picard.fingerprint

Class HaplotypeMap

java.lang.Object

picard.fingerprint.HaplotypeMap

public class HaplotypeMap
extends java.lang.Object

A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc. Also has the ability to read and write itself to and from files.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	HET_GENOTYPE_FOR_PHASING
static java.lang.String	PHASESET_PREFIX
static java.lang.String	SYNTHETIC_PHASESET_PREFIX

Constructor Summary

Constructors

Constructor and Description
HaplotypeMap(java.util.Collection<HaplotypeBlock> haplotypeBlocks) since this constructor doesn't initialize the HaplotypeMap "properly", it should be used carefully!
HaplotypeMap(java.io.File file)
HaplotypeMap(htsjdk.samtools.SAMFileHeader header) Constructs an empty HaplotypeMap using the provided SAMFileHeader's sequence dictionary.

Method Summary

Modifier and Type	Method and Description
void	addHaplotype(HaplotypeBlock haplotypeBlock) Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
java.util.Collection<htsjdk.variant.variantcontext.VariantContext>	asVcf(htsjdk.samtools.reference.ReferenceSequenceFile ref)
java.util.Set<Snp>	getAllSnps() Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
HaplotypeBlock	getHaplotype(Snp snp) Queries a HaplotypeBlock by Snp object.
HaplotypeBlock	getHaplotype(java.lang.String snpName) Queries a HaplotypeBlock by Snp name.
HaplotypeBlock	getHaplotype(java.lang.String chrom, int pos) Queries a HaplotypeBlock by Snp chromosome and position.
java.util.List<HaplotypeBlock>	getHaplotypes() Returns an unmodifiable collection of all the haplotype blocks in the map.
htsjdk.samtools.SAMFileHeader	getHeader()
htsjdk.samtools.util.IntervalList	getIntervalList() Returns an IntervalList with an entry for every SNP in every Haplotype in the map.
Snp	getSnp(java.lang.String chrom, int pos) Queries a Snp by chromosome and position.
HaplotypeMap	withoutChromosomes(java.util.Set<java.lang.String> chroms) Returns a copy of this haplotype map that excludes haplotypes on the chromosomes provided.
void	writeAsVcf(java.io.File output, java.io.File refFile)
void	writeToFile(java.io.File file) Writes out a HaplotypeMap file with the contents of this map.

Methods inherited from class java.lang.Object

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

Field Detail

HET_GENOTYPE_FOR_PHASING

public static final java.lang.String HET_GENOTYPE_FOR_PHASING

See Also:

Constant Field Values

SYNTHETIC_PHASESET_PREFIX

public static final java.lang.String SYNTHETIC_PHASESET_PREFIX

See Also:

Constant Field Values

PHASESET_PREFIX

public static final java.lang.String PHASESET_PREFIX

See Also:

Constant Field Values

Constructor Detail

HaplotypeMap

public HaplotypeMap(htsjdk.samtools.SAMFileHeader header)

Constructs an empty HaplotypeMap using the provided SAMFileHeader's sequence dictionary.

HaplotypeMap

public HaplotypeMap(java.io.File file)

HaplotypeMap

public HaplotypeMap(java.util.Collection<HaplotypeBlock> haplotypeBlocks)

since this constructor doesn't initialize the HaplotypeMap "properly", it should be used carefully!

Method Detail

addHaplotype

public void addHaplotype(HaplotypeBlock haplotypeBlock)

Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.

getHaplotype

public HaplotypeBlock getHaplotype(Snp snp)

Queries a HaplotypeBlock by Snp object. Returns NULL if none found.

getHaplotype

public HaplotypeBlock getHaplotype(java.lang.String snpName)

Queries a HaplotypeBlock by Snp name. Returns NULL if none found.

getHaplotype

public HaplotypeBlock getHaplotype(java.lang.String chrom,
                                   int pos)

Queries a HaplotypeBlock by Snp chromosome and position. Returns NULL if none found.

getHaplotypes

public java.util.List<HaplotypeBlock> getHaplotypes()

Returns an unmodifiable collection of all the haplotype blocks in the map.

getSnp

public Snp getSnp(java.lang.String chrom,
                  int pos)

Queries a Snp by chromosome and position. Returns NULL if none found.

getAllSnps

public java.util.Set<Snp> getAllSnps()

Returns an unmodifiable collection of all SNPs in all Haplotype blocks.

getIntervalList

public htsjdk.samtools.util.IntervalList getIntervalList()

Returns an IntervalList with an entry for every SNP in every Haplotype in the map.

withoutChromosomes

public HaplotypeMap withoutChromosomes(java.util.Set<java.lang.String> chroms)

Returns a copy of this haplotype map that excludes haplotypes on the chromosomes provided.

Parameters:

chroms - a set of zero or more chromosome names

writeAsVcf

public void writeAsVcf(java.io.File output,
                       java.io.File refFile)
                throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

asVcf

public java.util.Collection<htsjdk.variant.variantcontext.VariantContext> asVcf(htsjdk.samtools.reference.ReferenceSequenceFile ref)

writeToFile

public void writeToFile(java.io.File file)

Writes out a HaplotypeMap file with the contents of this map.

getHeader

public htsjdk.samtools.SAMFileHeader getHeader()