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Looks like the @WalkerName annotation doesn't work with the GATK docs, so I'm renaming the walkers.

This commit is contained in:
Eric Banks 2012-08-22 20:17:39 -04:00
parent 95a1337285
commit e5df91aa23
2 changed files with 3 additions and 5 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReference.java → public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
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@ -76,10 +76,9 @@ import java.util.List;
* *
*/ */
@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
@WalkerName("FastaAlternateReferenceMaker")
@Reference(window=@Window(start=-1,stop=50)) @Reference(window=@Window(start=-1,stop=50))
@Requires(value={DataSource.REFERENCE}) @Requires(value={DataSource.REFERENCE})
public class FastaAlternateReference extends FastaReference { public class FastaAlternateReferenceMaker extends FastaReferenceMaker {
/** /**
* Variants from these input files are used by this tool to construct an alternate reference. * Variants from these input files are used by this tool to construct an alternate reference.

5
public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReference.java → public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceMaker.java
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@ -62,15 +62,14 @@ import java.io.PrintStream;
* <pre> * <pre>
* java -Xmx2g -jar GenomeAnalysisTK.jar \ * java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \ * -R ref.fasta \
* -T FastaReference \ * -T FastaReferenceMaker \
* -o output.fasta \ * -o output.fasta \
* -L input.intervals * -L input.intervals
* </pre> * </pre>
* *
*/ */
@DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} ) @DocumentedGATKFeature( groupName = "Companion Utilities", extraDocs = {CommandLineGATK.class} )
@WalkerName("FastaReferenceMaker") public class FastaReferenceMaker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
public class FastaReference extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
@Output PrintStream out; @Output PrintStream out;