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makeUnbound now package protected 

-- Removed references to it in the codebase
-- Fixed documentation I saw that had the summary + body style
This commit is contained in:
Mark DePristo 2011-08-10 22:29:32 -04:00
parent cb6cf25bb0
commit 0086e27741
8 changed files with 15 additions and 18 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);
}

7
public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
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@ -39,10 +39,11 @@ 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 = RodBinding.makeUnbound(VariantContext.class);
public RodBinding<VariantContext> dbsnp;
}

12
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -61,13 +61,11 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
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.
*/
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="SnpEff file", required=false)
public RodBinding<SnpEffFeature> snpEffFile = RodBinding.makeUnbound(SnpEffFeature.class);
@Input(fullName="snpEffFile", shortName = "snpEffFile", doc="A SnpEff output file from which to add annotations", required=false)
public RodBinding<SnpEffFeature> snpEffFile;
/**
* A dbSNP VCF file from which to annotate.
@ -78,14 +76,12 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> {
protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
/**
* A comparisons VCF file 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).
*/
@Input(fullName="comp", shortName = "comp", doc="comparison VCF file", required=false)
public RodBinding<VariantContext> comps = RodBinding.makeUnbound(VariantContext.class);
@Input(fullName="comp", shortName = "comp", doc="A comparisons VCF file from which to annotate", required=false)
public RodBinding<VariantContext> comps;
@Output(doc="File to which variants should be written",required=true)
protected VCFWriter vcfWriter = null;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
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@ -55,7 +55,7 @@ public class BeagleOutputToVCFWalker extends RodWalker<Integer, Integer> {
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false)
public RodBinding<VariantContext> comp = RodBinding.makeUnbound(VariantContext.class);
public RodBinding<VariantContext> comp;
@Input(fullName="beagleR2", shortName = "beagleR2", doc="VCF file", required=true)
public RodBinding<BeagleFeature> beagleR2;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java
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@ -55,7 +55,7 @@ public class ProduceBeagleInputWalker extends RodWalker<Integer, Integer> {
@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false)
public RodBinding<VariantContext> validation = RodBinding.makeUnbound(VariantContext.class);
public RodBinding<VariantContext> validation;
@Output(doc="File to which BEAGLE input should be written",required=true)
protected PrintStream beagleWriter = null;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -52,7 +52,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
public List<RodBinding<VariantContext>> variants;
@Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
public RodBinding<VariantContext> snpmask = RodBinding.makeUnbound(VariantContext.class);
public RodBinding<VariantContext> snpmask;
private int deletionBasesRemaining = 0;

2
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -53,7 +53,7 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
@Input(fullName="mask", doc="Input ROD mask", required=false)
public RodBinding<Feature> mask = RodBinding.makeUnbound(Feature.class);
public RodBinding<Feature> mask;
@Output(doc="File to which variants should be written", required=true)
protected VCFWriter writer = null;

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;