Completed my documentation responsibilities - based on Mark's reasonable assignment and not the one Matt made up while on Meth.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2342 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java

@@ -9,6 +9,9 @@ import org.broadinstitute.sting.utils.pileup.*;
 
 import java.util.*;
 
+/**
+ * Computes the coverage per sample.
+ */
 public class CoverageBySample extends LocusWalker<Integer, Integer> {
 
     private HashSet<String> sampleNames = new HashSet<String>();

java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java

@@ -15,7 +15,7 @@ import java.io.*;
 
 
 /**
- * VariantAnnotator annotates variants.
+ * Annotates variant calls with context information.  Users can specify which of the available annotations to use.
  */
 //@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=VariationRod.class))
 @Allows(value={DataSource.READS, DataSource.REFERENCE})

java/src/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceWalker.java

@@ -13,7 +13,8 @@ import java.util.*;
 
 
 /**
- * CallsetConcordanceWalker finds the concordance between multiple VCF callsets (different tests are available).
+ * Determines the concordance between multiple VCF call sets at each position.
+ * Users can specify which concordance tests should be run.
  */
 @Requires(value={DataSource.REFERENCE})
 @Reference(window=@Window(start=-20,stop=20))

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

@@ -5,15 +5,16 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
+/**
+ * Computes the coverage per every <granularity> bases on the reference, or on the subset of the reference
+ * specified by the intervals provided. Moving to the next contig on the reference will always restart the
+ * count anew, even if the count of bases in the last chunk on the previous contig did not reach specified <granularity>.
+ */
 public class CoarseCoverageWalker extends ReadWalker<Integer,Integer> {
 	
-    @Argument(fullName="granularity",shortName="G",doc="Will print numbers of reads per every <granularity> bases "+
+    @Argument(fullName="granularity", shortName="G", doc="Granularity", required=true)
-    		"on the reference, or on the subset of the reference specified by Intervals (if given). Moving to the next "+
-    		"contig on the reference will always restart the count anew, even if the count of bases in the last chunk on"+
-    		" the previous contig did not reach specified <granularity>.",required=true)
     public Integer N;
 	
-
     private int chunkStart = 1; // start of the current chunk we are counting reads for
     private int contig = 0; // current contig we are on
     private int count = 0; // number of reads overlapping with the current chunk

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

@@ -9,6 +9,9 @@ import org.broadinstitute.sting.utils.genotype.Variation;
 
 import java.util.Iterator;
 
+/**
+ * Create a mask for use with the PickSequenomProbes walker.
+ */
 public class CreateSequenomMask extends RodWalker<Integer, Integer> {
 
     public void initialize() {}

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

@@ -12,8 +12,9 @@ import java.io.*;
 import java.util.Iterator;
 
 /**
- * Generates an alternative reference sequence over the specified interval.  Given a variant ROD track (named "snpmask"),
+ * 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.
+ * 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'.
  */
 @WalkerName("FastaAlternateReferenceMaker")
 @Requires(value={DataSource.REFERENCE})

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java

@@ -44,6 +44,10 @@ import java.io.File;
 import java.util.*;
 
 
+/**
+ * A variant caller which unifies the approaches of several disparate callers.  Works for single-sample,
+ * multi-sample, and pooled data.  The user can choose from several different incorporated calculation models.
+ */
 @Reference(window=@Window(start=-20,stop=20))
 public class UnifiedGenotyper extends LocusWalker<Pair<VariationCall, List<Genotype>>, Integer> {
 

java/src/org/broadinstitute/sting/gatk/walkers/indels/CleanedReadInjector.java

@@ -24,8 +24,8 @@ import java.util.*;
  */
 
 /**
- * Copies reads from the input stream into the <code>outputBAM</code>, replacing those
+ * Copies reads from the input stream into the outputBAM, replacing those
- * reads which have been cleaned with their new clean copies.
+ * reads which have been cleaned/realigned with their new clean copies.
  */
 @Requires({DataSource.READS, DataSource.REFERENCE})
 public class CleanedReadInjector extends ReadWalker<Integer,Integer> {

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelIntervalWalker.java

@@ -10,11 +10,9 @@ import net.sf.samtools.AlignmentBlock;
 
 import java.util.List;
 
-// A walker to determine intervals within which reads should be cleaned and realigned
+/**
-// because they contain one or more indels (which possibly caused them not to align perfectly).
+ * Emits intervals consisting of indels from the aligned reads.
-// Note that the reduce step assumes that reductions occur in order (i.e. no hierarchical reductions),
+ */
-// although this can easily be changed if necessary.
-
 @WalkerName("IndelIntervals")
 @Requires({DataSource.READS, DataSource.REFERENCE})
 @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
@@ -48,6 +46,8 @@ public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval
         return null;
     }
 
+    // Note that the reduce step assumes that reductions occur in order (i.e. no hierarchical reductions),
+    // although this can easily be changed if necessary.
     public Interval reduce(Interval value, Interval sum) {
         // if there is no interval to the left, then this is the first one
         if ( sum == null )

java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java

@@ -5,7 +5,6 @@ import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
@@ -15,7 +14,12 @@ import net.sf.samtools.*;
 import java.util.*;
 import java.io.File;
 import java.io.FileWriter;
- 
+
+/**
+ * Performs local realignment of reads based on misalignments due to the presence of indels.
+ * Unlike most mappers, this walker uses the full alignment context to determine whether an
+ * appropriate alternate reference (i.e. indel) exists and updates SAMRecords accordingly.
+ */
 @WalkerName("IntervalCleaner")
 @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
 public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer> {
@@ -60,8 +64,6 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
     private TreeSet<ComparableSAMRecord> readsToWrite = null;
     private TreeSet<ComparableSAMRecord> nextSetOfReadsToWrite = null;
 
-    private boolean debugOn = false;
-
     public void initialize() {
 
         if ( LOD_THRESHOLD < 0.0 )

java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java

@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.gatk.walkers.indels;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.filters.Platform454Filter;
 import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -36,7 +35,8 @@ import java.util.*;
 
 
 /**
- * Merges intervals based on reads which overlap them.
+ * Merges sets of intervals based on reads which overlap them; no two intervals in the final list
+ * will have a read that even partially spans them both.  A maximum interval size is enforced though. 
  */
 @WalkerName("IntervalMerger")
 @Requires({DataSource.READS, DataSource.REFERENCE})

java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java

@@ -14,6 +14,9 @@ import org.broadinstitute.sting.utils.cmdLine.Argument;
 
 import java.util.*;
 
+/**
+ * Emits intervals consisting of nearby loci with high mismatch rates.
+ */
 @WalkerName("MismatchIntervals")
 @ReadFilters({Platform454Filter.class, ZeroMappingQualityReadFilter.class})
 public class MismatchIntervalWalker extends LocusWalker<Pair<GenomeLoc, Boolean>, Pair<LinkedList<Boolean>, GenomeLoc>> {

java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java

@@ -10,6 +10,9 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.genotype.Variation;
 
+/**
+ * Given a ROD track SNP calls called "snps", emits intervals consisting of clustered SNPs.
+ */
 @WalkerName("SNPClusters")
 @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="snps",type= VariationRod.class)})
 public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {