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

variant eval allows non Variation rod objects 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1768 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-10-06 13:04:26 +00:00
parent 66fc8ea444
commit 1bd0c3c145
1 changed files with 2 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
View File

@ -25,9 +25,8 @@ import java.util.*;
* the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
* *
*/ */
@By(DataSource.REFERENCE) @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=ReferenceOrderedDatum.class)}) // right now we have no base variant class for rods, this should change
@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=VariationRod.class)}) // right now we have no base variant class for rods, this should change @Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class)})
@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=VariationRod.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class)})
public class VariantEvalWalker extends RefWalker<Integer, Integer> { public class VariantEvalWalker extends RefWalker<Integer, Integer> {
@Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false) @Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false)
public int minConfidenceScore = -1; public int minConfidenceScore = -1;