Removed cases where various toolkit functions were accessing GenomeAnalysisEngine.instance.

This will allow other programs like Queue to reuse the functionality.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4351 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/AbstractGenomeAnalysisEngine.java

@@ -30,9 +30,6 @@ import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.*;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.commandline.ArgumentSource;
-import org.broadinstitute.sting.gatk.DownsamplingMethod;
-import org.broadinstitute.sting.gatk.ReadMetrics;
-import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.datasources.sample.Sample;
@@ -43,6 +40,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadGroupBlackListFilter;
+import org.broadinstitute.sting.gatk.filters.SamRecordHeaderFilter;
 import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
@@ -203,7 +201,8 @@ public abstract class AbstractGenomeAnalysisEngine {
                                              List<GenomeLoc> additionalIntervals) {
 
         return IntervalUtils.sortAndMergeIntervals(IntervalUtils.mergeListsBySetOperator(additionalIntervals,
-                                                                                         IntervalUtils.parseIntervalArguments(argList),
+                                                                                         IntervalUtils.parseIntervalArguments(argList,
+                                                                                                 this.getArguments().unsafe != ValidationExclusion.TYPE.ALLOW_EMPTY_INTERVAL_LIST),
                                                                                          argCollection.BTIMergeRule),
                                                    mergingRule);
     }
@@ -278,7 +277,7 @@ public abstract class AbstractGenomeAnalysisEngine {
      * the caller must handle that directly.
      * @return A collection of available filters.
      */
-    protected Collection<SamRecordFilter> createFilters() {
+    public Collection<SamRecordFilter> createFilters() {
         Set<SamRecordFilter> filters = new HashSet<SamRecordFilter>();
         if (this.getArguments().readGroupBlackList != null && this.getArguments().readGroupBlackList.size() > 0)
             filters.add(new ReadGroupBlackListFilter(this.getArguments().readGroupBlackList));
@@ -291,7 +290,11 @@ public abstract class AbstractGenomeAnalysisEngine {
         logger.info("Strictness is " + argCollection.strictnessLevel);
 
         validateSuppliedReads();
-        readsDataSource = createReadsDataSource(extractSourceInfo());
+        readsDataSource = createReadsDataSource();
+
+        for (SamRecordFilter filter : filters)
+            if (filter instanceof SamRecordHeaderFilter)
+                ((SamRecordHeaderFilter)filter).setHeader(this.getSAMFileHeader());
         
         validateSuppliedReference();
         referenceDataSource = openReferenceSequenceFile(argCollection.referenceFile);
@@ -456,25 +459,6 @@ public abstract class AbstractGenomeAnalysisEngine {
 
     }
 
-    /**
-     * Bundles all the source information about the reads into a unified data structure.
-     *
-     * @return The reads object providing reads source info.
-     */
-    private ReadProperties extractSourceInfo() {
-
-        DownsamplingMethod method = getDownsamplingMethod();
-
-        return new ReadProperties(unpackBAMFileList(argCollection.samFiles),
-                argCollection.strictnessLevel,
-                argCollection.readBufferSize,
-                method,
-                new ValidationExclusion(Arrays.asList(argCollection.unsafe)),
-                filters,
-                includeReadsWithDeletionAtLoci(),
-                generateExtendedEvents());
-    }
-
     protected DownsamplingMethod getDownsamplingMethod() {
         DownsamplingMethod method;
         if(argCollection.getDownsamplingMethod() != null)
@@ -522,7 +506,7 @@ public abstract class AbstractGenomeAnalysisEngine {
             }
 
             // compare the reads to the reference
-            SequenceDictionaryUtils.validateDictionaries(logger, "reads", readsDictionary, "reference", referenceDictionary);
+            SequenceDictionaryUtils.validateDictionaries(logger, getArguments().unsafe, "reads", readsDictionary, "reference", referenceDictionary);
         }
 
         // compare the tracks to the reference, if they have a sequence dictionary
@@ -538,7 +522,7 @@ public abstract class AbstractGenomeAnalysisEngine {
             Set<String> trackSequences = new TreeSet<String>();
             for (SAMSequenceRecord dictionaryEntry : trackDict.getSequences())
                 trackSequences.add(dictionaryEntry.getSequenceName());
-            SequenceDictionaryUtils.validateDictionaries(logger, track.getName(), trackDict, "reference", referenceDictionary);
+            SequenceDictionaryUtils.validateDictionaries(logger, getArguments().unsafe, track.getName(), trackDict, "reference", referenceDictionary);
         }
 
     }
@@ -559,11 +543,21 @@ public abstract class AbstractGenomeAnalysisEngine {
     /**
      * Gets a data source for the given set of reads.
      *
-     * @param reads the read source information
      * @return A data source for the given set of reads.
      */
-    private SAMDataSource createReadsDataSource(ReadProperties reads) {
+    private SAMDataSource createReadsDataSource() {
-        return new SAMDataSource(reads);
+        DownsamplingMethod method = getDownsamplingMethod();
+
+        return new SAMDataSource(
+                unpackBAMFileList(argCollection.samFiles),
+                argCollection.useOriginalBaseQualities,
+                argCollection.strictnessLevel,
+                argCollection.readBufferSize,
+                method,
+                new ValidationExclusion(Arrays.asList(argCollection.unsafe)),
+                filters,
+                includeReadsWithDeletionAtLoci(),
+                generateExtendedEvents());
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java

@@ -76,6 +76,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
         try {
             engine.setArguments(getArgumentCollection());
             engine.setWalker(walker);
+            walker.setToolkit(engine);
 
             Collection<SamRecordFilter> filters = engine.createFilters();
             engine.setFilters(filters);
@@ -165,6 +166,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
         Walker walker = engine.getWalkerByName(getAnalysisName());
         engine.setArguments(getArgumentCollection());
         engine.setWalker(walker);
+        walker.setToolkit(engine);
         argumentSources.add(walker.getClass());
 
         Collection<SamRecordFilter> filters = engine.createFilters();

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

@@ -56,30 +56,13 @@ import java.util.*;
  * A GenomeAnalysisEngine that runs a specified walker.
  */
 public class GenomeAnalysisEngine extends AbstractGenomeAnalysisEngine {
-
-    // our instance of this genome analysis toolkit; it's used by other classes to extract the traversal engine
-    // TODO: public static without final tends to indicate we're thinking about this the wrong way
-    public static GenomeAnalysisEngine instance;
-
     /**
      * our walker manager
      */
-    private final WalkerManager walkerManager = new WalkerManager();;
+    private final WalkerManager walkerManager = new WalkerManager();
-
 
     private Walker<?, ?> walker;
 
-    /**
-     * our constructor, where all the work is done
-     * <p/>
-     * legacy traversal types are sent to legacyTraversal function; as we move more of the traversals to the
-     * new MicroScheduler class we'll be able to delete that function.
-     */
-    public GenomeAnalysisEngine() {
-        // make sure our instance variable points to this analysis engine
-        instance = this;
-    }
-
     public void setWalker(Walker<?, ?> walker) {
         this.walker = walker;
     }
@@ -150,7 +133,7 @@ public class GenomeAnalysisEngine extends AbstractGenomeAnalysisEngine {
      * @return A collection of available filters.
      */
     @Override
-    protected Collection<SamRecordFilter> createFilters() {
+    public Collection<SamRecordFilter> createFilters() {
         Set<SamRecordFilter> filters = new HashSet<SamRecordFilter>();
         filters.addAll(WalkerManager.getReadFilters(walker,this.getFilterManager()));
         filters.addAll(super.createFilters());
@@ -383,6 +366,6 @@ public class GenomeAnalysisEngine extends AbstractGenomeAnalysisEngine {
         for (Stub<?> stub : getOutputs())
             outputTracker.addOutput(stub);
 
-        outputTracker.prepareWalker(walker);
+        outputTracker.prepareWalker(walker, getArguments().strictnessLevel);
     }
 }

java/src/org/broadinstitute/sting/gatk/ReadProperties.java

@@ -1,11 +1,11 @@
 package org.broadinstitute.sting.gatk;
 
 import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Collection;
 /**
@@ -27,12 +27,14 @@ import java.util.Collection;
  */
 public class ReadProperties {
     private List<SAMReaderID> readers = null;
+    private SAMFileHeader header = null;
     private SAMFileReader.ValidationStringency validationStringency = SAMFileReader.ValidationStringency.STRICT;
     private Integer readBufferSize = null;
     private DownsamplingMethod downsamplingMethod = null;
     private ValidationExclusion exclusionList = null;
     private Collection<SamRecordFilter> supplementalFilters = null;
     private boolean includeReadsWithDeletionAtLoci = false;
+    private boolean useOriginalBaseQualities = false;
     private boolean generateExtendedEvents = false; // do we want to generate additional piles of "extended" events (indels)
 // immediately after the reference base such event is associated with?
 
@@ -66,6 +68,14 @@ public class ReadProperties {
         return readers;
     }
 
+    /**
+     * Gets the sam file header
+     * @return the sam file header
+     */
+    public SAMFileHeader getHeader() {
+        return header;
+    }
+
     /**
      * How strict should validation be?
      * @return Stringency of validation.
@@ -103,14 +113,11 @@ public class ReadProperties {
     }
 
     /**
-     * Simple constructor for unit testing.
+     * Return whether to use original base qualities.
-     * @param readsFiles List of reads files to open.
+     * @return Whether to use original base qualities.
      */
-    public ReadProperties( List<SAMReaderID> readsFiles ) {
+    public boolean useOriginalBaseQualities() {
-        this.readers = readsFiles;
+        return useOriginalBaseQualities;
-        this.downsamplingMethod = DownsamplingMethod.NONE;
-        this.supplementalFilters = new ArrayList<SamRecordFilter>();
-        this.exclusionList = new ValidationExclusion();
     }
 
     /**
@@ -118,6 +125,8 @@ public class ReadProperties {
      * files and store them in an easy-to-work-with package.  Constructor
      * is package protected.
      * @param samFiles list of reads files.
+     * @param header sam file header.
+     * @param useOriginalBaseQualities True if original base qualities should be used.
      * @param strictness Stringency of reads file parsing.
      * @param readBufferSize Number of reads to hold in memory per BAM.
      * @param downsamplingMethod Method for downsampling reads at a given locus.
@@ -131,6 +140,8 @@ public class ReadProperties {
      *        bases will be seen in the pileups, and the deletions will be skipped silently.
      */
     public ReadProperties( List<SAMReaderID> samFiles,
+           SAMFileHeader header,
+           boolean useOriginalBaseQualities,
            SAMFileReader.ValidationStringency strictness,
            Integer readBufferSize,
            DownsamplingMethod downsamplingMethod,
@@ -139,12 +150,14 @@ public class ReadProperties {
            boolean includeReadsWithDeletionAtLoci,
            boolean generateExtendedEvents) {
         this.readers = samFiles;
+        this.header = header;
         this.readBufferSize = readBufferSize;
         this.validationStringency = strictness;
-        this.downsamplingMethod = downsamplingMethod;
+        this.downsamplingMethod = downsamplingMethod == null ? DownsamplingMethod.NONE : downsamplingMethod;
         this.exclusionList = exclusionList == null ? new ValidationExclusion() : exclusionList;
         this.supplementalFilters = supplementalFilters;
         this.includeReadsWithDeletionAtLoci = includeReadsWithDeletionAtLoci;
         this.generateExtendedEvents = generateExtendedEvents;
+        this.useOriginalBaseQualities = useOriginalBaseQualities;
     }
 }

java/src/org/broadinstitute/sting/gatk/datasources/sample/SampleDataSource.java

@@ -37,6 +37,11 @@ import java.util.Collection;
  */
 public class SampleDataSource {
 
+    /**
+     * SAMFileHeader that has been created for this analysis.
+     */
+    private final SAMFileHeader header;
+
     /**
      * This is where Sample objects are stored. Samples are usually accessed by their ID, which is unique, so
      * this is stored as a HashMap.
@@ -63,7 +68,7 @@ public class SampleDataSource {
      * @param sampleFiles Sample files that were included on the command line
      */
     public SampleDataSource(SAMFileHeader header, List<File> sampleFiles) {
-
+        this.header = header;
         // create empty sample object for each sample referenced in the SAM header
         for (String sampleName : SampleUtils.getSAMFileSamples(header)) {
             if (!hasSample(sampleName)) {
@@ -85,7 +90,7 @@ public class SampleDataSource {
      * Hallucinates sample objects for all the samples in the SAM file and stores them
      */
     private void getSamplesFromSAMFile() {
-        for (String sampleName : SampleUtils.getSAMFileSamples(GenomeAnalysisEngine.instance.getSAMFileHeader())) {
+        for (String sampleName : SampleUtils.getSAMFileSamples(header)) {
             if (!hasSample(sampleName)) {
                 Sample newSample = new Sample(sampleName);
                 newSample.setSAMFileEntry(true);

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java

@@ -32,6 +32,7 @@ import net.sf.picard.sam.SamFileHeaderMerger;
 import net.sf.picard.sam.MergingSamRecordIterator;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.DownsamplingMethod;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.shards.BAMFormatAwareShard;
 import org.broadinstitute.sting.gatk.datasources.shards.MonolithicShard;
@@ -68,6 +69,11 @@ public class SAMDataSource implements SimpleDataSource {
      */
     protected final List<SAMReaderID> readerIDs;
 
+    /**
+     * How strict are the readers driving this data source.
+     */
+    protected final SAMFileReader.ValidationStringency validationStringency;
+
     /**
      * How far along is each reader?
      */
@@ -104,14 +110,54 @@ public class SAMDataSource implements SimpleDataSource {
 
     /**
      * Create a new SAM data source given the supplied read metadata.
-     * @param reads The read metadata.
+     * @param samFiles list of reads files.
      */
-    public SAMDataSource(ReadProperties reads) {
+    public SAMDataSource(List<SAMReaderID> samFiles) {
-        this.readProperties = reads;
+        this(
+                samFiles,
+                false,
+                SAMFileReader.ValidationStringency.STRICT,
+                null,
+                null,
+                new ValidationExclusion(),
+                new ArrayList<SamRecordFilter>(),
+                false,
+                false
+        );
+    }
+
+    /**
+     * Create a new SAM data source given the supplied read metadata.
+     * @param samFiles list of reads files.
+     * @param useOriginalBaseQualities True if original base qualities should be used.
+     * @param strictness Stringency of reads file parsing.
+     * @param readBufferSize Number of reads to hold in memory per BAM.
+     * @param downsamplingMethod Method for downsampling reads at a given locus.
+     * @param exclusionList what safety checks we're willing to let slide
+     * @param supplementalFilters additional filters to dynamically apply.
+     * @param generateExtendedEvents if true, the engine will issue an extra call to walker's map() with
+     *        a pile of indel/noevent extended events at every locus with at least one indel associated with it
+     *        (in addition to a "regular" call to map() at this locus performed with base pileup)
+     * @param includeReadsWithDeletionAtLoci if 'true', the base pileups sent to the walker's map() method
+     *         will explicitly list reads with deletion over the current reference base; otherwise, only observed
+     *        bases will be seen in the pileups, and the deletions will be skipped silently.
+     */
+    public SAMDataSource(
+            List<SAMReaderID> samFiles,
+            boolean useOriginalBaseQualities,
+            SAMFileReader.ValidationStringency strictness,
+            Integer readBufferSize,
+            DownsamplingMethod downsamplingMethod,
+            ValidationExclusion exclusionList,
+            Collection<SamRecordFilter> supplementalFilters,
+            boolean includeReadsWithDeletionAtLoci,
+            boolean generateExtendedEvents
+    ) {
         this.readMetrics = new ReadMetrics();
 
-        readerIDs = reads.getSAMReaderIDs();
+        readerIDs = samFiles;
-        for (SAMReaderID readerID : reads.getSAMReaderIDs()) {
+        validationStringency = strictness;
+        for (SAMReaderID readerID : samFiles) {
             if (!readerID.samFile.canRead())
                 throw new UserException.CouldNotReadInputFile(readerID.samFile,"file is not present or user does not have appropriate permissions.  " +
                                                                                "Please check that the file is present and readable and try again.");
@@ -136,10 +182,23 @@ public class SAMDataSource implements SimpleDataSource {
 
         initializeReaderPositions(readers);
 
-        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers.values(),SAMFileHeader.SortOrder.coordinate,true);
+        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,readers.headers(),true);
         mergedHeader = headerMerger.getMergedHeader();
         hasReadGroupCollisions = headerMerger.hasReadGroupCollisions();
 
+        readProperties = new ReadProperties(
+                samFiles,
+                mergedHeader,
+                useOriginalBaseQualities,
+                strictness,
+                readBufferSize,
+                downsamplingMethod,
+                exclusionList,
+                supplementalFilters,
+                includeReadsWithDeletionAtLoci,
+                generateExtendedEvents
+        );
+        
         // cache the read group id (original) -> read group id (merged) mapping.
         for(SAMReaderID id: readerIDs) {
             SAMFileReader reader = readers.getReader(id);
@@ -371,10 +430,10 @@ public class SAMDataSource implements SimpleDataSource {
      * @return An iterator over the selected data.
      */
     private StingSAMIterator getIterator(SAMReaders readers, BAMFormatAwareShard shard, boolean enableVerification) {
-        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers.values(),SAMFileHeader.SortOrder.coordinate,true);
+        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,readers.headers(),true);
 
         // Set up merging to dynamically merge together multiple BAMs.
-        MergingSamRecordIterator mergingIterator = new MergingSamRecordIterator(headerMerger,true);
+        MergingSamRecordIterator mergingIterator = new MergingSamRecordIterator(headerMerger,readers.values(),true);
         for(SAMReaderID id: getReaderIDs()) {
             if(shard.getFileSpans().get(id) == null)
                 continue;
@@ -388,6 +447,7 @@ public class SAMDataSource implements SimpleDataSource {
 
         return applyDecoratingIterators(shard.getReadMetrics(),
                 enableVerification,
+                readProperties.useOriginalBaseQualities(),
                 new ReleasingIterator(readers,StingSAMIteratorAdapter.adapt(mergingIterator)),
                 readProperties.getDownsamplingMethod().toFraction,
                 readProperties.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION),
@@ -403,13 +463,14 @@ public class SAMDataSource implements SimpleDataSource {
         SAMReaders readers = resourcePool.getAvailableReaders();
 
         // Set up merging and filtering to dynamically merge together multiple BAMs and filter out records not in the shard set.
-        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(readers.values(),SAMFileHeader.SortOrder.coordinate,true);
+        SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate,readers.headers(),true);
-        MergingSamRecordIterator mergingIterator = new MergingSamRecordIterator(headerMerger,true);
+        MergingSamRecordIterator mergingIterator = new MergingSamRecordIterator(headerMerger,readers.values(),true);
         for(SAMReaderID id: getReaderIDs())
             mergingIterator.addIterator(readers.getReader(id),readers.getReader(id).iterator());
 
         return applyDecoratingIterators(shard.getReadMetrics(),
                 shard instanceof ReadShard,
+                readProperties.useOriginalBaseQualities(),
                 new ReleasingIterator(readers,StingSAMIteratorAdapter.adapt(mergingIterator)),
                 readProperties.getDownsamplingMethod().toFraction,
                 readProperties.getValidationExclusionList().contains(ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION),
@@ -433,6 +494,7 @@ public class SAMDataSource implements SimpleDataSource {
      *
      * @param readMetrics metrics to track when using this iterator.
      * @param enableVerification Verify the order of reads.
+     * @param useOriginalBaseQualities True if original base qualities should be used.
      * @param wrappedIterator the raw data source.
      * @param downsamplingFraction whether and how much to downsample the reads themselves (not at a locus).
      * @param noValidationOfReadOrder Another trigger for the verifying iterator?  TODO: look into this.
@@ -441,11 +503,12 @@ public class SAMDataSource implements SimpleDataSource {
      */
     protected StingSAMIterator applyDecoratingIterators(ReadMetrics readMetrics,
                                                         boolean enableVerification,
+                                                        boolean useOriginalBaseQualities,
                                                         StingSAMIterator wrappedIterator,
                                                         Double downsamplingFraction,
                                                         Boolean noValidationOfReadOrder,
                                                         Collection<SamRecordFilter> supplementalFilters) {
-        wrappedIterator = new ReadFormattingIterator(wrappedIterator);
+        wrappedIterator = new ReadFormattingIterator(wrappedIterator, useOriginalBaseQualities);
 
         // NOTE: this (and other filtering) should be done before on-the-fly sorting
         //  as there is no reason to sort something that we will end of throwing away
@@ -530,7 +593,7 @@ public class SAMDataSource implements SimpleDataSource {
         private synchronized void createNewResource() {
             if(allResources.size() > maxEntries)
                 throw new ReviewedStingException("Cannot create a new resource pool.  All resources are in use.");
-            SAMReaders readers = new SAMReaders(readProperties);
+            SAMReaders readers = new SAMReaders(readerIDs, validationStringency);
             allResources.add(readers);
             availableResources.add(readers);
         }
@@ -548,14 +611,15 @@ public class SAMDataSource implements SimpleDataSource {
 
         /**
          * Derive a new set of readers from the Reads metadata.
-         * @param sourceInfo Metadata for the reads to load.
+         * @param readerIDs reads to load.
+         * @param validationStringency validation stringency.
          */
-        public SAMReaders(ReadProperties sourceInfo) {
+        public SAMReaders(Collection<SAMReaderID> readerIDs, SAMFileReader.ValidationStringency validationStringency) {
-            for(SAMReaderID readerID: sourceInfo.getSAMReaderIDs()) {
+            for(SAMReaderID readerID: readerIDs) {
                 SAMFileReader reader = new SAMFileReader(readerID.samFile);
                 reader.enableFileSource(true);
                 reader.enableIndexCaching(true);
-                reader.setValidationStringency(sourceInfo.getValidationStringency());
+                reader.setValidationStringency(validationStringency);
 
                 // If no read group is present, hallucinate one.
                 // TODO: Straw poll to see whether this is really required.
@@ -614,6 +678,17 @@ public class SAMDataSource implements SimpleDataSource {
         public Collection<SAMFileReader> values() {
             return readers.values();
         }
+
+        /**
+         * Gets all the actual readers out of this data structure.
+         * @return A collection of the readers.
+         */
+        public Collection<SAMFileHeader> headers() {
+            ArrayList<SAMFileHeader> headers = new ArrayList<SAMFileHeader>(readers.size());
+            for (SAMFileReader reader : values())
+                headers.add(reader.getFileHeader());
+            return headers;
+        }
     }
 
     private class ReleasingIterator implements StingSAMIterator {

java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

@@ -122,7 +122,7 @@ public abstract class MicroScheduler {
             throw new UnsupportedOperationException("Unable to determine traversal type, the walker is an unknown type.");
         }        
 
-        traversalEngine.initialize();                
+        traversalEngine.initialize(engine);
     }
 
     /**
@@ -147,7 +147,7 @@ public abstract class MicroScheduler {
      * @return an iterator over the reads specified in the shard.
      */
     protected StingSAMIterator getReadIterator(Shard shard) {
-        return (!reads.isEmpty()) ? reads.seek(shard) : new NullSAMIterator(new ReadProperties(Collections.<SAMReaderID>emptyList()));
+        return (!reads.isEmpty()) ? reads.seek(shard) : new NullSAMIterator();
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java

@@ -36,11 +36,18 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
  * @author mhanna
  * @version 0.1
  */
-public class MalformedReadFilter implements SamRecordFilter {
+public class MalformedReadFilter implements SamRecordHeaderFilter {
+    private SAMFileHeader header;
+    
+    @Override
+    public void setHeader(SAMFileHeader header) {
+        this.header = header;
+    }
+
     public boolean filterOut(SAMRecord read) {
         return !checkInvalidAlignmentStart(read) ||
                 !checkInvalidAlignmentEnd(read) ||
-                !checkAlignmentDisagreesWithHeader(GenomeAnalysisEngine.instance.getSAMFileHeader(),read) ||
+                !checkAlignmentDisagreesWithHeader(this.header,read) ||
                 !checkCigarDisagreesWithAlignment(read);
     }
 

java/src/org/broadinstitute/sting/gatk/filters/SamRecordHeaderFilter.java

@@ -0,0 +1,15 @@
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMFileHeader;
+
+/**
+ * A SamRecordFilter that also depends on the header.
+ */
+public interface SamRecordHeaderFilter extends SamRecordFilter {
+    /**
+     * Sets the header for use by this filter.
+     * @param header the header for use by this filter.
+     */
+    void setHeader(SAMFileHeader header);
+}

java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java

@@ -25,12 +25,12 @@
 
 package org.broadinstitute.sting.gatk.io;
 
+import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.commandline.ArgumentSource;
 import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.io.storage.StorageFactory;
@@ -74,7 +74,7 @@ public abstract class OutputTracker {
      */
     public abstract <T> T getStorage( Stub<T> stub );
 
-    public void prepareWalker( Walker walker ) {
+    public void prepareWalker( Walker walker, SAMFileReader.ValidationStringency strictnessLevel ) {
         for( Map.Entry<ArgumentSource,Object> io: inputs.entrySet() ) {
             ArgumentSource targetField = io.getKey();
             Object targetValue = io.getValue();
@@ -83,7 +83,7 @@ public abstract class OutputTracker {
             // TODO: Generalize this, and move it to its own initialization step.
             if( targetValue instanceof SAMFileReaderBuilder) {
                 SAMFileReaderBuilder builder = (SAMFileReaderBuilder)targetValue;
-                builder.setValidationStringency(GenomeAnalysisEngine.instance.getArguments().strictnessLevel);
+                builder.setValidationStringency(strictnessLevel);
                 targetValue = builder.build();
             }
 

java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java

@@ -273,16 +273,13 @@ public class LocusIteratorByState extends LocusIterator {
     }
     
     public LocusIteratorByState(final Iterator<SAMRecord> samIterator, ReadProperties readInformation, List<LocusIteratorFilter> filters ) {
+        this.readInfo = readInformation;
+        this.filters = filters;
         // Aggregate all sample names.
-        // TODO: Push in header via constructor
+        sampleNames.addAll(SampleUtils.getSAMFileSamples(readInfo.getHeader()));
-        if(GenomeAnalysisEngine.instance != null && GenomeAnalysisEngine.instance.getDataSource() != null) {
-            sampleNames.addAll(SampleUtils.getSAMFileSamples(GenomeAnalysisEngine.instance.getSAMFileHeader()));
-        }
         // Add a null sample name as a catch-all for reads without samples
         if(!sampleNames.contains(null)) sampleNames.add(null);        
         readStates = new ReadStateManager(samIterator,readInformation.getDownsamplingMethod(),sampleNames);
-        this.readInfo = readInformation;
-        this.filters = filters;
     }
 
     public Iterator<AlignmentContext> iterator() {

java/src/org/broadinstitute/sting/gatk/iterators/NullSAMIterator.java

@@ -22,9 +22,7 @@ import java.util.NoSuchElementException;
  * A placeholder for an iterator with no data.
  */
 public class NullSAMIterator implements StingSAMIterator {
-    private ReadProperties reads = null;
+    public NullSAMIterator() {}
-
-    public NullSAMIterator( ReadProperties reads ) { this.reads = reads; }
 
     public Iterator<SAMRecord> iterator() { return this; }
     public void close() { /* NO-OP */ }

java/src/org/broadinstitute/sting/gatk/iterators/ReadFormattingIterator.java

@@ -27,12 +27,19 @@ public class ReadFormattingIterator implements StingSAMIterator {
      */
     private StingSAMIterator wrappedIterator;
 
+    /**
+     * True if original base qualities should be used.
+     */
+    private final boolean useOriginalBaseQualities;
+
     /**
      * Decorate the given iterator inside a ReadWrappingIterator.
      * @param wrappedIterator iterator
+     * @param useOriginalBaseQualities true if original base qualities should be used
      */
-    public ReadFormattingIterator(StingSAMIterator wrappedIterator) {
+    public ReadFormattingIterator(StingSAMIterator wrappedIterator, boolean useOriginalBaseQualities) {
         this.wrappedIterator = wrappedIterator;
+        this.useOriginalBaseQualities = useOriginalBaseQualities;
     }
 
     /**
@@ -67,7 +74,7 @@ public class ReadFormattingIterator implements StingSAMIterator {
      *         no next exists.
      */
     public SAMRecord next() {
-        return new GATKSAMRecord(wrappedIterator.next());
+        return new GATKSAMRecord(wrappedIterator.next(), useOriginalBaseQualities);
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java

@@ -24,6 +24,8 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
     /** our log, which we want to capture anything from this class */
     protected static Logger logger = Logger.getLogger(TraversalEngine.class);
 
+    private GenomeAnalysisEngine engine;
+
     /**
      * Gets the named traversal type associated with the given traversal.
      * @return A user-friendly name for the given traversal type.
@@ -48,7 +50,7 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
     public void printProgress(Shard shard,GenomeLoc loc) {
         // A bypass is inserted here for unit testing.
         // TODO: print metrics outside of the traversal engine to more easily handle cumulative stats.
-        ReadMetrics cumulativeMetrics = GenomeAnalysisEngine.instance != null ? GenomeAnalysisEngine.instance.getCumulativeMetrics().clone() : new ReadMetrics();
+        ReadMetrics cumulativeMetrics = engine != null ? engine.getCumulativeMetrics().clone() : new ReadMetrics();
         cumulativeMetrics.incrementMetrics(shard.getReadMetrics());
         printProgress(loc, cumulativeMetrics, false);
     }
@@ -103,8 +105,12 @@ public abstract class TraversalEngine<M,T,WalkerType extends Walker<M,T>,Provide
         }
     }
 
-    /** Initialize the traversal engine.  After this point traversals can be run over the data */
+    /**
-    public void initialize() {
+     * Initialize the traversal engine.  After this point traversals can be run over the data
+     * @param engine GenomeAnalysisEngine for this traversal
+     */
+    public void initialize(GenomeAnalysisEngine engine) {
+        this.engine = engine;
         lastProgressPrintTime = startTime = System.currentTimeMillis();
     }
 

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

@@ -43,10 +43,20 @@ import org.apache.log4j.Logger;
 @ReadFilters(MalformedReadFilter.class)
 public abstract class Walker<MapType, ReduceType> {
     final protected static Logger logger = Logger.getLogger(Walker.class);
+    private GenomeAnalysisEngine toolkit;
 
     protected Walker() {
     }
 
+    /**
+     * Set the toolkit, for peering into internal structures that can't
+     * otherwise be read.
+     * @param toolkit The genome analysis toolkit.
+     */
+    public void setToolkit(GenomeAnalysisEngine toolkit) {
+        this.toolkit = toolkit;
+    }
+
     /**
      * Retrieve the toolkit, for peering into internal structures that can't
      * otherwise be read.  Use sparingly, and discuss uses with software engineering
@@ -54,7 +64,7 @@ public abstract class Walker<MapType, ReduceType> {
      * @return The genome analysis toolkit.
      */
     protected GenomeAnalysisEngine getToolkit() {
-        return GenomeAnalysisEngine.instance;
+        return toolkit;
     }
 
     /**
@@ -126,7 +136,7 @@ public abstract class Walker<MapType, ReduceType> {
 
     /**
      * General interval reduce routine called after all of the traversals are done
-     * @param results
+     * @param results interval reduce results
      */
     public void onTraversalDone(List<Pair<GenomeLoc, ReduceType>> results) {
         for ( Pair<GenomeLoc, ReduceType> result : results ) {
@@ -145,6 +155,8 @@ public abstract class Walker<MapType, ReduceType> {
      * However, onTraversalDone(reduce) will be called after each interval is processed.
      * The system will call onTraversalDone( GenomeLoc -> reduce ), after all reductions are done,
      *   which is overloaded here to call onTraversalDone(reduce) for each location
+     *
+     * @return true if your walker wants to reduce each interval separately.
      */
     public boolean isReduceByInterval() {
         return false;

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

@@ -31,6 +31,7 @@ import net.sf.samtools.util.SequenceUtil;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
@@ -179,7 +180,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             intervals = new IntervalFileMergingIterator( new java.io.File(intervalsFile), IntervalMergingRule.OVERLAPPING_ONLY );
         } else {
             // read in the whole list of intervals for cleaning
-            GenomeLocSortedSet locs = IntervalUtils.sortAndMergeIntervals(IntervalUtils.parseIntervalArguments(Arrays.asList(intervalsFile)), IntervalMergingRule.OVERLAPPING_ONLY);
+            GenomeLocSortedSet locs = IntervalUtils.sortAndMergeIntervals(IntervalUtils.parseIntervalArguments(Arrays.asList(intervalsFile),this.getToolkit().getArguments().unsafe != ValidationExclusion.TYPE.ALLOW_EMPTY_INTERVAL_LIST), IntervalMergingRule.OVERLAPPING_ONLY);
             intervals = locs.iterator();
         }
         currentInterval = intervals.hasNext() ? intervals.next() : null;

java/src/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerWalker.java

@@ -83,8 +83,6 @@ public class HLACallerWalker extends ReadWalker<Integer, Integer> {
     @Argument(fullName = "turnOffVerboseOutput", shortName = "noVerbose", doc = "Do not output verbose probability descriptions (INFO lines) ", required = false)
     protected boolean NO_VERBOSE = false;
 
-    GATKArgumentCollection args = this.getToolkit().getArguments();
-    
     // Initializing variables
     
     HLAFileReader HLADictionaryReader = new HLAFileReader();

java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java

@@ -53,7 +53,7 @@ public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
         }
         out.println("Header:");
         // enumerate the list of ROD's we've loaded
-        rodList = GenomeAnalysisEngine.instance.getRodDataSources();
+        rodList = this.getToolkit().getRodDataSources();
         for (ReferenceOrderedDataSource rod : rodList) {
             out.println(rod.getName() + DIVIDER + rod.getReferenceOrderedData().getType());
             out.println(rod.getName() + DIVIDER + rod.getReferenceOrderedData().getFile());

java/src/org/broadinstitute/sting/utils/GenomeLocParser.java

@@ -323,16 +323,17 @@ public class GenomeLocParser {
      * Where each locN can be:
      * 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
      *
-     * @param file_name
+     * @param file_name interval file
+     * @param allowEmptyIntervalList if false empty interval lists will return null
      * @return List<GenomeLoc> List of Genome Locs that have been parsed from file
      */
-    public static List<GenomeLoc> intervalFileToList(final String file_name) {
+    public static List<GenomeLoc> intervalFileToList(final String file_name, boolean allowEmptyIntervalList) {
         // try to open file
         File inputFile = new File(file_name);
 
         // check if file is empty
         if (inputFile.exists() && inputFile.length() < 1) {
-            if (GenomeAnalysisEngine.instance.getArguments().unsafe != ValidationExclusion.TYPE.ALLOW_EMPTY_INTERVAL_LIST)
+            if (allowEmptyIntervalList)
                 return new ArrayList<GenomeLoc>();
             else {
                 Utils.warnUser("The interval file " + file_name + " is empty. The GATK will continue processing but you " +

java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java

@@ -76,12 +76,12 @@ public class SequenceDictionaryUtils {
     }
 
     /**
+     * @param validationExclusion exclusions to validation
      * @return Returns true if the engine is in tolerant mode and we'll let through dangerous but not fatal dictionary inconsistency
      */
-    public static boolean allowNonFatalIncompabilities() {
+    public static boolean allowNonFatalIncompabilities(ValidationExclusion.TYPE validationExclusion) {
-        return GenomeAnalysisEngine.instance != null &&
+        return ( validationExclusion == ValidationExclusion.TYPE.ALLOW_SEQ_DICT_INCOMPATIBILITY ||
-                ( GenomeAnalysisEngine.instance.getArguments().unsafe == ValidationExclusion.TYPE.ALLOW_SEQ_DICT_INCOMPATIBILITY ||
+                        validationExclusion == ValidationExclusion.TYPE.ALL );
-                        GenomeAnalysisEngine.instance.getArguments().unsafe == ValidationExclusion.TYPE.ALL );
     }
 
     /**
@@ -89,12 +89,13 @@ public class SequenceDictionaryUtils {
      * thrown with detailed error messages.  If the engine is in permissive mode, then logger.warnings of generated instead
      *
      * @param logger for warnings
+     * @param validationExclusion exclusions to validation
      * @param name1 name associated with dict1
      * @param dict1 the sequence dictionary dict1
      * @param name2 name associated with dict2
      * @param dict2 the sequence dictionary dict2
      */
-    public static void validateDictionaries(Logger logger, String name1, SAMSequenceDictionary dict1, String name2, SAMSequenceDictionary dict2) {
+    public static void validateDictionaries(Logger logger, ValidationExclusion.TYPE validationExclusion, String name1, SAMSequenceDictionary dict1, String name2, SAMSequenceDictionary dict2) {
         SequenceDictionaryCompatability type = compareDictionaries(dict1, dict2);
         switch ( type ) {
             case IDENTICAL:
@@ -115,7 +116,7 @@ public class SequenceDictionaryUtils {
                         name2, elt2.getSequenceName(), elt2.getSequenceLength()),
                         name1, dict1, name2, dict2);
 
-                if ( allowNonFatalIncompabilities() )
+                if ( allowNonFatalIncompabilities(validationExclusion) )
                     logger.warn(ex.getMessage());
                 else
                     throw ex;
@@ -129,7 +130,7 @@ public class SequenceDictionaryUtils {
                 else
                     ex = new UserException.LexicographicallySortedSequenceDictionary(name2, dict2);
                 
-                if ( allowNonFatalIncompabilities() )
+                if ( allowNonFatalIncompabilities(validationExclusion) )
                     logger.warn(ex.getMessage());
                 else
                     throw ex;
@@ -137,7 +138,7 @@ public class SequenceDictionaryUtils {
 
             case OUT_OF_ORDER: {
                 UserException ex = new UserException.IncompatibleSequenceDictionaries("Order of contigs differences, which is unsafe", name1, dict1, name2, dict2);
-                if ( allowNonFatalIncompabilities() )
+                if ( allowNonFatalIncompabilities(validationExclusion) )
                     logger.warn(ex.getMessage());
                 else
                     throw ex;

java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java

@@ -26,9 +26,10 @@ public class IntervalUtils {
      * specifications.
      *
      * @param argList A list of strings containing interval data.
+     * @param allowEmptyIntervalList If false instead of an empty interval list will return null.
      * @return an unsorted, unmerged representation of the given intervals.  Null is used to indicate that all intervals should be used. 
      */
-    public static List<GenomeLoc> parseIntervalArguments(List<String> argList) {
+    public static List<GenomeLoc> parseIntervalArguments(List<String> argList, boolean allowEmptyIntervalList) {
         List<GenomeLoc> rawIntervals = new ArrayList<GenomeLoc>();    // running list of raw GenomeLocs
 
         if (argList != null) { // now that we can be in this function if only the ROD-to-Intervals was provided, we need to
@@ -50,7 +51,7 @@ public class IntervalUtils {
                     // if it's a file, add items to raw interval list
                     if (isIntervalFile(fileOrInterval)) {
                         try {
-                            rawIntervals.addAll(GenomeLocParser.intervalFileToList(fileOrInterval));
+                            rawIntervals.addAll(GenomeLocParser.intervalFileToList(fileOrInterval, allowEmptyIntervalList));
                         }
                         catch (Exception e) {
                             throw new UserException.MalformedFile(fileOrInterval, "Interval file could not be parsed in either format.", e);

java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java

@@ -39,7 +39,7 @@ public class GATKSAMRecord extends SAMRecord {
     // These attributes exist in memory only, and are never written to disk.
     private Map<Object, Object> temporaryAttributes;
 
-    public GATKSAMRecord(SAMRecord record) {
+    public GATKSAMRecord(SAMRecord record, boolean useOriginalBaseQualities) {
         super(null); // it doesn't matter - this isn't used
         if ( record == null )
             throw new IllegalArgumentException("The SAMRecord argument cannot be null");
@@ -55,8 +55,7 @@ public class GATKSAMRecord extends SAMRecord {
             setAttribute(attribute.tag, attribute.value);
 
         // if we are using original quals, set them now if t hey are present in the record
-        if ( GenomeAnalysisEngine.instance != null &&
+        if ( useOriginalBaseQualities ) {
-                GenomeAnalysisEngine.instance.getArguments().useOriginalBaseQualities ) {
             byte[] originalQuals = mRecord.getOriginalBaseQualities();
             if ( originalQuals != null )
                 mRecord.setBaseQualities(originalQuals);

java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java

@@ -50,7 +50,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator();
 
         GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1", 1, 5);
-        Shard shard = new LocusShard(new SAMDataSource(new ReadProperties(Collections.<SAMReaderID>emptyList())),Collections.singletonList(shardBounds),Collections.<SAMReaderID,SAMFileSpan>emptyMap());
+        Shard shard = new LocusShard(new SAMDataSource(Collections.<SAMReaderID>emptyList()),Collections.singletonList(shardBounds),Collections.<SAMReaderID,SAMFileSpan>emptyMap());
         WindowMaker windowMaker = new WindowMaker(shard,iterator,shard.getGenomeLocs(),LocusIteratorByState.NO_FILTERS);
         WindowMaker.WindowMakerIterator window = windowMaker.next();
         LocusShardDataProvider dataProvider = new LocusShardDataProvider(shard, null, window.getLocus(), window, null, null);

java/test/org/broadinstitute/sting/gatk/datasources/shards/MockLocusShard.java

@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 
@@ -40,6 +39,6 @@ import java.util.Collections;
  */
 public class MockLocusShard extends LocusShard {
     public MockLocusShard(final List<GenomeLoc> intervals) {
-        super(new SAMDataSource(new ReadProperties(Collections.<SAMReaderID>emptyList())),intervals,null);
+        super(new SAMDataSource(Collections.<SAMReaderID>emptyList()),intervals,null);
     }
 }

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java

@@ -86,10 +86,9 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
 
         // setup the data
         readers.add(new SAMReaderID(new File(validationDataLocation+"/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
-        ReadProperties reads = new ReadProperties(readers);
 
         // the sharding strat.
-        SAMDataSource data = new SAMDataSource(reads);
+        SAMDataSource data = new SAMDataSource(readers);
         ShardStrategy strat = ShardStrategyFactory.shatter(data,seq,ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL, seq.getSequenceDictionary(), 100000);
         int count = 0;
 
@@ -131,10 +130,9 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
 
         // setup the test files
         readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
-        ReadProperties reads = new ReadProperties(readers);
 
         // the sharding strat.
-        SAMDataSource data = new SAMDataSource(reads);
+        SAMDataSource data = new SAMDataSource(readers);
         ShardStrategy strat = ShardStrategyFactory.shatter(data,seq,ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL, seq.getSequenceDictionary(), 100000);
 
         ArrayList<Integer> readcountPerShard = new ArrayList<Integer>();
@@ -173,11 +171,10 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
         readers.clear();
         readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
         readers.add(new SAMReaderID(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"),Collections.<String>emptyList()));
-        reads = new ReadProperties(readers);
 
         count = 0;
         // the sharding strat.
-        data = new SAMDataSource(reads);
+        data = new SAMDataSource(readers);
         strat = ShardStrategyFactory.shatter(data,seq,ShardStrategyFactory.SHATTER_STRATEGY.LOCUS_EXPERIMENTAL, seq.getSequenceDictionary(), 100000);
 
         logger.debug("Pile two:");

java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java

@@ -1,11 +1,14 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import junit.framework.Assert;
+import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.ReadProperties;
+import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -15,11 +18,7 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
-import java.io.File;
+import java.util.*;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Arrays;
 
 /**
  * testing of the LocusIteratorByState
@@ -41,7 +40,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         final byte[] bases = new byte[] {'A','A','A','A','A','A','A','A','A','A'};
 
         // create a test version of the Reads object
-        ReadProperties readAttributes = new ReadProperties(new ArrayList<SAMReaderID>());
+        ReadProperties readAttributes = createTestReadProperties();
         JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
 
         SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
@@ -93,7 +92,7 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
         final byte[] quals = new byte[] { 20, 20, 20, 20, 20, 20, 20, 20, 20, 20};
 
         // create a test version of the Reads object
-        ReadProperties readAttributes = new ReadProperties(new ArrayList<SAMReaderID>());
+        ReadProperties readAttributes = createTestReadProperties();
         JVMUtils.setFieldValue(JVMUtils.findField(ReadProperties.class,"generateExtendedEvents"),readAttributes,true);
 
         SAMRecord before = ArtificialSAMUtils.createArtificialRead(header,"before",0,1,10);
@@ -132,6 +131,21 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
 
         Assert.assertTrue("Extended event pileup not found",foundExtendedEventPileup);
     }
+
+    private static ReadProperties createTestReadProperties() {
+        return new ReadProperties(
+                Collections.<SAMReaderID>emptyList(),
+                new SAMFileHeader(),
+                false,
+                SAMFileReader.ValidationStringency.STRICT,
+                null,
+                null,
+                new ValidationExclusion(),
+                new ArrayList<SamRecordFilter>(),
+                false,
+                false
+        );
+    }
 }
 
 class FakeCloseableIterator<T> implements CloseableIterator<T> {

java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java

@@ -99,7 +99,7 @@ public class TraverseReadsUnitTest extends BaseTest {
         ref = new IndexedFastaSequenceFile(refFile);
         GenomeLocParser.setupRefContigOrdering(ref);
 
-        SAMDataSource dataSource = new SAMDataSource(new ReadProperties(bamList));
+        SAMDataSource dataSource = new SAMDataSource(bamList);
         ShardStrategy shardStrategy = ShardStrategyFactory.shatter(dataSource,ref,ShardStrategyFactory.SHATTER_STRATEGY.READS_EXPERIMENTAL,
                 ref.getSequenceDictionary(),
                 readSize);