Adding docs to yet more walkers

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

@@ -40,18 +40,48 @@ import java.util.List;
 
 
 /**
- * Generates an alternative reference sequence over the specified interval.  Given variant ROD tracks,
- * it replaces the reference bases at variation sites with the bases supplied by the ROD(s).  Additionally,
- * allows for a "snpmask" ROD to set overlapping bases to 'N'.
+ * Generates an alternative reference sequence over the specified interval.
+ *
+ * <p>
+ * Given variant ROD tracks, it replaces the reference bases at variation sites with the bases supplied by the ROD(s).
+ * Additionally, allows for a "snpmask" ROD to set overlapping bases to 'N'.
+ *
+ * <h2>Input</h2>
+ * <p>
+ * The reference, requested intervals, and any number of variant rod files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * A fasta file representing the requested intervals.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T FastaAlternateReferenceMaker \
+ *   -o output.fasta \
+ *   -L input.intervals \
+ *   --variant input.vcf \
+ *   [--snpmask mask.vcf]
+ * </pre>
+ *
  */
 @WalkerName("FastaAlternateReferenceMaker")
 @Reference(window=@Window(start=-1,stop=50))
 @Requires(value={DataSource.REFERENCE})
 public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
 
+    /**
+     * Variants from these input files are used by this tool to construct an alternate reference.
+     */
     @Input(fullName = "variant", shortName = "V", doc="variants to model", required=false)
     public List<RodBinding<VariantContext>> variants = Collections.emptyList();
 
+    /**
+     * Snps from this file are used as a mask when constructing the alternate reference.
+     */
     @Input(fullName="snpmask", shortName = "snpmask", doc="SNP mask VCF file", required=false)
     public RodBinding<VariantContext> snpmask;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaReferenceWalker.java

@@ -38,14 +38,44 @@ import org.broadinstitute.sting.utils.collections.Pair;
 import java.io.PrintStream;
 
 /**
- * Renders a new reference in FASTA format consisting of only those loci provided in the input data set.  Has optional
- * features to control the output format.
+ * Renders a new reference in FASTA format consisting of only those loci provided in the input data set.
+ *
+ * <p>
+ * The output format can be partially controlled using the provided command-line arguments.
+ *
+ * <h2>Input</h2>
+ * <p>
+ * The reference and requested intervals.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * A fasta file representing the requested intervals.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T FastaReference \
+ *   -o output.fasta \
+ *   -L input.intervals
+ * </pre>
+ *
  */
 @WalkerName("FastaReferenceMaker")
 public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
+
     @Output PrintStream out;
-    @Argument(fullName="lineWidth", shortName="lw", doc="Maximum length of sequence to write per line", required=false) public int fastaLineWidth=60;
-    @Argument(fullName="rawOnelineSeq", shortName="raw", doc="Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity) - CAUTION: adjacent intervals will automatically be merged", required=false) public boolean fastaRawSeqs=false;
+
+    @Argument(fullName="lineWidth", shortName="lw", doc="Maximum length of sequence to write per line", required=false)
+    public int fastaLineWidth=60;
+
+    /**
+     *  Please note that when using this argument adjacent intervals will automatically be merged.
+     */
+    @Argument(fullName="rawOnelineSeq", shortName="raw", doc="Print sequences with no FASTA header lines, one line per interval (i.e. lineWidth = infinity)", required=false)
+    public boolean fastaRawSeqs=false;
 
     protected FastaSequence fasta;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java

@@ -53,6 +53,30 @@ import java.util.*;
 
 /**
  * Converts variants from other file formats to VCF format.
+ *
+ * <p>
+ * Note that there must be a Tribble feature/codec for the file format as well as an adaptor.
+ *
+ * <h2>Input</h2>
+ * <p>
+ * A variant file to filter.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * A VCF file.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T VariantsToVCF \
+ *   -o output.vcf \
+ *   --variant:RawHapMap input.hapmap \
+ *   --dbsnp dbsnp.vcf
+ * </pre>
+ *
  */
 @Reference(window=@Window(start=-40,stop=40))
 public class VariantsToVCF extends RodWalker<Integer, Integer> {
@@ -61,15 +85,24 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
     protected VCFWriter baseWriter = null;
     private SortingVCFWriter vcfwriter; // needed because hapmap/dbsnp indel records move
 
+    /**
+     * Variants from this input file are used by this tool as input.
+     */
     @Input(fullName="variant", shortName = "V", doc="Input variant file", required=true)
     public RodBinding<Feature> variants;
 
     @ArgumentCollection
     protected DbsnpArgumentCollection dbsnp = new DbsnpArgumentCollection();
 
-    @Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod (for data like GELI with genotypes)", required=false)
+    /**
+     * This argument is used for data (like GELI) with genotypes but no sample names encoded within.
+     */
+    @Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod", required=false)
     protected String sampleName = null;
 
+    /**
+     * This argument is useful for fixing input VCFs with bad reference bases (the output will be a fixed version of the VCF).
+     */
     @Argument(fullName="fixRef", shortName="fixRef", doc="Fix common reference base in case there's an indel without padding", required=false)
     protected boolean fixReferenceBase = false;