Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -34,10 +34,7 @@ import org.broadinstitute.sting.gatk.filters.ReadFilter;
 import org.broadinstitute.sting.gatk.walkers.Attribution;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.help.ApplicationDetails;
+import org.broadinstitute.sting.utils.help.*;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.GATKDocUtils;
-import org.broadinstitute.sting.utils.help.GATKDoclet;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 
 import java.util.*;
@@ -178,7 +175,7 @@ public class CommandLineGATK extends CommandLineExecutable {
         Formatter formatter = new Formatter(additionalHelp);
 
         formatter.format("For a full description of this walker, see its GATKdocs at:%n");
-        formatter.format("%s%n", GATKDocUtils.helpLinksToGATKDocs(walkerType));
+        formatter.format("%s%n", HelpUtils.helpLinksToGATKDocs(walkerType));
 
         return additionalHelp.toString();
     }

public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java

@@ -1,10 +1,11 @@
 package org.broadinstitute.sting.gatk.refdata;
 
+import net.sf.samtools.util.SequenceUtil;
 import org.broad.tribble.Feature;
+import org.broad.tribble.annotation.Strand;
 import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broad.tribble.gelitext.GeliTextFeature;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
@@ -92,6 +93,67 @@ public class VariantContextAdaptors {
     // --------------------------------------------------------------------------------------------------------------
 
     private static class DBSnpAdaptor implements VCAdaptor {
+        private static boolean isSNP(DbSNPFeature feature) {
+            return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
+        }
+
+        private static boolean isMNP(DbSNPFeature feature) {
+            return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
+        }
+
+        private static boolean isInsertion(DbSNPFeature feature) {
+            return feature.getVariantType().contains("insertion");
+        }
+
+        private static boolean isDeletion(DbSNPFeature feature) {
+            return feature.getVariantType().contains("deletion");
+        }
+
+        private static boolean isIndel(DbSNPFeature feature) {
+            return isInsertion(feature) || isDeletion(feature) || isComplexIndel(feature);
+        }
+
+        public static boolean isComplexIndel(DbSNPFeature feature) {
+            return feature.getVariantType().contains("in-del");
+        }
+
+        /**
+         * gets the alternate alleles.  This method should return all the alleles present at the location,
+         * NOT including the reference base.  This is returned as a string list with no guarantee ordering
+         * of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
+         * frequency).
+         *
+         * @return an alternate allele list
+         */
+        public static List<String> getAlternateAlleleList(DbSNPFeature feature) {
+            List<String> ret = new ArrayList<String>();
+            for (String allele : getAlleleList(feature))
+                if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
+            return ret;
+        }
+
+        /**
+         * gets the alleles.  This method should return all the alleles present at the location,
+         * including the reference base.  The first allele should always be the reference allele, followed
+         * by an unordered list of alternate alleles.
+         *
+         * @return an alternate allele list
+         */
+        public static List<String> getAlleleList(DbSNPFeature feature) {
+            List<String> alleleList = new ArrayList<String>();
+            // add ref first
+            if ( feature.getStrand() == Strand.POSITIVE )
+                alleleList = Arrays.asList(feature.getObserved());
+            else
+                for (String str : feature.getObserved())
+                    alleleList.add(SequenceUtil.reverseComplement(str));
+            if ( alleleList.size() > 0 && alleleList.contains(feature.getNCBIRefBase())
+                    && !alleleList.get(0).equals(feature.getNCBIRefBase()) )
+                Collections.swap(alleleList, alleleList.indexOf(feature.getNCBIRefBase()), 0);
+
+            return alleleList;
+        }
+
         /**
          * Converts non-VCF formatted dbSNP records to VariantContext. 
          * @return DbSNPFeature.
@@ -102,18 +164,18 @@ public class VariantContextAdaptors {
         @Override        
         public VariantContext convert(String name, Object input, ReferenceContext ref) {
             DbSNPFeature dbsnp = (DbSNPFeature)input;
-            if ( ! Allele.acceptableAlleleBases(DbSNPHelper.getReference(dbsnp)) )
+            if ( ! Allele.acceptableAlleleBases(dbsnp.getNCBIRefBase()) )
                 return null;
-            Allele refAllele = Allele.create(DbSNPHelper.getReference(dbsnp), true);
+            Allele refAllele = Allele.create(dbsnp.getNCBIRefBase(), true);
 
-            if ( DbSNPHelper.isSNP(dbsnp) || DbSNPHelper.isIndel(dbsnp) || DbSNPHelper.isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) {
+            if ( isSNP(dbsnp) || isIndel(dbsnp) || isMNP(dbsnp) || dbsnp.getVariantType().contains("mixed") ) {
                 // add the reference allele
                 List<Allele> alleles = new ArrayList<Allele>();
                 alleles.add(refAllele);
 
                 // add all of the alt alleles
                 boolean sawNullAllele = refAllele.isNull();
-                for ( String alt : DbSNPHelper.getAlternateAlleleList(dbsnp) ) {
+                for ( String alt : getAlternateAlleleList(dbsnp) ) {
                     if ( ! Allele.acceptableAlleleBases(alt) ) {
                         //System.out.printf("Excluding dbsnp record %s%n", dbsnp);
                         return null;

public/java/src/org/broadinstitute/sting/gatk/refdata/features/DbSNPHelper.java

@@ -1,169 +0,0 @@
-/*
- * Copyright (c) 2011, 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.
- */
-
-package org.broadinstitute.sting.gatk.refdata.features;
-
-import net.sf.samtools.util.SequenceUtil;
-import org.broad.tribble.annotation.Strand;
-import org.broad.tribble.dbsnp.DbSNPFeature;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.List;
-
-/**
- * this class contains static helper methods for DbSNP
- */
-public class DbSNPHelper {
-
-    private DbSNPHelper() {} // don't make a DbSNPHelper
-
-    public static String rsIDOfFirstRealVariant(List<VariantContext> VCs, VariantContext.Type type) {
-        if ( VCs == null )
-            return null;
-
-        String rsID = null;
-        for ( VariantContext vc : VCs ) {
-            if ( vc.getType() == type ) {
-                rsID = vc.getID();
-                break;
-            }
-        }
-
-        return rsID;
-    }
-
-    /**
-     * get the -1 * (log 10 of the error value)
-     *
-     * @return the log based error estimate
-     */
-    public static double getNegLog10PError(DbSNPFeature feature) {
-        return 4; // -log10(0.0001)
-    }
-
-    //
-    // What kind of variant are we?
-    //
-    // ----------------------------------------------------------------------
-    public static boolean isSNP(DbSNPFeature feature) {
-        return feature.getVariantType().contains("single") && feature.getLocationType().contains("exact");
-    }
-
-    public static boolean isMNP(DbSNPFeature feature) {
-        return feature.getVariantType().contains("mnp") && feature.getLocationType().contains("range");
-    }
-
-    public static String toMediumString(DbSNPFeature feature) {
-        String s = String.format("%s:%d:%s:%s", feature.getChr(), feature.getStart(), feature.getRsID(), Utils.join("",feature.getObserved()));
-        if (isSNP(feature)) s += ":SNP";
-        if (isIndel(feature)) s += ":Indel";
-        if (isHapmap(feature)) s += ":Hapmap";
-        if (is2Hit2Allele(feature)) s += ":2Hit";
-        return s;
-    }
-
-    public static boolean isInsertion(DbSNPFeature feature) {
-        return feature.getVariantType().contains("insertion");
-    }
-
-    public static boolean isDeletion(DbSNPFeature feature) {
-        return feature.getVariantType().contains("deletion");
-    }
-
-    public static boolean isIndel(DbSNPFeature feature) {
-        return DbSNPHelper.isInsertion(feature) || DbSNPHelper.isDeletion(feature) || DbSNPHelper.isComplexIndel(feature);
-    }
-
-    public static boolean isComplexIndel(DbSNPFeature feature) {
-        return feature.getVariantType().contains("in-del");
-    }
-
-    public static boolean isHapmap(DbSNPFeature feature) {
-        return feature.getValidationStatus().contains("by-hapmap");
-    }
-
-    public static boolean is2Hit2Allele(DbSNPFeature feature) {
-        return feature.getValidationStatus().contains("by-2hit-2allele");
-    }
-
-    public static boolean is1000genomes(DbSNPFeature feature) {
-        return feature.getValidationStatus().contains("by-1000genomes");
-    }
-
-    public static boolean isMQ1(DbSNPFeature feature) {
-        return feature.getWeight() == 1;
-    }
-
-    /**
-     * gets the alternate alleles.  This method should return all the alleles present at the location,
-     * NOT including the reference base.  This is returned as a string list with no guarantee ordering
-     * of alleles (i.e. the first alternate allele is not always going to be the allele with the greatest
-     * frequency).
-     *
-     * @return an alternate allele list
-     */
-    public static List<String> getAlternateAlleleList(DbSNPFeature feature) {
-        List<String> ret = new ArrayList<String>();
-        for (String allele : getAlleleList(feature))
-            if (!allele.equals(String.valueOf(feature.getNCBIRefBase()))) ret.add(allele);
-        return ret;
-    }
-
-    public static boolean onFwdStrand(DbSNPFeature feature) {
-        return feature.getStrand() == Strand.POSITIVE;
-    }
-
-    public static String getReference(DbSNPFeature feature) {
-        return feature.getNCBIRefBase();
-    }
-
-    public static String toSimpleString(DbSNPFeature feature) {
-        return String.format("%s:%s:%s", feature.getRsID(), feature.getObserved(), (feature.getStrand() == Strand.POSITIVE) ? "+" : "-");
-    }
-
-    /**
-     * gets the alleles.  This method should return all the alleles present at the location,
-     * including the reference base.  The first allele should always be the reference allele, followed
-     * by an unordered list of alternate alleles.
-     *
-     * @return an alternate allele list
-     */
-    public static List<String> getAlleleList(DbSNPFeature feature) {
-        List<String> alleleList = new ArrayList<String>();
-            // add ref first
-            if ( onFwdStrand(feature) )
-                alleleList = Arrays.asList(feature.getObserved());
-            else
-                for (String str : feature.getObserved())
-                    alleleList.add(SequenceUtil.reverseComplement(str));
-            if ( alleleList.size() > 0 && alleleList.contains(getReference(feature)) && !alleleList.get(0).equals(getReference(feature)) )
-                Collections.swap(alleleList, alleleList.indexOf(getReference(feature)), 0);
-
-        return alleleList;
-    }
-}

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

@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.gatk.walkers;
 
 import org.broad.tribble.Feature;
-import org.broad.tribble.dbsnp.DbSNPFeature;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
@@ -34,9 +33,6 @@ 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;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
-import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;

public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java

@@ -29,15 +29,11 @@ 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;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotationInterfaceManager;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
@@ -158,7 +154,7 @@ public class VariantAnnotatorEngine {
     private void annotateDBs(RefMetaDataTracker tracker, ReferenceContext ref, VariantContext vc, Map<String, Object> infoAnnotations) {
         for ( Map.Entry<RodBinding<VariantContext>, String> dbSet : dbAnnotations.entrySet() ) {
             if ( dbSet.getValue().equals(VCFConstants.DBSNP_KEY) ) {
-                String rsID = DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
+                String rsID = VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbSet.getKey(), ref.getLocus()), vc.getType());
                 infoAnnotations.put(VCFConstants.DBSNP_KEY, rsID != null);
                 // annotate dbsnp id if available and not already there
                 if ( rsID != null && (!vc.hasID() || vc.getID().equals(VCFConstants.EMPTY_ID_FIELD)) )

public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java

@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
+import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;

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

@@ -42,50 +42,190 @@ import java.io.PrintStream;
 /**
  * Emits a data file containing information about callable, uncallable, poorly mapped, and other parts of the genome
  *
- * @Author depristo
+ * <p>
- * @Date May 7, 2010
+ * A very common question about a NGS set of reads is what areas of the genome are considered callable. The system
+ * considers the coverage at each locus and emits either a per base state or a summary interval BED file that
+ * partitions the genomic intervals into the following callable states:
+ * <dl>
+ *     <dt>REF_N</dt>
+ *        <dd>the reference base was an N, which is not considered callable the GATK</dd>
+ *     <dt>CALLABLE</dt>
+ *        <dd>the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE</dd>
+ *     <dt>NO_COVERAGE</dt>
+ *        <dd>absolutely no reads were seen at this locus, regardless of the filtering parameters</dd>
+ *     <dt>LOW_COVERAGE</dt>
+ *        <dd>there were less than min. depth bases at the locus, after applying filters</dd>
+ *     <dt>EXCESSIVE_COVERAGE</dt>
+ *        <dd>more than -maxDepth read at the locus, indicating some sort of mapping problem</dd>
+ *     <dt>POOR_MAPPING_QUALITY</dt>
+ *        <dd>more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads</dd>
+ * </dl>
+ * </p>
+ *
+ * <h2>Input</h2>
+ * <p>
+ *     A BAM file containing <b>exactly one sample</b>.
+ * </p>
+ *
+ * <h2>Output</h2>
+ * <p>
+ * <ul>
+ *     <li>-o: a OutputFormatted (recommended BED) file with the callable status covering each base</li>
+ *     <li>-summary: a table of callable status x count of all examined bases</li>
+ * </ul>
+ * </p>
+ *
+ * <h2>Examples</h2>
+ * <pre>
+ *     -T CallableLociWalker \
+ *     -I my.bam \
+ *     -summary my.summary \
+ *     -o my.bed
+ * </pre>
+ *
+ * would produce a BED file (my.bed) that looks like:
+ *
+ * <pre>
+ *     20 10000000 10000864 CALLABLE
+ *     20 10000865 10000985 POOR_MAPPING_QUALITY
+ *     20 10000986 10001138 CALLABLE
+ *     20 10001139 10001254 POOR_MAPPING_QUALITY
+ *     20 10001255 10012255 CALLABLE
+ *     20 10012256 10012259 POOR_MAPPING_QUALITY
+ *     20 10012260 10012263 CALLABLE
+ *     20 10012264 10012328 POOR_MAPPING_QUALITY
+ *     20 10012329 10012550 CALLABLE
+ *     20 10012551 10012551 LOW_COVERAGE
+ *     20 10012552 10012554 CALLABLE
+ *     20 10012555 10012557 LOW_COVERAGE
+ *     20 10012558 10012558 CALLABLE
+ *     et cetera...
+ * </pre>
+ * as well as a summary table that looks like:
+ *
+ * <pre>
+ *                        state nBases
+ *                        REF_N 0
+ *                     CALLABLE 996046
+ *                  NO_COVERAGE 121
+ *                 LOW_COVERAGE 928
+ *           EXCESSIVE_COVERAGE 0
+ *         POOR_MAPPING_QUALITY 2906
+ * </pre>
+ *
+ * @author Mark DePristo
+ * @since May 7, 2010
  */
 @By(DataSource.REFERENCE)
 public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableBaseState, CallableLociWalker.Integrator> {
     @Output
     PrintStream out;
 
-    @Argument(fullName = "maxLowMAPQ", shortName = "mlmq", doc = "Maximum value for MAPQ to be considered a problematic mapped read.  The gap between this value and mmq are reads that are not sufficiently well mapped for calling but aren't indicative of mapping problems.", required = false)
+    /**
+     * Callable loci summary counts (see outputs) will be written to this file.
+     */
+    @Output(fullName = "summary", shortName = "summary", doc = "Name of file for output summary", required = true)
+    File summaryFile;
+
+    /**
+     * The gap between this value and mmq are reads that are not sufficiently well mapped for calling but
+     * aren't indicative of mapping problems.  For example, if maxLowMAPQ = 1 and mmq = 20, then reads with
+     * MAPQ == 0 are poorly mapped, MAPQ >= 20 are considered as contributing to calling, where
+     * reads with MAPQ >= 1 and < 20 are not bad in and of themselves but aren't sufficiently good to contribute to
+     * calling.  In effect this reads are invisible, driving the base to the NO_ or LOW_COVERAGE states
+     */
+    @Argument(fullName = "maxLowMAPQ", shortName = "mlmq", doc = "Maximum value for MAPQ to be considered a problematic mapped read.", required = false)
     byte maxLowMAPQ = 1;
 
-    @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth. Defaults to 50.", required = false)
+    /**
+     * Reads with MAPQ > minMappingQuality are treated as usable for variation detection, contributing to the CALLABLE
+     * state.
+     */
+    @Argument(fullName = "minMappingQuality", shortName = "mmq", doc = "Minimum mapping quality of reads to count towards depth.", required = false)
     byte minMappingQuality = 10;
 
-    @Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth. Defaults to 20.", required = false)
+    /**
+     * Bases with less than minBaseQuality are viewed as not sufficiently high quality to contribute to the CALLABLE state
+     */
+    @Argument(fullName = "minBaseQuality", shortName = "mbq", doc = "Minimum quality of bases to count towards depth.", required = false)
     byte minBaseQuality = 20;
 
+    /**
+     * If the number of QC+ bases (on reads with MAPQ > minMappingQuality and with base quality > minBaseQuality) exceeds this
+     * value and is less than maxDepth the site is considered CALLABLE.
+     */
     @Argument(fullName = "minDepth", shortName = "minDepth", doc = "Minimum QC+ read depth before a locus is considered callable", required = false)
     int minDepth = 4;
 
+    /**
+     * If the QC+ depth exceeds this value the site is considered to have EXCESSIVE_DEPTH
+     */
     @Argument(fullName = "maxDepth", shortName = "maxDepth", doc = "Maximum read depth before a locus is considered poorly mapped", required = false)
     int maxDepth = -1;
 
+    /**
+     * We don't want to consider a site as POOR_MAPPING_QUALITY just because it has two reads, and one is MAPQ.  We
+     * won't assign a site to the POOR_MAPPING_QUALITY state unless there are at least minDepthForLowMAPQ reads
+     * covering the site.
+     */
     @Argument(fullName = "minDepthForLowMAPQ", shortName = "mdflmq", doc = "Minimum read depth before a locus is considered a potential candidate for poorly mapped", required = false)
     int minDepthLowMAPQ = 10;
 
-    @Argument(fullName = "maxFractionOfReadsWithLowMAPQ", shortName = "frlmq", doc = "Maximum read depth before a locus is considered poorly mapped", required = false)
+    /**
+     * If the number of reads at this site is greater than minDepthForLowMAPQ and the fraction of reads with low mapping quality
+     * exceeds this fraction then the site has POOR_MAPPING_QUALITY.
+     */
+    @Argument(fullName = "maxFractionOfReadsWithLowMAPQ", shortName = "frlmq", doc = "If the fraction of reads at a base with low mapping quality exceeds this value, the site may be poorly mapped", required = false)
     double maxLowMAPQFraction = 0.1;
 
-    @Argument(fullName = "format", shortName = "format", doc = "Output format for the system: either BED or STATE_PER_BASE", required = false)
+    /**
+     * The output of this walker will be written in this format.  The recommended option is BED.
+     */
+    @Argument(fullName = "format", shortName = "format", doc = "Output format", required = false)
     OutputFormat outputFormat;
 
-    @Argument(fullName = "summary", shortName = "summary", doc = "Name of file for output summary", required = true)
+    public enum OutputFormat {
-    File summaryFile;
+        /**
+         * The output will be written as a BED file.  There's a BED element for each
+         * continuous run of callable states (i.e., CALLABLE, REF_N, etc).  This is the recommended
+         * format
+         */
+        BED,
 
-    public enum OutputFormat { BED, STATE_PER_BASE }
+        /**
+         * Emit chr start stop state quads for each base.  Produces a potentially disasterously
+         * large amount of output.
+         */
+        STATE_PER_BASE
+    }
+
+    public enum CalledState {
+        /** the reference base was an N, which is not considered callable the GATK */
+        REF_N,
+        /** the base satisfied the min. depth for calling but had less than maxDepth to avoid having EXCESSIVE_COVERAGE */
+        CALLABLE,
+        /** absolutely no reads were seen at this locus, regardless of the filtering parameters */
+        NO_COVERAGE,
+        /** there were less than min. depth bases at the locus, after applying filters */
+        LOW_COVERAGE,
+        /** more than -maxDepth read at the locus, indicating some sort of mapping problem */
+        EXCESSIVE_COVERAGE,
+        /** more than --maxFractionOfReadsWithLowMAPQ at the locus, indicating a poor mapping quality of the reads */
+        POOR_MAPPING_QUALITY
+    }
 
     ////////////////////////////////////////////////////////////////////////////////////
     // STANDARD WALKER METHODS
     ////////////////////////////////////////////////////////////////////////////////////
 
+    @Override
     public boolean includeReadsWithDeletionAtLoci() { return true; }
 
+    @Override
     public void initialize() {
+        if ( getToolkit().getSamples().size() > 1 )
+            throw new UserException.BadArgumentValue("-I", "CallableLoci only works for a single sample, but multiple samples were found in the provided BAM files: " + getToolkit().getSamples());
+
         try {
             PrintStream summaryOut = new PrintStream(summaryFile);
             summaryOut.close();
@@ -94,15 +234,15 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
         }
     }
 
-    public static class Integrator {
+    protected static class Integrator {
-        long counts[] = new long[CalledState.values().length];
+        final long counts[] = new long[CalledState.values().length];
         CallableBaseState state = null;
     }
 
-    public static class CallableBaseState implements HasGenomeLocation {
+    protected static class CallableBaseState implements HasGenomeLocation {
-        public GenomeLocParser genomeLocParser;
+        final public GenomeLocParser genomeLocParser;
         public GenomeLoc loc;
-        public CalledState state;
+        final public CalledState state;
 
         public CallableBaseState(GenomeLocParser genomeLocParser,GenomeLoc loc, CalledState state) {
             this.genomeLocParser = genomeLocParser;
@@ -133,16 +273,10 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
 
         public String toString() {
             return String.format("%s %d %d %s", loc.getContig(), loc.getStart(), loc.getStop(), state);
-            //return String.format("%s %d %d %d %s", loc.getContig(), loc.getStart(), loc.getStop(), loc.getStop() - loc.getStart() + 1, state);
         }
     }
 
-    public enum CalledState { REF_N, CALLABLE, NO_COVERAGE, LOW_COVERAGE, EXCESSIVE_COVERAGE, POOR_MAPPING_QUALITY }
+    @Override
-
-    public Integrator reduceInit() {
-        return new Integrator();
-    }
-
     public CallableBaseState map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         CalledState state;
 
@@ -179,6 +313,12 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
         return new CallableBaseState(getToolkit().getGenomeLocParser(),context.getLocation(), state);
     }
 
+    @Override
+    public Integrator reduceInit() {
+        return new Integrator();
+    }
+
+    @Override
     public Integrator reduce(CallableBaseState state, Integrator integrator) {
         // update counts
         integrator.counts[state.getState().ordinal()]++;
@@ -206,6 +346,7 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
     // INTERVAL ON TRAVERSAL DONE
     ////////////////////////////////////////////////////////////////////////////////////
 
+    @Override
     public void onTraversalDone(Integrator result) {
         // print out the last state
         if ( result != null ) {

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

@@ -32,8 +32,8 @@ 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.SeekableRODIterator;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;

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

@@ -39,9 +39,9 @@ import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
 import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.Transcript;
+import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqCodec;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
-import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
+import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;

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

@@ -32,7 +32,7 @@ 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;
-import org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature;
+import org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;

public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java

@@ -14,9 +14,8 @@ 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;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
-import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.BaseUtils;

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

@@ -33,7 +33,6 @@ 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.VariantContextAdaptors;
-import org.broadinstitute.sting.gatk.refdata.features.DbSNPHelper;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
@@ -120,7 +119,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
         if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) )
             return 0;
 
-        String rsID = dbsnp == null ? null : DbSNPHelper.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
+        String rsID = dbsnp == null ? null : VCFUtils.rsIDOfFirstRealVariant(tracker.getValues(dbsnp.dbsnp, context.getLocation()), VariantContext.Type.SNP);
 
         Collection<VariantContext> contexts = getVariantContexts(tracker, ref);
 

public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleCodec.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.beagle;
+package org.broadinstitute.sting.utils.codecs.beagle;
 /*
  * Copyright (c) 2010 The Broad Institute
  *

public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java

@@ -22,7 +22,7 @@
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
-package org.broadinstitute.sting.gatk.refdata.features.beagle;
+package org.broadinstitute.sting.utils.codecs.beagle;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.utils.variantcontext.Allele;

public/java/src/org/broadinstitute/sting/utils/codecs/completegenomics/CGVarCodec.java

@@ -117,7 +117,7 @@ public class CGVarCodec implements FeatureCodec {
         return new VariantContext("CGI", array[3], start, end, alleles, VariantContext.NO_NEG_LOG_10PERROR, null, attrs);
     }
 
-    public Class getFeatureType() {
+    public Class<VariantContext> getFeatureType() {
         return VariantContext.class;
     }
 

public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapCodec.java

@@ -82,7 +82,7 @@ public class RawHapMapCodec implements FeatureCodec {
                 headerLine);
     }
 
-    public Class getFeatureType() {
+    public Class<RawHapMapFeature> getFeatureType() {
         return RawHapMapFeature.class;
     }
 

public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqCodec.java

@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.gatk.refdata.features.refseq;
+package org.broadinstitute.sting.utils.codecs.refseq;
 
-import org.apache.commons.io.filefilter.FalseFileFilter;
 import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
@@ -104,7 +103,7 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
     }
 
     @Override
-    public Class getFeatureType() {
+    public Class<RefSeqFeature> getFeatureType() {
         return RefSeqFeature.class;
     }
 }

public/java/src/org/broadinstitute/sting/utils/codecs/refseq/RefSeqFeature.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.refseq;
+package org.broadinstitute.sting.utils.codecs.refseq;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;

public/java/src/org/broadinstitute/sting/utils/codecs/refseq/Transcript.java

@@ -1,53 +1,53 @@
-package org.broadinstitute.sting.gatk.refdata.features.refseq;
+package org.broadinstitute.sting.utils.codecs.refseq;
-
+
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.HasGenomeLocation;
+import org.broadinstitute.sting.utils.HasGenomeLocation;
-
+
-import java.util.List;
+import java.util.List;
-
+
-/**
+/**
- * Created by IntelliJ IDEA.
+ * Created by IntelliJ IDEA.
- * User: asivache
+ * User: asivache
- * Date: Sep 22, 2009
+ * Date: Sep 22, 2009
- * Time: 5:22:30 PM
+ * Time: 5:22:30 PM
- * To change this template use File | Settings | File Templates.
+ * To change this template use File | Settings | File Templates.
- */
+ */
-public interface Transcript extends HasGenomeLocation {
+public interface Transcript extends HasGenomeLocation {
-
+
-    /** Returns id of the transcript (RefSeq NM_* id) */
+    /** Returns id of the transcript (RefSeq NM_* id) */
-    public String getTranscriptId();
+    public String getTranscriptId();
-    /** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
+    /** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
-    public int getStrand();
+    public int getStrand();
-    /** Returns transcript's full genomic interval (includes all exons with UTRs) */
+    /** Returns transcript's full genomic interval (includes all exons with UTRs) */
-    public GenomeLoc getLocation();
+    public GenomeLoc getLocation();
-    /** Returns genomic interval of the coding sequence (does not include
+    /** Returns genomic interval of the coding sequence (does not include
-     * UTRs, but still includes introns, since it's a single interval on the DNA)
+     * UTRs, but still includes introns, since it's a single interval on the DNA)
-     */
+     */
-    public GenomeLoc getCodingLocation();
+    public GenomeLoc getCodingLocation();
-    /** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
+    /** Name of the gene this transcript corresponds to (typically NOT gene id such as Entrez etc,
-     * but the implementation can decide otherwise)
+     * but the implementation can decide otherwise)
-     */
+     */
-    public String getGeneName();
+    public String getGeneName();
-    /** Number of exons in this transcript */
+    /** Number of exons in this transcript */
-    public int getNumExons();
+    public int getNumExons();
-    /** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
+    /** Genomic location of the n-th exon; expected to throw an exception (runtime) if n is out of bounds */
-    public GenomeLoc getExonLocation(int n);
+    public GenomeLoc getExonLocation(int n);
-
+
-    /** Returns the list of all exons in this transcript, as genomic intervals */
+    /** Returns the list of all exons in this transcript, as genomic intervals */
-    public List<GenomeLoc> getExons();
+    public List<GenomeLoc> getExons();
-
+
-    /** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
+    /** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
-    public boolean overlapsP (GenomeLoc that);
+    public boolean overlapsP (GenomeLoc that);
-
+
-    /** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
+    /** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
-      * NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
+      * NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
-      * but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
+      * but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
-      * @see #overlapsExonP
+      * @see #overlapsExonP
-      */
+      */
-    public boolean overlapsCodingP (GenomeLoc that);
+    public boolean overlapsCodingP (GenomeLoc that);
-
+
-    /** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
+    /** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
-    public boolean overlapsExonP (GenomeLoc that);
+    public boolean overlapsExonP (GenomeLoc that);
-
+
-
+
-}
+}

public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupCodec.java

@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.refdata.features.sampileup;
+package org.broadinstitute.sting.utils.codecs.sampileup;
 
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
@@ -35,7 +35,7 @@ import java.util.ArrayList;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import static org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature.VariantType;
+import static org.broadinstitute.sting.utils.codecs.sampileup.SAMPileupFeature.VariantType;
 
 /**
  * A Tribble encoder / decoder for SAM pileup data. 

public/java/src/org/broadinstitute/sting/utils/codecs/sampileup/SAMPileupFeature.java

@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.refdata.features.sampileup;
+package org.broadinstitute.sting.utils.codecs.sampileup;
 
 import net.sf.samtools.util.StringUtil;
 import org.broad.tribble.Feature;

public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadCodec.java

@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.refdata.features.samread;
+package org.broadinstitute.sting.utils.codecs.samread;
 
 import net.sf.samtools.Cigar;
 import net.sf.samtools.TextCigarCodec;

public/java/src/org/broadinstitute/sting/utils/codecs/samread/SAMReadFeature.java

@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.refdata.features.samread;
+package org.broadinstitute.sting.utils.codecs.samread;
 
 import org.broad.tribble.Feature;
 

public/java/src/org/broadinstitute/sting/utils/codecs/snpEff/SnpEffCodec.java

@@ -222,7 +222,7 @@ public class SnpEffCodec implements FeatureCodec, SelfScopingFeatureCodec {
         return null;
     }
 
-    public Class getFeatureType() {
+    public Class<SnpEffFeature> getFeatureType() {
         return SnpEffFeature.class;
     }
 

public/java/src/org/broadinstitute/sting/utils/codecs/soapsnp/SoapSNPCodec.java

@@ -178,7 +178,7 @@ public class SoapSNPCodec implements FeatureCodec, NameAwareCodec {
     /**
      * @return VariantContext
      */
-    public Class getFeatureType() {
+    public Class<VariantContext> getFeatureType() {
         return VariantContext.class;
     }
 

public/java/src/org/broadinstitute/sting/utils/codecs/table/BedTableCodec.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.table;
+package org.broadinstitute.sting.utils.codecs.table;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;

public/java/src/org/broadinstitute/sting/utils/codecs/table/TableCodec.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.table;
+package org.broadinstitute.sting.utils.codecs.table;
 
 import org.broad.tribble.Feature;
 import org.broad.tribble.readers.LineReader;
@@ -51,7 +51,7 @@ public class TableCodec implements ReferenceDependentFeatureCodec {
     }
 
     @Override
-    public Class getFeatureType() {
+    public Class<TableFeature> getFeatureType() {
         return TableFeature.class;
     }
 

public/java/src/org/broadinstitute/sting/utils/codecs/table/TableFeature.java

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.gatk.refdata.features.table;
+package org.broadinstitute.sting.utils.codecs.table;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.utils.GenomeLoc;

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java

@@ -263,7 +263,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
      *
      * @return the type of record
      */
-    public Class getFeatureType() {
+    public Class<VariantContext> getFeatureType() {
         return VariantContext.class;
     }
 

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java

@@ -180,4 +180,19 @@ public class VCFUtils {
 
         return new HashSet<VCFHeaderLine>(map.values());
     }
+
+    public static String rsIDOfFirstRealVariant(List<VariantContext> VCs, VariantContext.Type type) {
+        if ( VCs == null )
+            return null;
+
+        String rsID = null;
+        for ( VariantContext vc : VCs ) {
+            if ( vc.getType() == type ) {
+                rsID = vc.getID();
+                break;
+            }
+        }
+
+        return rsID;
+    }
 }

public/java/src/org/broadinstitute/sting/utils/help/DocumentedGATKFeatureHandler.java

@@ -71,7 +71,7 @@ public abstract class DocumentedGATKFeatureHandler {
      * @return
      */
     public String getDestinationFilename(ClassDoc doc, Class clazz) {
-        return GATKDocUtils.htmlFilenameForClass(clazz);
+        return HelpUtils.htmlFilenameForClass(clazz);
     }
 
     /**

public/java/src/org/broadinstitute/sting/utils/help/GATKDocUtils.java

@@ -1,48 +0,0 @@
-/*
- * Copyright (c) 2011, 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.
- */
-
-package org.broadinstitute.sting.utils.help;
-
-/**
- * @author depristo
- * @since 8/8/11
- */
-public class GATKDocUtils {
-    private final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
-    private final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
-    private final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
-
-    public static String htmlFilenameForClass(Class c) {
-        return c.getName().replace(".", "_") + ".html";
-    }
-
-    public static String helpLinksToGATKDocs(Class c) {
-        String classPath = htmlFilenameForClass(c);
-        StringBuilder b = new StringBuilder();
-        b.append("release  version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
-        b.append("stable   version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
-        b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
-        return b.toString();
-    }
-}

public/java/src/org/broadinstitute/sting/utils/help/HelpUtils.java

@@ -32,6 +32,10 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import java.lang.reflect.Field;
 
 public class HelpUtils {
+    public final static String URL_ROOT_FOR_RELEASE_GATKDOCS = "http://www.broadinstitute.org/gsa/gatkdocs/release/";
+    public final static String URL_ROOT_FOR_STABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/stable/";
+    public final static String URL_ROOT_FOR_UNSTABLE_GATKDOCS = "http://iwww.broadinstitute.org/gsa/gatkdocs/unstable/";
+
     protected static boolean implementsInterface(ProgramElementDoc classDoc, Class... interfaceClasses) {
         for (Class interfaceClass : interfaceClasses)
             if (assignableToClass(classDoc, interfaceClass, false))
@@ -74,4 +78,17 @@ public class HelpUtils {
                 String.format("%s.%s", containingPackage.name(), doc.name()) :
                 String.format("%s", doc.name());
     }
+
+    public static String htmlFilenameForClass(Class c) {
+        return c.getName().replace(".", "_") + ".html";
+    }
+
+    public static String helpLinksToGATKDocs(Class c) {
+        String classPath = htmlFilenameForClass(c);
+        StringBuilder b = new StringBuilder();
+        b.append("release  version: ").append(URL_ROOT_FOR_RELEASE_GATKDOCS).append(classPath).append("\n");
+        b.append("stable   version: ").append(URL_ROOT_FOR_STABLE_GATKDOCS).append(classPath).append("\n");
+        b.append("unstable version: ").append(URL_ROOT_FOR_UNSTABLE_GATKDOCS).append(classPath).append("\n");
+        return b.toString();
+    }
 }

public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java

@@ -26,7 +26,6 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broad.tribble.Feature;
-import org.broadinstitute.sting.gatk.refdata.features.beagle.BeagleFeature;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.testng.Assert;
@@ -35,7 +34,6 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
-import javax.script.Bindings;
 import java.util.List;
 import java.util.EnumSet;
 /**

public/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java

@@ -10,7 +10,7 @@ import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.datasources.reads.Shard;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;

public/java/test/org/broadinstitute/sting/gatk/datasources/rmd/ReferenceOrderedDataPoolUnitTest.java

@@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;

public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java

@@ -31,7 +31,7 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.commandline.Tags;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GenomeLoc;

public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java

@@ -29,8 +29,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.refdata.features.table.BedTableCodec;
+import org.broadinstitute.sting.utils.codecs.table.BedTableCodec;
-import org.broadinstitute.sting.gatk.refdata.features.table.TableFeature;
+import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;