Documentation for more basic walkers.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2329 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java

@@ -36,7 +36,9 @@ import net.sf.samtools.SAMReadGroupRecord;
 import java.util.*;
 
 /**
- * Display the depth of coverage at a given locus.
+ * Computes the depth of coverage at all loci in the specified region of the reference.  Includes features to control
+ * grouping of results by read group or by sample, or filtering loci with either a small number of overlapping alignments
+ * or with alignments of poor mapping quality.  Can optionally include individual base counts at each locus. 
  */
 @By(DataSource.REFERENCE)
 public class DepthOfCoverageWalker extends LocusWalker<DepthOfCoverageWalker.DoCInfo, DepthOfCoverageWalker.DoCInfo> {

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

@@ -8,8 +8,10 @@ import net.sf.samtools.SAMRecord;
 
 import java.io.*;
 
-// create a fastq file from a bam file
-
+/**
+ * Converts reads from the input BAM file into fastq format, stripping away all alignment information.
+ * Optionally re-reverses the negative strand alignments using the --re-reverse command-line argument.
+ */
 @WalkerName("BamToFastq")
 public class BamToFastqWalker extends ReadWalker<Integer, Integer> {
 

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

@@ -10,8 +10,10 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Pair;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
-// create a fasta sequence file from a reference and intervals
-
+/**
+ * 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.
+ */
 @WalkerName("FastaReferenceMaker")
 public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, GenomeLoc> {
     @Argument(fullName="lineWidth", shortName="lw", doc="Maximum length of sequence to write per line", required=false) public int fastaLineWidth=60;