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

java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java

@@ -11,7 +11,10 @@ import org.broadinstitute.sting.utils.genotype.Variation;
 import java.io.*;
 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")
 @Requires(value={DataSource.REFERENCE})
 public class FastaAlternateReferenceWalker extends FastaReferenceWalker {

java/src/org/broadinstitute/sting/gatk/walkers/fasta/PickSequenomProbes.java

@@ -11,6 +11,10 @@ import org.broadinstitute.sting.utils.genotype.Variation;
 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")
 @Requires(value={DataSource.REFERENCE})
 @Reference(window=@Window(start=-200,stop=200))