public class Input
extends java.lang.Object
Constructor | Description |
---|---|
Input(java.io.File in,
java.util.List<PositionFilter> filters,
java.io.File out,
int maxdepth,
java.lang.String readsformat) |
Constructor
|
Input(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 input config
|
org.apache.commons.configuration2.tree.ImmutableNode |
getImputeConfig() |
Get the input config for the final imputation step
|
VCF |
getVCF() |
Get the VCF data
|
public Input(java.io.File in, java.util.List<PositionFilter> filters, java.io.File out, int maxdepth, java.lang.String readsformat)
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).public Input(org.apache.commons.configuration2.HierarchicalConfiguration<org.apache.commons.configuration2.tree.ImmutableNode> params)
params
- The configpublic VCF getVCF() throws VCFException, OutputException
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)public org.apache.commons.configuration2.tree.ImmutableNode getConfig()
public org.apache.commons.configuration2.tree.ImmutableNode getImputeConfig()