Total rewrite of the isGATKLite() functionality with help of Khalid/David. PluginManager was not working for us.

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

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.sting.gatk;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils;
 
 import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
 
-public class DummyProtectedWalker implements 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/bqsr/AdvancedRecalibrationEngine.java

@@ -31,7 +31,7 @@ import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
 
-public class AdvancedRecalibrationEngine extends RecalibrationEngine implements ProtectedPackageSource {
+public class AdvancedRecalibrationEngine extends StandardRecalibrationEngine implements ProtectedPackageSource {
 
     // optimizations: don't reallocate an array each time
     private byte[] tempQualArray;

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

@@ -51,7 +51,7 @@ import org.broadinstitute.sting.gatk.samples.SampleDBBuilder;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
-import org.broadinstitute.sting.utils.classloader.PluginManager;
+import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -199,20 +199,15 @@ public class GenomeAnalysisEngine {
     public BaseRecalibration getBaseRecalibration() { return baseRecalibration; }
     public boolean hasBaseRecalibration() { return baseRecalibration != null; }
     public void setBaseRecalibration(final File recalFile, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan) {
-        baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, disableIndelQuals, preserveQLessThan, isGATKLite());
+        baseRecalibration = new BaseRecalibration(recalFile, quantizationLevels, disableIndelQuals, preserveQLessThan);
     }
 
     /**
      * Utility method to determine whether this is the lite version of the GATK
      */
     public boolean isGATKLite() {
-        if ( isLiteVersion == null ) {
+        return JVMUtils.isGATKLite();
-            isLiteVersion = !(new PluginManager<Object>(Object.class).exists(DummyProtectedWalkerName));
-        }
-        return isLiteVersion;
     }
-    private static final String DummyProtectedWalkerName = "DummyProtectedWalker";
-    private static Boolean isLiteVersion = null;
 
     /**
      * Actually run the GATK with the specified walker.

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseQualityScoreRecalibrator.java

@@ -33,7 +33,6 @@ import org.broadinstitute.sting.gatk.filters.MappingQualityUnavailableFilter;
 import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
@@ -120,6 +119,8 @@ public class BaseQualityScoreRecalibrator extends LocusWalker<Long, Long> implem
 
     private RecalibrationEngine recalibrationEngine;
 
+    private int minimumQToUse;
+
     protected static final String SKIP_RECORD_ATTRIBUTE = "SKIP";                                                         // used to label reads that should be skipped.
     protected static final String SEEN_ATTRIBUTE = "SEEN";                                                                // used to label reads as processed.
     protected static final String COVARS_ATTRIBUTE = "COVARS";                                                            // used to store covariates array as a temporary attribute inside GATKSAMRecord.\
@@ -133,6 +134,10 @@ public class BaseQualityScoreRecalibrator extends LocusWalker<Long, Long> implem
      */
     public void initialize() {
 
+        // 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;
 
@@ -169,12 +174,14 @@ public class BaseQualityScoreRecalibrator extends LocusWalker<Long, Long> implem
 
         recalibrationEngine = initializeRecalibrationEngine();
         recalibrationEngine.initialize(requestedCovariates, recalibrationTables);
+
+        minimumQToUse = getToolkit().getArguments().PRESERVE_QSCORES_LESS_THAN;
     }
 
     private RecalibrationEngine initializeRecalibrationEngine() {
         List<Class<? extends RecalibrationEngine>> REclasses = new PluginManager<RecalibrationEngine>(RecalibrationEngine.class).getPlugins();
         if ( REclasses.isEmpty() )
-            throw new ReviewedStingException("There are no classes found that extend RecalibrationEngine; repository must be corrupted");
+            throw new ReviewedStingException("The RecalibrationEngine class is not found; repository must be corrupted");
 
         Class c = null;
         for ( Class<? extends RecalibrationEngine> REclass : REclasses ) {
@@ -201,7 +208,7 @@ public class BaseQualityScoreRecalibrator extends LocusWalker<Long, Long> implem
     }
 
     private boolean isLowQualityBase(GATKSAMRecord read, int offset) {
-        return read.getBaseQualities()[offset] < QualityUtils.MIN_USABLE_Q_SCORE;
+        return read.getBaseQualities()[offset] < minimumQToUse;
     }
 
     private boolean readNotSeen(GATKSAMRecord read) {

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java

@@ -1,110 +1,36 @@
 package org.broadinstitute.sting.gatk.walkers.bqsr;
 
-/*
- * 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.BaseUtils;
-import org.broadinstitute.sting.utils.classloader.PublicPackageSource;
-import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
-public class RecalibrationEngine implements PublicPackageSource {
+/*
+* 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.
+*/
+public interface RecalibrationEngine {
 
-    protected Covariate[] covariates;
+    public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables);
-    protected RecalibrationTables recalibrationTables;
 
-    public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables) {
+    public void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase);
-        this.covariates = covariates;
-        this.recalibrationTables = recalibrationTables;
-    }
 
-    /**
-     * Loop through the list of requested covariates and pick out the value from the read, offset, and reference
-     * Using the list of covariate values as a key, pick out the RecalDatum and increment,
-     * adding one to the number of observations and potentially one to the number of mismatches for mismatches only.
-     *
-     * @param pileupElement The pileup element to update
-     * @param refBase       The reference base at this locus
-     */
-    public synchronized void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) {
-        final int offset = pileupElement.getOffset();
-        final ReadCovariates readCovariates = covariateKeySetFrom(pileupElement.getRead());
-
-        final byte qual = pileupElement.getQual();
-        final boolean isError = !BaseUtils.basesAreEqual(pileupElement.getBase(), refBase);
-
-        final int[] keys = readCovariates.getKeySet(offset, EventType.BASE_SUBSTITUTION);
-        final int eventIndex = EventType.BASE_SUBSTITUTION.index;
-
-        final NestedIntegerArray<RecalDatum> rgRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE);
-        final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex);
-        final RecalDatum rgThisDatum = createDatumObject(qual, isError);
-        if (rgPreviousDatum == null)                                                                                // key doesn't exist yet in the map so make a new bucket and add it
-            rgRecalTable.put(rgThisDatum, keys[0], eventIndex);
-        else
-            rgPreviousDatum.combine(rgThisDatum);
-
-        final NestedIntegerArray<RecalDatum> qualRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE);
-        final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex);
-        if (qualPreviousDatum == null)
-            qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex);
-        else
-            qualPreviousDatum.increment(isError);
-
-        for (int i = 2; i < covariates.length; i++) {
-            if (keys[i] < 0)
-                continue;
-            final NestedIntegerArray<RecalDatum> covRecalTable = recalibrationTables.getTable(i);
-            final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex);
-            if (covPreviousDatum == null)
-                covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex);
-            else
-                covPreviousDatum.increment(isError);
-        }
-    }
-
-    /**
-     * creates a datum object with one observation and one or zero error
-     *
-     * @param reportedQual  the quality score reported by the instrument for this base
-     * @param isError       whether or not the observation is an error
-     * @return a new RecalDatum object with the observation and the error
-     */
-    protected RecalDatum createDatumObject(final byte reportedQual, final boolean isError) {
-        return new RecalDatum(1, isError ? 1:0, reportedQual);
-    }
-
-    /**
-     * Get the covariate key set from a read
-     *
-     * @param read the read
-     * @return the covariate keysets for this read
-     */
-    protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) {
-        return (ReadCovariates) read.getTemporaryAttribute(BaseQualityScoreRecalibrator.COVARS_ATTRIBUTE);
-    }
 }

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/StandardRecalibrationEngine.java

@@ -0,0 +1,110 @@
+package org.broadinstitute.sting.gatk.walkers.bqsr;
+
+/*
+ * 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.BaseUtils;
+import org.broadinstitute.sting.utils.classloader.PublicPackageSource;
+import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.recalibration.RecalibrationTables;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+public class StandardRecalibrationEngine implements RecalibrationEngine, PublicPackageSource {
+
+    protected Covariate[] covariates;
+    protected RecalibrationTables recalibrationTables;
+
+    public void initialize(final Covariate[] covariates, final RecalibrationTables recalibrationTables) {
+        this.covariates = covariates;
+        this.recalibrationTables = recalibrationTables;
+    }
+
+    /**
+     * Loop through the list of requested covariates and pick out the value from the read, offset, and reference
+     * Using the list of covariate values as a key, pick out the RecalDatum and increment,
+     * adding one to the number of observations and potentially one to the number of mismatches for mismatches only.
+     *
+     * @param pileupElement The pileup element to update
+     * @param refBase       The reference base at this locus
+     */
+    public synchronized void updateDataForPileupElement(final PileupElement pileupElement, final byte refBase) {
+        final int offset = pileupElement.getOffset();
+        final ReadCovariates readCovariates = covariateKeySetFrom(pileupElement.getRead());
+
+        final byte qual = pileupElement.getQual();
+        final boolean isError = !BaseUtils.basesAreEqual(pileupElement.getBase(), refBase);
+
+        final int[] keys = readCovariates.getKeySet(offset, EventType.BASE_SUBSTITUTION);
+        final int eventIndex = EventType.BASE_SUBSTITUTION.index;
+
+        final NestedIntegerArray<RecalDatum> rgRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.READ_GROUP_TABLE);
+        final RecalDatum rgPreviousDatum = rgRecalTable.get(keys[0], eventIndex);
+        final RecalDatum rgThisDatum = createDatumObject(qual, isError);
+        if (rgPreviousDatum == null)                                                                                // key doesn't exist yet in the map so make a new bucket and add it
+            rgRecalTable.put(rgThisDatum, keys[0], eventIndex);
+        else
+            rgPreviousDatum.combine(rgThisDatum);
+
+        final NestedIntegerArray<RecalDatum> qualRecalTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE);
+        final RecalDatum qualPreviousDatum = qualRecalTable.get(keys[0], keys[1], eventIndex);
+        if (qualPreviousDatum == null)
+            qualRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], eventIndex);
+        else
+            qualPreviousDatum.increment(isError);
+
+        for (int i = 2; i < covariates.length; i++) {
+            if (keys[i] < 0)
+                continue;
+            final NestedIntegerArray<RecalDatum> covRecalTable = recalibrationTables.getTable(i);
+            final RecalDatum covPreviousDatum = covRecalTable.get(keys[0], keys[1], keys[i], eventIndex);
+            if (covPreviousDatum == null)
+                covRecalTable.put(createDatumObject(qual, isError), keys[0], keys[1], keys[i], eventIndex);
+            else
+                covPreviousDatum.increment(isError);
+        }
+    }
+
+    /**
+     * creates a datum object with one observation and one or zero error
+     *
+     * @param reportedQual  the quality score reported by the instrument for this base
+     * @param isError       whether or not the observation is an error
+     * @return a new RecalDatum object with the observation and the error
+     */
+    protected RecalDatum createDatumObject(final byte reportedQual, final boolean isError) {
+        return new RecalDatum(1, isError ? 1:0, reportedQual);
+    }
+
+    /**
+     * Get the covariate key set from a read
+     *
+     * @param read the read
+     * @return the covariate keysets for this read
+     */
+    protected ReadCovariates covariateKeySetFrom(GATKSAMRecord read) {
+        return (ReadCovariates) read.getTemporaryAttribute(BaseQualityScoreRecalibrator.COVARS_ATTRIBUTE);
+    }
+}

public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java

@@ -105,6 +105,23 @@ public class JVMUtils {
         return allFields;
     }
 
+    /**
+     * Utility method to determine whether this is the lite version of the GATK
+     */
+    public static boolean isGATKLite() {
+        if ( isLiteVersion == null ) {
+            try {
+                Class.forName(DummyProtectedClassName);
+                isLiteVersion = false;
+            } catch ( ClassNotFoundException e) {
+                isLiteVersion = true;
+            }
+        }
+        return isLiteVersion;
+    }
+    private static final String DummyProtectedClassName = "org.broadinstitute.sting.gatk.DummyProtectedClass";
+    private static Boolean isLiteVersion = null;
+
     /**
      * Find the field with the given name in the class.  Will inspect all fields, independent
      * of access level.

public/java/src/org/broadinstitute/sting/utils/recalibration/BaseRecalibration.java

@@ -30,7 +30,6 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.collections.NestedIntegerArray;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.File;
@@ -66,13 +65,8 @@ public class BaseRecalibration {
      * @param quantizationLevels number of bins to quantize the quality scores
      * @param disableIndelQuals  if true, do not emit base indel qualities
      * @param preserveQLessThan  preserve quality scores less than this value
-     * @param isGATKLite         is this being called from the full or Lite version of the GATK
      */
-    public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan, final boolean isGATKLite) {
+    public BaseRecalibration(final File RECAL_FILE, final int quantizationLevels, final boolean disableIndelQuals, final int preserveQLessThan) {
-        // check for unsupported access
-        if (isGATKLite && !disableIndelQuals)
-            throw new UserException.NotSupportedInGATKLite("base insertion/deletion recalibration is not supported, please use the --disable_indel_quals argument");
-
         RecalibrationReport recalibrationReport = new RecalibrationReport(RECAL_FILE);
 
         recalibrationTables = recalibrationReport.getRecalibrationTables();