FilterSite

net.maizegenetics.dna.snp.FilterSite

All Implemented Interfaces:: Filter

public class FilterSite
implements Filter

Constructor Detail

FilterSite

public FilterSite(java.util.Map<java.lang.String,java.lang.Object> values)

Method Detail

attributes

public java.util.Map<net.maizegenetics.dna.snp.FilterSite.FILTER_SITES_ATTRIBUTES,java.lang.Object> attributes()

numAttributes
```
public int numAttributes()
```

filterName
```
public java.lang.String filterName()
```

siteMinCount
```
public int siteMinCount()
```

siteMinAlleleFreq
```
public double siteMinAlleleFreq()
```

siteMaxAlleleFreq
```
public double siteMaxAlleleFreq()
```

minHeterozygous
```
public double minHeterozygous()
```

maxHeterozygous
```
public double maxHeterozygous()
```

removeMinorSNPStates
```
public boolean removeMinorSNPStates()
```

removeSitesWithIndels

public boolean removeSitesWithIndels()

siteFilterType

public net.maizegenetics.dna.snp.FilterSite.SITE_RANGE_FILTER_TYPES siteFilterType()

startSite
```
public int startSite()
```

endSite
```
public int endSite()
```

startChr
```
public Chromosome startChr()
```

startPos
```
public int startPos()
```

endChr
```
public Chromosome endChr()
```

endPos
```
public int endPos()
```

includeSites
```
public boolean includeSites()
```

siteNames

public java.util.List<java.lang.String> siteNames()

chrPosFile
```
public java.lang.String chrPosFile()
```

positionList
```
public PositionList positionList()
```

bedFile
```
public java.lang.String bedFile()
```

Class FilterSite

Constructor Detail

FilterSite

Method Detail

attributes

numAttributes

filterName

siteMinCount

siteMinAlleleFreq

siteMaxAlleleFreq

minHeterozygous

maxHeterozygous

removeMinorSNPStates

removeSitesWithIndels

siteFilterType

startSite

endSite

startChr

startPos

endChr

endPos

includeSites

siteNames

chrPosFile

positionList

bedFile