public class ExacRecord extends Object
Constructor and Description |
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ExacRecord(String chrom,
int pos,
String id,
String ref,
List<String> alt,
Collection<String> filter,
Map<ExacPopulation,List<Integer>> alleleCounts,
Map<ExacPopulation,Integer> chromCounts) |
Modifier and Type | Method and Description |
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boolean |
equals(Object obj) |
com.google.common.collect.ImmutableMap<ExacPopulation,com.google.common.collect.ImmutableList<Integer>> |
getAlleleCounts() |
com.google.common.collect.ImmutableList<Integer> |
getAlleleCounts(ExacPopulation pop) |
com.google.common.collect.ImmutableMap<ExacPopulation,com.google.common.collect.ImmutableList<Double>> |
getAlleleFrequencies() |
com.google.common.collect.ImmutableList<Double> |
getAlleleFrequencies(ExacPopulation pop) |
com.google.common.collect.ImmutableList<String> |
getAlt() |
String |
getChrom() |
int |
getChromCount(ExacPopulation pop) |
com.google.common.collect.ImmutableMap<ExacPopulation,Integer> |
getChromCounts() |
com.google.common.collect.ImmutableList<String> |
getFilter() |
String |
getId() |
int |
getPos() |
String |
getRef() |
int |
hashCode() |
double |
highestAlleleFreq(int alleleNo) |
ExacPopulation |
popWithHighestAlleleFreq(int alleleNo) |
String |
toString() |
public ExacRecord(String chrom, int pos, String id, String ref, List<String> alt, Collection<String> filter, Map<ExacPopulation,List<Integer>> alleleCounts, Map<ExacPopulation,Integer> chromCounts)
public String getChrom()
public int getPos()
public String getId()
public String getRef()
public com.google.common.collect.ImmutableList<String> getAlt()
public com.google.common.collect.ImmutableList<String> getFilter()
public com.google.common.collect.ImmutableMap<ExacPopulation,com.google.common.collect.ImmutableList<Integer>> getAlleleCounts()
public com.google.common.collect.ImmutableMap<ExacPopulation,Integer> getChromCounts()
public com.google.common.collect.ImmutableMap<ExacPopulation,com.google.common.collect.ImmutableList<Double>> getAlleleFrequencies()
public com.google.common.collect.ImmutableList<Integer> getAlleleCounts(ExacPopulation pop)
pop
, for each allele, including reference onepublic int getChromCount(ExacPopulation pop)
pop
, for each allele, including the reference onepublic com.google.common.collect.ImmutableList<Double> getAlleleFrequencies(ExacPopulation pop)
public ExacPopulation popWithHighestAlleleFreq(int alleleNo)
ExacPopulation
with highest allele frequency for the given allele index (0 is first alternative
allele)public double highestAlleleFreq(int alleleNo)
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