From 0086e27741356df7c98152e9292bedfe89f24099 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Wed, 10 Aug 2011 22:29:32 -0400 Subject: [PATCH 1/2] makeUnbound now package protected -- Removed references to it in the codebase -- Fixed documentation I saw that had the summary + body style --- .../broadinstitute/sting/commandline/RodBinding.java | 2 +- .../gatk/arguments/DbsnpArgumentCollection.java | 7 ++++--- .../gatk/walkers/annotator/VariantAnnotator.java | 12 ++++-------- .../gatk/walkers/beagle/BeagleOutputToVCFWalker.java | 2 +- .../walkers/beagle/ProduceBeagleInputWalker.java | 2 +- .../walkers/fasta/FastaAlternateReferenceWalker.java | 2 +- .../walkers/filters/VariantFiltrationWalker.java | 2 +- .../gatk/walkers/variantutils/SelectVariants.java | 4 ++-- 8 files changed, 15 insertions(+), 18 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java b/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java index 41b5bf6f3..e0b1154c4 100644 --- a/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java +++ b/public/java/src/org/broadinstitute/sting/commandline/RodBinding.java @@ -64,7 +64,7 @@ public final class RodBinding { * @return the UNBOUND RodBinding producing objects of type T */ @Requires("type != null") - public final static RodBinding makeUnbound(Class type) { + protected final static RodBinding makeUnbound(Class type) { return new RodBinding(type); } diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java index b77b175bc..ce638ff2b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java @@ -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 dbsnp = RodBinding.makeUnbound(VariantContext.class); + public RodBinding dbsnp; } diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index ce9b9a5f0..a8fe46ab8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -61,13 +61,11 @@ public class VariantAnnotator extends RodWalker { 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 snpEffFile = RodBinding.makeUnbound(SnpEffFeature.class); + @Input(fullName="snpEffFile", shortName = "snpEffFile", doc="A SnpEff output file from which to add annotations", required=false) + public RodBinding snpEffFile; /** * A dbSNP VCF file from which to annotate. @@ -78,14 +76,12 @@ public class VariantAnnotator extends RodWalker { 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 comps = RodBinding.makeUnbound(VariantContext.class); + @Input(fullName="comp", shortName = "comp", doc="A comparisons VCF file from which to annotate", required=false) + public RodBinding comps; @Output(doc="File to which variants should be written",required=true) protected VCFWriter vcfWriter = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java index ee2e4853b..40e6748ed 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java @@ -55,7 +55,7 @@ public class BeagleOutputToVCFWalker extends RodWalker { protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); @Input(fullName="comp", shortName = "comp", doc="Comparison VCF file", required=false) - public RodBinding comp = RodBinding.makeUnbound(VariantContext.class); + public RodBinding comp; @Input(fullName="beagleR2", shortName = "beagleR2", doc="VCF file", required=true) public RodBinding beagleR2; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java index a46ec8b48..c1508cf83 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInputWalker.java @@ -55,7 +55,7 @@ public class ProduceBeagleInputWalker extends RodWalker { @ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); @Input(fullName="validation", shortName = "validation", doc="Input VCF file", required=false) - public RodBinding validation = RodBinding.makeUnbound(VariantContext.class); + public RodBinding validation; @Output(doc="File to which BEAGLE input should be written",required=true) protected PrintStream beagleWriter = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java index 93012ee10..60f9724e8 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java @@ -52,7 +52,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker { public List> variants; @Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false) - public RodBinding snpmask = RodBinding.makeUnbound(VariantContext.class); + public RodBinding snpmask; private int deletionBasesRemaining = 0; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 8ee1e3a89..c555e88cd 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -53,7 +53,7 @@ public class VariantFiltrationWalker extends RodWalker { protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection(); @Input(fullName="mask", doc="Input ROD mask", required=false) - public RodBinding mask = RodBinding.makeUnbound(Feature.class); + public RodBinding mask; @Output(doc="File to which variants should be written", required=true) protected VCFWriter writer = null; diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java index 13a1446b6..16733bc44 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java @@ -62,7 +62,7 @@ public class SelectVariants extends RodWalker { * 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 discordanceTrack = RodBinding.makeUnbound(VariantContext.class); + private RodBinding 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 { * 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 concordanceTrack = RodBinding.makeUnbound(VariantContext.class); + private RodBinding concordanceTrack; @Output(doc="File to which variants should be written",required=true) protected VCFWriter vcfWriter = null;