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

Class SVKmerizer

java.lang.Object

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

All Implemented Interfaces:

java.util.Iterator<SVKmer>

Direct Known Subclasses:

SVDUSTFilteredKmerizer

public class SVKmerizer
extends java.lang.Object
implements java.util.Iterator<SVKmer>

Iterator over successive Kmers from a sequence of characters. Silently skips over parts of the sequence that has characters other than A, C, G, or T.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SVKmerizer.ASCIICharSequence

Field Summary

Fields

Modifier and Type	Field and Description
protected int	idx
protected int	kAdvance
protected int	kSize
protected SVKmer	nextKmer
protected java.lang.CharSequence	seq

Constructor Summary

Constructors

Modifier	Constructor and Description
	SVKmerizer(byte[] seq, int kSize, int kSpace, SVKmer kmer)
	SVKmerizer(byte[] seq, int kSize, SVKmer kmer)
	SVKmerizer(java.lang.CharSequence seq, int kSize, int kSpace, SVKmer kmer)
	SVKmerizer(java.lang.CharSequence seq, int kSize, SVKmer kmer)
protected	SVKmerizer(int kSize, java.lang.CharSequence seq)
protected	SVKmerizer(int kSize, int kSpace, java.lang.CharSequence seq)

Method Summary

Modifier and Type	Method and Description
static java.util.stream.Stream<SVKmer>	canonicalStream(byte[] seq, int kSize, SVKmer kmer)
boolean	hasNext()
SVKmer	next()
protected SVKmer	nextKmer(SVKmer tmpKmer, int validBaseCount)
static java.util.stream.Stream<SVKmer>	stream(byte[] seq, int kSize, int kSpace, SVKmer kmer)
static java.util.stream.Stream<SVKmer>	stream(byte[] seq, int kSize, SVKmer kmer)
static java.util.stream.Stream<SVKmer>	stream(java.lang.CharSequence seq, int kSize, int kSpace, SVKmer kmer)
static SVKmer	toKmer(byte[] seq, SVKmer kmer)
static SVKmer	toKmer(java.lang.CharSequence seq, SVKmer kmer)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Iterator

forEachRemaining, remove

Field Detail

seq

protected final java.lang.CharSequence seq

kSize

protected final int kSize

kAdvance

protected final int kAdvance

idx

protected int idx

nextKmer

protected SVKmer nextKmer

Constructor Detail

SVKmerizer

public SVKmerizer(byte[] seq,
                  int kSize,
                  SVKmer kmer)

SVKmerizer

public SVKmerizer(byte[] seq,
                  int kSize,
                  int kSpace,
                  SVKmer kmer)

SVKmerizer

public SVKmerizer(java.lang.CharSequence seq,
                  int kSize,
                  SVKmer kmer)

SVKmerizer

public SVKmerizer(java.lang.CharSequence seq,
                  int kSize,
                  int kSpace,
                  SVKmer kmer)

SVKmerizer

protected SVKmerizer(int kSize,
                     java.lang.CharSequence seq)

SVKmerizer

protected SVKmerizer(int kSize,
                     int kSpace,
                     java.lang.CharSequence seq)

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface java.util.Iterator<SVKmer>

next

public SVKmer next()

Specified by:

next in interface java.util.Iterator<SVKmer>

toKmer

public static SVKmer toKmer(java.lang.CharSequence seq,
                            SVKmer kmer)

toKmer

public static SVKmer toKmer(byte[] seq,
                            SVKmer kmer)

stream

public static java.util.stream.Stream<SVKmer> stream(java.lang.CharSequence seq,
                                                     int kSize,
                                                     int kSpace,
                                                     SVKmer kmer)

stream

public static java.util.stream.Stream<SVKmer> stream(byte[] seq,
                                                     int kSize,
                                                     int kSpace,
                                                     SVKmer kmer)

stream

public static java.util.stream.Stream<SVKmer> stream(byte[] seq,
                                                     int kSize,
                                                     SVKmer kmer)

canonicalStream

public static java.util.stream.Stream<SVKmer> canonicalStream(byte[] seq,
                                                              int kSize,
                                                              SVKmer kmer)

nextKmer

protected SVKmer nextKmer(SVKmer tmpKmer,
                          int validBaseCount)