Package org.snpeff.ped
Class PlinkMap
- java.lang.Object
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- org.snpeff.ped.PlinkMap
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public class PlinkMap extends java.lang.Object
PLINK MAP file References: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
getChrName(int idx)
java.util.Collection<java.lang.String>
getGenotypeNames()
java.lang.Integer
getGenotypeNames(java.lang.String idStr)
java.lang.String
getId(int idx)
int
getPosition(int idx)
protected void
read(java.lang.String mapFileName)
Reads MAP file MAP file format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) Space separated or tab columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Genetic distance (morgans) Base-pair position (bp units)int
size()
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Method Detail
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getChrName
public java.lang.String getChrName(int idx)
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getGenotypeNames
public java.util.Collection<java.lang.String> getGenotypeNames()
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getGenotypeNames
public java.lang.Integer getGenotypeNames(java.lang.String idStr)
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getId
public java.lang.String getId(int idx)
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getPosition
public int getPosition(int idx)
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read
protected void read(java.lang.String mapFileName)
Reads MAP file MAP file format (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) Space separated or tab columns: chromosome (1-22, X, Y or 0 if unplaced) rs# or snp identifier Genetic distance (morgans) Base-pair position (bp units)- Parameters:
dataFileName
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size
public int size()
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