Documentation updates. Moved CountX.java walkers to QC

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2345 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/ClipReadsWalker.java

@@ -16,36 +16,9 @@ import java.io.File;
 
 import net.sf.samtools.util.StringUtil;
 
-/*
- * Copyright (c) 2009 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
 /**
- * This walker prints out the reads from the BAM files provided to the traversal engines.
- * It also supports the command line option '-outputBamFile filname', which outputs all the
- * reads to a specified BAM file
- * The walker now also optionally filters reads based on command line options.
+ * This ReadWalker provides simple, yet powerful read clipping capabilities.  It allows the user to clip bases in reads
+ * with poor quality scores, that match particular sequences, or that were generated by particular machine cycles.
  */
 @Requires({DataSource.READS})
 public class ClipReadsWalker extends ReadWalker<ClipReadsWalker.ReadClipper, ClipReadsWalker.ClippingData> {

java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodByRefWalker.java

@@ -11,8 +11,8 @@ import java.util.ArrayList;
 import java.util.List;
 
 /**
- * A very simple walker that prints out counts of the number of reference ordered data objects are
- * each locus.  For debugging RefWalkers.
+ * Prints out counts of the number of reference ordered data objects are
+ * each locus for debugging RefWalkers.
  */
 public class CountRodByRefWalker extends RefWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> {
     @Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false)

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

@@ -14,8 +14,8 @@ import java.util.Collection;
 import java.util.LinkedList;
 
 /**
- * A very simple walker that 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 are
+ * each locus for debugging RodWalkers.
  */
 public class CountRodWalker extends RodWalker<CountRodWalker.Datum, Pair<ExpandingArrayList<Long>, Long>> {
     @Argument(fullName = "verbose", shortName = "v", doc="If true, Countrod will print out detailed information about the rods it finds and locations", required = false)

java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceAssessor.java

@@ -25,6 +25,11 @@ import net.sf.samtools.SAMFileWriter;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 
+/**
+ * A completely experimental read walker that consumes a graphical reference emitted by GraphReferenceBuilder as a
+ * serialized java object and evaluates the number of mismatches to both the flat reference and the graphical
+ * reference for each read [Not for public use and will change drastically in the future].
+ */
 public class GraphReferenceAssessor extends ReadWalker<Integer, Integer> {
     @Argument(fullName="graphFile", shortName="GF", doc="", required=true)
     String graphFile = null;

java/src/org/broadinstitute/sting/playground/gatk/walkers/graphalign/GraphReferenceBuilder.java

@@ -25,6 +25,10 @@ import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.picard.reference.ReferenceSequenceFileFactory;
 import net.sf.samtools.util.StringUtil;
 
+/**
+ * A completely experimental walker that constructs a graphical reference that incorporates variation from provided
+ * RODs [Not for public use and will change drastically in the future].
+ */
 @WalkerName("GraphReferenceBuilder")
 @Requires(value={DataSource.REFERENCE})
 public class GraphReferenceBuilder extends RefWalker<Integer, Integer> {

java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java

@@ -16,14 +16,9 @@ import java.io.PrintStream;
 import java.util.*;
 
 /**
- * The Broad Institute
- * SOFTWARE COPYRIGHT NOTICE AGREEMENT
- * This software and its documentation are copyright 2009 by the
- * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
- *
- * This software is supplied without any warranty or guaranteed support whatsoever. Neither
- * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
- *
+ * A robust and general purpose tool for characterizing the quality of SNPs, Indels, and other variants that includes basic
+ * counting, ti/tv, dbSNP% (if -D is provided), concordance to chip or validation data, and will show interesting sites (-V)
+ * that are FNs, FP, etc.
  */
 @Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=ReferenceOrderedDatum.class)}) // right now we have no base variant class for rods, this should change
 //@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class), @RMD(name="validation",type=RodGenotypeChipAsGFF.class)})
@@ -35,7 +30,7 @@ public class VariantEvalWalker extends RefWalker<Integer, Integer> {
     @Argument(shortName="printVariants", doc="If true, prints the variants in all of the variant tracks that are examined", required=false)
     public boolean printVariants = false;
 
-    @Argument(shortName="badHWEThreshold", doc="XXX", required=false)
+    @Argument(shortName="badHWEThreshold", doc="Only sites with deviations froim Hardy-Weinberg equilibrium with P-values < than this threshold are flagged", required=false)
     public double badHWEThreshold = 1e-3;
 
     @Argument(fullName="evalContainsGenotypes", shortName = "G", doc="If true, the input list of variants will be treated as a genotyping file, containing assertions of actual genotype values for a particular person.  Analyses that only make sense on at the population level will be disabled, while those operating on genotypes will be enabled", required=false)