zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Oops, these VariantAnnotator input bindings aren't needed during the UG

This commit is contained in:
Ryan Poplin 2011-08-11 13:17:16 -04:00
parent 7fade88070
commit b705d9cf15
1 changed files with 3 additions and 29 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

32
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -66,35 +66,9 @@ public class UnifiedGenotyper extends LocusWalker<VariantCallContext, UnifiedGen
*/
@ArgumentCollection protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
/**
* The INFO field will be annotated with information on the most biologically-significant effect
* listed in the SnpEff output file for each variant.
*/
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
public RodBinding<SnpEffFeature> snpEffFile;
public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return snpEffFile; }
/**
* If a record in the 'variant' track overlaps with a record from the provided comp track, the INFO field will be annotated
* as such in the output with the track name (e.g. -comp:FOO will have 'FOO' in the INFO field). Records that are filtered in the comp track will be ignored.
* Note that 'dbSNP' has been special-cased (see the --dbsnp argument).
*/
@Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
public List<RodBinding<VariantContext>> comps = Collections.emptyList();
public List<RodBinding<VariantContext>> getCompRodBindings() { return comps; }
/**
* An external resource VCF file or files from which to annotate.
*
* One can add annotations from one of the resource VCFs to the output.
* For example, if you want to annotate your 'variant' VCF with the AC field value from the rod bound to 'resource',
* you can specify '-E resource.AC' and records in the output VCF will be annotated with 'resource.AC=N' when a record exists in that rod at the given position.
* If multiple records in the rod overlap the given position, one is chosen arbitrarily.
*/
@Input(fullName="resource", shortName = "resource", doc="external resource VCF file", required=false)
public List<RodBinding<VariantContext>> resources = Collections.emptyList();
public List<RodBinding<VariantContext>> getResourceRodBindings() { return resources; }
public RodBinding<SnpEffFeature> getSnpEffRodBinding() { return null; }
public List<RodBinding<VariantContext>> getCompRodBindings() { return Collections.emptyList(); }
public List<RodBinding<VariantContext>> getResourceRodBindings() { return Collections.emptyList(); }
// control the output
@Output(doc="File to which variants should be written",required=true)