HaplotypeMap (picard 2.18.2 API)

java.lang.Object
- picard.fingerprint.HaplotypeMap

```
public class HaplotypeMap
extends 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 Description

static String HET_GENOTYPE_FOR_PHASING

static String PHASESET_PREFIX

static String SYNTHETIC_PHASESET_PREFIX

Fields
Modifier and Type	Field	Description
`static String`	`HET_GENOTYPE_FOR_PHASING`
`static String`	`PHASESET_PREFIX`
`static String`	`SYNTHETIC_PHASESET_PREFIX`

Constructor Summary

Constructors
Constructor	Description
`HaplotypeMap(htsjdk.samtools.SAMFileHeader header)`	Constructs an empty HaplotypeMap using the provided SAMFileHeader's sequence dictionary.
`HaplotypeMap(File file)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addHaplotype(HaplotypeBlock haplotypeBlock)`	Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
`Collection<htsjdk.variant.variantcontext.VariantContext>`	`asVcf(htsjdk.samtools.reference.ReferenceSequenceFile ref)`
`Set<Snp>`	`getAllSnps()`	Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
`HaplotypeBlock`	`getHaplotype(String snpName)`	Queries a HaplotypeBlock by Snp name.
`HaplotypeBlock`	`getHaplotype(String chrom, int pos)`	Queries a HaplotypeBlock by Snp chromosome and position.
`HaplotypeBlock`	`getHaplotype(Snp snp)`	Queries a HaplotypeBlock by Snp object.
`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(String chrom, int pos)`	Queries a Snp by chromosome and position.
`HaplotypeMap`	`withoutChromosomes(Set<String> chroms)`	Returns a copy of this haplotype map that excludes haplotypes on the chromosomes provided.
`void`	`writeAsVcf(File output, File refFile)`
`void`	`writeToFile(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 String HET_GENOTYPE_FOR_PHASING
```
    See Also:
    
    Constant Field Values
  - SYNTHETIC_PHASESET_PREFIX
```
public static final String SYNTHETIC_PHASESET_PREFIX
```
    See Also:
    
    Constant Field Values
  - PHASESET_PREFIX
```
public static final 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(File file)
```
- 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(String snpName)
```
    Queries a HaplotypeBlock by Snp name. Returns NULL if none found.
  - getHaplotype
```
public HaplotypeBlock getHaplotype(String chrom,
                                   int pos)
```
    Queries a HaplotypeBlock by Snp chromosome and position. Returns NULL if none found.
  - getHaplotypes
```
public List<HaplotypeBlock> getHaplotypes()
```
    Returns an unmodifiable collection of all the haplotype blocks in the map.
  - getSnp
```
public Snp getSnp(String chrom,
                  int pos)
```
    Queries a Snp by chromosome and position. Returns NULL if none found.
  - getAllSnps
```
public 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(Set<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(File output,
                       File refFile)
                throws FileNotFoundException
```
    Throws:
    
    FileNotFoundException
  - asVcf
```
public Collection<htsjdk.variant.variantcontext.VariantContext> asVcf(htsjdk.samtools.reference.ReferenceSequenceFile ref)
```
  - writeToFile
```
public void writeToFile(File file)
```
    Writes out a HaplotypeMap file with the contents of this map.
  - getHeader
```
public htsjdk.samtools.SAMFileHeader getHeader()
```

Class HaplotypeMap

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

HET_GENOTYPE_FOR_PHASING

SYNTHETIC_PHASESET_PREFIX

PHASESET_PREFIX

Constructor Detail

HaplotypeMap

HaplotypeMap

Method Detail

addHaplotype

getHaplotype

getHaplotype

getHaplotype

getHaplotypes

getSnp

getAllSnps

getIntervalList

withoutChromosomes

writeAsVcf

asVcf

writeToFile

getHeader