VCFFilter
public class MAFFilter extends PositionFilter
Constructor | Description |
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MAFFilter(double maf,
int minDepth,
int maxDepth,
double error) |
Constructor
|
MAFFilter(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params) |
Constructor from a config (read in from a XML file)
|
Modifier and Type | Method | Description |
---|---|---|
org.apache.commons.configuration2.tree.ImmutableNode |
getConfig() |
Get the config for this filter
|
java.lang.String |
getSummary() |
Gets a string summary of this filter
|
boolean |
test(Position p) |
Tests whether a position should be filtered out
|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
change
public MAFFilter(double maf, int minDepth, int maxDepth, double error)
maf
- Minor allele frequencyminDepth
- A genotype must have at least this number of reads to be
used in the MAF calculationmaxDepth
- A genotype must have less than (or equal) this number of
reads to be used in the MAF calculationerror
- The error rate to be used when calling genotypespublic MAFFilter(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configpublic boolean test(Position p) throws VCFDataException
PositionFilter
test
in class PositionFilter
p
- The position to testVCFDataException
- If there is a problem with the
data in the VCFpublic org.apache.commons.configuration2.tree.ImmutableNode getConfig()
VCFFilter
public java.lang.String getSummary()
VCFFilter