All exceptions thrown by the GATK have been reviewed and UserErrors replaced where appropriate. Shazam. Another check-in will remove the GATKException and restore the StingException.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4252 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java

@@ -230,7 +230,7 @@ public class BWTFiles {
      * Convert the given reference sequence into a form suitable for building into
      * on-the-fly sequences.
      * @param referenceSequence The reference sequence to normalize.
-     * @throws StingException if normalized sequence cannot be generated.
+     * @throws GATKException if normalized sequence cannot be generated.
      */
     private static void normalizeReferenceSequence(byte[] referenceSequence) {
         StringUtil.toUpperCase(referenceSequence);

java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java

@@ -67,7 +67,7 @@ public class BWTReader {
             }
         }
         catch( IOException ex ) {
-            throw new StingException("Unable to read BWT from input stream.", ex);
+            throw new GATKException("Unable to read BWT from input stream.", ex);
         }
 
         return new BWT(inverseSA0, new Counts(count,true), sequenceBlocks);

java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.analyzecovariates;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.gatk.walkers.recalibration.*;
 import org.broadinstitute.sting.utils.classloader.PackageUtils;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
@@ -140,11 +141,8 @@ class AnalyzeCovariatesCLP extends CommandLineProgram {
                                     try {
                                         Covariate covariate = (Covariate)covClass.newInstance();
                                         requestedCovariates.add( covariate );
-
+                                    } catch (Exception e) {
-                                    } catch ( InstantiationException e ) {
+                                        throw new DynamicClassResolutionException(covClass, e);
-                                        throw new RuntimeException( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
-                                    } catch ( IllegalAccessException e ) {
-                                        throw new RuntimeException( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
                                     }
                                 }
                             }

java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java

@@ -31,6 +31,7 @@ import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.gatk.walkers.Multiplex;
 import org.broadinstitute.sting.gatk.walkers.Multiplexer;
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.lang.annotation.Annotation;
@@ -348,16 +349,13 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 Constructor ctor = type.getConstructor(String.class);
                 result = ctor.newInstance(value);
             }
-        }
-        catch (NoSuchMethodException e) {
-            throw new GATKException("constructFromString:NoSuchMethodException: Failed conversion " + e.getMessage());
-        } catch (IllegalAccessException e) {
-            throw new GATKException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
         } catch (InvocationTargetException e) {
             throw new GATKException("constructFromString:InvocationTargetException: Failed conversion - this is most likely caused by using an incorrect data type (e.g. a double when an int is required)");
-        } catch (InstantiationException e) {
+        } catch (Exception e) {
-            throw new GATKException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
+            throw new DynamicClassResolutionException(String.class, e);
         }
+
+
         // WARNING: Side effect!
         parsingEngine.addTags(result,tags);
 

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

@@ -101,7 +101,7 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
      */
     private void generateGATKRunReport(Walker<?,?> mWalker, Exception e) {
         if ( getArgumentCollection().phoneHomeType != GATKRunReport.PhoneHomeOption.NO_ET ) {
-            GATKRunReport report = new GATKRunReport(mWalker, e, GATKEngine);
+            GATKRunReport report = new GATKRunReport(mWalker, e, GATKEngine, getArgumentCollection().phoneHomeType );
             if ( getArgumentCollection().phoneHomeType == GATKRunReport.PhoneHomeOption.STDOUT )
                 report.postReport(System.out);
             else

java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java

@@ -68,7 +68,7 @@ public class AlignmentContext {
     }
 
     public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, long skippedBases,boolean hasPileupBeenDownsampled ) {
-        if ( loc == null ) throw new StingException("BUG: GenomeLoc in Alignment context is null");
+        if ( loc == null ) throw new GATKException("BUG: GenomeLoc in Alignment context is null");
         if ( basePileup == null ) throw new GATKException("BUG: ReadBackedPileup in Alignment context is null");
         if ( skippedBases < 0 ) throw new GATKException("BUG: skippedBases is -1 in Alignment context");
 

java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 /**
@@ -20,7 +21,7 @@ import org.broadinstitute.sting.utils.StingException;
  * This exception is throw when we're unable to generate a data source,
  * most likely due to an incomplete input source list
  */
-public class DataSourceGenerationException extends StingException {
+public class DataSourceGenerationException extends GATKException {
     public DataSourceGenerationException(String message) {
         super(message);
     }

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

@@ -216,7 +216,7 @@ class ReferenceOrderedQueryDataPool extends ResourcePool<FeatureSource, Location
                 return new SeekableRODIterator(new FeatureToGATKFeatureIterator(resource.iterator(),rod.getName()));
             }
         } catch (IOException e) {
-            throw new StingException("Unable to create iterator for rod named " + rod.getName(),e);
+            throw new GATKException("Unable to create iterator for rod named " + rod.getName(),e);
         }
     }
 

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 /**
@@ -28,7 +29,7 @@ import org.broadinstitute.sting.utils.StingException;
  * <p/>
  * Generate this on a simple data source load exception
  */
-public class SimpleDataSourceLoadException extends StingException {
+public class SimpleDataSourceLoadException extends GATKException {
     public SimpleDataSourceLoadException(String msg) {
         super(msg);
     }

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
 
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 
@@ -39,7 +40,7 @@ import org.broadinstitute.sting.utils.StingException;
  * <p/>
  * an exception that get's thrown if we can't split up a data source appropriately
  */
-public class SimpleDataSourceSplitException extends StingException {
+public class SimpleDataSourceSplitException extends GATKException {
     public SimpleDataSourceSplitException(String msg) {
         super(msg);
     }

java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java

@@ -98,7 +98,7 @@ public class OutputStreamStorage extends OutputStream implements Storage<OutputS
             outputStream.close();
         }
         catch( IOException ex ) {
-            throw new StingException( "Unable to close output stream" );
+            throw new UserError.CouldNotCreateOutputFile(file, "Unable to close output stream", ex );
         }
     }
 

java/src/org/broadinstitute/sting/gatk/io/stubs/OutputStreamArgumentTypeDescriptor.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.io.OutputStream;
 import java.io.File;
@@ -116,15 +117,8 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     private Object createInstanceOfClass(Class type,OutputStream outputStream) {
         try {
             return getConstructorForClass(type).newInstance(outputStream);
-        }
+        } catch (Exception e) {
-        catch( InstantiationException ex ) {
+            throw new DynamicClassResolutionException(type, e);
-            throw new GATKException("Could not instantiate class with OutputStream constructor: " + type.getName());
-        }
-        catch( IllegalAccessException ex ) {
-            throw new GATKException("Could not access class with OutputStream constructor: " + type.getName());
-        }
-        catch( InvocationTargetException ex ) {
-            throw new GATKException("Could not invoke constructor for class with OutputStream constructor: " + type.getName());
         }
     }
 }

java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java

@@ -155,6 +155,7 @@ public class GATKRunReport {
     public enum PhoneHomeOption {
         NO_ET,
         STANDARD,
+        DEV,
         STDOUT
     }
 
@@ -167,7 +168,10 @@ public class GATKRunReport {
      * @param e the exception caused by running this walker, or null if we completed successfully
      * @param engine the GAE we used to run the walker, so we can fetch runtime, args, etc
      */
-    public GATKRunReport(Walker<?,?> walker, Exception e, GenomeAnalysisEngine engine) {
+    public GATKRunReport(Walker<?,?> walker, Exception e, GenomeAnalysisEngine engine, PhoneHomeOption type) {
+        if ( type == PhoneHomeOption.NO_ET )
+            throw new GATKException("Trying to create a run report when type is NO_ET!");
+
         mGATKHeader = CommandLineGATK.createApplicationHeader();
         currentPath = System.getProperty("user.dir");
 

java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.GATKException;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.Utils;
@@ -232,12 +233,8 @@ public class RODRecordIterator<ROD extends ReferenceOrderedDatum> implements Ite
     private ROD instantiateROD(final String name) {
         try {
             return (ROD) named_constructor.newInstance(name);
-        } catch (java.lang.InstantiationException e) {
+        } catch (Exception e) {
-            throw new GATKException("Failed to instantiate ROD object of class "+type.getName());
+            throw new DynamicClassResolutionException(named_constructor.getDeclaringClass(), e);
-        } catch (java.lang.IllegalAccessException e) {
-            throw new GATKException("Access violation attempt while instantiating ROD object of class "+type.getName());
-        } catch (InvocationTargetException e) {
-            throw new GATKException("InvocationTargetException: Failed to instantiate ROD object of class "+type.getName());
         }
     }
 

java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java

@@ -23,6 +23,7 @@
 
 package org.broadinstitute.sting.gatk.refdata.tracks;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 
@@ -34,7 +35,7 @@ import org.broadinstitute.sting.utils.StingException;
  *
  * if we fail for some reason to make a track, throw this exception
  */
-public class RMDTrackCreationException extends StingException {
+public class RMDTrackCreationException extends GATKException {
     public RMDTrackCreationException(String msg) {
         super(msg);
     }

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

@@ -333,7 +333,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             do {
                 currentInterval = intervals.hasNext() ? intervals.next() : null;
             } while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) );
-        } catch (StingException e) {
+        } catch (GATKException e) {
             throw new UserError.MissortedFile(new File(intervalsFile), " *** Are you sure that your interval file is sorted? If not, you must use the --targetIntervalsAreNotSorted argument. ***", e);
         }
 

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java

@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@@ -213,10 +214,8 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
                         try {
                             final Covariate covariate = (Covariate)covClass.newInstance();
                             requestedCovariates.add( covariate );
-                        } catch ( InstantiationException e ) {
+                        } catch (Exception e) {
-                            throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
+                            throw new DynamicClassResolutionException(covClass, e);
-                        } catch ( IllegalAccessException e ) {
-                            throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
                         }
                     }
                 }
@@ -234,10 +233,8 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
                                 // Now that we've found a matching class, try to instantiate it
                                 final Covariate covariate = (Covariate)covClass.newInstance();
                                 requestedCovariates.add( covariate );
-                            } catch ( InstantiationException e ) {
+                            } catch (Exception e) {
-                                throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
+                                throw new DynamicClassResolutionException(covClass, e);
-                            } catch ( IllegalAccessException e ) {
-                                throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
                             }
                         }
                     }

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java

@@ -281,7 +281,7 @@ public class RecalDataManager {
                     if( attr instanceof String ) {
                         colorSpace = ((String)attr).getBytes();
                     } else {
-                        throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
+                        throw new UserError.MalformedBam(read, String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
                     }
 
                     // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java

@@ -47,6 +47,7 @@ import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.collections.NestedHashMap;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.Utils;
@@ -191,12 +192,10 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
                                     try {
                                         Covariate covariate = (Covariate)covClass.newInstance();
                                         requestedCovariates.add( covariate );
-
+                                    } catch (Exception e) {
-                                    } catch ( InstantiationException e ) {
+                                        throw new DynamicClassResolutionException(covClass, e);
-                                        throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
-                                    } catch ( IllegalAccessException e ) {
-                                        throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
                                     }
+
                                 }
                             }
 

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

@@ -51,6 +51,7 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
@@ -478,14 +479,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
                 Constructor constructor = c.getConstructor(argTypes);
                 VariantEvaluator eval = (VariantEvaluator)constructor.newInstance(args);
                 evals.add(eval);
-            } catch (InstantiationException e) {
+            } catch (Exception e) {
-                throw new StingException(String.format("Cannot instantiate class '%s': must be concrete class", c.getSimpleName()));
+                throw new DynamicClassResolutionException(c, e);
-            } catch (NoSuchMethodException e) {
-                throw new StingException(String.format("Cannot find expected constructor for class '%s': must have constructor accepting a single VariantEval2Walker object", c.getSimpleName()));
-            } catch (IllegalAccessException e) {
-                throw new StingException(String.format("Cannot instantiate class '%s' (Illegal Access):", c.getSimpleName()));
-            } catch (InvocationTargetException e) {
-                throw new StingException(String.format("Cannot instantiate class '%s' (Invocation): %s", c.getSimpleName(), e.getMessage()));
             }
         }
 
@@ -565,7 +560,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
                             if ( interesting != null ) interestingReasons.add(interesting);
                             break;
                         default:
-                            throw new StingException("BUG: Unexpected evaluation order " + evaluation);
+                            throw new GATKException("BUG: Unexpected evaluation order " + evaluation);
                     }
                 }
             }

java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java

@@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
@@ -127,7 +128,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
 
             return tranches;
         } catch( FileNotFoundException e ) {
-            throw new StingException("Can not find input file: " + f);
+            throw new UserError.CouldNotCreateOutputFile(f, e);
         }
     }
 
@@ -155,7 +156,7 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
                 firstLine = false;
             }
         } catch( FileNotFoundException e ) {
-            throw new StingException("Can not find input file: " + TRANCHES_FILE);
+            throw new UserError.CouldNotCreateOutputFile(TRANCHES_FILE, e);
         }
 
         // setup the header fields

java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/GenerateVariantClustersWalker.java

@@ -41,6 +41,7 @@ import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.File;
 import java.io.IOException;
@@ -147,7 +148,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
         }
 
         if(!foundDBSNP) {
-            throw new StingException("dbSNP track is required. This calculation is critically dependent on being able to distinguish known and novel sites.");
+            throw new UserError.CommandLineError("dbSNP track is required. This calculation is critically dependent on being able to distinguish known and novel sites.");
         }
     }
 
@@ -239,7 +240,7 @@ public class GenerateVariantClustersWalker extends RodWalker<ExpandingArrayList<
             //    theModel = new VariantNearestNeighborsModel( dataManager, TARGET_TITV, NUM_KNN );
             //    break;
             default:
-                throw new StingException( "Variant Optimization Model is unrecognized. Implemented options are GAUSSIAN_MIXTURE_MODEL and K_NEAREST_NEIGHBORS" );
+                throw new UserError.BadArgumentValue("OPTIMIZATION_MODEL", "Variant Optimization Model is unrecognized. Implemented options are GAUSSIAN_MIXTURE_MODEL and K_NEAREST_NEIGHBORS" );
         }
         
         theModel.run( CLUSTER_FILE );

java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java

@@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.PrintStream;
 
@@ -53,7 +54,7 @@ public class VariantDataManager {
         numVariants = dataList.size();
         data = dataList.toArray( new VariantDatum[numVariants] );
         if( numVariants <= 0 ) {
-            throw new StingException( "There are zero variants with > 0 clustering weight! Please provide sets of known polymorphic loci to be used as training data using the dbsnp, hapmap, or 1kg rod bindings. Clustering weights can be specified using -weightDBSNP, -weightHapMap, and -weight1KG" );
+            throw new UserError.BadInput("There are zero variants with > 0 clustering weight! Please provide sets of known polymorphic loci to be used as training data using the dbsnp, hapmap, or 1kg rod bindings. Clustering weights can be specified using -weightDBSNP, -weightHapMap, and -weight1KG" );
         }
         if( _annotationKeys == null ) {
             numAnnotations = 0;
@@ -62,7 +63,7 @@ public class VariantDataManager {
         } else {
             numAnnotations = _annotationKeys.size();
             if( numAnnotations <= 0 ) {
-                throw new StingException( "There are zero annotations!" );
+                throw new UserError.BadInput("There are zero annotations.  At least one annotation must be provided to use this walker!" );
             }
             meanVector = new double[numAnnotations];
             varianceVector = new double[numAnnotations];
@@ -110,7 +111,7 @@ public class VariantDataManager {
         }
         isNormalized = true; // Each data point is now [ (x - mean) / standard deviation ]
         if( foundZeroVarianceAnnotation ) {
-            throw new StingException("Found annotations with zero variance. They must be excluded before proceeding.");
+            throw new UserError.BadInput("Found annotations with zero variance. They must be excluded before proceeding.");
         }
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java

@@ -28,9 +28,11 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 import org.apache.log4j.Logger;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.text.XReadLines;
 
 import Jama.*; 
@@ -130,11 +132,11 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
                 } else if( CLUSTER_PATTERN.matcher(line).matches() ) {
                     clusterLines.add(line);
                 } else {
-                    throw new StingException("Malformed input file: " + clusterFile);
+                    throw new UserError.MalformedFile(clusterFile, "Could not parse line: " + line);
                 }
             }
         } catch ( FileNotFoundException e ) {
-            throw new StingException("Can not find input file: " + clusterFile);
+            throw new UserError.CouldNotReadInputFile(clusterFile, e);
         }
 
         dataManager = new VariantDataManager( annotationLines );
@@ -427,9 +429,8 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
         } else {
             try {
                 value = Double.parseDouble( (String)vc.getAttribute( annotationKey ) );
-            } catch( Exception e ) {
+            } catch( NumberFormatException e ) {
-                throw new StingException("No double value detected for annotation = " + annotationKey +
+                throw new UserError.MalformedFile(vc.getName(), "No double value detected for annotation = " + annotationKey + " in variant at " + VariantContextUtils.getLocation(vc) + ", reported annotation value = " + vc.getAttribute( annotationKey ), e );
-                        " in variant at " + VariantContextUtils.getLocation(vc) + ", reported annotation value = " + vc.getAttribute( annotationKey ) );
             }
         }
         return value;
@@ -488,10 +489,11 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
         int annIndex = 0;
         for( final String annotation : dataManager.annotationKeys ) {
             PrintStream outputFile;
+            File file = new File(outputPrefix + "." + annotation + ".dat");
             try {
-                outputFile = new PrintStream( outputPrefix + "." + annotation + ".dat" );
+                outputFile = new PrintStream( file );
-            } catch (Exception e) {
+            } catch (FileNotFoundException e) {
-                throw new StingException( "Unable to create output file: " + outputPrefix + ".dat" );
+                throw new UserError.CouldNotCreateOutputFile( file, e );
             }
 
             outputFile.println("annotationValue,knownDist,novelDist");
@@ -506,7 +508,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
         }
     }
 
-    public final void outputOptimizationCurve( final VariantDatum[] data, final PrintStream outputReportDatFile, final PrintStream outputTranchesFile,
+    public final void outputOptimizationCurve( final VariantDatum[] data, final PrintStream outputReportDatFile, final PrintStream tranchesOutputFile,
                                                final int desiredNumVariants, final Double[] FDRtranches, final double QUAL_STEP ) {
 
         final int numVariants = data.length;
@@ -530,19 +532,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
             markedVariant[iii] = false;
         }
 
-        PrintStream outputFile;
+        tranchesOutputFile.println("FDRtranche,novelTITV,pCut,numNovel,filterName");
-        try {
-            outputFile = new PrintStream( outputReportDatFile );
-        } catch (Exception e) {
-            throw new StingException( "Unable to create output file: " + outputReportDatFile );
-        }
-        PrintStream tranchesOutputFile;
-        try {
-            tranchesOutputFile = new PrintStream( outputTranchesFile );
-            tranchesOutputFile.println("FDRtranche,novelTITV,pCut,numNovel,filterName");
-        } catch (Exception e) {
-            throw new StingException( "Unable to create output file: " + outputTranchesFile );
-        }
 
         int numKnown = 0;
         int numNovel = 0;
@@ -552,7 +542,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
         int numNovelTv = 0;
         boolean foundDesiredNumVariants = false;
         int jjj = 0;
-        outputFile.println("pCut,numKnown,numNovel,knownTITV,novelTITV");
+        outputReportDatFile.println("pCut,numKnown,numNovel,knownTITV,novelTITV");
         for( double qCut = MAX_QUAL; qCut >= -0.001; qCut -= QUAL_STEP ) {
             for( int iii = 0; iii < numVariants; iii++ ) {
                 if( !markedVariant[iii] ) {
@@ -584,7 +574,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
                 logger.info("\t" + String.format("%.4f novel Ti/Tv ratio", ((double)numNovelTi) / ((double)numNovelTv)));
                 foundDesiredNumVariants = true;
             }
-            outputFile.println( qCut + "," + numKnown + "," + numNovel + "," +
+            outputReportDatFile.println( qCut + "," + numKnown + "," + numNovel + "," +
                     ( numKnownTi == 0 || numKnownTv == 0 ? "NaN" : ( ((double)numKnownTi) / ((double)numKnownTv) ) ) + "," +
                     ( numNovelTi == 0 || numNovelTv == 0 ? "NaN" : ( ((double)numNovelTi) / ((double)numNovelTv) ) ));
 
@@ -710,7 +700,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
 
                     logger.warn("About to throw exception due to numerical instability. Try running with fewer annotations and then with fewer Gaussians. " +
                             "It is best to only use the annotations which appear to be Gaussianly distributed for this Gaussian mixture model.");
-                    throw new StingException("Numerical Instability! Found NaN after performing log10: " + pVarInClusterLog10[kkk] + ", cluster = " + kkk + ", variant index = " + iii);
+                    throw new GATKException("Numerical Instability! Found NaN after performing log10: " + pVarInClusterLog10[kkk] + ", cluster = " + kkk + ", variant index = " + iii);
                 }
             }
 
@@ -720,7 +710,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
                 if( Double.isNaN(pVarInCluster[kkk][iii]) ) {
                     logger.warn("About to throw exception due to numerical instability. Try running with fewer annotations and then with fewer Gaussians. " +
                             "It is best to only use the annotations which appear to be Gaussianly distributed for this Gaussian mixture model.");
-                    throw new StingException("Numerical Instability! Found NaN after rescaling log10 values: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii);
+                    throw new GATKException("Numerical Instability! Found NaN after rescaling log10 values: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii);
                 }
             }
         }
@@ -786,7 +776,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
                 if( Double.isNaN(prob) ) {
                     logger.warn("About to throw exception due to numerical instability. Try running with fewer annotations and then with fewer Gaussians. " +
                             "It is best to only use the annotations which appear to be Gaussianly distributed for this Gaussian mixture model.");
-                    throw new StingException("Numerical Instability! Found NaN in M-step: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii);
+                    throw new GATKException("Numerical Instability! Found NaN in M-step: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii);
                 }
                 sumProb += prob;
                 for( int jjj = 0; jjj < numAnnotations; jjj++ ) {

java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java

@@ -41,6 +41,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.io.File;
@@ -143,7 +144,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             //    theModel = new VariantNearestNeighborsModel( dataManager, TARGET_TITV, NUM_KNN );
             //    break;
             default:
-                throw new StingException( "Variant Optimization Model is unrecognized. Implemented options are GAUSSIAN_MIXTURE_MODEL and K_NEAREST_NEIGHBORS" );
+                throw new UserError.BadArgumentValue("OPTIMIZATION_MODEL", "Variant Optimization Model is unrecognized. Implemented options are GAUSSIAN_MIXTURE_MODEL and K_NEAREST_NEIGHBORS" );
         }
 
         boolean foundDBSNP = false;
@@ -166,7 +167,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
         }
 
         if(!foundDBSNP) {
-            throw new StingException("dbSNP track is required. This calculation is critically dependent on being able to distinguish known and novel sites.");
+            throw new UserError.CommandLineError("dbSNP track is required. This calculation is critically dependent on being able to distinguish known and novel sites.");
         }
 
         // setup the header fields
@@ -232,7 +233,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                     final double totalPrior = 1.0 - ((1.0 - acPrior) * (1.0 - knownPrior));
 
                     if( MathUtils.compareDoubles(totalPrior, 1.0, 1E-8) == 0 || MathUtils.compareDoubles(totalPrior, 0.0, 1E-8) == 0 ) {
-                        throw new StingException("Something is wrong with the prior that was entered by the user:  Prior = " + totalPrior); // TODO - fix this up later
+                        throw new UserError.CommandLineError("Something is wrong with the prior that was entered by the user:  Prior = " + totalPrior); // TODO - fix this up later
                     }
 
                     final double pVar = theModel.evaluateVariant( vc );
@@ -285,7 +286,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
             PrintStream reportDatFilePrintStream = new PrintStream(REPORT_DAT_FILE);
             theModel.outputOptimizationCurve( dataManager.data, reportDatFilePrintStream, TRANCHES_FILE, DESIRED_NUM_VARIANTS, FDR_TRANCHES, QUAL_STEP );
         } catch ( FileNotFoundException e ) {
-            throw new StingException("Can't create report dat file: " + REPORT_DAT_FILE.getName());
+            throw new UserError.CouldNotCreateOutputFile(REPORT_DAT_FILE, e);
         }
 
         // Execute Rscript command to plot the optimization curve

java/src/org/broadinstitute/sting/oneoffprojects/walkers/AnnotationByAlleleFrequencyWalker.java

@@ -37,6 +37,8 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.classloader.PackageUtils;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.util.*;
 
@@ -90,7 +92,7 @@ public class AnnotationByAlleleFrequencyWalker  extends RodWalker<Integer, Integ
             if ( interfaceClass == null )
                 interfaceClass = classMap.get(group + "Annotation");
             if ( interfaceClass == null )
-                throw new StingException("Class " + group + " is not found; please check that you have specified the class name correctly");
+                throw new UserError.BadArgumentValue("group", "Class " + group + " is not found; please check that you have specified the class name correctly");
             classes.addAll(PackageUtils.getClassesImplementingInterface(interfaceClass));
         }
 
@@ -100,7 +102,7 @@ public class AnnotationByAlleleFrequencyWalker  extends RodWalker<Integer, Integ
             if ( annotationClass == null )
                 annotationClass = classMap.get(annotation + "Annotation");
             if ( annotationClass == null )
-                throw new StingException("Class " + annotation + " is not found; please check that you have specified the class name correctly");
+                throw new UserError.BadArgumentValue("annotation", "Class " + annotation + " is not found; please check that you have specified the class name correctly");
             classes.add(annotationClass);
         }
 
@@ -128,10 +130,8 @@ public class AnnotationByAlleleFrequencyWalker  extends RodWalker<Integer, Integ
     private static <T> T getInstance(Class<T> c) {
         try {
             return c.newInstance();
-        } catch (InstantiationException e) {
+        } catch (Exception e) {
-            throw new StingException(String.format("Cannot instantiate annotation class '%s': must be concrete class", c.getSimpleName()));
+            throw new DynamicClassResolutionException(c, e);
-        } catch (IllegalAccessException e) {
-            throw new StingException(String.format("Cannot instantiate annotation class '%s': must have no-arg constructor", c.getSimpleName()));
         }
     }
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BaseTransitionTableCalculatorJavaWalker.java

@@ -33,8 +33,10 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
+import java.io.File;
 import java.util.*;
 import java.io.PrintStream;
 import java.io.FileNotFoundException;
@@ -85,7 +87,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
 
     public void initialize() {
         if ( nPreviousBases > 3 || ( nPreviousReadBases > 3 && readBasesMustMatchRef ) ) {
-            throw new StingException("You have opted to use a number of previous bases in excess of 3. In order to do this you must change the reference window size in the walker itself.");
+            throw new UserError.CommandLineError("You have opted to use a number of previous bases in excess of 3. In order to do this you must change the reference window size in the walker itself.");
         }
         UnifiedArgumentCollection uac = new UnifiedArgumentCollection();
         uac.baseModel = BaseMismatchModel.THREE_STATE;
@@ -149,7 +151,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
             String errMsg = "Parallelization cannot be used with UsePreviousBases due to the fact that internal walker data specifies whether a previous reference base is usable or not.";
             String errMsg2 = " This can cause cause concurrency issues and unpredictable behavior when used with parallelization. Either do not specify -nt, or try a the conjunction of ";
             String errMsg3 = "--usePreviousReadBases and --forcePreviousReadBasesToMatchRef.";
-            throw new StingException(errMsg+errMsg2+errMsg3);
+            throw new UserError.CommandLineError(errMsg+errMsg2+errMsg3);
         }
         return reduce(reduce1,reduce2);
     }
@@ -162,7 +164,7 @@ public class BaseTransitionTableCalculatorJavaWalker extends LocusWalker<Set<Bas
             try {
                 output = new PrintStream(outFilePath);
             } catch ( FileNotFoundException e ) {
-                throw new StingException("File given as input to -of, "+outFilePath+" could not be opened.",e);
+                throw new UserError.CouldNotCreateOutputFile(new File(outFilePath), e);
             }
         }
         output.print(createHeaderFromConditions());

java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java

@@ -35,6 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 
@@ -156,7 +157,7 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
                 else if (compGenotype.isHomVar())
                     hg = 2;
                 else
-                    throw new StingException("Bug! invalid genotype!");
+                    throw new GATKException("Bug! invalid genotype!");
 
                 if (postbglGenotype.isNoCall())
                     bg = -1;
@@ -167,7 +168,7 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
                 else if (postbglGenotype.isHomVar())
                     bg = 2;
                 else
-                    throw new StingException("Bug! invalid genotype!");
+                    throw new GATKException("Bug! invalid genotype!");
 
 
                 if (prebglGenotype.isNoCall())
@@ -179,7 +180,7 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
                 else if (prebglGenotype.isHomVar())
                     pg = 2;
                 else
-                    throw new StingException("Bug! invalid genotype!");
+                    throw new GATKException("Bug! invalid genotype!");
 
                 outputWriter.format("%d %d %d %d\n",dp, hg, pg, bg);
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DSBWalkerV3.java

@@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import net.sf.samtools.SAMRecord;
 
@@ -390,7 +391,7 @@ public class DSBWalkerV3 extends ReadWalker<Integer,Integer> {
         } else if ( controlReadGroups.contains( read.getReadGroup().getReadGroupId() )) {
             addControl(read);
         } else {
-            throw new StingException("Read "+read + " belongs to unrecognized read group");
+            throw new UserError.MalformedBam(read, "Read "+read + " belongs to unrecognized read group");
         }
         return 1;
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DbSNPWindowCounter.java

@@ -17,6 +17,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -68,7 +69,7 @@ public class DbSNPWindowCounter extends LocusWalker<Integer, Long> {
                     windowStart,
                     windowStop);
         } catch (IOException e) {
-            throw new StingException("Unable to query dbSNP track due to IO Exception",e);
+            throw new UserError.CouldNotReadInputFile(myDbSNPFile, e);
         }
 
         // count the number of dbSNPs we've seen

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java

@@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
@@ -196,7 +197,7 @@ class IntervalInfoBuilder {
                     }
                 }
             } else {
-                throw new StingException("Attempting to update an IntervalInfoBuilder twice with the same (non-TCGA) gene: "+gene);
+                throw new GATKException("Attempting to update an IntervalInfoBuilder twice with the same (non-TCGA) gene: "+gene);
             }
         } else {
 

java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.features.samread.SAMReadFeature;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
@@ -71,7 +72,7 @@ public class DownsamplingValidationWalker extends LocusWalker<Integer,Long> {
         int matchingReadsFound = 0;
         if(unsampledReadsStartingAtThisLocus.isEmpty()) {
             if(!sampledReadsStartingAtThisLocus.isEmpty())
-                throw new StingException("Downsampler hallucinated a read starting at locus "+ref.getLocus());
+                throw new GATKException("Downsampler hallucinated a read starting at locus "+ref.getLocus());
         }
         else {
             boolean foundMatch = false;
@@ -86,10 +87,10 @@ public class DownsamplingValidationWalker extends LocusWalker<Integer,Long> {
             }
 
             if(!foundMatch)
-                throw new StingException("Downsampler failed to include any read starting at locus "+ref.getLocus());
+                throw new GATKException("Downsampler failed to include any read starting at locus "+ref.getLocus());
 
             if(matchingReadsFound > maxExpectedNumberOfReads)
-                throw new StingException("Downsampler found too many reads starting at locus "+ref.getLocus());                
+                throw new GATKException("Downsampler found too many reads starting at locus "+ref.getLocus());
         }
 
         return matchingReadsFound;

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelAnnotator.java

@@ -19,6 +19,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.io.File;
@@ -42,7 +43,7 @@ public class IndelAnnotator extends RodWalker<Integer,Long> {
             try {
                 refseqIterator = new SeekableRODIterator(new FeatureToGATKFeatureIterator(refseq.iterator(),"refseq"));
             } catch (IOException e) {
-                throw new StingException("Unable to open file " + RefseqFileName, e);
+                throw new UserError.CouldNotReadInputFile(RefseqFileName, e);
             }
 
             logger.info("Using RefSeq annotations from " + RefseqFileName);

java/src/org/broadinstitute/sting/oneoffprojects/walkers/IndelDBRateWalker.java

@@ -18,6 +18,7 @@ import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
 import java.io.PrintStream;
@@ -45,7 +46,7 @@ public class IndelDBRateWalker extends RodWalker<OverlapTable,OverlapTabulator>
 
     public void initialize() {
         if ( indelWindow > 40 ) {
-            throw new StingException("Indel windows have a maximum size of 40");
+            throw new UserError.CommandLineError("Indel windows have a maximum size of 40");
         }
 
         if ( outVCF != null ) {

java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java

@@ -19,10 +19,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -422,7 +419,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
                 } else if ( isOppositeHomozygote(varContext) ) {
                     violation = assessOppositeHomozygote(varContext,tracker,reference,context);
                 } else {
-                    throw new StingException("Mendelian violation that is neither deNovo nor opposite homozygote. Should never see this.");
+                    throw new GATKException("Mendelian violation that is neither deNovo nor opposite homozygote. Should never see this.");
                 }
             } else {
                 violation = new MendelianViolation(varContext,MendelianViolationType.NONE);
@@ -466,7 +463,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
         if ( ! trio.isFiltered() ) {
             Allele parental = trio.getGenotype(trioStructure.mom).getAllele(0); // guaranteed homozygous
             if ( parental.getBases().length < 1 ) {
-                throw new StingException("Parental bases have length zero at "+trio.toString());
+                throw new GATKException("Parental bases have length zero at "+trio.toString());
             }
 
             Map<String,StratifiedAlignmentContext> splitContext = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());

java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java

@@ -25,9 +25,13 @@
 
 package org.broadinstitute.sting.oneoffprojects.walkers;
 
+import java.io.File;
 import java.io.IOException;
+
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.commandline.Argument;
@@ -166,7 +170,7 @@ public class QualityScoreByStrandWalker extends LocusWalker<StrandedCounts,Stran
             pairOut.close();
         }
 	} catch ( IOException e ) {
-	    throw new StingException("Outputfile could not be opened");
+	    throw new UserError.CouldNotCreateOutputFile(new File(pairOutput), e);
 	}
     }
 }
@@ -207,7 +211,7 @@ class StrandedCounts {
 
     public void updateReadPair( int fQual, int rQual, int fOff, int rOff ) {  // hehe f Off
         if ( rOff < 0 || fOff < 0 )
-	    throw new StingException("Offset is negative. Should never happen.");
+	    throw new GATKException("Offset is negative. Should never happen.");
 	forwardCountsByOffset[fOff][fQual < 0 ? 0 : fQual > 40 ? 40 : fQual]++;
         reverseCountsByOffset[rOff][rQual < 0 ? 0 : rQual > 40 ? 40 : rQual]++;
     }

java/src/org/broadinstitute/sting/oneoffprojects/walkers/ReadQualityScoreWalker.java

@@ -35,6 +35,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileWriter;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.*;
 
@@ -79,9 +80,9 @@ public class ReadQualityScoreWalker extends ReadWalker<SAMRecord, SAMFileWriter>
         try {
             inputReader = new BufferedReader( new FileReader ( inputQualityFile ) );
         } catch ( FileNotFoundException e) {
-			throw new StingException("Could not find required input file: " + inputQualityFile);
+            throw new UserError.CouldNotReadInputFile(new File(inputQualityFile), e);
 		} catch (IOException e) {
-			throw new StingException("Failed while reading data from input file: " + inputQualityFile);
+            throw new UserError.CouldNotReadInputFile(new File(inputQualityFile), e);
 		}
         return outputBamFile;
     }
@@ -103,13 +104,13 @@ public class ReadQualityScoreWalker extends ReadWalker<SAMRecord, SAMFileWriter>
             try {
                 if( line == null ) {
                     line = inputReader.readLine();
-                    if( line == null ) { throw new StingException( "Input file is empty: " + inputQualityFile ); }
+                    if( line == null ) { throw new UserError.MalformedFile(new File(inputQualityFile), "Input file is empty" ); }
                 }
                 String[] halves = line.split( " ", 2 );
                 GenomeLoc curLoc = GenomeLocParser.parseGenomeLoc( halves[0] );
                 while( curLoc.isBefore( readLoc ) ) { // Loop until the beginning of the read
                     line = inputReader.readLine();
-                    if( line == null ) { throw new StingException( "Input file doesn't encompass all reads. Can't find beginning of read: " + readLoc ); }
+                    if( line == null ) { throw new UserError.MalformedFile(new File(inputQualityFile), "Input file doesn't encompass all reads. Can't find beginning of read: " + readLoc ); }
                     halves = line.split( " ", 2 );
                     curLoc = GenomeLocParser.parseGenomeLoc( halves[0] );
                 }
@@ -122,7 +123,7 @@ public class ReadQualityScoreWalker extends ReadWalker<SAMRecord, SAMFileWriter>
                     sumNeighborhoodQuality += Float.parseFloat( halves[1] );
                     numLines++;
                     line = inputReader.readLine();
-                    if( line == null ) { throw new StingException( "Input file doesn't encompass all reads. Can't find end of read: " + readLoc ); }
+                    if( line == null ) { throw new UserError.MalformedFile(new File(inputQualityFile), "Input file doesn't encompass all reads. Can't find end of read: " + readLoc ); }
                     halves = line.split( " ", 2 );
                     curLoc = GenomeLocParser.parseGenomeLoc( halves[0] );
                 }
@@ -132,9 +133,9 @@ public class ReadQualityScoreWalker extends ReadWalker<SAMRecord, SAMFileWriter>
                 line = savedLine;
 
             } catch ( FileNotFoundException e ) {
-                throw new StingException( "Could not find required input file: " + inputQualityFile );
+                throw new UserError.CouldNotReadInputFile(new File(inputQualityFile), e);
             } catch (IOException e ) {
-                throw new StingException( "Failed while reading data from input file: " + inputQualityFile + " Also, " + e.getMessage() );
+                throw new UserError.CouldNotReadInputFile(new File(inputQualityFile), e);
             }
 
             meanNeighborhoodQuality = sumNeighborhoodQuality / ((float) numLines);

java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -41,6 +42,7 @@ import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.StringUtil;
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.File;
 import java.io.FileInputStream;
@@ -85,7 +87,7 @@ public class TestReadFishingWalker extends ReadWalker<Integer,Long> {
             indelCallInputStream = new FileInputStream(indelCalls);
         }
         catch(IOException ex) {
-            throw new StingException("Unable to load indel calls.");
+            throw new UserError.CouldNotReadInputFile(indelCalls, ex);
         }
 
         Scanner indelCallReader = new Scanner(indelCallInputStream);
@@ -127,7 +129,7 @@ public class TestReadFishingWalker extends ReadWalker<Integer,Long> {
                 System.arraycopy(referenceSequence.getBases(),eventStart,revisedReference,eventStart+eventLength,bufferWidth);
             }
             else
-                throw new StingException("Invalid indel type: " + type);                
+                throw new GATKException("Invalid indel type: " + type);
 
             aligners.put(GenomeLocParser.createGenomeLoc(contig,start,stop),new BWACAligner(revisedReference,new BWAConfiguration()));
             if(++numAlignersCreated % 100 == 0)

java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java

@@ -11,6 +11,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
@@ -95,7 +96,7 @@ public class VCF4WriterTestWalker extends RodWalker<Integer, Integer> {
                     out.printf("Read %d header lines%n", header.getMetaData().size());
                 }
                 catch (FileNotFoundException e ) {
-                    throw new StingException(e.getMessage());
+                    throw new GATKException(e.getMessage());
                 }
 
                 final Set<String> vcfSamples = header.getGenotypeSamples();

java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval/AminoAcidTransition.java

@@ -9,10 +9,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.analysis.AminoAcid;
 import org.broadinstitute.sting.utils.analysis.AminoAcidTable;
 import org.broadinstitute.sting.utils.analysis.AminoAcidUtils;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 /*
  * Copyright (c) 2010 The Broad Institute
@@ -143,11 +145,11 @@ public class AminoAcidTransition extends VariantEvaluator {
             infoValueSplit = parent.aminoAcidTransitionSplit;
             useCodons = parent.aatUseCodons;
             if ( infoKey == null ) {
-                throw new StingException("No info-field key provided for amino acid tabulation. Please provide the appropriate key with -aatk.");
+                throw new UserError.CommandLineError("No info-field key provided for amino acid tabulation. Please provide the appropriate key with -aatk.");
             }
 
             if ( infoValueSplit == null ) {
-                throw new StingException("No split string provided for amino acid tabulation. Please provide the split string with -aats");
+                throw new UserError.CommandLineError("No split string provided for amino acid tabulation. Please provide the split string with -aats");
             }
         }
     }

java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.playground.analyzeconcordance;
 
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
@@ -91,11 +92,8 @@ public class AnalyzeConcordance extends CommandLineProgram {
 			logger.info("Generating html report...");
 			generateHtmlReport();
 			logger.info("...Done!");
-			
-        } catch (StingException se) {
-            throw se;
         } catch (Exception e) {
-            throw new StingException("Error analyzing concordance", e);
+            throw new GATKException("Error analyzing concordance", e);
         }
 
         return result;
@@ -105,7 +103,7 @@ public class AnalyzeConcordance extends CommandLineProgram {
         // create the output directory where all the data tables and plots will go
         File outputDir = new File(this.outputDir);
         if (!outputDir.exists() && !outputDir.mkdirs()) {
-            throw new StingException("Couldn't create directory: " + this.outputDir);
+            throw new GATKException("Couldn't create directory: " + this.outputDir);
         }
     }
 

java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java

@@ -1,7 +1,9 @@
 package org.broadinstitute.sting.playground.examples;
 
 import org.apache.log4j.BasicConfigurator;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.simpleframework.xml.Element;
 import org.simpleframework.xml.Root;
 import org.simpleframework.xml.Serializer;
@@ -121,7 +123,7 @@ public class SampleXmlMarshaller {
             SampleXmlMarshaller example = serializer.read(SampleXmlMarshaller.class, source);
             return example;
         } catch (Exception e) {
-            throw new StingException("Failed to marshal the data to file " + filename,e);
+            throw new GATKException("Failed to marshal the data to file " + filename,e);
         }
     }
 }

java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java

@@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -155,7 +156,7 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
         if ( g.isHomRef() ) return "HOM-REF";
         else if ( g.isHet() ) return "HET";
         else if ( g.isHom() ) return "HOM-NONREF";
-        else throw new StingException("Unexpected genotype in getGenotypeClass " + g);
+        else throw new GATKException("Unexpected genotype in getGenotypeClass " + g);
     }
 
     public boolean useRead( PileupElement e ) {

java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java

@@ -300,7 +300,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
                         }
                     }
                     if (logger.isDebugEnabled() && (phasingSiteIndex == -1 || phasingSiteIndex == 0))
-                        throw new StingException("Internal error: could NOT find vr and/or prevVr!");
+                        throw new GATKException("Internal error: could NOT find vr and/or prevVr!");
 
                     if (sampleWindowVaList.size() > maxPhaseSites) {
                         logger.warn("Trying to phase sample " + samp + " at locus " + VariantContextUtils.getLocation(vc) + " within a window of " + cacheWindow + " bases yields " + sampleWindowVaList.size() + " heterozygous sites to phase:\n" + toStringVRL(sampleWindowVaList));
@@ -432,7 +432,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
 
     public static void ensurePhasing(BialleleSNP curBiall, BialleleSNP prevBiall, Haplotype hap) {
         if (hap.size() < 2)
-            throw new StingException("LOGICAL ERROR: Only considering haplotypes of length > 2!");
+            throw new GATKException("LOGICAL ERROR: Only considering haplotypes of length > 2!");
 
         byte prevBase = hap.getBase(0); // The 1st base in the haplotype
         byte curBase = hap.getBase(1);  // The 2nd base in the haplotype
@@ -745,7 +745,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         private Haplotype complement(Haplotype hap) {
             int numSites = bialleleSNPs.length;
             if (hap.size() != numSites)
-                throw new StingException("INTERNAL ERROR: hap.size() != numSites");
+                throw new GATKException("INTERNAL ERROR: hap.size() != numSites");
 
             // Take the other base at EACH position of the Haplotype:
             byte[] complementBases = new byte[numSites];
@@ -953,7 +953,7 @@ class Haplotype extends BaseArray implements Cloneable {
 
     public void updateBase(int index, Byte base) {
         if (base == null) {
-            throw new StingException("Internal error: CANNOT have null for a missing Haplotype base!");
+            throw new GATKException("Internal error: CANNOT have null for a missing Haplotype base!");
         }
         super.updateBase(index, base);
     }
@@ -1053,7 +1053,7 @@ class Read extends BaseArray {
 
         int sz = this.bases.length;
         if (sz != hap.bases.length)
-            throw new StingException("Read and Haplotype should have same length to be compared!");
+            throw new GATKException("Read and Haplotype should have same length to be compared!");
 
         for (int i = 0; i < sz; i++) {
             Byte thisBase = this.getBase(i);

java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/MatePairLibrarySize.java

@@ -7,6 +7,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.util.*;
 import java.io.File;
@@ -59,11 +60,12 @@ public class MatePairLibrarySize extends ReadWalker<Integer, Integer> {
         String[] libraries = matePairSize.keySet().toArray(new String[1]);
 
         for (String library : libraries) {
+            File file =  new File(String.format("%s/%s.pairdist", OUT_DIR.getAbsolutePath(), library));
             try {
                 Integer[] sizes = matePairSize.get(library).keySet().toArray(new Integer[1]);
 
                 if (sizes != null && sizes.length > 1) {
-                    PrintWriter pw = new PrintWriter(String.format("%s/%s.pairdist", OUT_DIR.getAbsolutePath(), library));
+                    PrintWriter pw = new PrintWriter(file);
                     Arrays.sort(sizes);
 
                     pw.printf("%s\t%s%n", "insert", "frequency");
@@ -77,7 +79,7 @@ public class MatePairLibrarySize extends ReadWalker<Integer, Integer> {
                     pw.close();
                 }
             } catch (IOException e) {
-                throw new StingException("Unable to initialize output files.");
+                throw new UserError.CouldNotCreateOutputFile(file, e);
             }
         }
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java

@@ -33,6 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.By;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.StingException;
@@ -90,7 +91,7 @@ public class CoverageAcrossBaitsWalker extends LocusWalker<Pair<Integer, Integer
         IntervalRod intervalROD = tracker.lookup("interval",IntervalRod.class);
 
         GenomeLoc interval = intervalROD == null ? null : intervalROD.getLocation();
-        if (interval == null) { throw new StingException("No intervals at locus; should not happen"); }
+        if (interval == null) { throw new GATKException("No intervals at locus; should not happen"); }
         int offset = (int)(context.getPosition() - interval.getStart());
 
         int depth[] = new int[2];

java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/HybSelPerformanceWalker.java

@@ -51,6 +51,7 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.File;
 import java.io.IOException;
@@ -120,7 +121,7 @@ public class HybSelPerformanceWalker extends LocusWalker<Integer, HybSelPerforma
             try {
                 refseqIterator = new SeekableRODIterator(new FeatureToGATKFeatureIterator(refseq.iterator(), "refseq"));
             } catch (IOException e) {
-                throw new StingException("Unable to open file " + REFSEQ_FILE, e);
+                throw new UserError.CouldNotReadInputFile(REFSEQ_FILE, e);
             }
 
             logger.info("Using RefSeq annotations from "+REFSEQ_FILE);

java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java

@@ -25,6 +25,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing;
 
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import java.util.ArrayList;
 import java.util.List;
@@ -35,7 +36,7 @@ public class Biallele {
 
     public Biallele(Genotype gt) {
         if (gt.getPloidy() != 2)
-            throw new StingException("Biallele must have ploidy of 2!");
+            throw new GATKException("Biallele must have ploidy of 2!");
 
         this.top = gt.getAllele(0);
         this.bottom = gt.getAllele(1);

java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java

@@ -26,6 +26,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 public class BialleleSNP extends Biallele {
@@ -34,9 +35,9 @@ public class BialleleSNP extends Biallele {
         super(gt);
 
         if (getTopAllele().getBases().length != 1)
-            throw new StingException("LOGICAL ERROR: BialleleSNP may not contain non-SNP site!");
+            throw new GATKException("LOGICAL ERROR: BialleleSNP may not contain non-SNP site!");
         if (getBottomAllele().getBases().length != 1)
-            throw new StingException("LOGICAL ERROR: BialleleSNP may not contain non-SNP site!");
+            throw new GATKException("LOGICAL ERROR: BialleleSNP may not contain non-SNP site!");
     }
 
     public byte getTopBase() {
@@ -62,7 +63,7 @@ public class BialleleSNP extends Biallele {
         else if (BaseUtils.basesAreEqual(base, botBase))
             return topBase;
         else
-            throw new StingException("LOGICAL ERROR: base MUST match either TOP or BOTTOM!");
+            throw new GATKException("LOGICAL ERROR: base MUST match either TOP or BOTTOM!");
     }
 
     public static byte getSingleBase(byte[] bases) {

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

@@ -10,6 +10,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
@@ -49,7 +50,7 @@ public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
         try {
             digest = MessageDigest.getInstance("MD5");
         } catch (NoSuchAlgorithmException e) {
-            throw new StingException("Unable to find MD5 checksumer");
+            throw new GATKException("Unable to find MD5 checksumer");
         }
         out.println("Header:");
         // enumerate the list of ROD's we've loaded

java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java

@@ -49,6 +49,7 @@ import net.sf.samtools.SAMRecord;
 
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 
@@ -75,8 +76,8 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 	 * @param c mapping of the custom contig sequence onto intervals on the master reference
 	 */
 	public void addCustomContig(String name, Collection<GenomeLoc> c) {
-		if ( name == null ) throw new StingException("Custom contig name can not be null");
+		if ( name == null ) throw new GATKException("Custom contig name can not be null");
-		if ( map.containsKey(name)) throw new StingException("Custom contig "+name+" already exists");
+		if ( map.containsKey(name)) throw new GATKException("Custom contig "+name+" already exists");
 		map.put(name, c);
 	}
 	
@@ -102,7 +103,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 			while( ( line = reader.readLine() ) != null ) {
 				String[] halves = line.split("#",2);
 				if ( halves.length < 2 ) 
-					throw new StingException("Line: "+line+"\nin map file "+f+"\n does not contain contig name");
+					throw new UserError.MalformedFile(f, "Line: "+line+"\nin map file "+f+"\n does not contain contig name");
 				
 				int p1 = 0;
 				for ( ;  p1 < halves[1].length() && Character.isWhitespace(halves[1].charAt(p1) ); p1++ ); 
@@ -112,13 +113,13 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 				// p2 is index of first whitespace after first word
 				
 				if ( p1 == p2 ) 
-					throw new StingException("Line: "+line+"\n in map file "+f+"\nNo contig name found after '#'");
+					throw new UserError.MalformedFile(f, "Line: "+line+"\n in map file "+f+"\nNo contig name found after '#'");
 				
 				String name = halves[1].substring(p1, p2);
 								
 				String[] coord_parts = halves[0].split("\\s");
 				if ( coord_parts.length % 3 != 0 ) 
-					throw new StingException("Line: "+line+"\n in map file "+f+"\nNumber of coordinate fields is not a multiple of 3");
+					throw new UserError.MalformedFile(f, "Line: "+line+"\n in map file "+f+"\nNumber of coordinate fields is not a multiple of 3");
 				
 				List<GenomeLoc> segments = new ArrayList<GenomeLoc>( coord_parts.length / 3 );
 				
@@ -135,9 +136,9 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 			}
 			reader.close();
 		} catch ( FileNotFoundException e) {
-			throw new StingException("Can not find map file "+f);
+			throw new UserError.CouldNotReadInputFile(f, e);
 		} catch (IOException e) {
-			throw new StingException("Failed while reading data from map file "+f);			
+			throw new UserError.CouldNotReadInputFile(f, e);
 		}
 	}
 
@@ -182,14 +183,14 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 					p2 = p1;
 					while ( p2 < line.length() && line.charAt(p2) != ',') p2++; // next comma or end-of-line
 				}
-				if ( segments.size() == 0 ) throw new StingException("Line "+line+" has no intervals specified");
+				if ( segments.size() == 0 ) throw new GATKException("Line "+line+" has no intervals specified");
 				addCustomContig(name, segments);
 			}
 			reader.close();
 		} catch ( FileNotFoundException e) {
-			throw new StingException("Can not find map file "+f);
+			throw new UserError.CouldNotReadInputFile(f, e);
 		} catch (IOException e) {
-			throw new StingException("Failed while reading data from map file "+f);			
+            throw new UserError.CouldNotReadInputFile(f, e);
 		}
 	}
 
@@ -208,7 +209,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 			}
 			writer.close();
 		} catch (IOException e) {
-			throw new StingException("Failed while writing data to map file "+f);
+			throw new UserError.CouldNotCreateOutputFile(f, e);
 		}
 	}
 	
@@ -241,7 +242,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 
         // get mapping from read's contig onto a "global" contig (as a list of intervals on the latter):
 		Collection<GenomeLoc> segments = getContigMapping(r.getReferenceName());
-		if ( segments == null ) throw new StingException("Can not remap a record: unknown custom contig name "+r.getReferenceName());
+		if ( segments == null ) throw new UserError.MalformedBam(r, "Can not remap a record: unknown custom contig name "+r.getReferenceName());
 
         // scroll the list of intervals until we find the interval that the alignment start falls into:
 		Pair<? extends Iterator<GenomeLoc>, Integer> p = seekForward(segments,customStart);
@@ -277,7 +278,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 			case S: // soft clip
 			case H: // or hard clip - these are not included in getAlignmentStart, so pass them through
 				if ( k != 0 && k != N-1 ) // paranoid
-					throw new StingException("Don't know what to do with S or N cigar element that is not at the either end of the cigar. Cigar: "+
+					throw new GATKException("Don't know what to do with S or N cigar element that is not at the either end of the cigar. Cigar: "+
 							r.getCigarString());
 			case I: // insertions are passed through as well
 				newCigar.add(new CigarElement(len,ce.getOperator()));
@@ -315,7 +316,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
                         if ( discardCrossContig ) {
                 //			System.out.println("WARNING: ALIGNMENT DISCARDED: "+message);
                             return null;
-                        } else throw new StingException(message);
+                        } else throw new UserError.MalformedBam(r, message);
                     }
 
                     gl = iter.next(); // advance to next segment
@@ -323,11 +324,11 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
                     refPos = (int)gl.getStart(); // we jump to the start of next segment on the master ref
 
                     if ( gl.getContigIndex() != r.getReferenceIndex() )
-                        throw new StingException("Contig "+oldRefName+
+                        throw new UserError.MalformedBam(r, "Contig "+oldRefName+
                         " has segments on different master contigs: currently unsupported");
 
                     if ( refPos < currStop + 1 )
-                        throw new StingException("Contig "+oldRefName+
+                        throw new UserError.MalformedBam(r, "Contig "+oldRefName+
                         " has segments that are out of order or strictly adjacent: currently unsupported");
                     if ( len > 0 && refPos > currStop + 1 ) {
                         // add "panning" N's w/respect to the master ref over the region between adjacent segments
@@ -375,7 +376,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 	 */
 	private Pair<PushbackIterator<GenomeLoc>,Integer> seekForward(Collection<GenomeLoc> segments,int position) {
 		
-		if ( position < 1 ) throw new StingException("Position "+position + " is outside of custom contig boundaries");
+		if ( position < 1 ) throw new GATKException("Position "+position + " is outside of custom contig boundaries");
 		
 		PushbackIterator<GenomeLoc> iter = new PushbackIterator<GenomeLoc>(segments.iterator());
 		
@@ -390,7 +391,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 			position -= length;
 		}
 		// if we get here, position is to the right of the last segment; not good.
-		throw new StingException("Position "+position + " is outside of custom contig boundaries");
+		throw new GATKException("Position "+position + " is outside of custom contig boundaries");
 	}
 
 	private long contigLength(Collection<GenomeLoc> segments) {

java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.playground.utils;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.StingException;
 import org.apache.log4j.Logger;
@@ -60,7 +61,7 @@ public class ProcessUtils {
 
 			return result;
 		} catch (Exception e) {
-			throw new StingException("Error running command:" + command, e);
+			throw new GATKException("Error running command:" + command, e);
 		}
 	}
 }

java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java

@@ -26,6 +26,7 @@ package org.broadinstitute.sting.playground.utils.report;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.tags.Param;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.annotation.Annotation;
@@ -74,7 +75,7 @@ public class AnalysisModuleScanner {
     /** scan the class and find all appropriate fields and tables */
     public void scan() {
         if (cls == null || !cls.isAnnotationPresent(Analysis.class))
-            throw new StingException("The class passed in cannot be null, " + "" +
+            throw new GATKException("The class passed in cannot be null, " + "" +
                                      "and must contain the @Analysis annotation, class " + cls + " was the input");
 
         // get the annotation off of the class

java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.playground.utils.report;
 import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
 import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils;
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
@@ -195,7 +196,7 @@ public class ReportMarshaller {
             else
                 node.addAllChildren(nodes);
         } catch (IllegalAccessException e) {
-            throw new StingException("Unable to access field " + f);
+            throw new GATKException("Unable to access field " + f);
         }
     }
 }

java/src/org/broadinstitute/sting/playground/utils/report/VE2ReportFactory.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.playground.utils.report;
 import org.broadinstitute.sting.playground.utils.report.templates.*;
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.io.*;
 import java.util.List;
@@ -84,13 +85,8 @@ public class VE2ReportFactory {
     public static ReportFormat createByType(Class formatType) {
         try {
             return ((Class<? extends ReportFormat>) formatType).newInstance();
-        }
+        } catch (Exception e) {
-        catch (InstantiationException ex) {
+            throw new DynamicClassResolutionException(formatType, e);
-            throw new StingException(String.format("Unable to instantiate %s", formatType), ex);
-        }
-        catch (IllegalAccessException ex) {
-            throw new StingException(String.format("Unable to access %s", formatType), ex);
         }
     }
-
 }

java/src/org/broadinstitute/sting/playground/utils/report/templates/GrepFormat.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.utils.report.templates;
 
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -31,7 +32,7 @@ public class GrepFormat implements ReportFormat {
         try {
             stream = new PrintWriter(baseFile);
         } catch (FileNotFoundException e) {
-            throw new StingException("Unable to write to file " + baseFile, e);
+            throw new UserError.CouldNotCreateOutputFile(baseFile, e);
         }
         privateWrite(baseNode);
     }

java/src/org/broadinstitute/sting/playground/utils/report/templates/TableBasedFormat.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.playground.utils.report.templates;
 
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.*;
 import java.util.*;
@@ -36,7 +37,7 @@ public abstract class TableBasedFormat implements ReportFormat {
      * @param baseNode the root node
      */
     public void write(Writer writeLocation, Node baseNode) {
-        if (splitFilesByAnalysis()) throw new StingException("Unable to write output report, we require a file input for multi-file formats");
+        if (splitFilesByAnalysis()) throw new UserError.CommandLineError("Unable to write output report, we require a file input for multi-file formats");
         // if there is only a single output file, create it
         stream = new PrintWriter(writeLocation);
         traverseAnalysisNodes(baseNode);
@@ -222,12 +223,13 @@ public abstract class TableBasedFormat implements ReportFormat {
      */
     public void newStream(String analysisOrTableName) {
         String name = analysisOrTableName.replaceAll("\\s+","_").replaceAll("\\/","_slash_");
+        File file = new File(this.baseLocation + "." + name + this.extension());
         if (stream == null || splitFilesByAnalysis()) {
             if (stream != null) stream.close();
             try {
-                stream = new PrintWriter(this.baseLocation + "." + name + this.extension());
+                stream = new PrintWriter(file);
             } catch (FileNotFoundException e) {
-                throw new StingException("Unable to create Report file at location " + this.baseLocation + "." + name + this.extension(), e);
+                throw new UserError.CouldNotCreateOutputFile(file, e);
             }
         }
     }

java/src/org/broadinstitute/sting/playground/utils/report/templates/TextTable.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.playground.utils.report.templates;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.IOException;
 import java.io.Writer;
@@ -103,7 +104,7 @@ class TextTable {
         try {
             writer.append("\n");
         } catch (IOException e) {
-            throw new StingException("Unable to write to the Writer");
+            throw new UserError.CouldNotCreateOutputFile(writer.toString(), "Unable to write to the Writer", e);
         }
     }
 
@@ -128,7 +129,7 @@ class TextTable {
             if (y != rows.size() - 1)
                 writer.append(seperator);
         } catch (IOException e) {
-            throw new StingException("Unable to write to the Writer");
+            throw new UserError.CouldNotCreateOutputFile(writer.toString(), "Unable to write to the Writer", e);
         }
     }
 

java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java

@@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescripto
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
@@ -94,7 +95,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
     protected int execute() {
         try {
             if (!outputDirectory.isDirectory() && !outputDirectory.mkdirs())
-                throw new StingException("Unable to create output directory: " + outputDirectory);
+                throw new GATKException("Unable to create output directory: " + outputDirectory);
 
             for (Class<? extends CommandLineProgram> clp: clpManager.getValues()) {
 

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

@@ -35,7 +35,7 @@ public class CardinalityCounter implements Iterator<int[]>, Iterable<int[]> {
 
     public int[] next() {
         if (!hasNext())
-            throw new StingException("CANNOT iterate past end!");
+            throw new GATKException("CANNOT iterate past end!");
 
         // Copy the assignment to be returned:
         int[] nextList = new int[valList.length];

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

@@ -164,7 +164,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
 
     public GenomeLoc merge( GenomeLoc that ) throws GATKException {
         if (!(this.contiguousP(that))) {
-            throw new StingException("The two genome loc's need to be contigous");
+            throw new GATKException("The two genome loc's need to be contigous");
         }
 
         return new GenomeLoc(getContig(), this.contigIndex,
@@ -174,7 +174,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
 
     public GenomeLoc intersect( GenomeLoc that ) throws GATKException {
         if (!(this.overlapsP(that))) {
-            throw new StingException("GenomeLoc::intersect(): The two genome loc's need to overlap");
+            throw new GATKException("GenomeLoc::intersect(): The two genome loc's need to overlap");
         }
 
         return new GenomeLoc(getContig(), this.contigIndex,

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

@@ -193,13 +193,13 @@ public class GenomeLocParser {
                     stop = parsePosition(str.substring(dashIndex + 1));
                 }
             } catch(Exception e) {
-                throw new StingException("Failed to parse Genome Location string: " + str, e);
+                throw new UserError("Failed to parse Genome Location string: " + str, e);
             }
         }
 
         // is the contig valid?
         if (!isContigValid(contig))
-            throw new StingException("Contig '" + contig + "' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?");
+            throw new UserError("Contig '" + contig + "' does not match any contig in the GATK sequence dictionary derived from the reference; are you sure you are using the correct reference fasta file?");
 
         if (stop == Integer.MAX_VALUE && hasKnownContigOrdering())
             // lookup the actually stop position!
@@ -319,13 +319,7 @@ public class GenomeLocParser {
      */
     public static List<GenomeLoc> intervalFileToList(final String file_name) {
         // try to open file
-        File inputFile = null;
+        File inputFile = new File(file_name);
-        try {
-            inputFile = new File(file_name);
-        }
-        catch (Exception e) {
-            throw new StingException("Could not open file", e);
-        }
 
         // check if file is empty
         if (inputFile.exists() && inputFile.length() < 1) {
@@ -377,7 +371,7 @@ public class GenomeLocParser {
                 return ret.isEmpty() ? null : ret;
             }
             catch (IOException e2) {
-                throw new StingException("An I/O error occurred while reading the interval file.", e);
+                throw new UserError.CouldNotReadInputFile(new File(file_name), e);
             }
         }
     }
@@ -433,10 +427,10 @@ public class GenomeLocParser {
     public static GenomeLoc createGenomeLoc(int contigIndex, final long start, final long stop) {
         checkSetup();
         if (start < 0) {
-            throw new StingException("Bad start position " + start);
+            throw new GATKException("Bad start position " + start);
         }
         if (stop < -1) {
-            throw new StingException("Bad stop position " + stop);
+            throw new GATKException("Bad stop position " + stop);
         }    // a negative -1 indicates it's not a meaningful end position
 
 
@@ -503,16 +497,16 @@ public class GenomeLocParser {
      */
     private static GenomeLoc exceptionOnInvalidGenomeLoc(GenomeLoc toReturn) {
         if (toReturn.getStart() < 0) {
-            throw new StingException("Parameters to GenomeLocParser are incorrect: the start position is less than 0");
+            throw new GATKException("Parameters to GenomeLocParser are incorrect: the start position is less than 0");
         }
         if ((toReturn.getStop() != -1) && (toReturn.getStop() < 0)) {
-            throw new StingException("Parameters to GenomeLocParser are incorrect: the stop position is less than 0");
+            throw new GATKException("Parameters to GenomeLocParser are incorrect: the stop position is less than 0");
         }
         if (toReturn.getContigIndex() < 0) {
-            throw new StingException("Parameters to GenomeLocParser are incorrect: the contig index is less than 0");
+            throw new GATKException("Parameters to GenomeLocParser are incorrect: the contig index is less than 0");
         }
         if (toReturn.getContigIndex() >= contigInfo.getSequences().size()) {
-            throw new StingException("Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count");
+            throw new GATKException("Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count");
 
         }
         return toReturn;
@@ -533,11 +527,11 @@ public class GenomeLocParser {
     private static void exceptionOnInvalidGenomeLocBounds(GenomeLoc locus) {
         int contigSize = contigInfo.getSequence(locus.getContigIndex()).getSequenceLength();
         if(locus.getStart() > contigSize)
-            throw new StingException(String.format("GenomeLoc is invalid: locus start %d is after the end of contig %s",locus.getStart(),locus.getContig()));
+            throw new GATKException(String.format("GenomeLoc is invalid: locus start %d is after the end of contig %s",locus.getStart(),locus.getContig()));
         if(locus.getStop() > contigSize)
-            throw new StingException(String.format("GenomeLoc is invalid: locus stop %d is after the end of contig %s",locus.getStop(),locus.getContig()));
+            throw new GATKException(String.format("GenomeLoc is invalid: locus stop %d is after the end of contig %s",locus.getStop(),locus.getContig()));
         if (locus.getStart() > locus.getStop()) {
-            throw new StingException("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position");
+            throw new GATKException("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position");
         }
     }
 
@@ -629,7 +623,7 @@ public class GenomeLocParser {
 
         int index = -1;
         if ((index = contigInfo.getSequenceIndex(contig)) < 0) {
-            throw new StingException("Contig name ( " + contig + " ) not in the set sequence dictionary.");
+            throw new GATKException("Contig name ( " + contig + " ) not in the set sequence dictionary.");
         }
         return exceptionOnInvalidGenomeLoc(new GenomeLoc(contig, index, loc.start, loc.getStop()));
     }
@@ -642,7 +636,7 @@ public class GenomeLocParser {
     public static GenomeLoc setContigIndex(GenomeLoc loc, int contig) {
         checkSetup();
         if ((contig >= GenomeLocParser.contigInfo.getSequences().size()) || (contig < 0)) {
-            throw new StingException("Contig index ( " + contig + " ) is not in the sequence dictionary set.");
+            throw new GATKException("Contig index ( " + contig + " ) is not in the sequence dictionary set.");
         }
         return exceptionOnInvalidGenomeLoc(new GenomeLoc(GenomeLocParser.contigInfo.getSequence(contig).getSequenceName(), contig, loc.start, loc.getStop()));
     }
@@ -715,7 +709,7 @@ public class GenomeLocParser {
     /** check to make sure that we've setup the contig information */
     private static void checkSetup() {
         if (contigInfo == null) {
-            throw new StingException("The GenomeLocParser hasn't been setup with a contig sequence yet");
+            throw new GATKException("The GenomeLocParser hasn't been setup with a contig sequence yet");
         }
     }
 

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

@@ -109,7 +109,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
         } else {
             int loc = Collections.binarySearch(mArray,e);
             if (loc >= 0) {
-                throw new StingException("Genome Loc Sorted Set already contains the GenomicLoc " + e.toString());
+                throw new GATKException("Genome Loc Sorted Set already contains the GenomicLoc " + e.toString());
             } else {
                 mArray.add((loc+1) * -1,e);
                 return true;
@@ -193,7 +193,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
             } else if ( e.getStop() < p.getStart() ) {
                 toExclude.pop();                 // p starts after e stops, e is done
             } else {
-                throw new StingException("BUG: unexpected condition: p=" + p + ", e=" + e);
+                throw new GATKException("BUG: unexpected condition: p=" + p + ", e=" + e);
             }
 
             if ( i++ % 10000 == 0 )

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

@@ -40,7 +40,7 @@ public class HeapSizeMonitor {
             monitorThread.join();
         }
         catch(InterruptedException ex) {
-            throw new StingException("Unable to connect to monitor thread");
+            throw new GATKException("Unable to connect to monitor thread");
         }
         monitorThread = null;        
     }
@@ -72,7 +72,7 @@ public class HeapSizeMonitor {
                     Thread.sleep(monitorFrequencyMillis);
                 }
                 catch(InterruptedException ex) {
-                    throw new StingException("Unable to continue monitoring heap consumption",ex);
+                    throw new GATKException("Unable to continue monitoring heap consumption",ex);
                 }
             }
         }

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

@@ -17,7 +17,7 @@ package org.broadinstitute.sting.utils;
  * bad sequence id out of bounds, etc.
  */
 
-public class MalformedGenomeLocException extends StingException {
+public class MalformedGenomeLocException extends GATKException {
     /**
      * Create a new MalformedGenomeLocException with the given message.  Does not preserve the existing stack trace.
      * @param message The message.

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

@@ -112,7 +112,7 @@ public class PathUtils {
         }
 
         if (dir.listFiles() == null) {
-            throw new StingException("The volume '" + dir.getAbsolutePath() + "' could not be accessed.");
+            throw new GATKException("The volume '" + dir.getAbsolutePath() + "' could not be accessed.");
         }
     }
 

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

@@ -35,7 +35,7 @@ public class ReservoirDownsampler<T> {
      */
     public ReservoirDownsampler(final int maxElements) {
         if(maxElements < 0)
-            throw new StingException("Unable to work with an negative size collection of elements");
+            throw new GATKException("Unable to work with an negative size collection of elements");
         this.reservoir = new ArrayList<T>(maxElements);
         this.maxElements = maxElements;
     }

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

@@ -185,7 +185,7 @@ public class WilcoxonRankSum {
                 U = n1 < n2 ? U1 : U2;
                 break;
             default:
-                throw new StingException("Unexpected WILCOXON H0: " + h0);
+                throw new GATKException("Unexpected WILCOXON H0: " + h0);
         }
 
         // data is nA nB then
@@ -232,7 +232,7 @@ public class WilcoxonRankSum {
                 pvalue = NORMAL.cdf(z);
                 break;
             default:
-                throw new StingException("Unexpected WILCOXON H0: " + h0);
+                throw new GATKException("Unexpected WILCOXON H0: " + h0);
         }
 
         return pvalue;

java/src/org/broadinstitute/sting/utils/bed/BedParser.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.utils.bed;
 
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
@@ -33,7 +34,7 @@ public class BedParser {
         try {
             mIn = new BufferedReader(new FileReader(fl));
         } catch (FileNotFoundException e) {
-            throw new StingException("Unable to open the bed file = " + fl);
+            throw new UserError.CouldNotReadInputFile(fl, e);
         }
         mLocations = parseLocations();
     }
@@ -61,7 +62,7 @@ public class BedParser {
                 locArray.add(parseLocation(line));
             }
         } catch (IOException e) {
-            throw new StingException("Unable to parse line in BED file.");
+            throw new UserError.MalformedFile("Unable to parse line in BED file.");
         }
         return locArray;
     }
@@ -82,7 +83,7 @@ public class BedParser {
             start = Integer.valueOf(parts[1]) + TO_ONE_BASED_ADDITION;
             stop = Integer.valueOf(parts[2]); // the ending point is an open interval
         } catch (Exception e) {
-            throw new StingException("Unable to process bed file line = " + line);
+            throw new UserError.MalformedFile("Unable to process bed file line = " + line, e);
         }
 
         // we currently drop the rest of the bed record, which can contain names, scores, etc

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.utils.classloader;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.reflect.Modifier;
@@ -127,7 +128,7 @@ public class JVMUtils {
             field.set(instance, value);
         }
         catch( IllegalAccessException ex ) {
-            throw new StingException(String.format("Could not set %s in instance %s to %s",field.getName(),instance.getClass().getName(),value.toString()));
+            throw new GATKException(String.format("Could not set %s in instance %s to %s",field.getName(),instance.getClass().getName(),value.toString()));
         }
     }
 
@@ -143,7 +144,7 @@ public class JVMUtils {
             return field.get(instance);
         }
         catch( IllegalAccessException ex ) {
-            throw new StingException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName()));
+            throw new GATKException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName()));
         }
     }
 

java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java

@@ -28,7 +28,9 @@ package org.broadinstitute.sting.utils.classloader;
 import ch.qos.logback.classic.Level;
 import ch.qos.logback.classic.Logger;
 import ch.qos.logback.classic.LoggerContext;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.reflections.Reflections;
 import org.reflections.scanners.SubTypesScanner;
 import org.reflections.util.ClasspathHelper;
@@ -95,10 +97,8 @@ public class PackageUtils {
     public static <T> T getSimpleInstance(Class<T> c) {
         try {
             return c.newInstance();
-        } catch (InstantiationException e) {
+        } catch (Exception e) {
-            throw new StingException(String.format("Cannot instantiate class '%s': must be concrete class", c.getSimpleName()));
+            throw new DynamicClassResolutionException(c, e);
-        } catch (IllegalAccessException e) {
-            throw new StingException(String.format("Cannot instantiate class '%s': must have no-arg constructor", c.getSimpleName()));
         }
     }
 
@@ -138,7 +138,7 @@ public class PackageUtils {
           method.invoke(ClassLoader.getSystemClassLoader(), url);
           resetReflections();
       } catch (Exception e) {
-          throw new StingException("Error adding url to the current classloader.", e);
+          throw new GATKException("Error adding url to the current classloader.", e);
       }
     }
 

java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java

@@ -25,8 +25,10 @@
 
 package org.broadinstitute.sting.utils.classloader;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.util.HashMap;
 import java.util.List;
@@ -84,17 +86,13 @@ public abstract class PluginManager<PluginType> {
      * @return The plugin object if found; null otherwise.
      */
     public PluginType createByName(String pluginName) {
+        Class<? extends PluginType> plugin = pluginsByName.get(pluginName);
         try {
-            Class<? extends PluginType> plugin = pluginsByName.get(pluginName);
             if( plugin == null )
-                throw new StingException(String.format("Could not find %s with name: %s", pluginCategory,pluginName));
+                throw new GATKException(String.format("Could not find %s with name: %s", pluginCategory,pluginName));
             return plugin.newInstance();
-        }
+        } catch (Exception e) {
-        catch( InstantiationException ex ) {
+            throw new DynamicClassResolutionException(plugin, e);
-            throw new StingException(String.format("Unable to instantiate %s %s",pluginCategory,pluginName), ex);
-        }
-        catch( IllegalAccessException ex ) {
-            throw new StingException(String.format("Unable to access %s %s",pluginCategory,pluginName), ex);
         }
     }
 
@@ -107,12 +105,8 @@ public abstract class PluginManager<PluginType> {
     public PluginType createByType(Class pluginType) {
         try {
             return ((Class<? extends PluginType>) pluginType).newInstance();
-        }
+        } catch (Exception e) {
-        catch( InstantiationException ex ) {
+            throw new DynamicClassResolutionException(pluginType, e);
-            throw new StingException(String.format("Unable to instantiate %s",pluginCategory), ex);
-        }
-        catch( IllegalAccessException ex ) {
-            throw new StingException(String.format("Unable to access %s",pluginCategory), ex);
         }
     }
 

java/src/org/broadinstitute/sting/utils/collections/CircularArray.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.utils.collections;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 
@@ -69,7 +70,7 @@ public class CircularArray <T> {
 	
 	/** Creates an array of fixed length */
 	public CircularArray(int length) {
-		if ( length <= 0 ) throw new StingException("CircularArray length must be positive. Passed: "+length);
+		if ( length <= 0 ) throw new GATKException("CircularArray length must be positive. Passed: "+length);
 		data = new Object[length]; 
 		offset = 0;
 	}
@@ -150,7 +151,7 @@ public class CircularArray <T> {
 		
 		/** Creates an array of fixed length */
 		public Int(int length) {
-			if ( length <= 0 ) throw new StingException("CircularArray length must be positive. Passed: "+length);
+			if ( length <= 0 ) throw new GATKException("CircularArray length must be positive. Passed: "+length);
 			data = new int[length]; // automaticaly initialized to zeros
 			offset = 0;
 		}

java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.collections;
 
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 
@@ -42,10 +43,10 @@ public class MergingIterator implements Iterator<RODRecordList>, Iterable<RODRec
         public Element(Iterator<RODRecordList> it) {
             if ( it instanceof LocationAwareSeekableRODIterator) {
                 this.it = (LocationAwareSeekableRODIterator)it;
-                if ( ! it.hasNext() ) throw new StingException("Iterator is empty");
+                if ( ! it.hasNext() ) throw new GATKException("Iterator is empty");
                 update();
             } else {
-                throw new StingException("Iterator passed to MergingIterator is not LocationAwareSeekableRODIterator");
+                throw new GATKException("Iterator passed to MergingIterator is not LocationAwareSeekableRODIterator");
             }
         }
 

java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java

@@ -40,7 +40,7 @@ public class DupUtils {
         try {
             return (SAMRecord)read.clone();
         } catch ( CloneNotSupportedException e ) {
-            throw new StingException("Unexpected Clone failure!");
+            throw new GATKException("Unexpected Clone failure!");
         }
     }
 

java/src/org/broadinstitute/sting/utils/exceptions/DynamicClassResolutionException.java

@@ -0,0 +1,64 @@
+/*
+ * 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.utils.exceptions;
+
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMSequenceDictionary;
+import org.broadinstitute.sting.utils.GATKException;
+import org.broadinstitute.sting.utils.StingException;
+
+import java.io.File;
+import java.lang.reflect.InvocationTargetException;
+
+/**
+ * Class for handling common failures of dynamic class resolution
+ *
+ * User: depristo
+ * Date: Sep 3, 2010
+ * Time: 2:24:09 PM
+ */
+public class DynamicClassResolutionException extends UserError {
+    public DynamicClassResolutionException(Class c, Exception ex) {
+        super(String.format("Could not create module %s because %s caused by exception %s",
+                c.getSimpleName(), moreInfo(ex), ex.getMessage()));
+    }
+
+    private static String moreInfo(Exception ex) {
+        try {
+            throw ex;
+        } catch (InstantiationException e) {
+            return "BUG: cannot instantiate class: must be concrete class";
+        } catch (NoSuchMethodException e) {
+            return "BUG: Cannot find expected constructor for class";
+        } catch (IllegalAccessException e) {
+            return "Cannot instantiate class (Illegal Access)";
+        } catch (InvocationTargetException e) {
+            return "Cannot instantiate class (Invocation failure)";
+        } catch ( Exception e ) {
+            return "A general exception occurred";
+        }
+    }
+}

java/src/org/broadinstitute/sting/utils/exceptions/UserError.java

@@ -27,9 +27,11 @@ package org.broadinstitute.sting.utils.exceptions;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMSequenceDictionary;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
+import java.lang.reflect.InvocationTargetException;
 
 /**
  * Represents the common user errors detected by Sting / GATK
@@ -40,7 +42,7 @@ import java.io.File;
  * Date: Sep 3, 2010
  * Time: 2:24:09 PM
  */
-public class UserError extends StingException {
+public class UserError extends GATKException {
     public UserError(String msg) { super(msg); }
     public UserError(String msg, Throwable e) { super(msg, e); }
     private UserError(Throwable e) { super("", e); } // cannot be called, private access                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
@@ -51,6 +53,12 @@ public class UserError extends StingException {
         }
     }
 
+    public static class BadInput extends UserError {
+        public BadInput(String message) {
+            super(String.format("Bad input: %s", message));
+        }
+    }
+
     // todo -- fix up exception cause passing
     public static class MissingArgument extends CommandLineError {
         public MissingArgument(String arg, String message) {
@@ -156,7 +164,11 @@ public class UserError extends StingException {
         public MalformedFile(File f, String message, Exception e) {
             super(String.format("File %s is malformed: %s caused by %s", f.getAbsolutePath(), message, e.getMessage()));
         }
-    }
+
+        public MalformedFile(String name, String message, Exception e) {
+            super(String.format("File associated with name %s is malformed: %s caused by %s", name, message, e.getMessage()));
+        }
+     }
 
     public static class CannotExecuteRScript extends UserError {
         public CannotExecuteRScript(String message, Exception e) {
@@ -183,5 +195,4 @@ public class UserError extends StingException {
             super(String.format("Walker %s is not available: %s", walkerName, message));
         }
     }
-
 }

java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.utils.fasta;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.FileNotFoundException;
@@ -34,7 +35,7 @@ public class ArtificialFastaUtils {
         try {
             s = new PrintStream(new FileOutputStream(fileName));
         } catch (FileNotFoundException e) {
-            throw new StingException("Filename " + fileName + " passed to the ArtificialFastaUtils generated a FileNotFound exception", e);
+            throw new GATKException("Filename " + fileName + " passed to the ArtificialFastaUtils generated a FileNotFound exception", e);
         }
         generateFakeFasta(contigNames, contigSizes, pattern, s);
     }
@@ -58,7 +59,7 @@ public class ArtificialFastaUtils {
      */
     private static void generateFakeFasta(List<String> contigNames, List<Integer> contigSizes, BASE_PATTERN pattern, PrintStream s) {
         if (contigNames.size() != contigSizes.size()) {
-            throw new StingException("ArtificialContig name and size arrays are not equal sizes");
+            throw new GATKException("ArtificialContig name and size arrays are not equal sizes");
         }
         for (int x = 0; x < contigNames.size(); x++) {
             ArtificialContig tig = new ArtificialContig(contigNames.get(x), contigSizes.get(x), pattern);
@@ -122,7 +123,7 @@ class ArtificialContig {
             case ALL_G:
                 return "G";
             default:
-                throw new StingException("Unknown base pattern");
+                throw new GATKException("Unknown base pattern");
         }
     }
 

java/src/org/broadinstitute/sting/utils/fastq/FastqReader.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.utils.fastq;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.util.Iterator;
 import java.util.zip.GZIPInputStream;
@@ -23,7 +24,7 @@ public class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord>
 
             nextRecord = readNextRecord();
         } catch (IOException e) {
-            throw new StingException(String.format("Error opening '%s'", fastqFile.getAbsolutePath()));
+            throw new UserError.CouldNotReadInputFile(file, String.format("Error opening '%s'", fastqFile.getAbsolutePath()));
         }
     }
 
@@ -36,7 +37,7 @@ public class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord>
 
             return new FastqRecord(seqHeader, seqLine, qualHeader, qualLine);
         } catch (IOException e) {
-            throw new StingException(String.format("Error reading '%s'", fastqFile.getAbsolutePath()));
+            throw new UserError.CouldNotReadInputFile(fastqFile, e);
         }
     }
 
@@ -52,7 +53,7 @@ public class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord>
                 nextRecord = null;
             }
         } catch (IOException e) {
-            throw new StingException("IO problem");
+            throw new UserError.CouldNotReadInputFile(fastqFile, e);
         }
 
         return rec;
@@ -66,7 +67,7 @@ public class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord>
         try {
             in.close();
         } catch (IOException e) {
-            
+            throw new UserError.CouldNotReadInputFile(fastqFile, e);
         }
     }
 }

java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.utils.file;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
@@ -143,7 +144,7 @@ public class FSLockWithShared {
                 channel.close();
         }
         catch (Exception e) {
-            throw new StingException("An error occurred while unlocking file", e);
+            throw new GATKException("An error occurred while unlocking file", e);
         }
     }
 }

java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.utils.genotype;
 import edu.mit.broad.picard.genotype.DiploidGenotype;
 import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
 import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.HashMap;
@@ -234,15 +235,15 @@ public class LikelihoodObject {
         switch (mLikelihoodType) {
             case NEGATIVE_LOG:
                 if (score < 0)
-                    throw new StingException("Likelikhood score of " + score + " is invalid, for NEGATIVE_LOG it must be greater than or equal to 0");
+                    throw new GATKException("Likelikhood score of " + score + " is invalid, for NEGATIVE_LOG it must be greater than or equal to 0");
                 break;
             case LOG:
                 if (score > 0)
-                    throw new StingException("Likelikhood score of " + score + " is invalid, for LOG it must be less than or equal to 0");
+                    throw new GATKException("Likelikhood score of " + score + " is invalid, for LOG it must be less than or equal to 0");
                 break;
             case RAW:
                 if (score < 0 || score > 1)
-                    throw new StingException("Likelikhood score of " + score + " is invalid, for RAW it must be [0,1]");
+                    throw new GATKException("Likelikhood score of " + score + " is invalid, for RAW it must be [0,1]");
                 break;
         }
     }

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java

@@ -3,7 +3,9 @@ package org.broadinstitute.sting.utils.genotype.glf;
 import net.sf.samtools.util.BinaryCodec;
 import net.sf.samtools.util.BlockCompressedInputStream;
 import net.sf.samtools.util.RuntimeEOFException;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
 
 import java.io.DataInputStream;
@@ -63,23 +65,28 @@ public class GLFReader implements Iterator<GLFRecord> {
     // we have this variable becuase there is no eof for glf's
     private int lastRecordType = -1;
 
+    private File myFile;
+
     /**
      * create a glf reader
      *
      * @param readFrom the file to read from
      */
     public GLFReader(File readFrom) {
+        myFile = readFrom;
+
         try {
             inputBinaryCodec = new BinaryCodec(new DataInputStream(new BlockCompressedInputStream(readFrom)));
         } catch (IOException e) {
-            throw new StingException("Unable to open " + readFrom.getName(), e);
+            throw new UserError.CouldNotReadInputFile(myFile, e);
         }
+
         inputBinaryCodec.setInputFileName(readFrom.getName());
 
         // first verify that it's a valid GLF
         for (short s : glfMagic) {
             if (inputBinaryCodec.readUByte() != s)
-                throw new StingException("Verification of GLF format failed: magic string doesn't match)");
+                throw new UserError.MalformedFile(myFile, "Verification of GLF format failed: magic string doesn't match)");
         }
 
         // get the header string
@@ -170,7 +177,7 @@ public class GLFReader implements Iterator<GLFRecord> {
             }
             //nextRecord = null;
         } else {
-            throw new StingException("Unkonwn GLF record type (type = " + recordType + ")");
+            throw new UserError.MalformedFile(myFile, "Unknown GLF record type (type = " + recordType + ")");
         }
         if (nextRecord != null) currentLocation = nextRecord.getPosition();
         return ret;
@@ -219,7 +226,7 @@ public class GLFReader implements Iterator<GLFRecord> {
     }
 
     public void remove() {
-        throw new StingException("GLFReader doesn't support remove()");
+        throw new GATKException("GLFReader doesn't support remove()");
     }
 
     public void close() {

java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.utils.genotype.glf;
 
 import net.sf.samtools.util.BinaryCodec;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 
@@ -251,7 +252,7 @@ public abstract class GLFRecord {
      * @return the minimum value
      */
     protected static double findMin(double vals[]) {
-        if (vals.length < 1) throw new StingException("findMin: an array of size < 1 was passed in");
+        if (vals.length < 1) throw new GATKException("findMin: an array of size < 1 was passed in");
 
         double min = vals[0];
         for (double d : vals)

java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.utils.help;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
@@ -80,7 +81,7 @@ public class ApplicationDetails {
             runningInstructions = JVMUtils.getLocationFor( application ).getName();
         }
         catch( IOException ex ) {
-            throw new StingException("Unable to determine running instructions", ex);
+            throw new GATKException("Unable to determine running instructions", ex);
         }
 
         if( runningInstructions.endsWith(".jar") )

java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java

@@ -31,6 +31,7 @@ import java.util.*;
 import java.io.PrintStream;
 import java.io.IOException;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.Utils;
@@ -181,7 +182,7 @@ public class ResourceBundleExtractorDoclet {
         for(Tag tag: element.tags()) {
             if(tag.name().equals("@"+DisplayNameTaglet.NAME)) {
                 if(name != null)
-                    throw new StingException("Only one display name tag can be used per package / walker.");
+                    throw new GATKException("Only one display name tag can be used per package / walker.");
                 name = tag.text();
             }
             else if(tag.name().equals("@"+VERSION_TAGLET_NAME))

java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java

@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.utils.instrumentation;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.instrument.Instrumentation;
@@ -73,7 +74,7 @@ public class Sizeof {
      */
     public static long getObjectSize(Object o) {
         if(!isEnabled())
-            throw new StingException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
+            throw new GATKException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
         return instrumentation.getObjectSize(o);
     }
 
@@ -84,7 +85,7 @@ public class Sizeof {
      */
     public static long getObjectGraphSize(Object o) {
         if(!isEnabled())
-            throw new StingException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
+            throw new GATKException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
         IdentityHashMap<Object,Object> objectsSeen = new IdentityHashMap<Object,Object>();
         return getObjectGraphSize(o,objectsSeen);
     }
@@ -134,7 +135,7 @@ public class Sizeof {
                     fieldValue = field.get(o);
                 }
                 catch(IllegalAccessException ex) {
-                    throw new StingException("Unable to access field " + field.getName(),ex);
+                    throw new GATKException("Unable to access field " + field.getName(),ex);
                 }
                 totalSize += getObjectGraphSize(fieldValue,objectsSeen);
             }

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

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.interval;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.StringToGenomeLocIteratorAdapter;
@@ -52,11 +53,13 @@ import java.io.FileNotFoundException;
  * iterator is a merging one).
  */
 public class IntervalFileMergingIterator implements Iterator<GenomeLoc> {
-
     private PushbackIterator<GenomeLoc> it ;
     private IntervalMergingRule myRule;
+    private File myFile;
 
     public IntervalFileMergingIterator(File f, IntervalMergingRule rule) {
+        myFile = f;
+
         try {
             XReadLines reader = new XReadLines(f);
 
@@ -68,7 +71,7 @@ public class IntervalFileMergingIterator implements Iterator<GenomeLoc> {
                                                               StringToGenomeLocIteratorAdapter.FORMAT.GATK ) ) ;
             }
         } catch ( FileNotFoundException e ) {
-            throw new StingException("Can not open interval file "+f);
+            throw new UserError.CouldNotReadInputFile(f, e);
         }
         myRule = rule;
     }
@@ -91,7 +94,7 @@ public class IntervalFileMergingIterator implements Iterator<GenomeLoc> {
             GenomeLoc next = it.next();
 
             if ( next.isBefore(current)) {
-                throw new StingException("Interval "+next+" in the interval file is out of order.");
+                throw new UserError.MalformedFile(myFile, "Interval "+next+" in the interval file is out of order.");
             }
 
             if (current.overlapsP(next)) {

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

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.util.LinkedList;
 import java.util.List;
@@ -39,7 +40,7 @@ public class IntervalUtils {
                 if (argument.equals("all")) {
                     if (argList.size() != 1) {
                         // throw error if '-L all' is not only interval - potentially conflicting commands
-                        throw new StingException(String.format("Conflicting arguments: Intervals given along with \"-L all\""));
+                        throw new UserError.CommandLineError(String.format("Conflicting arguments: Intervals given along with \"-L all\""));
                     }
                     return null;
                 }
@@ -53,9 +54,7 @@ public class IntervalUtils {
                             rawIntervals.addAll(GenomeLocParser.intervalFileToList(fileOrInterval));
                         }
                         catch (Exception e) {
-                            throw new StingException(String.format("Interval file %s could not be parsed in either format. " +
+                            throw new UserError.MalformedFile(fileOrInterval, "Interval file could not be parsed in either format.", e);
-                                    "The problem is:%n%s",
-                                    fileOrInterval, e.getMessage()), e);
                         }
                     }
 
@@ -147,11 +146,11 @@ public class IntervalUtils {
             if (file.exists())
                 return true;
             else
-                throw new StingException(String.format("The interval file %s does not exist.", file.getAbsolutePath()));
+                throw new UserError.CouldNotReadInputFile(file, "The interval file does not exist.");
         }
 
         if(file.exists())
-            throw new StingException(String.format("The interval file %s does not have one of " +
+            throw new UserError.CouldNotReadInputFile(file, String.format("The interval file %s does not have one of " +
                     "the supported extensions (.bed, .list, .picard, .interval_list, or .intervals). " +
                     "Please rename your file with the appropriate extension. If %s is NOT supposed to be a file, " +
                     "please move or rename the file at location %s", str, str, file.getAbsolutePath()));

java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java

@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.utils.pileup;
 
 import net.sf.samtools.SAMReadGroupRecord;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -83,8 +84,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      *
      */
     public AbstractReadBackedPileup(GenomeLoc loc, List<PE> pileup) {
-        if ( loc == null ) throw new StingException("Illegal null genomeloc in ReadBackedPileup");
+        if ( loc == null ) throw new GATKException("Illegal null genomeloc in ReadBackedPileup");
-        if ( pileup == null ) throw new StingException("Illegal null pileup in ReadBackedPileup");
+        if ( pileup == null ) throw new GATKException("Illegal null pileup in ReadBackedPileup");
 
         this.loc = loc;
         this.pileupElementTracker = new UnifiedPileupElementTracker<PE>(pileup);
@@ -97,8 +98,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @param pileup
      */
     public AbstractReadBackedPileup(GenomeLoc loc, List<PE> pileup, int size, int nDeletions, int nMQ0Reads) {
-        if ( loc == null ) throw new StingException("Illegal null genomeloc in UnifiedReadBackedPileup");
+        if ( loc == null ) throw new GATKException("Illegal null genomeloc in UnifiedReadBackedPileup");
-        if ( pileup == null ) throw new StingException("Illegal null pileup in UnifiedReadBackedPileup");
+        if ( pileup == null ) throw new GATKException("Illegal null pileup in UnifiedReadBackedPileup");
 
         this.loc = loc;
         this.pileupElementTracker = new UnifiedPileupElementTracker<PE>(pileup);
@@ -159,9 +160,9 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @return
      */
     private PileupElementTracker<PE> readsOffsets2Pileup(List<SAMRecord> reads, List<Integer> offsets ) {
-        if ( reads == null ) throw new StingException("Illegal null read list in UnifiedReadBackedPileup");
+        if ( reads == null ) throw new GATKException("Illegal null read list in UnifiedReadBackedPileup");
-        if ( offsets == null ) throw new StingException("Illegal null offsets list in UnifiedReadBackedPileup");
+        if ( offsets == null ) throw new GATKException("Illegal null offsets list in UnifiedReadBackedPileup");
-        if ( reads.size() != offsets.size() ) throw new StingException("Reads and offset lists have different sizes!");
+        if ( reads.size() != offsets.size() ) throw new GATKException("Reads and offset lists have different sizes!");
 
         UnifiedPileupElementTracker<PE> pileup = new UnifiedPileupElementTracker<PE>();
         for ( int i = 0; i < reads.size(); i++ ) {
@@ -179,8 +180,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @return
      */
     private PileupElementTracker<PE> readsOffsets2Pileup(List<SAMRecord> reads, int offset ) {
-        if ( reads == null ) throw new StingException("Illegal null read list in UnifiedReadBackedPileup");
+        if ( reads == null ) throw new GATKException("Illegal null read list in UnifiedReadBackedPileup");
-        if ( offset < 0 ) throw new StingException("Illegal offset < 0 UnifiedReadBackedPileup");
+        if ( offset < 0 ) throw new GATKException("Illegal offset < 0 UnifiedReadBackedPileup");
 
         UnifiedPileupElementTracker<PE> pileup = new UnifiedPileupElementTracker<PE>();
         for ( int i = 0; i < reads.size(); i++ ) {

java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java

@@ -23,6 +23,7 @@
  */
 package org.broadinstitute.sting.utils.pileup;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -140,7 +141,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
                 case INSERTION: v[i] = 'I'; break;
                 case DELETION: v[i] = 'D'; break;
                 case NOEVENT: v[i] = '.'; break;
-                default: throw new StingException("Unknown event type encountered: "+e.getType());
+                default: throw new GATKException("Unknown event type encountered: "+e.getType());
             }
             i++;
         }
@@ -190,7 +191,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
                     indel = getDeletionString(e.getEventLength(),refBases);
                     break;
                 case NOEVENT: continue;
-                default: throw new StingException("Unknown event type encountered: "+e.getType());
+                default: throw new GATKException("Unknown event type encountered: "+e.getType());
             }
 
             cnt = events.get(indel);

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

@@ -31,6 +31,7 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
@@ -146,7 +147,7 @@ public class AlignmentUtils {
                 case H:
                 case P:
                     break;
-                default: throw new StingException("The " + ce.getOperator() + " cigar element is not currently supported");
+                default: throw new GATKException("The " + ce.getOperator() + " cigar element is not currently supported");
             }
 
         }
@@ -298,7 +299,7 @@ public class AlignmentUtils {
             case P:
                 break;
             default:
-                throw new StingException( "Unsupported cigar operator: " + ce.getOperator() );
+                throw new GATKException( "Unsupported cigar operator: " + ce.getOperator() );
             }
         }
         return alignment;
@@ -337,7 +338,7 @@ public class AlignmentUtils {
             case P:
                 break;
             default:
-                throw new StingException( "Unsupported cigar operator: " + ce.getOperator() );
+                throw new GATKException( "Unsupported cigar operator: " + ce.getOperator() );
             }
         }
         return alignment;

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

@@ -10,6 +10,7 @@ import java.io.ByteArrayInputStream;
 import java.io.UnsupportedEncodingException;
 import java.util.*;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -93,7 +94,7 @@ public class ArtificialSAMFileReader extends SAMFileReader {
             return new ByteArrayInputStream(byteArray);
         }
         catch( UnsupportedEncodingException ex ) {
-            throw new StingException("Unable to build empty input stream",ex);
+            throw new GATKException("Unable to build empty input stream",ex);
         }
     }
 }

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

@@ -6,6 +6,7 @@ import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 
@@ -126,7 +127,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {
         // sanity check that we have an actual matching read next
         SAMRecord rec = this.peek();
         if (rec == null) {
-            throw new StingException("The next read doesn't match");
+            throw new GATKException("The next read doesn't match");
         }
         // set the seeked variable to true
         seeked = true;
@@ -165,7 +166,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {
             super.next();
         }
         if (!super.hasNext()) {
-            throw new StingException("Unable to find the target chromosome");
+            throw new GATKException("Unable to find the target chromosome");
         }
         while (super.hasNext() && this.peek().getAlignmentStart() < start) {
             super.next();
@@ -173,7 +174,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {
         // sanity check that we have an actual matching read next
         SAMRecord rec = this.peek();
         if (!matches(rec)) {
-            throw new StingException("The next read doesn't match");
+            throw new GATKException("The next read doesn't match");
         }
         // set the seeked variable to true
         seeked = true;

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
@@ -115,7 +116,7 @@ public class ArtificialSAMUtils {
      */
     public static SAMFileHeader createEnumeratedReadGroups( SAMFileHeader header, List<String> readGroupIDs, List<String> sampleNames ) {
         if (readGroupIDs.size() != sampleNames.size()) {
-            throw new StingException("read group count and sample name count must be the same");
+            throw new GATKException("read group count and sample name count must be the same");
         }
 
         List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>();
@@ -145,7 +146,7 @@ public class ArtificialSAMUtils {
     public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, int length ) {
         if( (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) ||
             (refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START) )
-            throw new StingException("Invalid alignment start for artificial read, start = " + alignmentStart);
+            throw new GATKException("Invalid alignment start for artificial read, start = " + alignmentStart);
         SAMRecord record = new SAMRecord(header);
         record.setReadName(name);
         record.setReferenceIndex(refIndex);
@@ -183,7 +184,7 @@ public class ArtificialSAMUtils {
      */
     public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual ) {
         if (bases.length != qual.length) {
-            throw new StingException("Passed in read string is different length then the quality array");
+            throw new GATKException("Passed in read string is different length then the quality array");
         }
         SAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
         rec.setReadBases(bases);

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

@@ -5,6 +5,7 @@ import java.util.*;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 /**
  * @author ebanks
@@ -64,7 +65,7 @@ public class GATKSAMRecord extends SAMRecord {
 
         // sanity check that the lengths of the base and quality strings are equal
         if ( getBaseQualities().length  != getReadLength() )
-            throw new StingException(String.format("Error: the number of base qualities does not match the number of bases in %s (and the GATK does not currently support '*' for the quals)", mRecord.getReadName()));
+            throw new UserError.MalformedBam(this, String.format("Error: the number of base qualities does not match the number of bases in %s (and the GATK does not currently support '*' for the quals)", mRecord.getReadName()));
     }
 
     ///////////////////////////////////////////////////////////////////////////////

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

@@ -29,6 +29,7 @@ import net.sf.samtools.SAMFileReader;
 
 import java.io.File;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 /**
@@ -72,9 +73,9 @@ public class SAMFileReaderBuilder {
      */
     public SAMFileReader build() {
         if( samFile == null )
-            throw new StingException( "Filename for output sam file must be supplied.");
+            throw new GATKException( "Filename for output sam file must be supplied.");
         if( validationStringency == null )
-            throw new StingException( "Header for output sam file must be supplied.");
+            throw new GATKException( "Header for output sam file must be supplied.");
 
         SAMFileReader reader = new SAMFileReader( samFile );
         reader.setValidationStringency( validationStringency );

java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.utils.text;
 
 import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
@@ -110,7 +111,7 @@ public class TextFormattingUtils {
                 bundle = new PropertyResourceBundle(new StringReader(""));
             }
             catch(IOException ioe) {
-                throw new StingException("No resource bundle found, and unable to create an empty placeholder.",ioe);
+                throw new GATKException("No resource bundle found, and unable to create an empty placeholder.",ioe);
             }
         }
         return bundle;

java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java

@@ -1,7 +1,9 @@
 package org.broadinstitute.sting.utils.wiggle;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.*;
 
@@ -40,12 +42,15 @@ public class WiggleWriter {
     private StepType type = StepType.variable;
     // the type of step for the wiggle file, todo -- allow this to change
 
+    private String myFile = "unknown";
+
     public WiggleWriter(File outputFile) {
+        myFile = outputFile.getAbsolutePath();
         FileOutputStream outputStream;
         try {
             outputStream = new FileOutputStream(outputFile);
         } catch ( FileNotFoundException e ) {
-            throw new StingException("Unable to create a wiggle file at location: %s"+outputFile.getAbsolutePath(),e);
+            throw new UserError.CouldNotCreateOutputFile(outputFile, "Unable to create a wiggle file ", e);
         }
 
         wWriter = new BufferedWriter(new OutputStreamWriter(outputStream));
@@ -72,7 +77,7 @@ public class WiggleWriter {
             write(wWriter,String.format("%d\t%s",loc.getStart(),dataPoint.toString()));
         } else {
             // todo -- maybe allow this to open a new file for the new chromosome?
-            throw new StingException("Attempting to write multiple contigs into wiggle file, first contig was "+firstLoc.getContig()+" most recent "+loc.getContig());
+            throw new GATKException("Attempting to write multiple contigs into wiggle file, first contig was "+firstLoc.getContig()+" most recent "+loc.getContig());
         }
     }
 
@@ -82,7 +87,7 @@ public class WiggleWriter {
             w.flush();
             // flush required so writing to output stream will work
         } catch (IOException e) {
-            throw new StingException(String.format("Error writing the wiggle line %s",s),e);
+            throw new UserError.CouldNotCreateOutputFile(myFile, String.format("Error writing the wiggle line %s", s), e);
         }
     }
 }