org.broadinstitute.hellbender.utils

Interface IntervalPileup

public interface IntervalPileup

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static interface	IntervalPileup.Element
static interface	IntervalPileup.Insert

Field Summary

Fields

Modifier and Type	Field and Description
static byte	GAP
static byte	NO_BASE
static byte	NO_BQ

Method Summary

Modifier and Type	Method and Description
byte	baseAt(int row, int column)
IntervalPileup.Element	element(GATKRead read)
default IntervalPileup.Element	element(int row)
boolean	hasInsertAt(int i, int j)
int	height()
IntervalPileup.Insert	insertAt(int row, int column)
byte[]	insertBasesAt(int i, int j)
byte[]	insertQualsAt(int i, int j)
static IntervalPileup	of(java.util.List<GATKRead> reads, ReferenceBases referenceBases)
static IntervalPileup	of(htsjdk.samtools.util.Locatable loc, ReadsDataSource aln, ReferenceDataSource ref)
byte	qualAt(int row, int column)
GATKRead	readAt(int row, int column)
java.util.List<GATKRead>	reads()
java.util.List<GATKRead>	readsAt(int row, int column)
ReferenceBases	reference()
int	width()

Field Detail

NO_BQ

static final byte NO_BQ

See Also:

Constant Field Values

GAP

static final byte GAP

See Also:

Constant Field Values

NO_BASE

static final byte NO_BASE

See Also:

Constant Field Values

Method Detail

reads

java.util.List<GATKRead> reads()

reference

ReferenceBases reference()

width

int width()

height

int height()

baseAt

byte baseAt(int row,
            int column)

qualAt

byte qualAt(int row,
            int column)

insertAt

IntervalPileup.Insert insertAt(int row,
                               int column)

readAt

GATKRead readAt(int row,
                int column)

readsAt

java.util.List<GATKRead> readsAt(int row,
                                 int column)

element

IntervalPileup.Element element(GATKRead read)

element

default IntervalPileup.Element element(int row)

hasInsertAt

boolean hasInsertAt(int i,
                    int j)

insertBasesAt

byte[] insertBasesAt(int i,
                     int j)

insertQualsAt

byte[] insertQualsAt(int i,
                     int j)

of

static IntervalPileup of(htsjdk.samtools.util.Locatable loc,
                         ReadsDataSource aln,
                         ReferenceDataSource ref)

of

static IntervalPileup of(java.util.List<GATKRead> reads,
                         ReferenceBases referenceBases)