Package Executable
Class Input
- java.lang.Object
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- Executable.Input
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public class Input extends java.lang.Object
Represents the input to LinkImputeR
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Constructor Summary
Constructors Constructor Description Input(java.io.File in, java.util.List<PositionFilter> filters, java.io.File out, int maxdepth, java.lang.String readsformat)
ConstructorInput(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 input configorg.apache.commons.configuration2.tree.ImmutableNode
getImputeConfig()
Get the input config for the final imputation stepVCF
getVCF()
Get the VCF data
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Constructor Detail
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Input
public Input(java.io.File in, java.util.List<PositionFilter> filters, java.io.File out, int maxdepth, java.lang.String readsformat)
Constructor- Parameters:
in
- The input VCF filefilters
- The filters to apply to the VCF as it is read inout
- The file to output the VCF to IMMEDIATELY after the VCF has been read in and the input parameters applied. Input filters are applied in all cases so it can save time in the final imputation step to save a VCF with the filters applied rather than read it in from scratch and reapply the filters.maxdepth
- The maximum read depth for a genotype. Genotypes with a higher read depth are set to have no reads and a missing genotype.readsformat
- The formats to read read depths from. If a single value then assumes the format contains comma separated data for reference alt read depths. If readsformat is itself comma seperated then assumes the first item is the format containing the reference allele depth, the second the alt allele depth. If null defaults to the current VCF standard (AD).
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Input
public Input(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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Method Detail
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getVCF
public VCF getVCF() throws VCFException, OutputException
Get the VCF data- Returns:
- The VCF data
- Throws:
VCFException
- If there is a problem with VCF file or the data in it.OutputException
- If there is a problem writing out the immediate output file (see constructor)
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getConfig
public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
Get the input config- Returns:
- The config
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getImputeConfig
public org.apache.commons.configuration2.tree.ImmutableNode getImputeConfig()
Get the input config for the final imputation step- Returns:
- The config
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