Merge branch 'master' of gsa2:/humgen/gsa-scr1/chartl/dev/unstable

protected/java/src/org/broadinstitute/sting/gatk/DummyProtectedClass.java

@@ -1,34 +0,0 @@
-package org.broadinstitute.sting.gatk;
-
-/*
- * 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.
- */
-
-import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
-
-public class DummyProtectedClass implements ProtectedPackageSource {
-
-    // THIS CLASS IS USED JUST SO THAT WE CAN TEST WHETHER WE ARE USING THE LITE OR FULL VERSION OF THE GATK
-    // **** DO NOT REMOVE! ****
-}

protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java

@@ -35,10 +35,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
@@ -52,12 +50,6 @@ import java.util.*;
  */
 public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnnotation, ActiveRegionBasedAnnotation {
 
-    public static final String[] keyNames = { VCFConstants.ALLELE_NUMBER_KEY, VCFConstants.ALLELE_COUNT_KEY, VCFConstants.ALLELE_FREQUENCY_KEY };
-    public static final VCFInfoHeaderLine[] descriptions = {
-            VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_FREQUENCY_KEY),
-            VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_COUNT_KEY),
-            VCFStandardHeaderLines.getInfoLine(VCFConstants.ALLELE_NUMBER_KEY) };
-
     private Set<String> founderIds = new HashSet<String>();
 
     public Map<String, Object> annotate(final RefMetaDataTracker tracker,
@@ -78,8 +70,8 @@ public class ChromosomeCounts extends InfoFieldAnnotation implements StandardAnn
     }
 
     public List<String> getKeyNames() {
-        return Arrays.asList(keyNames);
+        return Arrays.asList(ChromosomeCountConstants.keyNames);
     }
 
-    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(descriptions); }
+    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(ChromosomeCountConstants.descriptions); }
 }

protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java

@@ -41,7 +41,6 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -55,7 +54,6 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintStream;
-import java.lang.reflect.Constructor;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -159,10 +157,6 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
     public void initialize() {
         baq = new BAQ(BAQGOP); // setup the BAQ object with the provided gap open penalty
 
-        // check for unsupported access
-        if (getToolkit().isGATKLite() && !getToolkit().getArguments().disableIndelQuals)
-            throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument");
-
         if (RAC.FORCE_PLATFORM != null)
             RAC.DEFAULT_PLATFORM = RAC.FORCE_PLATFORM;
 

protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationPerformance.java

@@ -0,0 +1,110 @@
+/*
+ * Copyright (c) 2010 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.walkers.bqsr;
+
+import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.filters.*;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.report.GATKReport;
+import org.broadinstitute.sting.gatk.report.GATKReportTable;
+import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.recalibration.*;
+
+import java.io.*;
+
+/**
+ */
+
+@ReadFilters({MappingQualityZeroFilter.class, MappingQualityUnavailableFilter.class, UnmappedReadFilter.class, NotPrimaryAlignmentFilter.class, DuplicateReadFilter.class, FailsVendorQualityCheckFilter.class})
+@PartitionBy(PartitionType.READ)
+public class RecalibrationPerformance extends RodWalker<Integer, Integer> implements NanoSchedulable {
+
+    @Output(doc="Write output to this file", required = true)
+    public PrintStream out;
+
+    @Input(fullName="recal", shortName="recal", required=false, doc="The input covariates table file")
+    public File RECAL_FILE = null;
+
+    public void initialize() {
+        out.println("Cycle\tQrep\tQemp\tIsJoint\tObservations\tErrors");
+
+        final GATKReport report = new GATKReport(RECAL_FILE);
+        final GATKReportTable table = report.getTable(RecalUtils.ALL_COVARIATES_REPORT_TABLE_TITLE);
+        for ( int row = 0; row < table.getNumRows(); row++ ) {
+
+            final int nObservations = (int)asDouble(table.get(row, RecalUtils.NUMBER_OBSERVATIONS_COLUMN_NAME));
+            final int nErrors = (int)Math.round(asDouble(table.get(row, RecalUtils.NUMBER_ERRORS_COLUMN_NAME)));
+            final double empiricalQuality = asDouble(table.get(row, RecalUtils.EMPIRICAL_QUALITY_COLUMN_NAME));
+
+            final byte QReported = Byte.parseByte((String) table.get(row, RecalUtils.QUALITY_SCORE_COLUMN_NAME));
+
+            final double jointEstimateQemp = RecalDatum.bayesianEstimateOfEmpiricalQuality(nObservations, nErrors, QReported);
+
+            //if ( Math.abs((int)(jointEstimateQemp - empiricalQuality)) > 1 )
+            //    System.out.println(String.format("Qreported = %f, nObservations = %f, nErrors = %f, point Qemp = %f, joint Qemp = %f", estimatedQReported, nObservations, nErrors, empiricalQuality, jointEstimateQemp));
+
+            if ( table.get(row, RecalUtils.COVARIATE_NAME_COLUMN_NAME).equals("Cycle") &&
+                    table.get(row, RecalUtils.EVENT_TYPE_COLUMN_NAME).equals("M") &&
+                    table.get(row, RecalUtils.READGROUP_COLUMN_NAME).equals("20FUKAAXX100202.6") &&
+                    (QReported == 6 || QReported == 10 || QReported == 20 || QReported == 30 || QReported == 45) ) {
+                out.println(String.format("%s\t%d\t%d\t%s\t%d\t%d", table.get(row, RecalUtils.COVARIATE_VALUE_COLUMN_NAME), QReported, Math.round(empiricalQuality), "False", (int)nObservations, (int)nErrors));
+                out.println(String.format("%s\t%d\t%d\t%s\t%d\t%d", table.get(row, RecalUtils.COVARIATE_VALUE_COLUMN_NAME), QReported, (int)jointEstimateQemp, "True", (int)nObservations, (int)nErrors));
+            }
+        }
+
+    }
+
+    @Override
+    public boolean isDone() {
+        return true;
+    }
+
+    private double asDouble(final Object o) {
+        if ( o instanceof Double )
+            return (Double)o;
+        else if ( o instanceof Integer )
+            return (Integer)o;
+        else if ( o instanceof Long )
+            return (Long)o;
+        else
+            throw new ReviewedStingException("Object " + o + " is expected to be either a double, long or integer but its not either: " + o.getClass());
+    }
+
+    @Override
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { return 0; }
+
+    @Override
+    public Integer reduceInit() { return 0; }
+
+    @Override
+    public Integer reduce(Integer counter, Integer sum) { return 0; }
+
+    @Override
+    public void onTraversalDone(Integer sum) {}
+}

protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java

@@ -124,7 +124,7 @@ public class ErrorRatePerCycle extends LocusWalker<Integer, Integer> {
 
     public void initialize() {
         report = new GATKReport();
-        report.addTable(reportName, reportDescription, 6);
+        report.addTable(reportName, reportDescription, 6, GATKReportTable.TableSortingWay.SORT_BY_ROW);
         table = report.getTable(reportName);
         table.addColumn("readgroup");
         table.addColumn("cycle");

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java

@@ -31,6 +31,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fragments.FragmentCollection;
+import org.broadinstitute.sting.utils.genotyper.DiploidGenotype;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java

@@ -60,7 +60,7 @@ public class ErrorModel  {
 
         boolean hasCalledAlleles = false;
 
-        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
+        final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
         if (refSampleVC != null) {
 
             for (Allele allele : refSampleVC.getAlleles()) {

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java

@@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -231,7 +232,7 @@ public abstract class GeneralPloidyGenotypeLikelihoodsCalculationModel extends G
             ReadBackedPileup pileup = AlignmentContextUtils.stratify(sample.getValue(), contextType).getBasePileup();
             if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
                 // no likelihoods have been computed for this sample at this site
-                perReadAlleleLikelihoodMap.put(sample.getKey(), org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap());
+                perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
             }
 
             // create the GenotypeLikelihoods object

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java

@@ -119,7 +119,7 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
 
             if (!perReadAlleleLikelihoodMap.containsKey(sample.getKey())){
                 // no likelihoods have been computed for this sample at this site
-                perReadAlleleLikelihoodMap.put(sample.getKey(), PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap());
+                perReadAlleleLikelihoodMap.put(sample.getKey(), new PerReadAlleleLikelihoodMap());
             }
             final ReadBackedPileup pileup = context.getBasePileup();
             if (pileup != null) {

protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java

@@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
+import org.broadinstitute.sting.utils.genotyper.DiploidGenotype;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
@@ -55,7 +56,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
     protected SNPGenotypeLikelihoodsCalculationModel(UnifiedArgumentCollection UAC, Logger logger) {
         super(UAC, logger);
         useAlleleFromVCF = UAC.GenotypingMode == GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
-        perReadAlleleLikelihoodMap = PerReadAlleleLikelihoodMap.getBestAvailablePerReadAlleleLikelihoodMap();
+        perReadAlleleLikelihoodMap = new PerReadAlleleLikelihoodMap();
     }
 
     public VariantContext getLikelihoods(final RefMetaDataTracker tracker,

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

@@ -28,7 +28,6 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
-import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.downsampling.DownsampleType;
@@ -41,7 +40,6 @@ import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -230,25 +228,6 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
      **/
     public void initialize() {
 
-        // Check for protected modes
-        if (GATKLiteUtils.isGATKLite()) {
-            // no polyploid/pooled mode in GATK Like
-            if (UAC.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY ||
-                    UAC.referenceSampleName != null ||
-                    UAC.referenceSampleRod.isBound())  {
-                throw new UserException.NotSupportedInGATKLite("you cannot enable usage of ploidy values other than 2");
-            }
-
-            if ( UAC.CONTAMINATION_FRACTION > 0.0 ) {
-                if ( UAC.CONTAMINATION_FRACTION == StandardCallerArgumentCollection.DEFAULT_CONTAMINATION_FRACTION ) {
-                    UAC.CONTAMINATION_FRACTION = 0.0;
-                    logger.warn("setting contamination down-sampling fraction to 0.0 because it is not enabled in GATK-lite");
-                } else {
-                    throw new UserException.NotSupportedInGATKLite("you cannot enable usage of contamination down-sampling");
-                }
-            }
-        }
-
         if ( UAC.TREAT_ALL_READS_AS_SINGLE_POOL ) {
             samples.add(GenotypeLikelihoodsCalculationModel.DUMMY_SAMPLE_NAME);
         } else {