Adding docs to 3 more walkers

public/java/src/org/broadinstitute/sting/gatk/walkers/indels/LeftAlignIndels.java

@@ -35,16 +35,46 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 
+
 /**
- * Left aligns indels in reads.
+ * Left-aligns indels from reads in a bam file.
+ *
+ * <p>
+ * LeftAlignIndels is a tool that takes a bam file and left-aligns any indels inside it.  The same indel can often be
+ * placed at multiple positions and still represent the same haplotype.  While a standard convention is to place an
+ * indel at the left-most position this doesn't always happen, so this tool can be used to left-align them.
+ *
+ * <h2>Input</h2>
+ * <p>
+ * A bam file to left-align.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * A left-aligned bam.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx3g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T LeftAlignIndels \
+ *   -I input.bam \
+ *   -o output.vcf
+ * </pre>
+ *
  */
 public class LeftAlignIndels extends ReadWalker<Integer, Integer> {
 
     @Output(required=false, doc="Output bam")
     protected StingSAMFileWriter writer = null;
 
-    @Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the SAMFileWriter. "+
-                "If too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool may run out of memory.", required=false)
+    /**
+     * If set too low, the tool may run out of system file descriptors needed to perform sorting; if too high, the tool
+     * may run out of memory.  We recommend that you additionally tell Java to use a temp directory with plenty of available
+     * space (by setting java.io.tempdir on the command-line).
+     */
+    @Argument(fullName="maxReadsInRam", shortName="maxInRam", doc="max reads allowed to be kept in memory at a time by the output writer", required=false)
     protected int MAX_RECORDS_IN_RAM = 500000;
 
     public void initialize() {

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

@@ -46,6 +46,31 @@ import java.util.*;
 
 /**
  * Left-aligns indels from a variants file.
+ *
+ * <p>
+ * LeftAlignVariants is a tool that takes a VCF file and left-aligns any indels inside it.  The same indel can often be
+ * placed at multiple positions and still represent the same haplotype.  While the standard convention with VCF is to
+ * place an indel at the left-most position this doesn't always happen, so this tool can be used to left-align them.
+ *
+ * <h2>Input</h2>
+ * <p>
+ * A variant set to left-align.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * A left-aligned VCF.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T LeftAlignVariants \
+ *   --variant input.vcf \
+ *   -o output.vcf
+ * </pre>
+ *
  */
 @Reference(window=@Window(start=-200,stop=200))
 public class LeftAlignVariants extends RodWalker<Integer, Integer> {

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

@@ -25,7 +25,6 @@
 
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
-import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broadinstitute.sting.commandline.*;
@@ -34,7 +33,6 @@ import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgume
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
@@ -48,7 +46,32 @@ import java.util.Set;
 
 
 /**
- * Validates a variants file.
+ * Strictly validates a variants file.
+ *
+ * <p>
+ * ValidateVariants is a GATK tool that takes a VCF file and validates much of the information inside it.
+ * Checks include the correctness of the reference base(s), accuracy of AC & AN values, tests against rsIDs
+ * when a dbSNP file is provided, and that all alternate alleles are present in at least one sample.
+ *
+ * <h2>Input</h2>
+ * <p>
+ * A variant set to filter.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * A filtered VCF.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T ValidateVariants \
+ *   --variant input.vcf \
+ *   --dbsnp dbsnp.vcf
+ * </pre>
+ *
  */
 @Reference(window=@Window(start=0,stop=100))
 public class ValidateVariants extends RodWalker<Integer, Integer> {
@@ -67,10 +90,13 @@ public class ValidateVariants extends RodWalker<Integer, Integer> {
     @Argument(fullName = "validationType", shortName = "type", doc = "which validation type to run", required = false)
     protected ValidationType type = ValidationType.ALL;
 
-    @Argument(fullName = "doNotValidateFilteredRecords", shortName = "doNotValidateFilteredRecords", doc = "should we skip validation on filtered records?", required = false)
+    /**
+     * By default, even filtered records are validated.
+     */
+    @Argument(fullName = "doNotValidateFilteredRecords", shortName = "doNotValidateFilteredRecords", doc = "skip validation on filtered records", required = false)
     protected Boolean DO_NOT_VALIDATE_FILTERED = false;
 
-    @Argument(fullName = "warnOnErrors", shortName = "warnOnErrors", doc = "should we just emit warnings on errors instead of terminating the run?", required = false)
+    @Argument(fullName = "warnOnErrors", shortName = "warnOnErrors", doc = "just emit warnings on errors instead of terminating the run at the first instance", required = false)
     protected Boolean WARN_ON_ERROR = false;
 
     private long numErrors = 0;