mapping string for a read.

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Constructor Detail

Mapping

public Mapping(java.lang.String str)

Mapping

public Mapping(GATKRead read)

Method Detail

isMapped

public boolean isMapped()

getContig

public java.lang.String getContig()

Returns the contig as per the primary interval, or null if unmapped.

Specified by:

getContig in interface htsjdk.samtools.util.Locatable

Returns:

may return a null.

getStart

public int getStart()

Returns the primary interval start position, or SAMRecord.NO_ALIGNMENT_START if unmapped.

Specified by:

getStart in interface htsjdk.samtools.util.Locatable

Returns:

SAMRecord.NO_ALIGNMENT_START or a strictly positive value.

getEnd

public int getEnd()

Returns the primary interval end position, or SAMRecord.NO_ALIGNMENT_START if unmapped.

Specified by:

getEnd in interface htsjdk.samtools.util.Locatable

Returns:

SAMRecord.NO_ALIGNMENT_START or a strictly positive value.

getCigar

public htsjdk.samtools.Cigar getCigar()

Returns the cigar of the primary interval, or the empty cigar if unmapped.

Returns:

isForwardStrand

public boolean isForwardStrand()

getPrimaryInterval

public AlignmentInterval getPrimaryInterval()

getSupplementaryIntervals

public java.util.List<AlignmentInterval> getSupplementaryIntervals()

getAllIntervals

public java.util.List<AlignmentInterval> getAllIntervals()

toString

public static java.lang.String toString(GATKRead read)

Generates the mapping string for a read. This contains the read own coordinates plus the content of the SA tag if present.

Parameters:

read - the source read.

Returns:

never null. SVFastqUtils.UNMAPPED_DESCRIPTION_STR if the read is unmapped.

toString

public java.lang.String toString()

Generates the mapping string as it would be included in the Fastq read header.

Overrides:

toString in class java.lang.Object

Returns:

never null. SVFastqUtils.UNMAPPED_DESCRIPTION_STR if the read is unmapped.