Package org.snpeff.stats
Class GeneCountByTypeTable
java.lang.Object
org.snpeff.stats.GeneCountByTypeTable
- All Implemented Interfaces:
Serializable
,Iterable<String>
Count for each 'type' and 'gene'.
Tries to avoid multiple counting by comparing to latest variants.
WARNING: This strategy does not work if changeEffect are out of order.
- Author:
- pcingola
- See Also:
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetBioType
(String key) getCounter
(String type) Get counter for this typegetCounterSize
(String type) Get size counter for this typeGet a sorted list of keysint
getSizeByType
(String key, String type) Get a sorted list of keysiterator()
void
sample
(Gene gene, Transcript tr, String type, VariantEffect variantEffect) Sample this <gene, marker, type, variant> tuple to update statisticsMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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GENE_CPG_NUM_BINS
public static int GENE_CPG_NUM_BINS -
debug
public static boolean debug
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Constructor Details
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GeneCountByTypeTable
public GeneCountByTypeTable()
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Method Details
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getBioType
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getCounter
Get counter for this type -
getCounterSize
Get size counter for this type -
getKeyList
Get a sorted list of keys -
getSizeByType
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getTypeList
Get a sorted list of keys -
iterator
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sample
Sample this <gene, marker, type, variant> tuple to update statistics
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