public class HaplotypeMap extends Object
Constructor and Description |
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HaplotypeMap(File file)
Constructs a HaplotypeMap from the provided file.
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HaplotypeMap(SAMFileHeader header)
Constructs an empty HaplotypeMap using the provided SAMFileHeader's sequence dictionary.
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Modifier and Type | Method and Description |
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void |
addHaplotype(HaplotypeBlock haplotypeBlock)
Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
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Set<Snp> |
getAllSnps()
Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
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HaplotypeBlock |
getHaplotype(Snp snp)
Queries a HaplotypeBlock by Snp object.
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HaplotypeBlock |
getHaplotype(String snpName)
Queries a HaplotypeBlock by Snp name.
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HaplotypeBlock |
getHaplotype(String chrom,
int pos)
Queries a HaplotypeBlock by Snp chromosome and position.
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List<HaplotypeBlock> |
getHaplotypes()
Returns an unmodifiable collection of all the haplotype blocks in the map.
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SAMFileHeader |
getHeader() |
IntervalList |
getIntervalList()
Returns an IntervalList with an entry for every SNP in every Haplotype in the map.
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Snp |
getSnp(String chrom,
int pos)
Queries a Snp by chromosome and position.
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HaplotypeMap |
withoutChromosomes(Set<String> chroms)
Returns a copy of this haplotype map that excludes haplotypes on the chromosomes provided.
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void |
writeToFile(File file)
Writes out a HaplotypeMap file with the contents of this map.
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public HaplotypeMap(File file)
public HaplotypeMap(SAMFileHeader header)
public void addHaplotype(HaplotypeBlock haplotypeBlock)
public HaplotypeBlock getHaplotype(Snp snp)
public HaplotypeBlock getHaplotype(String snpName)
public HaplotypeBlock getHaplotype(String chrom, int pos)
public List<HaplotypeBlock> getHaplotypes()
public Snp getSnp(String chrom, int pos)
public Set<Snp> getAllSnps()
public IntervalList getIntervalList()
public HaplotypeMap withoutChromosomes(Set<String> chroms)
chroms
- a set of zero or more chromosome namespublic void writeToFile(File file)
public SAMFileHeader getHeader()