public class PrintStats
extends java.lang.Object
Constructor | Description |
---|---|
PrintStats(java.io.File pretty,
java.io.File depth,
java.io.File geno,
java.io.File depthGeno,
java.io.File eachMasked,
boolean partial) |
Constructor
|
PrintStats(java.lang.String root,
boolean partial) |
Constructor that creates file names for the different output based on a
root string
|
PrintStats(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 imputer options config
|
void |
writeEachMasked(java.util.List<SingleGenotypeCall> correct,
java.util.List<SingleGenotypeCall> imputed,
java.lang.String[] samples,
PositionMeta[] positions) |
Writes data on each masked sample / snp if appropriate
|
void |
writeStats(AccuracyStats stats,
AccuracyStats cstats,
AccuracyStats istats) |
Write stats to the appropriate files
|
public PrintStats(java.io.File pretty, java.io.File depth, java.io.File geno, java.io.File depthGeno, java.io.File eachMasked, boolean partial)
pretty
- File to print pretty stats todepth
- File to print depth stats togeno
- File to print geno stats todepthGeno
- File to print depth-geno stats toeachMasked
- File to print information for each masked sample / position topartial
- Whether to print partial stats (i.e. for imputed and called
as well as for combined)public PrintStats(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configpublic PrintStats(java.lang.String root, boolean partial)
root
- The root stringpartial
- Whether to print partial stats (i.e. for imputed and called
as well as for combined)public void writeStats(AccuracyStats stats, AccuracyStats cstats, AccuracyStats istats) throws OutputException
stats
- Accuracy stats for combinedcstats
- Accuracy stats for calledistats
- Accuracy stats for imputedOutputException
- If there is an IO problempublic void writeEachMasked(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> imputed, java.lang.String[] samples, PositionMeta[] positions) throws OutputException
correct
- List of correct genotypesimputed
- List of imputed genotypessamples
- List of samples (sample names)positions
- List of positions (position meta data)OutputException
- If there is an IO problempublic org.apache.commons.configuration2.tree.ImmutableNode getConfig()