Package Executable
Class PrintStats
- java.lang.Object
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- Executable.PrintStats
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public class PrintStats extends java.lang.Object
Class used to print stats
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Constructor Summary
Constructors 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)
ConstructorPrintStats(java.lang.String root, boolean partial)
Constructor that creates file names for the different output based on a root stringPrintStats(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description org.apache.commons.configuration2.tree.ImmutableNode
getConfig()
Get the imputer options configvoid
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 appropriatevoid
writeStats(AccuracyStats stats, AccuracyStats cstats, AccuracyStats istats)
Write stats to the appropriate files
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Constructor Detail
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PrintStats
public PrintStats(java.io.File pretty, java.io.File depth, java.io.File geno, java.io.File depthGeno, java.io.File eachMasked, boolean partial)
Constructor- Parameters:
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)
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PrintStats
public PrintStats(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
Constructor from a config (read in from a XML file)- Parameters:
params
- The config
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PrintStats
public PrintStats(java.lang.String root, boolean partial)
Constructor that creates file names for the different output based on a root string- Parameters:
root
- The root stringpartial
- Whether to print partial stats (i.e. for imputed and called as well as for combined)
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Method Detail
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writeStats
public void writeStats(AccuracyStats stats, AccuracyStats cstats, AccuracyStats istats) throws OutputException
Write stats to the appropriate files- Parameters:
stats
- Accuracy stats for combinedcstats
- Accuracy stats for calledistats
- Accuracy stats for imputed- Throws:
OutputException
- If there is an IO problem
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writeEachMasked
public void writeEachMasked(java.util.List<SingleGenotypeCall> correct, java.util.List<SingleGenotypeCall> imputed, java.lang.String[] samples, PositionMeta[] positions) throws OutputException
Writes data on each masked sample / snp if appropriate- Parameters:
correct
- List of correct genotypesimputed
- List of imputed genotypessamples
- List of samples (sample names)positions
- List of positions (position meta data)- Throws:
OutputException
- If there is an IO problem
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getConfig
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Get the imputer options config- Returns:
- The config
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