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Resolving merge conflicts

This commit is contained in:
Eric Banks 2011-08-10 22:45:11 -04:00
parent bdb1da30fd 8a0338c7b7
commit 75985c2fa0
4 changed files with 6 additions and 9 deletions
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2
public/java/src/org/broadinstitute/sting/commandline/RodBinding.java
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@ -64,7 +64,7 @@ public final class RodBinding<T extends Feature> {
* @return the UNBOUND RodBinding producing objects of type T
*/
@Requires("type != null")
public final static <T extends Feature> RodBinding<T> makeUnbound(Class<T> type) {
protected final static <T extends Feature> RodBinding<T> makeUnbound(Class<T> type) {
return new RodBinding<T>(type);
}

5
public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
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@ -39,8 +39,9 @@ import org.simpleframework.xml.*;
public class DbsnpArgumentCollection {
/**
* A dbSNP VCF file.
*/
* A dbSNP VCF file. Variants in this track will be treated as "known" variants
* in tools using this track.
*/
@Input(fullName="dbsnp", shortName = "D", doc="dbSNP file", required=false)
public RodBinding<VariantContext> dbsnp;

4
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -61,8 +61,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
/**
* A SnpEff output file from which to add annotations.
*
* The INFO field will be annotated with information on the most biologically-significant effect
* listed in the SnpEff output file for each variant.
*/
@ -80,8 +78,6 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
public RodBinding<VariantContext> getDbsnpRodBinding() { return dbsnp.dbsnp; }
/**
* A comparisons VCF file or files from which to annotate.
*
* 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).

4
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -62,7 +62,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
* or the sample is called reference in this track.
*/
@Input(fullName="discordance", shortName = "disc", doc="Output variants that were not called in this Feature comparison track", required=false)
private RodBinding<VariantContext> discordanceTrack = RodBinding.makeUnbound(VariantContext.class);
private RodBinding<VariantContext> discordanceTrack;
/**
* A site is considered concordant if (1) we are not looking for specific samples and there is a variant called
@ -70,7 +70,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
* track and they have the sample genotype call.
*/
@Input(fullName="concordance", shortName = "conc", doc="Output variants that were also called in this Feature comparison track", required=false)
private RodBinding<VariantContext> concordanceTrack = RodBinding.makeUnbound(VariantContext.class);
private RodBinding<VariantContext> concordanceTrack;
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;