Constructor and Description |
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VariantAnnotator(ReferenceDictionary refDict,
com.google.common.collect.ImmutableMap<Integer,Chromosome> chromosomeMap,
AnnotationBuilderOptions options)
Construct new VariantAnnotator, given a chromosome map.
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Modifier and Type | Method and Description |
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ReferenceDictionary |
ReferenceDictionaryBuilder.build() |
ReferenceDictionary |
JannovarData.getRefDict() |
ReferenceDictionary |
Chromosome.getRefDict() |
Constructor and Description |
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Chromosome(ReferenceDictionary refDict,
int chrID,
IntervalArray<TranscriptModel> tmIntervalTree)
Initialize object.
|
JannovarData(ReferenceDictionary refDict,
com.google.common.collect.ImmutableList<TranscriptModel> transcriptInfos)
Initialize the object with the given values.
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Modifier and Type | Method and Description |
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ReferenceDictionary |
ReferenceDictParser.parse()
Load accessions and chromInfo file and return resulting ReferenceDictionary.
|
Constructor and Description |
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EnsemblParser(ReferenceDictionary refDict,
String basePath,
org.ini4j.Profile.Section iniSection) |
Constructor and Description |
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FlatBEDParser(ReferenceDictionary refDict,
String basePath,
org.ini4j.Profile.Section iniSection,
boolean printProgressBars) |
Constructor and Description |
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RefSeqParser(ReferenceDictionary refDict,
String basePath,
org.ini4j.Profile.Section iniSection) |
Constructor and Description |
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UCSCParser(ReferenceDictionary refDict,
String basePath,
org.ini4j.Profile.Section iniSection) |
Modifier and Type | Method and Description |
---|---|
static ReferenceDictionary |
HG19RefDictBuilder.build() |
ReferenceDictionary |
GenomeInterval.getRefDict() |
ReferenceDictionary |
GenomePosition.getRefDict() |
Constructor and Description |
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GenomeInterval(ReferenceDictionary refDict,
Strand strand,
int chr,
int beginPos,
int endPos)
construct genome interval with zero-based coordinate system
|
GenomeInterval(ReferenceDictionary refDict,
Strand strand,
int chr,
int beginPos,
int endPos,
PositionType positionType)
construct genome interval with selected coordinate system
|
GenomePosition(ReferenceDictionary refDict,
Strand strand,
int chr,
int pos)
construct genome position with zero-based coordinate system
|
GenomePosition(ReferenceDictionary refDict,
Strand strand,
int chr,
int pos,
PositionType positionType)
construct genome position with selected coordinate system
|
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