@Override public boolean equals(Object o) { if (this == o) return true; if (!(o instanceof VariantSetStats)) return false; VariantSetStats that = (VariantSetStats) o; return !(impl != null ? !impl.equals(that.impl) : that.impl != null); }
public Map<String, ChromosomeStats> getChromosomeStats() { return impl.getChromosomeStats(); }
public Map<String, Integer> getConsequenceTypesCounts() { return impl.getConsequenceTypesCounts(); }
public void addNumPass(int passCount) { this.impl.setNumPass(impl.getNumPass() + passCount); }
public VariantSetStats() { this.impl = new org.opencb.biodata.models.variant.metadata.VariantSetStats(); this.impl.setVariantTypeCounts(new HashMap<>()); this.impl.setChromosomeStats(new HashMap<>()); this.impl.setNumRareVariants(new ArrayList<>()); this.impl.setVariantBiotypeCounts(new HashMap<>()); this.setNumVariants(0); this.setNumSamples(0); this.setSnpsCount(0); this.setIndelsCount(0); this.setStructuralCount(0); this.setNumPass(0); this.setConsequenceTypesCounts(new LinkedHashMap<>(20)); }
public VariantSetStats(int numRecords, int samplesCount, int snpsCount, int indelsCount, int structuralCount, int passCount, float meanQuality, Map<String, Integer> consequenceTypesCount) { this.impl = new org.opencb.biodata.models.variant.metadata.VariantSetStats(); this.impl.setVariantTypeCounts(new HashMap<>()); this.impl.setChromosomeStats(new HashMap<>()); this.setNumVariants(numRecords); this.setNumSamples(samplesCount); this.setSnpsCount(snpsCount); this.setIndelsCount(indelsCount); this.setStructuralCount(structuralCount); this.setNumPass(passCount); this.setMeanQuality(meanQuality); this.setConsequenceTypesCounts(consequenceTypesCount); }
public List<VariantsByFrequency> getNumRareVariants() { return impl.getNumRareVariants(); }
public int getNumSamples() { return impl.getNumSamples(); }
public int getNumPass() { return impl.getNumPass(); }
public float getStdDevQuality(){ return impl.getStdDevQuality(); }
public int getNumVariants() { return impl.getNumVariants() == null ? 0 : impl.getNumVariants(); }
public Float getMeanQuality() { return impl.getMeanQuality(); }
@Override public VariantSetStats build() { try { VariantSetStats record = new VariantSetStats(); record.numVariants = fieldSetFlags()[0] ? this.numVariants : (java.lang.Integer) defaultValue(fields()[0]); record.numSamples = fieldSetFlags()[1] ? this.numSamples : (java.lang.Integer) defaultValue(fields()[1]); record.numPass = fieldSetFlags()[2] ? this.numPass : (java.lang.Integer) defaultValue(fields()[2]); record.tiTvRatio = fieldSetFlags()[3] ? this.tiTvRatio : (java.lang.Float) defaultValue(fields()[3]); record.meanQuality = fieldSetFlags()[4] ? this.meanQuality : (java.lang.Float) defaultValue(fields()[4]); record.stdDevQuality = fieldSetFlags()[5] ? this.stdDevQuality : (java.lang.Float) defaultValue(fields()[5]); record.numRareVariants = fieldSetFlags()[6] ? this.numRareVariants : (java.util.List<org.opencb.biodata.models.variant.metadata.VariantsByFrequency>) defaultValue(fields()[6]); record.variantTypeCounts = fieldSetFlags()[7] ? this.variantTypeCounts : (java.util.Map<java.lang.String,java.lang.Integer>) defaultValue(fields()[7]); record.variantBiotypeCounts = fieldSetFlags()[8] ? this.variantBiotypeCounts : (java.util.Map<java.lang.String,java.lang.Integer>) defaultValue(fields()[8]); record.consequenceTypesCounts = fieldSetFlags()[9] ? this.consequenceTypesCounts : (java.util.Map<java.lang.String,java.lang.Integer>) defaultValue(fields()[9]); record.chromosomeStats = fieldSetFlags()[10] ? this.chromosomeStats : (java.util.Map<java.lang.String,org.opencb.biodata.models.variant.metadata.ChromosomeStats>) defaultValue(fields()[10]); return record; } catch (Exception e) { throw new org.apache.avro.AvroRuntimeException(e); } } }
private int getChromosomeCount(String chromosome) { ChromosomeStats chromosomeStats = impl.getChromosomeStats().get(chromosome); return chromosomeStats == null ? 0 : chromosomeStats.getCount(); }
public Map<String, Integer> getChromosomeCounts() { return impl.getChromosomeStats().entrySet().stream().collect(Collectors.toMap(Map.Entry::getKey, o -> o.getValue().getCount())); }
public void setChromosomeCount(String chromosome, int count) { impl.getChromosomeStats().compute(chromosome, (key, chromosomeStats) -> { if (chromosomeStats == null) { return new ChromosomeStats(count, 0F); } else { chromosomeStats.setCount(count); return chromosomeStats; } }); }
public void addChromosomeCount(String chromosome, int count) { impl.getChromosomeStats().compute(chromosome, (key, chromosomeStats) -> { if (chromosomeStats == null) { return new ChromosomeStats(count, 0F); } else { chromosomeStats.setCount(chromosomeStats.getCount() + count); return chromosomeStats; } }); }