Added short documentation for each class so that it appears in the walker command-line documentation.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2340 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java

@@ -13,7 +13,7 @@ import org.apache.commons.jexl.*;
 
 
 /**
- * VariantFiltrationWalker filters variant calls in VCF format.
+ * Filters variant calls using a number of user-selectable, parameterizable criteria.
  */
 @Requires(value={},referenceMetaData=@RMD(name="variant",type= RodVCF.class))
 public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {

java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java

@@ -24,13 +24,8 @@ import cern.jet.stat.Probability;
 
 /**
  * FindContaminatingReadGroupsWalker lists read groups in a single-sample BAM file that appear
- * to be contaminants by searching for evidence of systematic underperformance at likely
- * homozygous-variant sites.  First, sites that are likely homozygous-variant but are called
- * as heterozygous are identified.  Next, per each site and read group, we compute the proportion
- * of bases in the pileup supporting an alternate allele.  Finally, a one-sample, left-tailed
- * t-test is performed with the null hypothesis being that the alternate allele distribution has
- * a mean of 0.95 and the alternate hypothesis being that the true mean is statistically
- * significantly less than expected.
+ * to be contaminants (i.e. a read group that's not actually associated with the sample) by searching
+ * for evidence of systematic underperformance at likely homozygous-variant sites.
  *
  * @author Kiran Garimella
  */

java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java

@@ -20,6 +20,9 @@ import java.io.File;
 import java.io.PrintStream;
 import java.util.*;
 
+/**
+ * Converts variants from other file formats (anything that implements the Variation interface) to VCF format.
+ */
 public class VariantsToVCF extends RefWalker<Integer, Integer> {
     @Argument(fullName="vcfout", shortName="VO", doc="The output VCF file") public File VCF_OUT;
     @Argument(fullName="verbose", shortName="V", doc="Show extended output", required=false) public boolean VERBOSE = false;

java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java

@@ -12,6 +12,9 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 import java.util.*;
 import java.io.File;
 
+/**
+ * Extracts subsets of a VCF file like one or more samples, all or only variant loci, all or filtered loci.
+ */
 public class VCFSubsetWalker extends RefWalker<ArrayList<VCFRecord>, VCFWriter> {
     @Argument(fullName="sample", shortName="SN", doc="Sample to include (or nothing to specify all samples)", required=false)
     private HashSet<String> SAMPLES;