PlinkMap (SnpEff 5.1 API)

java.lang.Object
- org.snpeff.ped.PlinkMap

```
public class PlinkMap
extends java.lang.Object
```
PLINK MAP file References: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml

Author:

pcingola

Field Summary

Fields
Modifier and Type Field Description

static boolean debug

Constructor Summary

Constructors
Constructor Description

PlinkMap()

PlinkMap(java.lang.String mapFileName)

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()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - debug
```
public static boolean debug
```
- Constructor Detail
  - PlinkMap
```
public PlinkMap()
```
  - PlinkMap
```
public PlinkMap(java.lang.String mapFileName)
```
- Method Detail
  - getChrName
```
public java.lang.String getChrName(int idx)
```
  - getGenotypeNames
```
public java.util.Collection<java.lang.String> getGenotypeNames()
```
  - getGenotypeNames
```
public java.lang.Integer getGenotypeNames(java.lang.String idStr)
```
  - getId
```
public java.lang.String getId(int idx)
```
  - getPosition
```
public int getPosition(int idx)
```
  - 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 -
  - size
```
public int size()
```