public class MemoryMappedVcfDataStore
extends java.lang.Object
| Modifier and Type | Class and Description |
|---|---|
static class |
MemoryMappedVcfDataStore.Genotype |
protected static class |
MemoryMappedVcfDataStore.Locus |
| Constructor and Description |
|---|
MemoryMappedVcfDataStore() |
| Modifier and Type | Method and Description |
|---|---|
java.util.Collection<VcfPosition> |
getAllPositions() |
java.util.Collection<java.util.List<VcfSample>> |
getAllSamples() |
MemoryMappedVcfDataStore.Genotype |
getGenotypeAtLocus(java.lang.String chromosome,
long position,
int sampleIndex) |
MemoryMappedVcfDataStore.Genotype |
getGenotypeAtLocus(java.lang.String chromosome,
long position,
java.lang.String sampleId) |
MemoryMappedVcfDataStore.Genotype |
getGenotypeForId(java.lang.String positionId,
int sampleIndex) |
MemoryMappedVcfDataStore.Genotype |
getGenotypeForId(java.lang.String positionId,
java.lang.String sampleId) |
protected java.util.Map<java.lang.String,VcfPosition> |
getIdToPosition() |
protected java.util.Map<java.lang.String,java.util.List<VcfSample>> |
getIdToSamples() |
protected java.util.Map<MemoryMappedVcfDataStore.Locus,VcfPosition> |
getLocusToPosition() |
protected java.util.Map<MemoryMappedVcfDataStore.Locus,java.util.List<VcfSample>> |
getLocusToSamples() |
VcfMetadata |
getMetadata() |
VcfPosition |
getPositionAtLocus(java.lang.String chromosome,
long position) |
VcfPosition |
getPositionForId(java.lang.String id) |
VcfSample |
getSampleAtLocus(java.lang.String chromosome,
long position,
int sampleIndex) |
VcfSample |
getSampleAtLocus(java.lang.String chromosome,
long position,
java.lang.String sampleId) |
VcfSample |
getSampleForId(java.lang.String positionId,
int sampleIndex) |
VcfSample |
getSampleForId(java.lang.String positionId,
java.lang.String sampleId) |
java.util.List<VcfSample> |
getSamplesAtLocus(java.lang.String chromosome,
long position) |
java.util.List<VcfSample> |
getSamplesForId(java.lang.String id) |
protected void |
setIdToPosition(java.util.Map<java.lang.String,VcfPosition> idToPosition) |
protected void |
setIdToSamples(java.util.Map<java.lang.String,java.util.List<VcfSample>> idToSamples) |
protected void |
setLocusToPosition(java.util.Map<MemoryMappedVcfDataStore.Locus,VcfPosition> locusToPosition) |
protected void |
setLocusToSamples(java.util.Map<MemoryMappedVcfDataStore.Locus,java.util.List<VcfSample>> locusToSamples) |
protected void |
setMetadata(VcfMetadata metadata) |
@Nullable public java.util.Collection<VcfPosition> getAllPositions()
@Nullable public java.util.Collection<java.util.List<VcfSample>> getAllSamples()
@Nullable public VcfMetadata getMetadata()
protected void setMetadata(VcfMetadata metadata)
@Nullable public VcfPosition getPositionForId(@Nonnull java.lang.String id)
@Nullable public java.util.List<VcfSample> getSamplesForId(@Nonnull java.lang.String id)
@Nullable public VcfPosition getPositionAtLocus(@Nonnull java.lang.String chromosome, long position)
@Nullable public java.util.List<VcfSample> getSamplesAtLocus(@Nonnull java.lang.String chromosome, long position)
@Nullable public VcfSample getSampleForId(@Nonnull java.lang.String positionId, @Nonnull java.lang.String sampleId)
@Nullable public VcfSample getSampleForId(@Nonnull java.lang.String positionId, int sampleIndex)
@Nullable public VcfSample getSampleAtLocus(@Nonnull java.lang.String chromosome, long position, @Nonnull java.lang.String sampleId)
@Nullable public VcfSample getSampleAtLocus(@Nonnull java.lang.String chromosome, long position, int sampleIndex)
@Nullable public MemoryMappedVcfDataStore.Genotype getGenotypeForId(@Nonnull java.lang.String positionId, java.lang.String sampleId)
@Nullable public MemoryMappedVcfDataStore.Genotype getGenotypeAtLocus(@Nonnull java.lang.String chromosome, long position, java.lang.String sampleId)
@Nullable public MemoryMappedVcfDataStore.Genotype getGenotypeForId(@Nonnull java.lang.String positionId, int sampleIndex)
@Nullable public MemoryMappedVcfDataStore.Genotype getGenotypeAtLocus(@Nonnull java.lang.String chromosome, long position, int sampleIndex)
protected java.util.Map<java.lang.String,VcfPosition> getIdToPosition()
protected void setIdToPosition(java.util.Map<java.lang.String,VcfPosition> idToPosition)
protected java.util.Map<MemoryMappedVcfDataStore.Locus,VcfPosition> getLocusToPosition()
protected void setLocusToPosition(java.util.Map<MemoryMappedVcfDataStore.Locus,VcfPosition> locusToPosition)
protected java.util.Map<java.lang.String,java.util.List<VcfSample>> getIdToSamples()
protected void setIdToSamples(java.util.Map<java.lang.String,java.util.List<VcfSample>> idToSamples)
protected java.util.Map<MemoryMappedVcfDataStore.Locus,java.util.List<VcfSample>> getLocusToSamples()
protected void setLocusToSamples(java.util.Map<MemoryMappedVcfDataStore.Locus,java.util.List<VcfSample>> locusToSamples)