Adding docs to QC walkers

public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java

@@ -40,26 +40,65 @@ import java.util.TreeSet;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+
 /**
- * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear
- * in the input file.  It can dynamically merge the contents of multiple input BAM files, resulting
- * in merged output sorted in coordinate order.  Can also optionally filter reads based on the --read-filter
- * command line argument.
+ * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear in the input file.
+ *
+ * <p>
+ * PrintReads can dynamically merge the contents of multiple input BAM files, resulting
+ * in merged output sorted in coordinate order.  Can also optionally filter reads based on the
+ * --read_filter command line argument.
+ *
+ * <h2>Input</h2>
+ * <p>
+ * One or more bam files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * A single processed bam file.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T PrintReads \
+ *   -o output.bam \
+ *   -I input1.bam \
+ *   -I input2.bam \
+ *   --read_filter MappingQualityZero
+ * </pre>
+ *
  */
 @BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
-    /** an optional argument to dump the reads out to a BAM file */
+
     @Output(doc="Write output to this BAM filename instead of STDOUT")
     SAMFileWriter out;
+
     @Argument(fullName = "readGroup", shortName = "readGroup", doc="Exclude all reads with this read group from the output", required = false)
     String readGroup = null;
+
+    /**
+     * For example, --platform ILLUMINA or --platform 454.
+     */
     @Argument(fullName = "platform", shortName = "platform", doc="Exclude all reads with this platform from the output", required = false)
-    String platform = null; // E.g. ILLUMINA, 454
+    String platform = null;
+
     @Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false)
     int nReadsToPrint = -1;
+
+    /**
+     * Only reads from samples listed in the provided file(s) will be included in the output.
+     */
     @Argument(fullName="sample_file", shortName="sf", doc="File containing a list of samples (one per line). Can be specified multiple times", required=false)
     public Set<File> sampleFile = new TreeSet<File>();
+
+    /**
+     * Only reads from the sample(s) will be included in the output.
+     */
     @Argument(fullName="sample_name", shortName="sn", doc="Sample name to be included in the analysis. Can be specified multiple times.", required=false)
     public Set<String> sampleNames = new TreeSet<String>();
 

public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByIntervalWalker.java

@@ -38,12 +38,32 @@ import java.util.List;
 
 /**
  * Walks along reference and calculates the GC content for each interval.
+ *
+ *
+ * <h2>Input</h2>
+ * <p>
+ * One or more BAM files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * GC content calculations per interval.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T GCContentByInterval \
+ *   -o output.txt \
+ *   -I input.bam \
+ *   -L input.intervals
+ * </pre>
+ *
  */
 @Allows(value = {DataSource.REFERENCE})
 @Requires(value = {DataSource.REFERENCE})
-
 @By(DataSource.REFERENCE)
-
 public class GCContentByIntervalWalker extends LocusWalker<Long, Long> {
     @Output
     protected PrintStream out;

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java

@@ -11,7 +11,31 @@ import java.io.PrintStream;
 
 /**
  * Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.
+ *
+ * <p>
  * Simplest example of a locus walker.
+ *
+ *
+ * <h2>Input</h2>
+ * <p>
+ * One or more BAM files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * Number of loci traversed.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T CountLoci \
+ *   -o output.txt \
+ *   -I input.bam \
+ *   [-L input.intervals]
+ * </pre>
+ *
  */
 public class CountLociWalker extends LocusWalker<Integer, Long> implements TreeReducible<Long> {
     @Output(doc="Write count to this file instead of STDOUT")

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountPairsWalker.java

@@ -39,6 +39,26 @@ import java.util.List;
  * query name order.  Breaks counts down by total pairs and number
  * of paired reads.
  *
+ *
+ * <h2>Input</h2>
+ * <p>
+ * One or more bam files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * Number of pairs seen.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T CountPairs \
+ *   -o output.txt \
+ *   -I input.bam
+ * </pre>
+ *
  * @author mhanna
  */
 public class CountPairsWalker extends ReadPairWalker<Integer,Long> {

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java

@@ -9,8 +9,32 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
 
 /**
  * Walks over the input data set, calculating the number of reads seen for diagnostic purposes.
+ *
+ * <p>
  * Can also count the number of reads matching a given criterion using read filters (see the
  * --read-filter command line argument).  Simplest example of a read-backed analysis.
+ *
+ *
+ * <h2>Input</h2>
+ * <p>
+ * One or more BAM files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * Number of reads seen.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T CountReads \
+ *   -o output.txt \
+ *   -I input.bam \
+ *   [-L input.intervals]
+ * </pre>
+ *
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CountReadsWalker extends ReadWalker<Integer, Integer> {

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java

@@ -27,8 +27,11 @@ package org.broadinstitute.sting.gatk.walkers.qc;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
+import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -41,23 +44,46 @@ import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.collections.Pair;
 
 import java.io.PrintStream;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.LinkedList;
-import java.util.List;
+import java.util.*;
 
 /**
- * Prints out counts of the number of reference ordered data objects are
- * each locus for debugging RodWalkers.
+ * Prints out counts of the number of reference ordered data objects encountered.
+ *
+ *
+ * <h2>Input</h2>
+ * <p>
+ * One or more rod files.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * Number of rods seen.
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -R ref.fasta \
+ *   -T CountRod \
+ *   -o output.txt \
+ *   --rod input.vcf
+ * </pre>
+ *
  */
 public class CountRodWalker extends RodWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
     @Output
     public PrintStream out;
 
-    @Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false)
+    /**
+     * One or more input rod files
+     */
+    @Input(fullName="rod", shortName = "rod", doc="Input VCF file(s)", required=false)
+    public List<RodBinding<Feature>> rods = Collections.emptyList();
+
+    @Argument(fullName = "verbose", shortName = "v", doc="If true, CountRod will print out detailed information about the rods it finds and locations", required = false)
     public boolean verbose = false;
 
-    @Argument(fullName = "showSkipped", shortName = "s", doc="If true, CountRod will print out the skippped locations", required = false)
+    @Argument(fullName = "showSkipped", shortName = "s", doc="If true, CountRod will print out the skipped locations", required = false)
     public boolean showSkipped = false;
 
     @Override