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documentation updates for the new help system. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2323 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-12-11 16:15:44 +00:00
parent 23d96b1d43
commit 420725441a
2 changed files with 8 additions and 1 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
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@ -11,7 +11,10 @@ import org.broadinstitute.sting.utils.genotype.Variation;
import java.io.*; import java.io.*;
import java.util.Iterator; import java.util.Iterator;
/**
* Generates an alternative reference sequence over the specified interval. Given a variant ROD track (named "snpmask"),
* it replaces the reference bases at variation sites with the bases supplied by the ROD.
*/
@WalkerName("FastaAlternateReferenceMaker") @WalkerName("FastaAlternateReferenceMaker")
@Requires(value={DataSource.REFERENCE}) @Requires(value={DataSource.REFERENCE})
public class FastaAlternateReferenceWalker extends FastaReferenceWalker { public class FastaAlternateReferenceWalker extends FastaReferenceWalker {

4
java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java
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@ -11,6 +11,10 @@ import org.broadinstitute.sting.utils.genotype.Variation;
import java.util.*; import java.util.*;
/**
* Generates Sequenom probe information given a single variant track. Emitted is the variant
* along with the 200 reference bases on each side of the variant.
*/
@WalkerName("PickSequenomProbes") @WalkerName("PickSequenomProbes")
@Requires(value={DataSource.REFERENCE}) @Requires(value={DataSource.REFERENCE})
@Reference(window=@Window(start=-200,stop=200)) @Reference(window=@Window(start=-200,stop=200))