Massive review of maybe 50% of the exceptions in the GATK. GATKException is a tmp. tracker so that I can tell which StingExceptions I've reviewed. Please don't use it. If you are working on new code and are considering throwing exceptions, it's either UserError or StingException, please

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4246 348d0f76-0448-11de-a6fe-93d51630548a

java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java

@@ -26,6 +26,7 @@
 package net.sf.picard.reference;
 
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSourceProgressListener;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*;
 
@@ -33,6 +34,7 @@ import java.io.*;
 import java.util.Iterator;
 
 import net.sf.picard.reference.FastaSequenceIndex;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 /**
  * Builds FastaSequenceIndex from fasta file.
@@ -83,7 +85,7 @@ public class FastaSequenceIndexBuilder {
             in = new DataInputStream(new BufferedInputStream(new FileInputStream(fastaFile)));
         }
         catch (Exception e) {
-            throw new StingException(String.format("Could not read fasta file %s", fastaFile.getAbsolutePath()));
+            throw new UserError.CouldNotReadInputFile(fastaFile, "Could not read fasta file", e);
         }
 
         /*
@@ -166,7 +168,7 @@ public class FastaSequenceIndexBuilder {
                         // validate base character
                         else {
                             if (!isValidBase(currentByte))
-                                throw new StingException(String.format("An invalid base was found in the contig: %s", contig));
+                                throw new UserError.MalformedFile(fastaFile, String.format("An invalid base was found in the contig: %s", contig));
                         }
                         break;
 
@@ -192,7 +194,7 @@ public class FastaSequenceIndexBuilder {
                                     // error if next char is a valid base, end of contig otherwise
                                 else if (basesThisLine != basesPerLine || bytesPerLine != bytesRead - endOfLastLine) {
                                     if (isValidBase(nextByte) && nextByte != -1) {
-                                        throw new StingException(String.format("An invalid line was found in the contig: %s", contig));
+                                        throw new UserError.MalformedFile(fastaFile, String.format("An invalid line was found in the contig: %s", contig));
                                     }
                                     else
                                         finishReadingContig(sequenceIndex);
@@ -204,7 +206,7 @@ public class FastaSequenceIndexBuilder {
                         // validate base character
                         else {
                             if (!isValidBase(currentByte))
-                                throw new StingException(String.format("An invalid base was found in the contig: %s", contig));
+                                throw new UserError.MalformedFile(fastaFile, String.format("An invalid base was found in the contig: %s", contig));
                         }
                         break;
                 }
@@ -212,9 +214,10 @@ public class FastaSequenceIndexBuilder {
             return sequenceIndex;
         }
         catch (IOException e) {
-            throw new StingException(String.format("Could not read fasta file %s", fastaFile.getAbsolutePath()), e);        }
+            throw new UserError.CouldNotReadInputFile(fastaFile, String.format("Could not read fasta file"), e);
+        }
         catch (Exception e) {
-            throw new StingException(e.getMessage(), e);
+            throw new GATKException(e.getMessage(), e);
         }
     }
 
@@ -270,8 +273,7 @@ public class FastaSequenceIndexBuilder {
             out = new BufferedWriter(new FileWriter(faiFile));
         }
         catch (Exception e) {
-            throw new StingException(String.format("Could not open file %s for writing. Check that GATK is permitted to write to disk.",
+            throw new UserError.CouldNotCreateOutputFile(faiFile, e);
-                    faiFile.getAbsolutePath()), e);
         }
 
         try {
@@ -282,7 +284,7 @@ public class FastaSequenceIndexBuilder {
             out.close();
         }
         catch (Exception e) {
-            throw new StingException(String.format("An error occurred while writing file %s", e));
+            throw new UserError.CouldNotCreateOutputFile(faiFile, e);
         }
     }
 

java/src/org/broadinstitute/sting/alignment/Alignment.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.alignment;
 
 import net.sf.samtools.*;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
@@ -189,7 +190,7 @@ public class Alignment {
             read = (SAMRecord)unmappedRead.clone();
         }
         catch(CloneNotSupportedException ex) {
-            throw new StingException("Unable to create aligned read from template.");
+            throw new GATKException("Unable to create aligned read from template.");
         }
 
         if(newSAMHeader != null)

java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 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.alignment.bwa.c.BWACAligner;
@@ -120,7 +121,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
                     logger.error(String.format("    Mapping quality: %s%n", alignmentsByScore[i].getMappingQuality()));
                 }
             }
-            throw new StingException(String.format("Read %s mismatches!", read.getReadName()));
+            throw new GATKException(String.format("Read %s mismatches!", read.getReadName()));
         }
 
         return 1;

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.bwa;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
@@ -76,7 +77,7 @@ public class BWTFiles {
      */
     public BWTFiles(String prefix) {
         if(prefix == null)
-            throw new StingException("Prefix must not be null.");
+            throw new GATKException("Prefix must not be null.");
         annFile = new File(prefix + ".ann");
         ambFile = new File(prefix + ".amb");
         pacFile = new File(prefix + ".pac");
@@ -135,7 +136,7 @@ public class BWTFiles {
             success &= reverseSAFile.delete();
 
             if(!success)
-                throw new StingException("Unable to clean up autogenerated representation");
+                throw new GATKException("Unable to clean up autogenerated representation");
         }
     }
 
@@ -183,7 +184,7 @@ public class BWTFiles {
             writeEncodedReferenceSequence(reverseReferenceSequence,rpacFile,rbwtFile,rsaFile);
         }
         catch(IOException ex) {
-            throw new StingException("Unable to write autogenerated reference sequence to temporary files");
+            throw new GATKException("Unable to write autogenerated reference sequence to temporary files");
         }
 
         // Make sure that, at the very least, all temporary files are deleted on exit.
@@ -235,7 +236,7 @@ public class BWTFiles {
         StringUtil.toUpperCase(referenceSequence);
         for(byte base: referenceSequence) {
             if(base != 'A' && base != 'C' && base != 'G' && base != 'T')
-                throw new StingException(String.format("Base type %c is not supported when building references on-the-fly",(char)base));
+                throw new GATKException(String.format("Base type %c is not supported when building references on-the-fly",(char)base));
         }
     }
 }

java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.c;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
@@ -29,15 +30,15 @@ public class BWACAligner extends BWAAligner {
     public BWACAligner(BWTFiles bwtFiles, BWAConfiguration configuration) {
         super(bwtFiles,configuration);
         if(thunkPointer != 0)
-            throw new StingException("BWA/C attempting to reinitialize.");
+            throw new GATKException("BWA/C attempting to reinitialize.");
 
-        if(!bwtFiles.annFile.exists()) throw new StingException("ANN file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.annFile.exists()) throw new GATKException("ANN file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.ambFile.exists()) throw new StingException("AMB file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.ambFile.exists()) throw new GATKException("AMB file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.pacFile.exists()) throw new StingException("PAC file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.pacFile.exists()) throw new GATKException("PAC file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.forwardBWTFile.exists()) throw new StingException("Forward BWT file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.forwardBWTFile.exists()) throw new GATKException("Forward BWT file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.forwardSAFile.exists()) throw new StingException("Forward SA file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.forwardSAFile.exists()) throw new GATKException("Forward SA file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.reverseBWTFile.exists()) throw new StingException("Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.reverseBWTFile.exists()) throw new GATKException("Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.reverseSAFile.exists()) throw new StingException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.reverseSAFile.exists()) throw new GATKException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it.");
 
         thunkPointer = create(bwtFiles,configuration);
     }
@@ -60,7 +61,7 @@ public class BWACAligner extends BWAAligner {
     @Override
     public void updateConfiguration(BWAConfiguration configuration) {
         if(thunkPointer != 0)
-            throw new StingException("BWA/C: attempting to update configuration of uninitialized aligner.");
+            throw new GATKException("BWA/C: attempting to update configuration of uninitialized aligner.");
         updateConfiguration(thunkPointer,configuration);
     }
 
@@ -70,7 +71,7 @@ public class BWACAligner extends BWAAligner {
     @Override
     public void close() {
         if(thunkPointer == 0)
-            throw new StingException("BWA/C close attempted, but BWA/C is not properly initialized.");
+            throw new GATKException("BWA/C close attempted, but BWA/C is not properly initialized.");
         destroy(thunkPointer);
     }
 
@@ -82,7 +83,7 @@ public class BWACAligner extends BWAAligner {
     @Override
     public Alignment getBestAlignment(final byte[] bases) {
         if(thunkPointer == 0)
-            throw new StingException("BWA/C getBestAlignment attempted, but BWA/C is not properly initialized.");
+            throw new GATKException("BWA/C getBestAlignment attempted, but BWA/C is not properly initialized.");
         return getBestAlignment(thunkPointer,bases);
     }
 
@@ -193,7 +194,7 @@ public class BWACAligner extends BWAAligner {
      */
     public BWAPath[] getPaths(byte[] bases) {
         if(thunkPointer == 0)
-            throw new StingException("BWA/C getPaths attempted, but BWA/C is not properly initialized.");
+            throw new GATKException("BWA/C getPaths attempted, but BWA/C is not properly initialized.");
         return getPaths(thunkPointer,bases);
     }
 
@@ -226,7 +227,7 @@ public class BWACAligner extends BWAAligner {
      */
     protected Alignment[] convertPathsToAlignments(byte[] bases, BWAPath[] paths) {
         if(thunkPointer == 0)
-            throw new StingException("BWA/C convertPathsToAlignments attempted, but BWA/C is not properly initialized.");
+            throw new GATKException("BWA/C convertPathsToAlignments attempted, but BWA/C is not properly initialized.");
         return convertPathsToAlignments(thunkPointer,bases,paths);
     }
 

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.java;
 
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 
@@ -61,7 +62,7 @@ public class AlignerTestHarness {
                 alignmentCleaned = (SAMRecord)read.clone();
             }
             catch( CloneNotSupportedException ex ) {
-                throw new StingException("SAMRecord clone not supported", ex);
+                throw new GATKException("SAMRecord clone not supported", ex);
             }
 
             if( alignmentCleaned.getReadNegativeStrandFlag() )

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

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
 import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Deque;
@@ -33,7 +34,7 @@ public class AlignmentMatchSequence implements Cloneable {
             copy = (AlignmentMatchSequence)super.clone(); 
         }
         catch( CloneNotSupportedException ex ) {
-            throw new StingException("Unable to clone AlignmentMatchSequence.");
+            throw new GATKException("Unable to clone AlignmentMatchSequence.");
         }
 
         copy.entries = new ArrayDeque<AlignmentMatchSequenceEntry>();
@@ -53,7 +54,7 @@ public class AlignmentMatchSequence implements Cloneable {
                 case MATCH_MISMATCH: operator = CigarOperator.MATCH_OR_MISMATCH; break;
                 case INSERTION: operator = CigarOperator.INSERTION; break;
                 case DELETION: operator = CigarOperator.DELETION; break;
-                default: throw new StingException("convertToCigar: cannot process state: " + entry.getAlignmentState());
+                default: throw new GATKException("convertToCigar: cannot process state: " + entry.getAlignmentState());
             }
             cigar.add( new CigarElement(entry.count,operator) );
         }
@@ -129,7 +130,7 @@ public class AlignmentMatchSequence implements Cloneable {
                 return (AlignmentMatchSequenceEntry)super.clone(); 
             }
             catch( CloneNotSupportedException ex ) {
-                throw new StingException("Unable to clone AlignmentMatchSequenceEntry.");
+                throw new GATKException("Unable to clone AlignmentMatchSequenceEntry.");
             }
         }
 

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

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.alignment.bwa.java.BWAJavaAligner;
 import org.broadinstitute.sting.alignment.bwa.java.AlignmentMatchSequence;
 import org.broadinstitute.sting.alignment.bwa.java.AlignmentState;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.Cigar;
 
@@ -151,7 +152,7 @@ public class BWAAlignment extends Alignment implements Cloneable {
             newAlignment = (BWAAlignment)super.clone();
         }
         catch( CloneNotSupportedException ex ) {
-            throw new StingException("Unable to clone BWAAlignment.");
+            throw new GATKException("Unable to clone BWAAlignment.");
         }
         newAlignment.creationNumber = numCreated++;
         newAlignment.alignmentMatchSequence = alignmentMatchSequence.clone();

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

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 /**
@@ -124,7 +125,7 @@ public class BWT {
      */
     protected byte getBase(long index) {
         if(index == inverseSA0)
-            throw new StingException(String.format("Base at index %d does not have a text representation",index));
+            throw new GATKException(String.format("Base at index %d does not have a text representation",index));
 
         SequenceBlock block = getSequenceBlock(index);
         int position = getSequencePosition(index);

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
@@ -28,7 +29,7 @@ public class BWTReader {
             this.inputStream = new FileInputStream(inputFile);
         }
         catch( FileNotFoundException ex ) {
-            throw new StingException("Unable to open input file", ex);
+            throw new GATKException("Unable to open input file", ex);
         }
     }
 
@@ -80,7 +81,7 @@ public class BWTReader {
             inputStream.close();
         }
         catch( IOException ex ) {
-            throw new StingException("Unable to close input file", ex);
+            throw new GATKException("Unable to close input file", ex);
         }
     }
 }

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;
@@ -28,7 +29,7 @@ public class BWTWriter {
             this.outputStream = new BufferedOutputStream(new FileOutputStream(outputFile));
         }
         catch( FileNotFoundException ex ) {
-            throw new StingException("Unable to open output file", ex);
+            throw new GATKException("Unable to open output file", ex);
         }
     }
 
@@ -53,7 +54,7 @@ public class BWTWriter {
             intPackedOutputStream.write(bwt.counts.toArray(false));
         }
         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);
         }
     }
 
@@ -65,7 +66,7 @@ public class BWTWriter {
             outputStream.close();
         }
         catch( IOException ex ) {
-            throw new StingException("Unable to close input file", ex);
+            throw new GATKException("Unable to close input file", ex);
         }
     }
 }

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
@@ -87,7 +88,7 @@ public class Bases implements Iterable<Byte>
             if( entry.getValue().equals(ascii) )
                 return entry.getKey();
         }
-        throw new StingException(String.format("Base %c is an invalid base to pack", (char)ascii));
+        throw new GATKException(String.format("Base %c is an invalid base to pack", (char)ascii));
     }
 
     /**

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.HashMap;
@@ -96,7 +97,7 @@ public class Counts implements Cloneable {
             other = (Counts)super.clone();
         }
         catch(CloneNotSupportedException ex) {
-            throw new StingException("Unable to clone counts object", ex);
+            throw new GATKException("Unable to clone counts object", ex);
         }
         other.counts = new HashMap<Byte,Long>(counts);
         other.cumulativeCounts = new HashMap<Byte,Long>(cumulativeCounts);

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

@@ -31,6 +31,7 @@ import net.sf.picard.reference.ReferenceSequence;
 
 import java.io.*;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 
@@ -182,7 +183,7 @@ public class CreateBWTFromReference {
 
         for( int i = 0; i < bwt.length(); i++ ) {
             if( bwtSequence[i] != existingBWTSequence[i] )
-                throw new StingException("BWT mismatch at " + i);
+                throw new GATKException("BWT mismatch at " + i);
         }
 
         File existingSAFile = new File(inputFileName+".sa");
@@ -193,7 +194,7 @@ public class CreateBWTFromReference {
             if( i % 10000 == 0 )
                 System.out.printf("Validating suffix array entry %d%n", i);
             if( suffixArray.get(i) != existingSuffixArray.get(i) )
-                throw new StingException(String.format("Suffix array mismatch at %d; SA is %d; should be %d",i,existingSuffixArray.get(i),suffixArray.get(i)));
+                throw new GATKException(String.format("Suffix array mismatch at %d; SA is %d; should be %d",i,existingSuffixArray.get(i),suffixArray.get(i)));
         }
     }
 

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Comparator;
@@ -53,7 +54,7 @@ public class SuffixArray {
         this.bwt = bwt;
 
         if(sequenceInterval != 1 && bwt == null)
-            throw new StingException("A BWT must be provided if the sequence interval is not 1");
+            throw new GATKException("A BWT must be provided if the sequence interval is not 1");
     }
 
     /**
@@ -118,7 +119,7 @@ public class SuffixArray {
                 inverseSA0 = i;
         }
         if(inverseSA0 < 0)
-            throw new StingException("Unable to find first inverse SA entry in generated suffix array.");
+            throw new GATKException("Unable to find first inverse SA entry in generated suffix array.");
 
         return new SuffixArray(inverseSA0,occurrences,suffixArray);
     }    

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
@@ -35,7 +36,7 @@ public class SuffixArrayReader {
             this.bwt = bwt;
         }
         catch( FileNotFoundException ex ) {
-            throw new StingException("Unable to open input file", ex);
+            throw new GATKException("Unable to open input file", ex);
         }
     }
 
@@ -61,7 +62,7 @@ public class SuffixArrayReader {
             uintPackedInputStream.read(suffixArray);
         }
         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 SuffixArray(inverseSA0, new Counts(occurrences,true), suffixArray, suffixArrayInterval, bwt);
@@ -76,7 +77,7 @@ public class SuffixArrayReader {
             inputStream.close();
         }
         catch( IOException ex ) {
-            throw new StingException("Unable to close input file", ex);
+            throw new GATKException("Unable to close input file", ex);
         }
     }    
 }

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 
@@ -27,7 +28,7 @@ public class SuffixArrayWriter {
             this.outputStream = new BufferedOutputStream(new FileOutputStream(outputFile));
         }
         catch( FileNotFoundException ex ) {
-            throw new StingException("Unable to open input file", ex);
+            throw new GATKException("Unable to open input file", ex);
         }
     }
 
@@ -48,7 +49,7 @@ public class SuffixArrayWriter {
             uintPackedOutputStream.write(suffixArray.sequence,1,suffixArray.sequence.length-1);
         }
         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);
         }
     }
 
@@ -61,7 +62,7 @@ public class SuffixArrayWriter {
             outputStream.close();
         }
         catch( IOException ex ) {
-            throw new StingException("Unable to close input file", ex);
+            throw new GATKException("Unable to close input file", ex);
         }
     }
 }

java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
@@ -51,7 +52,7 @@ public class BasePackedInputStream<T> {
 
     public BasePackedInputStream( Class<T> type, FileInputStream inputStream, ByteOrder byteOrder ) {
         if( type != Integer.class )
-            throw new StingException("Only bases packed into 32-bit words are currently supported by this input stream.  Type specified: " + type.getName());
+            throw new GATKException("Only bases packed into 32-bit words are currently supported by this input stream.  Type specified: " + type.getName());
         this.type = type;
         this.targetInputStream = inputStream;
         this.targetInputChannel = inputStream.getChannel();

java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.*;
@@ -134,7 +135,7 @@ public class BasePackedOutputStream<T> {
         else if( type == Byte.class )
             buffer.put((byte)packedBases);
         else
-            throw new StingException("Cannot pack bases into type " + type.getName());
+            throw new GATKException("Cannot pack bases into type " + type.getName());
         targetOutputStream.write(buffer.array());        
     }
 }

java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
@@ -58,14 +59,14 @@ public class PackUtils {
             long typeSize = type.getField("MAX_VALUE").getLong(null) - type.getField("MIN_VALUE").getLong(null)+1;
             long intTypeSize = (long)Integer.MAX_VALUE - (long)Integer.MIN_VALUE + 1;
             if( typeSize > intTypeSize )
-                throw new StingException("Cannot determine number of bits available in type: " + type.getName());
+                throw new GATKException("Cannot determine number of bits available in type: " + type.getName());
             return (int)(Math.log(typeSize)/Math.log(2));
         }
         catch( NoSuchFieldException ex ) {
-            throw new StingException("Cannot determine number of bits available in type: " + type.getName(),ex);
+            throw new GATKException("Cannot determine number of bits available in type: " + type.getName(),ex);
         }
         catch( IllegalAccessException ex ) {
-            throw new StingException("Cannot determine number of bits available in type: " + type.getName(),ex);
+            throw new GATKException("Cannot determine number of bits available in type: " + type.getName(),ex);
         }
     }
 
@@ -85,7 +86,7 @@ public class PackUtils {
             case 'T':
                 return 3;
             default:
-                throw new StingException("Unknown base type: " + base);
+                throw new GATKException("Unknown base type: " + base);
         }
     }
 
@@ -105,7 +106,7 @@ public class PackUtils {
             case 3:
                 return 'T';
             default:
-                throw new StingException("Unknown pack type: " + pack);
+                throw new GATKException("Unknown pack type: " + pack);
         }
     }
 

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
@@ -69,7 +70,7 @@ public class ArgumentDefinitionGroup implements Iterable<ArgumentDefinition> {
      */
     public ArgumentDefinitionGroup merge( ArgumentDefinitionGroup other ) {
         if( !groupNameMatches(other) )
-            throw new StingException("Unable to merge two argument groups with differing names.");
+            throw new GATKException("Unable to merge two argument groups with differing names.");
 
         // Create a merged definition group.
         List<ArgumentDefinition> mergedDefinitions = new ArrayList<ArgumentDefinition>();

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Set;
@@ -56,9 +57,9 @@ public class ArgumentDefinitions implements Iterable<ArgumentDefinition> {
             if( definition.fullName.length() == 0 )
                 throw new IllegalArgumentException( "Argument cannot have 0-length fullname." );
             if( hasArgumentDefinition( definition.fullName, FullNameDefinitionMatcher ) )
-                throw new StingException("Duplicate definition of argument with full name: " + definition.fullName);
+                throw new GATKException("Duplicate definition of argument with full name: " + definition.fullName);
             if( definition.shortName != null && hasArgumentDefinition( definition.shortName, ShortNameDefinitionMatcher ) )
-                throw new StingException("Duplicate definition of argument with short name: " + definition.shortName);
+                throw new GATKException("Duplicate definition of argument with short name: " + definition.shortName);
 
             argumentDefinitions.add( definition );
         }

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

@@ -24,6 +24,7 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.annotation.Annotation;
@@ -46,6 +47,6 @@ public enum ArgumentIOType {
         for (ArgumentIOType ioType: ArgumentIOType.values())
             if (ioType.annotationClass.isAssignableFrom(annotation.getClass()))
                 return ioType;
-        throw new StingException("Unknown annotation type: " + annotation);
+        throw new GATKException("Unknown annotation type: " + annotation);
     }
 }

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.lang.reflect.Field;
@@ -209,7 +210,7 @@ public class ArgumentSource {
      */
     public MultiplexArgumentTypeDescriptor createDependentTypeDescriptor(Object containingObject) {
         if(!isDependent())
-            throw new StingException("Field " + field.getName() + " is independent; no dependent type descriptor can be derived.");
+            throw new GATKException("Field " + field.getName() + " is independent; no dependent type descriptor can be derived.");
         return ((MultiplexArgumentTypeDescriptor)typeDescriptor).createCustomTypeDescriptor(this,containingObject);
     }
 

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

@@ -25,11 +25,13 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 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.UserError;
 
 import java.lang.annotation.Annotation;
 import java.lang.reflect.*;
@@ -81,7 +83,7 @@ public abstract class ArgumentTypeDescriptor {
             if( descriptor.supports(type) )
                 return descriptor;
         }
-        throw new StingException("Can't process command-line arguments of type: " + type.getName());
+        throw new GATKException("Can't process command-line arguments of type: " + type.getName());
     }
 
     /**
@@ -219,7 +221,7 @@ public abstract class ArgumentTypeDescriptor {
     protected String getArgumentValue( ArgumentDefinition definition, ArgumentMatches matches ) {
         Collection<String> argumentValues = getArgumentValues( definition, matches );
         if( argumentValues.size() > 1 )
-            throw new StingException("Multiple values associated with given definition, but this argument expects only one: " + definition.fullName);
+            throw new UserError.CommandLineError("Multiple values associated with given definition, but this argument expects only one: " + definition.fullName);
         return argumentValues.size() > 0 ? argumentValues.iterator().next() : null;
     }
 
@@ -263,7 +265,7 @@ public abstract class ArgumentTypeDescriptor {
         for (Class annotation: ARGUMENT_ANNOTATIONS)
             if (source.field.isAnnotationPresent(annotation))
                 return source.field.getAnnotation(annotation);
-        throw new StingException("ArgumentAnnotation is not present for the argument field: " + source.field.getName());
+        throw new GATKException("ArgumentAnnotation is not present for the argument field: " + source.field.getName());
     }
 
     /**
@@ -331,7 +333,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 for (Object val : vals) {
                     if (String.valueOf(val).equalsIgnoreCase(value)) return val;
                     try { if (type.getField(val.toString()).isAnnotationPresent(EnumerationArgumentDefault.class)) defaultEnumeration = val; }
-                    catch (NoSuchFieldException e) { throw new StingException("parsing " + type.toString() + "doesn't contain the field " + val.toString()); }
+                    catch (NoSuchFieldException e) { throw new GATKException("parsing " + type.toString() + "doesn't contain the field " + val.toString()); }
                 }
                 // if their argument has no value (null), and there's a default, return that default for the enum value
                 if (defaultEnumeration != null && value == null)
@@ -348,13 +350,13 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             }
         }
         catch (NoSuchMethodException e) {
-            throw new StingException("constructFromString:NoSuchMethodException: Failed conversion " + e.getMessage());
+            throw new GATKException("constructFromString:NoSuchMethodException: Failed conversion " + e.getMessage());
         } catch (IllegalAccessException e) {
-            throw new StingException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
+            throw new GATKException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
         } catch (InvocationTargetException e) {
-            throw new StingException("constructFromString:InvocationTargetException: Failed conversion - this is most likely caused by using an incorrect data type (e.g. a double when an int is required)");
+            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) {
-            throw new StingException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
+            throw new GATKException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
         }
         // WARNING: Side effect!
         parsingEngine.addTags(result,tags);
@@ -417,11 +419,11 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             }
             catch (InstantiationException e) {
                 logger.fatal("ArgumentParser: InstantiationException: cannot convert field " + source.field.getName());
-                throw new StingException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
+                throw new GATKException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
             }
             catch (IllegalAccessException e) {
                 logger.fatal("ArgumentParser: IllegalAccessException: cannot convert field " + source.field.getName());
-                throw new StingException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
+                throw new GATKException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
             }
 
             for( ArgumentMatch match: matches ) {
@@ -453,7 +455,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             }
         }
         else
-            throw new StingException("Unsupported compound argument type: " + type);
+            throw new GATKException("Unsupported compound argument type: " + type);
 
         // WARNING: Side effect!
         parsingEngine.addTags(result,tags);
@@ -521,7 +523,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     @Override
     public Object createTypeDefault(ArgumentSource source,Class type) {
         if(multiplexer == null || multiplexedIds == null)
-            throw new StingException("No multiplexed ids available");
+            throw new GATKException("No multiplexed ids available");
 
         Map<Object,Object> multiplexedMapping = new HashMap<Object,Object>();
         Class componentType = getCollectionComponentType(source.field);
@@ -540,7 +542,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     @Override
     public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) {
         if(multiplexedIds == null)
-            throw new StingException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first.");
+            throw new GATKException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first.");
 
         Map<Object,Object> multiplexedMapping = new HashMap<Object,Object>();
 
@@ -571,14 +573,14 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 if(!source.field.getName().equals(sourceField))
                     continue;
                 if(source.field.isAnnotationPresent(Multiplex.class))
-                    throw new StingException("Command-line arguments can only depend on independent fields");
+                    throw new GATKException("Command-line arguments can only depend on independent fields");
                 sourceTypes[currentField] = source.field.getType();
                 sourceValues[currentField] = JVMUtils.getFieldValue(source.field,containingObject);
                 currentField++;
                 fieldFound = true;
             }
             if(!fieldFound)
-                throw new StingException(String.format("Unable to find source field %s, referred to by dependent field %s",sourceField,dependentArgument.field.getName()));
+                throw new GATKException(String.format("Unable to find source field %s, referred to by dependent field %s",sourceField,dependentArgument.field.getName()));
         }
 
         Class<? extends Multiplexer> multiplexerType = dependentArgument.field.getAnnotation(Multiplex.class).value();
@@ -588,7 +590,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             multiplexerConstructor.setAccessible(true);
         }
         catch(NoSuchMethodException ex) {
-            throw new StingException(String.format("Unable to find constructor for class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new GATKException(String.format("Unable to find constructor for class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
 
         Multiplexer multiplexer = null;
@@ -596,13 +598,13 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             multiplexer = multiplexerConstructor.newInstance(sourceValues);
         }
         catch(IllegalAccessException ex) {
-            throw new StingException(String.format("Constructor for class %s with parameters %s is inaccessible",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new GATKException(String.format("Constructor for class %s with parameters %s is inaccessible",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
         catch(InstantiationException ex) {
-            throw new StingException(String.format("Can't create class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new GATKException(String.format("Can't create class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
         catch(InvocationTargetException ex) {
-            throw new StingException(String.format("Can't invoke constructor of class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new GATKException(String.format("Can't invoke constructor of class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
 
         return new MultiplexArgumentTypeDescriptor(multiplexer,multiplexer.multiplex());

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -124,7 +125,7 @@ public class CommandLineUtils {
         try {
             return annotation.getClass().getMethod(method).invoke(annotation);
         } catch (Exception e) {
-            throw new StingException("Unable to access method " + method + " on annotation " + annotation.getClass(), e);
+            throw new GATKException("Unable to access method " + method + " on annotation " + annotation.getClass(), e);
         }
     }
 }

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

@@ -25,10 +25,12 @@
 
 package org.broadinstitute.sting.commandline;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.help.ApplicationDetails;
 import org.broadinstitute.sting.utils.help.HelpFormatter;
 import org.apache.log4j.Logger;
@@ -293,9 +295,9 @@ public class ParsingEngine {
         // Grab the first argument definition and report that one as the failure.  Theoretically, we should notify of all failures.
         List<ArgumentDefinition> definitions = argumentSource.createArgumentDefinitions();
         if(definitions.size() < 1)
-            throw new StingException("Internal error.  Argument source creates no definitions.");
+            throw new GATKException("Internal error.  Argument source creates no definitions.");
         ArgumentDefinition definition = definitions.get(0);
-        throw new StingException(String.format("The parameter %s is deprecated.  %s",definition.fullName,definition.doc));
+        throw new UserError.DeprecatedArgument(definition.fullName,definition.doc);
     }
 
     /**
@@ -314,7 +316,7 @@ public class ParsingEngine {
 
         // Abort if no home is found for the object.
         if( targets.size() == 0 )
-            throw new StingException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
+            throw new GATKException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
 
         for( Object target: targets ) {
             Object value = (argumentMatches.size() != 0) ? source.parse(this,argumentMatches) : source.createDefault();

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

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk;
 
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 /**
  * Describes the method for downsampling reads at a given locus.
@@ -35,15 +36,15 @@ public class DownsamplingMethod {
 
         // Can't leave toFraction and toCoverage null unless type is experimental naive duplicate eliminator.
         if(type != DownsampleType.NONE && toFraction == null && toCoverage == null)
-            throw new StingException("Must specify either toFraction or toCoverage when downsampling.");
+            throw new UserError.CommandLineError("Must specify either toFraction or toCoverage when downsampling.");
 
         // Fraction and coverage cannot both be specified.
         if(toFraction != null && toCoverage != null)
-            throw new StingException("Downsampling coverage and fraction are both specified.  Please choose only one.");
+            throw new UserError.CommandLineError("Downsampling coverage and fraction are both specified.  Please choose only one.");
 
         // Experimental by sample downsampling does not work with a fraction of reads.
         if(type == DownsampleType.BY_SAMPLE && toFraction != null)
-            throw new StingException("Cannot downsample to fraction with new EXPERIMENTAL_BY_SAMPLE method");
+            throw new UserError.CommandLineError("Cannot downsample to fraction with new EXPERIMENTAL_BY_SAMPLE method");
 
         this.type = type;
         this.toCoverage = toCoverage;

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

@@ -31,6 +31,7 @@ import net.sf.samtools.*;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
@@ -42,7 +43,6 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.*;
 import org.broadinstitute.sting.gatk.executive.MicroScheduler;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.filters.ReadGroupBlackListFilter;
-import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.gatk.io.stubs.*;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
@@ -155,12 +155,12 @@ public class GenomeAnalysisEngine {
 
         // validate our parameters
         if (args == null) {
-            throw new StingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null.");
+            throw new GATKException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null.");
         }
 
         // validate our parameters              
         if (my_walker == null)
-            throw new StingException("The walker passed to GenomeAnalysisEngine can not be null.");
+            throw new GATKException("The walker passed to GenomeAnalysisEngine can not be null.");
 
         // save our argument parameter
         this.argCollection = args;
@@ -267,7 +267,7 @@ public class GenomeAnalysisEngine {
 
             // check to make sure we have a rod of that name
             if (!rodNames.containsKey(rodName))
-                throw new StingException("--rodToIntervalTrackName (-BTI) was pass the name '"+rodName+"', which wasn't given as a ROD name in the -B option");
+                throw new UserError.CommandLineError("--rodToIntervalTrackName (-BTI) was passed the name '"+rodName+"', which wasn't given as a ROD name in the -B option");
 
             for (String str : rodNames.keySet())
                 if (str.equals(rodName)) {
@@ -400,7 +400,7 @@ public class GenomeAnalysisEngine {
         // Temporarily require all walkers to have a reference, even if that reference is not conceptually necessary.
         if ((my_walker instanceof ReadWalker || my_walker instanceof DuplicateWalker || my_walker instanceof ReadPairWalker) && 
                 argCollection.referenceFile == null) {
-            Utils.scareUser(String.format("Read-based traversals require a reference file but none was given"));
+            throw new UserError.CommandLineError("Read-based traversals require a reference file but none was given");
         }
 
         return MicroScheduler.create(this,my_walker,readsDataSource,referenceDataSource.getReference(),rodDataSources,argCollection.numberOfThreads);
@@ -720,7 +720,7 @@ public class GenomeAnalysisEngine {
             error.append(String.format(compareToName + " contigs:     %s%n", prettyPrintSequenceRecords(comparedToDictionary)));
             error.append(String.format("Reference contigs: %s%n", prettyPrintSequenceRecords(referenceDictionary)));
             logger.error(error.toString());
-            Utils.scareUser("No overlap exists between sequence dictionary of " + compareToName + " and the sequence dictionary of the reference.");
+            throw new UserError.IncompatibleSequenceDictionaries(referenceDictionary, comparedToDictionary, compareToName);
         }
 
         // If the two datasets are not equal and neither is a strict subset of the other, warn the user.
@@ -773,20 +773,20 @@ public class GenomeAnalysisEngine {
         // sharding system; it's required with the new sharding system only for locus walkers.
         if(readsDataSource != null && !readsDataSource.hasIndex() ) { 
             if(!exclusions.contains(ValidationExclusion.TYPE.ALLOW_UNINDEXED_BAM))
-                throw new StingException("The GATK cannot currently process unindexed BAM files without the -U ALLOW_UNINDEXED_BAM");
+                throw new UserError.CommandLineError("The GATK cannot currently process unindexed BAM files without the -U ALLOW_UNINDEXED_BAM");
             if(intervals != null && WalkerManager.getWalkerDataSource(walker) != DataSource.REFERENCE)
-                throw new StingException("Cannot shard input by interval when walker is not driven by reference.");
+                throw new UserError.CommandLineError("Cannot perform interval processing when walker is not driven by reference and no index is available.");
 
             Shard.ShardType shardType;
             if(walker instanceof LocusWalker) {
                 if (readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.coordinate)
-                    Utils.scareUser("Locus walkers can only walk over coordinate-sorted data.  Please resort your input BAM file.");                
+                    throw new UserError.MissortedBAM(SAMFileHeader.SortOrder.coordinate, "Locus walkers can only walk over coordinate-sorted data.  Please resort your input BAM file(s).");
                 shardType = Shard.ShardType.LOCUS;
             }
             else if(walker instanceof ReadWalker || walker instanceof DuplicateWalker || walker instanceof ReadPairWalker)
                 shardType = Shard.ShardType.READ;
             else
-                throw new StingException("The GATK cannot currently process unindexed BAM files");
+                throw new UserError.CommandLineError("The GATK cannot currently process unindexed BAM files");
 
             List<GenomeLoc> region;
             if(intervals != null)
@@ -810,7 +810,7 @@ public class GenomeAnalysisEngine {
 
             if (intervals != null && !intervals.isEmpty()) {
                 if(!readsDataSource.isEmpty() && readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.coordinate)
-                    Utils.scareUser("Locus walkers can only walk over coordinate-sorted data.  Please resort your input BAM file.");
+                    throw new UserError.MissortedBAM(SAMFileHeader.SortOrder.coordinate, "Locus walkers can only walk over coordinate-sorted data.  Please resort your input BAM file(s).");
 
                 shardStrategy = ShardStrategyFactory.shatter(readsDataSource,
                         referenceDataSource.getReference(),
@@ -844,9 +844,9 @@ public class GenomeAnalysisEngine {
             }
         } else if (walker instanceof ReadPairWalker) {
             if(readsDataSource != null && readsDataSource.getSortOrder() != SAMFileHeader.SortOrder.queryname)
-                Utils.scareUser("Read pair walkers can only walk over query name-sorted data.  Please resort your input BAM file.");            
+                throw new UserError.MissortedBAM(SAMFileHeader.SortOrder.queryname, "Read pair walkers can only walk over query name-sorted data.  Please resort your input BAM file.");
             if(intervals != null && !intervals.isEmpty())
-                Utils.scareUser("Pairs traversal cannot be used in conjunction with intervals.");
+                throw new UserError.CommandLineError("Pairs traversal cannot be used in conjunction with intervals.");
 
             shardStrategy = ShardStrategyFactory.shatter(readsDataSource,
                     referenceDataSource.getReference(),
@@ -854,7 +854,7 @@ public class GenomeAnalysisEngine {
                     drivingDataSource.getSequenceDictionary(),
                     SHARD_SIZE);
         } else
-            throw new StingException("Unable to support walker of type" + walker.getClass().getName());
+            throw new GATKException("Unable to support walker of type" + walker.getClass().getName());
 
         return shardStrategy;
     }
@@ -996,7 +996,7 @@ public class GenomeAnalysisEngine {
                         unpackedReads.add(new SAMReaderID(new File(fileName),getTags(inputFile)));
                 }
                 catch( FileNotFoundException ex ) {
-                    throw new StingException("Unable to find file while unpacking reads", ex);
+                    throw new UserError.CouldNotReadInputFile(inputFile, "Unable to find file while unpacking reads", ex);
                 }
             }
             else if(inputFile.getName().toLowerCase().endsWith(".bam")) {
@@ -1006,9 +1006,9 @@ public class GenomeAnalysisEngine {
                 unpackedReads.add(new SAMReaderID(new File("/dev/stdin"),Collections.<String>emptyList()));
             }
             else {
-                Utils.scareUser(String.format("The GATK reads argument (-I) supports only BAM files with the .bam extension and lists of BAM files " +
+                throw new UserError.CommandLineError(String.format("The GATK reads argument (-I) supports only BAM files with the .bam extension and lists of BAM files " +
-                                              "with the .list extension, but the file %s has neither extension.  Please ensure that your BAM file or list " +
+                        "with the .list extension, but the file %s has neither extension.  Please ensure that your BAM file or list " +
-                                              "of BAM files is in the correct format, update the extension, and try again.",inputFile.getName()));
+                        "of BAM files is in the correct format, update the extension, and try again.",inputFile.getName()));
             }
         }
         return unpackedReads;

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

@@ -30,6 +30,7 @@ import java.util.Map;
 import java.util.HashMap;
 import java.util.Collections;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 /**
@@ -78,7 +79,7 @@ public class ReadMetrics implements Cloneable {
             newMetrics = (ReadMetrics)super.clone();
         }
         catch(CloneNotSupportedException ex) {
-            throw new StingException("Unable to clone runtime metrics",ex);
+            throw new GATKException("Unable to clone runtime metrics",ex);
         }
         newMetrics.nRecords = nRecords;
         newMetrics.nReads = nReads;

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

@@ -30,6 +30,7 @@ import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
@@ -168,7 +169,7 @@ public class WalkerManager extends PluginManager<Walker> {
     public static DataSource getWalkerDataSource(Class<? extends Walker> walkerClass) {
         By byDataSource = walkerClass.getAnnotation(By.class);
         if( byDataSource == null )
-            throw new StingException("Unable to find By annotation for walker class " + walkerClass.getName());
+            throw new GATKException("Unable to find By annotation for walker class " + walkerClass.getName());
         return byDataSource.value();
     }
 
@@ -397,7 +398,7 @@ public class WalkerManager extends PluginManager<Walker> {
     private static Requires getWalkerRequirements(Class<? extends Walker> walkerClass) {
         Requires requiresDataSource = walkerClass.getAnnotation(Requires.class);
         if( requiresDataSource == null )
-            throw new StingException( "Unable to find data types required by walker class " + walkerClass.getName());
+            throw new GATKException( "Unable to find data types required by walker class " + walkerClass.getName());
         return requiresDataSource;
     }
 

java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.arguments;
 
 import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.commandline.Argument;
@@ -191,7 +192,7 @@ public class GATKArgumentCollection {
         try {
             serializer.write(collection, result);
         } catch (Exception e) {
-            throw new StingException("Failed to marshal the data to the file " + outputFile, e);
+            throw new GATKException("Failed to marshal the data to the file " + outputFile, e);
         }
     }
 
@@ -206,7 +207,7 @@ public class GATKArgumentCollection {
         try {
             serializer.write(collection, outputFile);
         } catch (Exception e) {
-            throw new StingException("Failed to marshal the data to the file " + outputFile, e);
+            throw new GATKException("Failed to marshal the data to the file " + outputFile, e);
         }
     }
 
@@ -222,7 +223,7 @@ public class GATKArgumentCollection {
             GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, source);
             return example;
         } catch (Exception e) {
-            throw new StingException("Failed to marshal the data from file " + filename, e);
+            throw new GATKException("Failed to marshal the data from file " + filename, e);
         }
     }
 
@@ -237,7 +238,7 @@ public class GATKArgumentCollection {
             GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, file);
             return example;
         } catch (Exception e) {
-            throw new StingException("Failed to marshal the data from file " + file.toString(), e);
+            throw new GATKException("Failed to marshal the data from file " + file.toString(), e);
         }
     }
 

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

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.contexts;
 
 import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -68,8 +69,8 @@ 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 ( basePileup == null ) throw new StingException("BUG: ReadBackedPileup in Alignment context is null");
+        if ( basePileup == null ) throw new GATKException("BUG: ReadBackedPileup in Alignment context is null");
-        if ( skippedBases < 0 ) throw new StingException("BUG: skippedBases is -1 in Alignment context");
+        if ( skippedBases < 0 ) throw new GATKException("BUG: skippedBases is -1 in Alignment context");
 
         this.loc = loc;
         this.basePileup = basePileup;
@@ -90,7 +91,7 @@ public class AlignmentContext {
      */
     public ReadBackedPileup getBasePileup() {
         if(!hasBasePileup())
-            throw new StingException("No base pileup is available.  Please check for a base pileup with hasBasePileup() before attempting to retrieve a pileup.");
+            throw new GATKException("No base pileup is available.  Please check for a base pileup with hasBasePileup() before attempting to retrieve a pileup.");
         return basePileup;
     }
 
@@ -100,7 +101,7 @@ public class AlignmentContext {
      */
     public ReadBackedExtendedEventPileup getExtendedEventPileup() {
         if(!hasExtendedEventPileup())
-            throw new StingException("No extended event pileup is present.");
+            throw new GATKException("No extended event pileup is present.");
         return (ReadBackedExtendedEventPileup)basePileup; 
     }
 

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.contexts;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.BaseUtils;
@@ -191,7 +192,7 @@ public class ReferenceContext {
         byte[] b = new byte[stop-start];
 
         if ( stop > bases.length )
-            throw new StingException("Bases beyond the current window requested: window="+window+", requested="+n);
+            throw new GATKException("Bases beyond the current window requested: window="+window+", requested="+n);
 
         int i = 0;
         for ( int j = start ;  j < stop ; j++) b[i++]=bases[j];

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

@@ -27,8 +27,10 @@ package org.broadinstitute.sting.gatk.contexts;
 
 import net.sf.samtools.SAMRecord;
 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.exceptions.UserError;
 import org.broadinstitute.sting.utils.pileup.*;
 
 import java.util.*;
@@ -73,7 +75,7 @@ public class StratifiedAlignmentContext<RBP extends ReadBackedPileup> {
             case REVERSE:
                 return new AlignmentContext(loc,basePileup.getNegativeStrandPileup());
             default:
-                throw new StingException("Unable to get alignment context for type = " + type);
+                throw new GATKException("Unable to get alignment context for type = " + type);
         }
     }
 
@@ -113,8 +115,9 @@ public class StratifiedAlignmentContext<RBP extends ReadBackedPileup> {
             if(sampleName != null)
                 contexts.put(sampleName,new StratifiedAlignmentContext<RBP>(loc,pileupBySample));
             else {
-                if(assumedSingleSample == null)
+                if(assumedSingleSample == null) {
-                    throw new StingException("Missing read group for read " + pileupBySample.iterator().next().getRead());
+                    throw new UserError.MalformedBam(pileupBySample.iterator().next().getRead(), "Missing read group for read");
+                }
                 contexts.put(assumedSingleSample,new StratifiedAlignmentContext<RBP>(loc,pileupBySample));
             }
         }
@@ -144,9 +147,9 @@ public class StratifiedAlignmentContext<RBP extends ReadBackedPileup> {
         boolean isExtended = contexts.iterator().next().basePileup instanceof ReadBackedExtendedEventPileup;
         for(StratifiedAlignmentContext context: contexts) {
             if(!loc.equals(context.getLocation()))
-                throw new StingException("Illegal attempt to join contexts from different genomic locations");
+                throw new GATKException("Illegal attempt to join contexts from different genomic locations");
             if(isExtended != (context.basePileup instanceof ReadBackedExtendedEventPileup))
-                throw new StingException("Illegal attempt to join simple and extended contexts");
+                throw new GATKException("Illegal attempt to join simple and extended contexts");
         }
 
         AlignmentContext jointContext;

java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java

@@ -110,7 +110,7 @@ public class VariantContextUtils {
      */
     public static List<JexlVCMatchExp> initializeMatchExps(String[] names, String[] exps) {
         if ( names == null || exps == null )
-            throw new StingException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) );
+            throw new GATKException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) );
 
         if ( names.length != exps.length )
             throw new UserError("Inconsistent number of provided filter names and expressions: names=" + Arrays.toString(names) + " exps=" + Arrays.toString(exps));
@@ -322,7 +322,7 @@ public class VariantContextUtils {
 
         for ( VariantContext vc : VCs ) {
             if ( loc.getStart() != vc.getStart() ) // || !first.getReference().equals(vc.getReference()) )
-                throw new StingException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString());
+                throw new GATKException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString());
 
             if ( getLocation(vc).size() > loc.size() )
                 loc = getLocation(vc); // get the longest location
@@ -449,7 +449,7 @@ public class VariantContextUtils {
             if ( ref == null || ref.length() < myRef.length() )
                 ref = myRef;
             else if ( ref.length() == myRef.length() && ! ref.equals(myRef) )
-                throw new StingException("BUG: equal length references with difference bases: "+ ref + " " + myRef);
+                throw new GATKException("BUG: equal length references with difference bases: "+ ref + " " + myRef);
         }
 
         return ref;
@@ -471,7 +471,7 @@ public class VariantContextUtils {
             //
 
             Allele myRef = vc.getReference();
-            if ( refAllele.length() <= myRef.length() ) throw new StingException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele);
+            if ( refAllele.length() <= myRef.length() ) throw new GATKException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele);
             byte[] extraBases = Arrays.copyOfRange(refAllele.getBases(), myRef.length(), refAllele.length());
 
 //            System.out.printf("Remapping allele at %s%n", vc);
@@ -576,7 +576,7 @@ public class VariantContextUtils {
             padVC = false;
         else if (refAllele.length() == locLength-1)
             padVC = true;
-        else throw new StingException("Badly formed variant context, reference length must be at most one base shorter than location size");
+        else throw new GATKException("Badly formed variant context, reference length must be at most one base shorter than location size");
 
 
         // nothing to do if we don't need to pad bases
@@ -590,7 +590,7 @@ public class VariantContextUtils {
             else if (attributes.containsKey(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY))
                 refByte = (Byte)attributes.get(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY);
             else
-                throw new StingException("Error when trying to pad Variant Context: either input reference base must be a regular base, or input VC must contain reference base key");
+                throw new GATKException("Error when trying to pad Variant Context: either input reference base must be a regular base, or input VC must contain reference base key");
 
             List<Allele> alleles = new ArrayList<Allele>();
             Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();

java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantJEXLContext.java

@@ -27,9 +27,11 @@ import org.apache.commons.jexl2.JexlContext;
 import org.apache.commons.jexl2.MapContext;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broad.tribble.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.util.*;
 
@@ -272,7 +274,7 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
         try {
             jexl.put (exp, (Boolean) exp.exp.evaluate(jContext));
         } catch (Exception e) {
-            throw new StingException(e.getMessage());
+            throw new UserError.CommandLineError(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
         }
     }
 

java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
@@ -88,8 +89,8 @@ public class LocusReferenceView extends ReferenceView {
         if( walker.getClass().isAnnotationPresent(Reference.class) ) {
             Window window = walker.getClass().getAnnotation(Reference.class).window();
 
-            if( window.start() > 0 ) throw new StingException( "Reference window starts after current locus" );
+            if( window.start() > 0 ) throw new GATKException( "Reference window starts after current locus" );
-            if( window.stop() < 0 ) throw new StingException( "Reference window ends before current locus" );
+            if( window.stop() < 0 ) throw new GATKException( "Reference window ends before current locus" );
 
             windowStart = window.start();
             windowStop = window.stop();
@@ -124,7 +125,7 @@ public class LocusReferenceView extends ReferenceView {
         if ( bounds==null || loc==null) return; // can bounds be null actually???
         if ( isLocationWithinBounds(loc) ) return;
         if ( loc.getContigIndex() != bounds.getContigIndex() )
-            throw new StingException("Illegal attempt to expand reference view bounds to accommodate location on a different contig.");
+            throw new GATKException("Illegal attempt to expand reference view bounds to accommodate location on a different contig.");
 
         bounds = GenomeLocParser.createGenomeLoc(bounds.getContigIndex(),
                                                  Math.min(bounds.getStart(),loc.getStart()),

java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java

@@ -1,10 +1,7 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Collections;
 import java.util.Collection;
@@ -84,7 +81,7 @@ public class ReferenceView implements View {
         int overhang = (int)(genomeLoc.getStop() - stop);
         if ( overhang > 0 ) {
             if ( overhang > BUFFER ) // todo -- this is a bit dangerous
-                throw new StingException("Insufficient buffer size for Xs overhanging genome -- expand BUFFER");
+                throw new GATKException("Insufficient buffer size for Xs overhanging genome -- expand BUFFER");
             byte[] all = new byte[subsequence.getBases().length + overhang];
             System.arraycopy(subsequence.getBases(), 0, all, 0, subsequence.getBases().length);
             System.arraycopy(Xs, 0, all, subsequence.getBases().length, overhang);

java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.ArrayList;
@@ -110,7 +111,7 @@ public abstract class ShardDataProvider {
             Collection<Class<? extends View>> conflicts = registeredView.getConflictingViews();
             for( Class<? extends View> conflict: conflicts ) {
                 if( conflict.isInstance(view) )
-                    throw new StingException(String.format("Tried to register two conflicting views: %s and %s",
+                    throw new GATKException(String.format("Tried to register two conflicting views: %s and %s",
                                                            registeredView.getClass().getSimpleName(),
                                                            view.getClass().getSimpleName()));
             }
@@ -120,7 +121,7 @@ public abstract class ShardDataProvider {
         for( Class<? extends View> conflict: view.getConflictingViews() ) {
             for( View registeredView: registeredViews ) {
                 if( conflict.isInstance(registeredView) )
-                    throw new StingException(String.format("Tried to register two conflicting views: %s and %s",
+                    throw new GATKException(String.format("Tried to register two conflicting views: %s and %s",
                                                            registeredView.getClass().getSimpleName(),
                                                            view.getClass().getSimpleName()));
             }

java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java

@@ -123,7 +123,7 @@ public class IntervalSharder {
 
         for(GenomeLoc location: loci) {
             if(!location.getContig().equals(contig))
-                throw new StingException("Location outside bounds of contig");
+                throw new GATKException("Location outside bounds of contig");
 
             if(!binIterator.hasNext())
                 break;
@@ -190,7 +190,7 @@ public class IntervalSharder {
                 }
                 else {
                     if(lastFilePointer == null)
-                        throw new StingException("Illegal state: initializer failed to create cached file pointer.");
+                        throw new GATKException("Illegal state: initializer failed to create cached file pointer.");
 
                     // The start of the region overlaps the bin.  Add the overlapping subset.
                     final int regionStop = Math.min(locationStop,binStop);
@@ -474,7 +474,7 @@ class BinQueueState implements Comparable<BinQueueState> {
         // Both BinQueueStates have next bins.  Before proceeding, make sure the bin cache is valid.
         if(this.firstLocusInCurrentBin <= 0 || this.lastLocusInCurrentBin <= 0 ||
            other.firstLocusInCurrentBin <= 0 || other.lastLocusInCurrentBin <= 0) {
-            throw new StingException("Sharding mechanism error - bin->locus cache is invalid.");
+            throw new GATKException("Sharding mechanism error - bin->locus cache is invalid.");
         }
 
         // Straight integer subtraction works here because lhsStart, rhsStart always positive.

java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.ReadMetrics;
@@ -42,7 +43,7 @@ public class MonolithicShard implements Shard {
     public MonolithicShard(SAMDataSource readsDataSource, ShardType shardType, List<GenomeLoc> locs) {
         this.readsDataSource = readsDataSource;
         if(shardType != ShardType.LOCUS && shardType != ShardType.READ)
-            throw new StingException("Invalid shard type for monolithic shard: " + shardType);
+            throw new GATKException("Invalid shard type for monolithic shard: " + shardType);
         this.shardType = shardType;
         this.locs = locs;
     }

java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
@@ -71,7 +72,7 @@ public class ShardStrategyFactory {
             case READS_EXPERIMENTAL:
                 return new ReadShardStrategy(readsDataSource,null);
             default:
-                throw new StingException("Strategy: " + strat + " isn't implemented for this type of shatter request");
+                throw new GATKException("Strategy: " + strat + " isn't implemented for this type of shatter request");
         }
 
     }
@@ -109,7 +110,7 @@ public class ShardStrategyFactory {
             case READS_EXPERIMENTAL:
                 return new ReadShardStrategy(readsDataSource,lst);
             default:
-                throw new StingException("Strategy: " + strat + " isn't implemented");
+                throw new GATKException("Strategy: " + strat + " isn't implemented");
         }
 
     }

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.picard.reference.FastaSequenceIndexBuilder;
 import net.sf.picard.sam.CreateSequenceDictionary;
@@ -68,7 +69,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
             try {
                 // get exclusive lock
                 if (!indexLock.exclusiveLock())
-                    throw new StingException("Index file could not be written because a lock could not be obtained." +
+                    throw new GATKException("Index file could not be written because a lock could not be obtained." +
                             "If you are running multiple instances of GATK, another process is probably creating this " +
                             "file now. Please wait until it is finished and try again.");
                 FastaSequenceIndexBuilder faiBuilder = new FastaSequenceIndexBuilder(fastaFile, this);
@@ -82,7 +83,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
             catch (Exception e) {
                 // If lock creation succeeded, the failure must have been generating the index.
                 // If lock creation failed, just skip over index creation entirely.
-                throw new StingException("Index file does not exist and could not be created because " + e.getMessage(), e);
+                throw new GATKException("Index file does not exist and could not be created because " + e.getMessage(), e);
             }
             finally {
                 indexLock.unlock();
@@ -108,7 +109,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
             try {
                 // get shared lock on dict file so nobody else can start creating it
                 if (!dictLock.exclusiveLock())
-                    throw new StingException("Dictionary file could not be written because a lock could not be obtained." +
+                    throw new GATKException("Dictionary file could not be written because a lock could not be obtained." +
                             "If you are running multiple instances of GATK, another process is probably creating this " +
                             "file now. Please wait until it is finished and try again.");
                 // dict will be written to random temporary file in same directory (see note above)
@@ -121,7 +122,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
                 new CreateSequenceDictionary().instanceMain(args);
 
                 if (!tempFile.renameTo(dictFile))
-                    throw new StingException("Error transferring temp file " + tempFile + " to dict file " + dictFile);
+                    throw new GATKException("Error transferring temp file " + tempFile + " to dict file " + dictFile);
             }
             catch(FileSystemInabilityToLockException ex) {
                 logger.info("Unable to create write lock: " + ex.getMessage());
@@ -130,7 +131,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
             catch (Exception e) {
                 // If lock creation succeeded, the failure must have been generating the index.
                 // If lock creation failed, just skip over index creation entirely.
-                throw new StingException("Dictionary file does not exist and could not be created because " + e.getMessage(), e);
+                throw new GATKException("Dictionary file does not exist and could not be created because " + e.getMessage(), e);
             }
             finally {
                 dictLock.unlock();
@@ -149,7 +150,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
         try {
             try {
                 if (!dictLock.sharedLock()) {
-                    throw new StingException("Could not open dictionary file because a lock could not be obtained.");
+                    throw new GATKException("Could not open dictionary file because a lock could not be obtained.");
                 }
             }
             catch(FileSystemInabilityToLockException ex) {
@@ -159,7 +160,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
 
             try {
                 if (!indexLock.sharedLock()) {
-                    throw new StingException("Could not open index file because a lock could not be obtained.");
+                    throw new GATKException("Could not open index file because a lock could not be obtained.");
                 }
             }
             catch(FileSystemInabilityToLockException ex) {

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

@@ -11,8 +11,10 @@ import org.broadinstitute.sting.gatk.refdata.utils.FlashBackIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+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.IOException;
 import java.util.List;
@@ -155,7 +157,7 @@ class ReferenceOrderedDataPool extends ResourcePool<LocationAwareSeekableRODIter
             return null;
         }
         else {
-            throw new StingException("Unable to find a ROD iterator for segments of type " + segment.getClass());
+            throw new GATKException("Unable to find a ROD iterator for segments of type " + segment.getClass());
         }
     }
 
@@ -223,7 +225,7 @@ class ReferenceOrderedQueryDataPool extends ResourcePool<FeatureSource, Location
         try {
             resource.close();
         } catch (IOException e) {
-            throw new StingException("Unable to close reader for rod named " + rod.getName(),e);
+            throw new UserError.CouldNotReadInputFile("Unable to close reader for rod named " + rod.getName(),e);
         }
     }
 }

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
@@ -88,10 +89,10 @@ abstract class ResourcePool <T,I extends Iterator> {
 
             // make sure we actually removed the assignment
             if (obj == null)
-                    throw new StingException("Failed to remove resource assignment; target key had no associated value in the resource assignment map");
+                    throw new GATKException("Failed to remove resource assignment; target key had no associated value in the resource assignment map");
             // Return the resource to the pool.
             if( !allResources.contains(resource) )
-                throw new StingException("Iterator does not belong to the given pool.");
+                throw new GATKException("Iterator does not belong to the given pool.");
             availableResources.add(resource);
         }
     }

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

@@ -41,7 +41,9 @@ import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.File;
 import java.util.*;
@@ -126,7 +128,7 @@ public class SAMDataSource implements SimpleDataSource {
 
             // Validate that all input files are sorted in the same order.
             if(this.sortOrder != null && this.sortOrder != sortOrder)
-                throw new StingException(String.format("Attempted to process mixed of files sorted as %s and %s.",this.sortOrder,sortOrder));
+                throw new UserError.MissortedBAM(String.format("Attempted to process mixed of files sorted as %s and %s.",this.sortOrder,sortOrder));
 
             // Update the sort order.
             this.sortOrder = sortOrder;
@@ -293,7 +295,7 @@ public class SAMDataSource implements SimpleDataSource {
      */
     public void fillShard(BAMFormatAwareShard shard) {
         if(!shard.buffersReads())
-            throw new StingException("Attempting to fill a non-buffering shard.");
+            throw new GATKException("Attempting to fill a non-buffering shard.");
 
         SAMReaders readers = resourcePool.getAvailableReaders();
         // Cache the most recently viewed read so that we can check whether we've reached the end of a pair.
@@ -325,7 +327,7 @@ public class SAMDataSource implements SimpleDataSource {
             return seekMonolithic(shard);
 
         if(!(shard instanceof BAMFormatAwareShard))
-            throw new StingException("BlockDrivenSAMDataSource cannot operate on shards of type: " + shard.getClass());
+            throw new GATKException("BlockDrivenSAMDataSource cannot operate on shards of type: " + shard.getClass());
         BAMFormatAwareShard bamAwareShard = (BAMFormatAwareShard)shard;
 
         if(bamAwareShard.buffersReads()) {
@@ -348,7 +350,7 @@ public class SAMDataSource implements SimpleDataSource {
             if(readers.getReader(id) == read.getFileSource().getReader())
                 return id;
         }
-        throw new StingException("Unable to find id for reader associated with read " + read.getReadName());
+        throw new GATKException("Unable to find id for reader associated with read " + read.getReadName());
     }
 
     /**
@@ -507,7 +509,7 @@ public class SAMDataSource implements SimpleDataSource {
 
         public synchronized void releaseReaders(SAMReaders readers) {
             if(!allResources.contains(readers))
-                throw new StingException("Tried to return readers from the pool that didn't originate in the pool.");
+                throw new GATKException("Tried to return readers from the pool that didn't originate in the pool.");
             availableResources.add(readers);
         }
 
@@ -522,12 +524,12 @@ public class SAMDataSource implements SimpleDataSource {
                 if(id != null)
                     return id;
             }
-            throw new StingException("No such reader id is available");
+            throw new GATKException("No such reader id is available");
         }
 
         private synchronized void createNewResource() {
             if(allResources.size() > maxEntries)
-                throw new StingException("Cannot create a new resource pool.  All resources are in use.");
+                throw new GATKException("Cannot create a new resource pool.  All resources are in use.");
             SAMReaders readers = new SAMReaders(readProperties);
             allResources.add(readers);
             availableResources.add(readers);

java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.datasources.utilities;
 
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.instrumentation.Sizeof;
 
@@ -58,7 +59,7 @@ public class BAMFileStat extends CommandLineProgram {
     public int execute() {
         switch(command) {
             case ShowBlocks:
-                throw new StingException("The BAM block inspector has been disabled.");
+                throw new GATKException("The BAM block inspector has been disabled.");
             case ShowIndex:
                 showIndexBins(new File(bamFileName),range);
                 break;
@@ -171,7 +172,7 @@ public class BAMFileStat extends CommandLineProgram {
             }
         }
         catch(IllegalAccessException ex) {
-            throw new StingException("Unable to examine cached index",ex);
+            throw new GATKException("Unable to examine cached index",ex);
         }
 
         System.out.printf("%nOverall: %d bins, %d chunks, %d linear index entries",numBins,numChunks,numLinearIndexEntries);

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

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
@@ -184,7 +185,7 @@ public abstract class Accumulator {
          */
         public void accumulate( ShardDataProvider provider, Object result ) {
             if(!(provider instanceof LocusShardDataProvider))
-                throw new StingException("Unable to reduce by interval on reads traversals at this time.");
+                throw new GATKException("Unable to reduce by interval on reads traversals at this time.");
 
             GenomeLoc location = ((LocusShardDataProvider)provider).getLocus();
 

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

@@ -9,6 +9,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde
 import org.broadinstitute.sting.gatk.io.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.ReadMetrics;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
@@ -110,7 +111,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
             mbs.registerMBean(this, name);
         }
         catch (JMException ex) {
-            throw new StingException("Unable to register microscheduler with JMX", ex);
+            throw new GATKException("Unable to register microscheduler with JMX", ex);
         }
     }
 
@@ -130,7 +131,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         while (isShardTraversePending() || isTreeReducePending()) {
             // Check for errors during execution.
             if(hasTraversalErrorOccurred())
-                throw new StingException("An error has occurred during the traversal.",getTraversalError());
+                throw new GATKException("An error has occurred during the traversal.",getTraversalError());
 
             // Too many files sitting around taking up space?  Merge them.
             if (isMergeLimitExceeded())
@@ -159,7 +160,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
             notifyTraversalDone(walker,result);
         }
         catch (Exception ex) {
-            throw new StingException("Unable to retrieve result", ex);
+            throw new GATKException("Unable to retrieve result", ex);
         }
 
         outputTracker.close();
@@ -359,7 +360,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
 
     private synchronized Throwable getTraversalError() {
         if(!hasTraversalErrorOccurred())
-            throw new StingException("User has attempted to retrieve a traversal error when none exists");
+            throw new GATKException("User has attempted to retrieve a traversal error when none exists");
         return error;
     }
 

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

@@ -8,6 +8,7 @@ import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.concurrent.Callable;
@@ -83,7 +84,7 @@ public class ShardTraverser implements Callable {
         catch(Throwable t) {
             // Notify that an exception has occurred and rethrow it.
             microScheduler.notifyOfTraversalError(t);
-            throw new StingException("An error has occurred during traversal",t);
+            throw new GATKException("An error has occurred during traversal",t);
         }
         finally {
             synchronized(this) {
@@ -115,7 +116,7 @@ public class ShardTraverser implements Callable {
             }
         }
         catch( InterruptedException ex ) {
-            throw new StingException("Interrupted while waiting for more output to be finalized.",ex);
+            throw new GATKException("Interrupted while waiting for more output to be finalized.",ex);
         }
     }
 

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

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.concurrent.Callable;
@@ -90,11 +91,11 @@ public class TreeReducer implements Callable {
         }
         catch( InterruptedException ex ) {
             microScheduler.notifyOfTraversalError(ex);
-            throw new StingException("Hierarchical reduce interrupted", ex);
+            throw new GATKException("Hierarchical reduce interrupted", ex);
         }
         catch( ExecutionException ex ) {
             microScheduler.notifyOfTraversalError(ex);
-            throw new StingException("Hierarchical reduce failed", ex);
+            throw new GATKException("Hierarchical reduce failed", ex);
         }
 
         long endTime = System.currentTimeMillis();

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.io;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.ArgumentSource;
@@ -140,7 +141,7 @@ public abstract class OutputTracker {
      */
     protected <T> T getTargetStream( Stub<T> stub ) {
         if( !outputs.containsKey(stub) )
-            throw new StingException("OutputTracker was not notified that this stub exists: " + stub);
+            throw new GATKException("OutputTracker was not notified that this stub exists: " + stub);
         Storage<T> storage = outputs.get(stub);
         if( storage == null ) {
             storage = StorageFactory.createStorage(stub);

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.io.storage;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.storage.Storage;
@@ -60,7 +61,7 @@ public class OutputStreamStorage extends OutputStream implements Storage<OutputS
             this.outputStream = stub.getOutputStream();           
         }
         else
-            throw new StingException("Not enough information to create storage for an OutputStream; need either a file or an existing output stream");
+            throw new GATKException("Not enough information to create storage for an OutputStream; need either a file or an existing output stream");
     }
 
     public OutputStreamStorage( OutputStreamStub stub, File file ) {

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

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.File;
@@ -85,7 +86,7 @@ public class StorageFactory {
                 storage = new VCFWriterStorage(vcfWriterStub);
         }
         else
-            throw new StingException("Unsupported stub type: " + stub.getClass().getName());
+            throw new GATKException("Unsupported stub type: " + stub.getClass().getName());
 
         return storage;
     }

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

@@ -5,6 +5,7 @@ import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 
@@ -48,7 +49,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
             this.stream = stub.getOutputStream();
         }
         else
-            throw new StingException("Unable to create target to which to write; storage was provided with neither a file nor a stream.");
+            throw new GATKException("Unable to create target to which to write; storage was provided with neither a file nor a stream.");
 
         writer = new StandardVCFWriter(stream);
     }

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

@@ -26,6 +26,7 @@
 package org.broadinstitute.sting.gatk.io.stubs;
 
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 
@@ -117,13 +118,13 @@ public class OutputStreamArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             return getConstructorForClass(type).newInstance(outputStream);
         }
         catch( InstantiationException ex ) {
-            throw new StingException("Could not instantiate class with OutputStream constructor: " + type.getName());
+            throw new GATKException("Could not instantiate class with OutputStream constructor: " + type.getName());
         }
         catch( IllegalAccessException ex ) {
-            throw new StingException("Could not access class with OutputStream constructor: " + type.getName());
+            throw new GATKException("Could not access class with OutputStream constructor: " + type.getName());
         }
         catch( InvocationTargetException ex ) {
-            throw new StingException("Could not invoke constructor for class with OutputStream constructor: " + type.getName());
+            throw new GATKException("Could not invoke constructor for class with OutputStream constructor: " + type.getName());
         }
     }
 }

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

@@ -28,6 +28,7 @@ import org.broadinstitute.sting.commandline.ArgumentTypeDescriptor;
 import org.broadinstitute.sting.commandline.ArgumentSource;
 import org.broadinstitute.sting.commandline.ArgumentMatches;
 import org.broadinstitute.sting.commandline.ParsingEngine;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
@@ -66,7 +67,7 @@ public class SAMFileReaderArgumentTypeDescriptor extends ArgumentTypeDescriptor
         String readerFileName = getArgumentValue( createDefaultArgumentDefinition(source), matches );
 
         if( readerFileName == null )
-            throw new StingException("SAM file compression was supplied, but no associated writer was supplied with it.");
+            throw new UserError.CommandLineError("SAM file compression was supplied, but no associated writer was supplied with it.");
 
         builder.setSAMFile(new File(readerFileName));
 

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

@@ -30,6 +30,7 @@ import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import net.sf.samtools.SAMFileWriter;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.lang.annotation.Annotation;
 import java.util.List;
@@ -94,7 +95,7 @@ public class SAMFileWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor
     public Object parse( ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches )  {
         String writerFileName = getArgumentValue( createBAMArgumentDefinition(source), matches );
         if( writerFileName == null )
-            throw new StingException("SAM file compression was supplied, but no associated writer was supplied with it.");
+            throw new UserError.CommandLineError("SAM file compression was supplied, but no associated writer was supplied with it.");
 
         SAMFileWriterStub stub = new SAMFileWriterStub(engine, new File(writerFileName));
 

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

@@ -35,6 +35,7 @@ import java.io.OutputStream;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 /**
@@ -150,7 +151,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     public void setCompressionLevel( Integer compressionLevel ) {
         if(writeStarted)
-            throw new StingException("User attempted to change the compression level of a file with alignments already in it.");        
+            throw new GATKException("Attempted to change the compression level of a file with alignments already in it.");
         this.compressionLevel = compressionLevel;
     }
 
@@ -168,7 +169,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     public void setPresorted(boolean presorted) {
         if(writeStarted)
-            throw new StingException("User attempted to change the presorted state of a file with alignments already in it.");
+            throw new GATKException("Attempted to change the presorted state of a file with alignments already in it.");
         this.presorted = presorted;
     }
 
@@ -186,7 +187,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     public void setMaxRecordsInRam(int maxRecordsInRam) {
         if(writeStarted)
-            throw new StingException("User attempted to change the max records in RAM of a file with alignments already in it.");
+            throw new GATKException("Attempted to change the max records in RAM of a file with alignments already in it.");
         this.maxRecordsInRam = maxRecordsInRam;
     }
 
@@ -204,7 +205,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     public void writeHeader(SAMFileHeader header) {
         if(writeStarted)
-            throw new StingException("User attempted to change the header of a file with alignments already in it.");
+            throw new GATKException("Attempted to change the header of a file with alignments already in it.");
         this.headerOverride = header;
     }
 

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

@@ -32,6 +32,7 @@ import java.util.LinkedList;
 import java.util.Iterator;
 import java.util.NoSuchElementException;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 /**
@@ -67,7 +68,7 @@ public class BufferingReadIterator implements CloseableIterator<SAMRecord> {
     }
 
     public void remove() {
-        throw new StingException("Unable to remove from a BufferingReadIterator");
+        throw new GATKException("Unable to remove from a BufferingReadIterator");
     }
 
     /**

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

@@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.Walker;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.simpleframework.xml.Element;
@@ -241,7 +242,7 @@ public class GATKRunReport {
             serializer.write(this, stream);
             //throw new StingException("test");
         } catch (Exception e) {
-            throw new StingException("Failed to marshal the data to the file " + stream, e);
+            throw new GATKException("Failed to marshal the data to the file " + stream, e);
         }
     }
 

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

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.refdata;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 
@@ -29,7 +30,7 @@ public class IntervalRod extends BasicReferenceOrderedDatum {
 	}
 
 	public String repl() {
-		throw new StingException("repl() is not implemented yet");
+		throw new GATKException("repl() is not implemented yet");
 	}
 
 	public String toSimpleString() { return loc.toString(); }

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

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import org.broad.tribble.util.variantcontext.Allele;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
@@ -65,7 +66,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         try {
             plink.initialize(file);
         } catch (FileNotFoundException e) {
-            throw new StingException("Unable to find file " + file);
+            throw new GATKException("Unable to find file " + file);
         }
         return plink;
     }
@@ -188,9 +189,9 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
             return seqVars;
 
         } catch ( FileNotFoundException e ) {
-            throw new StingException("File "+file.getAbsolutePath()+" could not be found. This was checked earlier. Should never happen.",e);
+            throw new GATKException("File "+file.getAbsolutePath()+" could not be found. This was checked earlier. Should never happen.",e);
         } catch ( IOException e ) {
-            throw new StingException("Error reading file "+file.getAbsolutePath()+".",e);
+            throw new GATKException("Error reading file "+file.getAbsolutePath()+".",e);
         }
     }
 
@@ -200,7 +201,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         }
 
         if ( plinkFileType != PlinkFileType.STANDARD_PED )
-            throw new StingException("Plink file is likely of .raw or recoded format. Please use an uncoded .ped file.");
+            throw new GATKException("Plink file is likely of .raw or recoded format. Please use an uncoded .ped file.");
 
         StringTokenizer st = new StringTokenizer(plinkLine, "\t");
         int offset = 0;
@@ -224,7 +225,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         // if the first line is not a comment (what we're used to seeing),
         // then it's the raw header (comes from de-binary-ing a .bed file)
         if ( !header.startsWith("#") )
-            throw new StingException("Plink file is likely of .raw or recoded format. Please use an uncoded .ped file.");
+            throw new GATKException("Plink file is likely of .raw or recoded format. Please use an uncoded .ped file.");
 
         plinkFileType = PlinkFileType.STANDARD_PED;
 
@@ -281,7 +282,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         try {
             reader = new BufferedReader( new FileReader( bimFile ));
         } catch ( FileNotFoundException e) {
-            throw new StingException("The SNP information file accompanying the binary ped file was not found (the .bim file). "+
+            throw new GATKException("The SNP information file accompanying the binary ped file was not found (the .bim file). "+
                                      "Please ensure that it is in the same directory as the .bed and .fam files. The file we "+
                                      "Were looking for was "+bimFile.getAbsolutePath(),e);
         }
@@ -300,7 +301,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
                 line = reader.readLine();
             }
         } catch ( IOException e ) {
-            throw new StingException("There was an error reading the .bim file "+bimFile.getAbsolutePath(), e);
+            throw new GATKException("There was an error reading the .bim file "+bimFile.getAbsolutePath(), e);
         }
 
         return variants;
@@ -311,7 +312,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         try {
             reader = new BufferedReader( new FileReader( famFile ));
         } catch ( FileNotFoundException e) {
-            throw new StingException("The Family information file accompanying the binary ped file was not found (the .fam file). "+
+            throw new GATKException("The Family information file accompanying the binary ped file was not found (the .fam file). "+
                                      "Please ensure that it is in the same directory as the .bed and .bim files. The file we "+
                                      "Were looking for was "+famFile.getAbsolutePath(),e);
         }
@@ -327,7 +328,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
                 }
             } while ( line != null );
         } catch (IOException e) {
-            throw new StingException("There was an error reading the .fam file "+famFile.getAbsolutePath(),e);
+            throw new GATKException("There was an error reading the .fam file "+famFile.getAbsolutePath(),e);
         }
 
         return sampleNames;
@@ -338,7 +339,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         try {
             inStream = new FileInputStream(bedFile);
         } catch (FileNotFoundException e) {
-            throw new StingException("The Binary pedigree file file accompanying the family file was not found (the .bed file). "+
+            throw new GATKException("The Binary pedigree file file accompanying the family file was not found (the .bed file). "+
                                      "Please ensure that it is in the same directory as the .bim and .fam files. The file we "+
                                      "Were looking for was "+bedFile.getAbsolutePath(),e);
         }
@@ -378,7 +379,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
                 }
             } while ( genotype != -1 );
         } catch ( IOException e) {
-            throw new StingException("Error reading binary ped file "+bedFile.getAbsolutePath(), e);
+            throw new GATKException("Error reading binary ped file "+bedFile.getAbsolutePath(), e);
         }
 
         return variants;

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.refdata;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.Utils;
@@ -115,7 +116,7 @@ public class RODRecordIterator<ROD extends ReferenceOrderedDatum> implements Ite
         try {
             reader = new PushbackIterator<String>(new XReadLines(file));
         } catch (FileNotFoundException e) {
-            Utils.scareUser("Couldn't open file: " + file);
+            throw new UserError.CouldNotReadInputFile(file, e);
         }
         this.file = file;
         this.name = name;
@@ -124,7 +125,7 @@ public class RODRecordIterator<ROD extends ReferenceOrderedDatum> implements Ite
             named_constructor = type.getConstructor(String.class);
         }
         catch (java.lang.NoSuchMethodException e) {
-            throw new StingException("ROD class "+type.getName()+" does not have constructor that accepts a single String argument (track name)");
+            throw new GATKException("ROD class "+type.getName()+" does not have constructor that accepts a single String argument (track name)");
         }
         ROD rod = instantiateROD(name);
         fieldDelimiter = rod.delimiterRegex(); // get delimiter from the ROD itself
@@ -232,11 +233,11 @@ public class RODRecordIterator<ROD extends ReferenceOrderedDatum> implements Ite
         try {
             return (ROD) named_constructor.newInstance(name);
         } catch (java.lang.InstantiationException e) {
-            throw new StingException("Failed to instantiate ROD object of class "+type.getName());
+            throw new GATKException("Failed to instantiate ROD object of class "+type.getName());
         } catch (java.lang.IllegalAccessException e) {
-            throw new StingException("Access violation attempt while instantiating ROD object of class "+type.getName());
+            throw new GATKException("Access violation attempt while instantiating ROD object of class "+type.getName());
         } catch (InvocationTargetException e) {
-            throw new StingException("InvocationTargetException: Failed to instantiate ROD object of class "+type.getName());
+            throw new GATKException("InvocationTargetException: Failed to instantiate ROD object of class "+type.getName());
         }
     }
 

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

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 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;
 
@@ -47,10 +48,10 @@ public class RODRecordListImpl extends AbstractList<GATKFeature> implements Comp
             records.add(r);
             if ( r == null ) continue;
             if ( ! this.name.equals(r.getName() ) ) {
-                throw new StingException("Attempt to add GATKFeature with non-matching name "+r.getName()+" to the track "+name);
+                throw new GATKException("Attempt to add GATKFeature with non-matching name "+r.getName()+" to the track "+name);
             }
             if ( location != null && ! location.overlapsP(r.getLocation()) ) {
-                    throw new StingException("Attempt to add GATKFeature that lies outside of specified interval "+location+"; offending GATKFeature:\n"+r.toString());
+                    throw new GATKException("Attempt to add GATKFeature that lies outside of specified interval "+location+"; offending GATKFeature:\n"+r.toString());
             }
         }
     }
@@ -72,7 +73,7 @@ public class RODRecordListImpl extends AbstractList<GATKFeature> implements Comp
     public void add(GATKFeature record, boolean allowNameMismatch) {
         if ( record != null ) {
             if ( ! allowNameMismatch && ! name.equals(record.getName() ) )
-                throw new StingException("Attempt to add GATKFeature with non-matching name "+record.getName()+" to the track "+name);
+                throw new GATKException("Attempt to add GATKFeature with non-matching name "+record.getName()+" to the track "+name);
         }
         records.add(record);
     }

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

@@ -5,8 +5,10 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 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;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.util.*;
 
@@ -106,8 +108,8 @@ public class RefMetaDataTracker {
 
         Object obj = objects.get(0).getUnderlyingObject();
         if (!(clazz.isAssignableFrom(obj.getClass())))
-            throw new StingException("Unable to case track named " + name + " to type of " + clazz.toString()
+            throw new UserError.CommandLineError("Unable to case track named " + name + " to type of " + clazz.toString()
-                                     + " it's of type " + obj.getClass());
+                    + " it's of type " + obj.getClass());
 
         return (T)obj;
     }
@@ -289,7 +291,7 @@ public class RefMetaDataTracker {
         Collection<VariantContext> contexts = getVariantContexts(ref, name, allowedTypes, curLocation, requireStartHere, false );
 
         if ( contexts.size() > 1 )
-            throw new StingException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation);
+            throw new GATKException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation);
         else if ( contexts.size() == 0 )
             return null;
         else

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

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 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.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
@@ -131,7 +132,7 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator {
      */
      public RODRecordList next() {
          if ( ! next_is_allowed )
-             throw new StingException("Illegal use of iterator: Can not advance iterator with next() after seek-forward query of length > 1");
+             throw new GATKException("Illegal use of iterator: Can not advance iterator with next() after seek-forward query of length > 1");
 
          curr_position++;
  //        curr_query_end = -1;
@@ -178,7 +179,7 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator {
              r = it.next(); // we got here only if we do need next record, time to load it for real
 
              long stop = r.getLocation().getStop();
-             if ( stop < curr_position ) throw new StingException("DEBUG: encountered contig that should have been loaded earlier"); // this should never happen
+             if ( stop < curr_position ) throw new GATKException("DEBUG: encountered contig that should have been loaded earlier"); // this should never happen
              if ( stop > max_position ) max_position = stop; // max_position keeps the rightmost stop position across all loaded records
              records.add(r);
          }
@@ -257,14 +258,14 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator {
     public RODRecordList seekForward(GenomeLoc interval) {
 
         if ( interval.getContigIndex() < curr_contig )
-            throw new StingException("Out of order query: query contig "+interval.getContig()+" is located before "+
+            throw new GATKException("Out of order query: query contig "+interval.getContig()+" is located before "+
                                      "the iterator's current contig");
         if ( interval.getContigIndex() == curr_contig ) {
             if ( interval.getStart() < curr_position )
-                throw new StingException("Out of order query: query position "+interval +" is located before "+
+                throw new GATKException("Out of order query: query position "+interval +" is located before "+
                         "the iterator's current position "+curr_contig + ":" + curr_position);
             if ( interval.getStop() < curr_query_end )
-                throw new StingException("Unsupported querying sequence: current query interval " +
+                throw new GATKException("Unsupported querying sequence: current query interval " +
                         interval+" ends before the end of previous query interval ("+curr_query_end+")");
         }
 

java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java

@@ -4,6 +4,7 @@ import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.Transcript;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 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.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
@@ -60,7 +61,7 @@ public class RefSeqFeature implements Transcript, Feature {
 
     /** Genomic location of the n-th exon; throws an exception if n is out of bounds */
     public GenomeLoc getExonLocation(int n) {
-        if ( n >= exons.size() || n < 0 ) throw new StingException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
+        if ( n >= exons.size() || n < 0 ) throw new GATKException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
         return exons.get(n);
     }
 

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

@@ -28,8 +28,10 @@ package org.broadinstitute.sting.gatk.refdata.tracks;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.io.File;
 import java.util.*;
@@ -175,7 +177,7 @@ public class RMDTrackManager extends PluginManager<RMDTrackBuilder> {
         // create instances of each of the requested types
         for (RMDTriplet trip : inputs) {
             RMDTrackBuilder b = availableTrackBuilders.get(trip.getType().toUpperCase());
-            if (b == null) throw new StingException("Unable to find track for " + trip.getType());
+            if (b == null) throw new UserError.CommandLineError("Unable to find track for " + trip.getType());
             tracks.add(b.createInstanceOfTrack(availableTrackTypes.get(trip.getType().toUpperCase()), trip.getName(), new File(trip.getFile())));
         }
         return tracks;

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

@@ -30,6 +30,7 @@ import org.broad.tribble.FeatureSource;
 import org.broad.tribble.source.BasicFeatureSource;
 import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
+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;
@@ -115,7 +116,7 @@ public class TribbleTrack extends RMDTrack implements QueryableTrack {
         try {
             reader.close();
         } catch (IOException e) {
-            throw new StingException("Unable to close reader " + reader.toString(),e);
+            throw new GATKException("Unable to close reader " + reader.toString(),e);
         }
         reader = null;
     }

java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java

@@ -39,6 +39,7 @@ import org.broad.tribble.util.LittleEndianOutputStream;
 import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.StingException;
@@ -230,7 +231,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
             locked = lock.sharedLock();
         }
         catch(FileSystemInabilityToLockException ex) {
-            throw new StingException("Unexpected inability to lock exception", ex);
+            throw new GATKException("Unexpected inability to lock exception", ex);
         }
         Index idx;
         try {
@@ -297,7 +298,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
             return index;
         }
         catch(FileSystemInabilityToLockException ex) {
-            throw new StingException("Unexpected inability to lock exception", ex);
+            throw new GATKException("Unexpected inability to lock exception", ex);
         }
         finally {
             if (locked) lock.unlock();

java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.Comparator;
@@ -114,7 +115,7 @@ public class AnnotationDatum implements Comparator<AnnotationDatum> {
     final public float calcTiTv( final int INDEX ) {
 
         if( ti[INDEX] < 0 || tv[INDEX] < 0 ) {
-            throw new StingException( "Integer overflow detected! There are too many variants piled up in one annotation bin." );
+            throw new GATKException( "Integer overflow detected! There are too many variants piled up in one annotation bin." );
         }
 
         if( tv[INDEX] == 0 ) { // Don't divide by zero

java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java

@@ -197,7 +197,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
         String b = haplotypeB.toString();
 
         if (a.length() != b.length())
-            throw new StingException("Haplotypes a and b must be of same length");
+            throw new GATKException("Haplotypes a and b must be of same length");
 
         char chA, chB;
         char wc = REGEXP_WILDCARD.charAt(0);

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

@@ -49,6 +49,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.exceptions.UserError;
@@ -168,7 +169,7 @@ public class VariantAnnotatorEngine {
         Collection<VariantContext> results = this.annotateContext(tracker, ref, EMPTY_STRATIFIED_ALIGNMENT_CONTEXT, vc);
 
         if ( results.size() != 1 )
-            throw new StingException("BUG: annotateContext call requires 1 resulting annotated VC, but got " + results);
+            throw new GATKException("BUG: annotateContext call requires 1 resulting annotated VC, but got " + results);
 
         return results.iterator().next();
 

java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java

@@ -33,6 +33,7 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserError;
 
@@ -83,7 +84,7 @@ public class JoinTable
      */
     public void parseFromFile(String filename, String localBindingName, String localColumnName, String externalBindingName, String externalColumnName)  {
         if(parsedFromFile) {
-            throw new StingException("parseFromFile(" + filename +", ..) called more than once");
+            throw new GATKException("parseFromFile(" + filename +", ..) called more than once");
         }
         parsedFromFile = true;
 
@@ -135,7 +136,7 @@ public class JoinTable
                     br.close();
                 }
             } catch(IOException e) {
-                throw new StingException("Unable to close file: " + filename, e);
+                throw new GATKException("Unable to close file: " + filename, e);
             }
         }
     }

java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java

@@ -31,6 +31,7 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.UserError;
@@ -63,7 +64,7 @@ public class JoinTableParser
     public List<String> readHeader(BufferedReader br) throws IOException
     {
         if(header != null) {
-            throw new StingException("readHeader(..) called more than once. Header is currently set to: " + header);
+            throw new GATKException("readHeader(..) called more than once. Header is currently set to: " + header);
         }
 
         header = Collections.unmodifiableList(parseHeader(br));

java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java

@@ -44,7 +44,9 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 
 /**
@@ -173,12 +175,12 @@ public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> {
         try {
             header = AnnotatorInputTableCodec.readHeader(transcriptsDataSource.getReferenceOrderedData().getFile());
         } catch(Exception e) {
-            throw new StingException("Failed when attempting to read header from file: " + transcriptsDataSource.getReferenceOrderedData().getFile(), e);
+            throw new UserError.MalformedFile(transcriptsDataSource.getReferenceOrderedData().getFile(), "Failed when attempting to read header from file", e);
         }
 
         for ( String columnName : GENE_NAME_COLUMNS ) {
             if ( !header.contains(columnName) )
-                throw new StingException("The column name '" + columnName + "' provided to -n doesn't match any of the column names in: " + transcriptsDataSource.getReferenceOrderedData().getFile());
+                throw new UserError.CommandLineError("The column name '" + columnName + "' provided to -n doesn't match any of the column names in: " + transcriptsDataSource.getReferenceOrderedData().getFile());
         }
 
         //init outputColumnNames list
@@ -973,7 +975,7 @@ public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> {
          */
         public int computeInitialCodingCoord() {
             if(!isProteinCodingTranscript()) {
-                throw new StingException("This method should only be called for protein-coding transcripts");
+                throw new GATKException("This method should only be called for protein-coding transcripts");
             }
 
             if(positiveStrand)

java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToInfo.java

@@ -42,6 +42,7 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 
 /**
@@ -70,7 +71,7 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer> implements Tre
     private String[] GENE_NAME_COLUMNS = {};
 
     public void initialize() {
-        throw new StingException("This walker is no longer supported.  We are actively working on a bug-free replacement.  We thank you for your patience at this time.");
+        throw new UserError.MissingWalker("TranscriptToInfo", "This walker is no longer supported.  We are actively working on a bug-free replacement.  We thank you for your patience at this time.");
     }
 
     public Integer reduceInit() { return 0; }

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

@@ -29,6 +29,7 @@ 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.*;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -91,7 +92,7 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
             PrintStream summaryOut = new PrintStream(summaryFile);
             summaryOut.close();
         } catch (FileNotFoundException e) {
-            throw new StingException("Cannot write to summary file " + summaryFile);
+            throw new UserError.CouldNotCreateOutputFile(summaryFile, e);
         }
     }
 
@@ -219,7 +220,7 @@ public class CallableLociWalker extends LocusWalker<CallableLociWalker.CallableB
 
                 summaryOut.close();
             } catch (FileNotFoundException e) {
-                throw new StingException(e.getMessage());
+                throw new UserError.CouldNotCreateOutputFile(summaryFile, e);
             }
         }
     }

java/src/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalker.java

@@ -32,6 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broad.tribble.bed.FullBEDFeature;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 import java.util.*;
 import java.io.PrintStream;
@@ -94,7 +95,7 @@ public class CompareCallableLociWalker extends RodWalker<List<CallableLociWalker
         //System.out.printf("tracker %s%n", tracker);
         List<Object> bindings = tracker.getReferenceMetaData(track);
         if ( bindings.size() != 1 || ! (bindings.get(0) instanceof FullBEDFeature)) {
-            throw new StingException(String.format("%s track isn't a properly formated CallableBases object!", track));
+            throw new UserError.MalformedFile(String.format("%s track isn't a properly formated CallableBases object!", track));
         }
 
         FullBEDFeature bed = (FullBEDFeature)bindings.get(0);

java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java

@@ -4,7 +4,9 @@ import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 
 import java.util.*;
@@ -56,7 +58,7 @@ public class CoverageUtils {
         } else if ( type == DoCOutputType.Partition.sample_by_platform_by_center ) {
             return String.format("%s_pl_%s_cn_%s",r.getSample(),r.getPlatform(),r.getSequencingCenter());
         } else {
-            throw new StingException("Invalid type ID sent to getTypeID. This is a BUG!");
+            throw new GATKException("Invalid type ID sent to getTypeID. This is a BUG!");
         }
     }
 
@@ -118,7 +120,7 @@ public class CoverageUtils {
             try {
                 counts[BaseUtils.simpleBaseToBaseIndex(e.getBase())]++;
             } catch (ArrayIndexOutOfBoundsException exc) {
-                throw new StingException("Expected a simple base, but actually received"+(char)e.getBase());
+                throw new GATKException("Expected a simple base, but actually received"+(char)e.getBase());
             }
         }
     }
@@ -126,10 +128,8 @@ public class CoverageUtils {
     private static SAMReadGroupRecord getReadGroup(SAMRecord r) {
         SAMReadGroupRecord rg = r.getReadGroup();
         if ( rg == null ) {
-            String msg = "Read "+r.getReadName()+" lacks read group information.";
+            String msg = "Read "+r.getReadName()+" lacks read group information; Please associate all reads with read groups";
-            msg += " Please associate all reads with read groups [recommended]\n";
+            throw new UserError.MalformedBam(r, msg);
-            msg += " Or run with -rf MissingReadGroup [not recommended]";
-            throw new StingException(msg);
         }
 
         return rg;

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

@@ -36,13 +36,11 @@ import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder;
 import org.broadinstitute.sting.gatk.refdata.utils.*;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.StingException;
 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;
@@ -227,7 +225,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
                 partition.add(String.format("%s_pl_%s_cn_%s",rg.getSample(),rg.getPlatform(),rg.getSequencingCenter()));
             }
         } else {
-            throw new StingException("Invalid aggregation type sent to getSamplesFromToolKit");
+            throw new GATKException("Invalid aggregation type sent to getSamplesFromToolKit");
         }
 
         return partition;
@@ -290,7 +288,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
                         getCorrectStream(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.statistics),
                         partition);
             } else {
-                throw new StingException("Partition type "+partition.toString()+" had no entries. Please check that your .bam header has all appropriate partition types.");
+                throw new GATKException("Partition type "+partition.toString()+" had no entries. Please check that your .bam header has all appropriate partition types.");
             }
         }
 
@@ -405,7 +403,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
         try {
             return new SeekableRODIterator(new FeatureToGATKFeatureIterator(refseq.iterator(),"refseq"));
         } catch (IOException e) {
-            throw new StingException("Unable to open file " + refSeqGeneList, e);
+            throw new UserError.CouldNotReadInputFile(refSeqGeneList, "Unable to open file", e);
         }
     }
 
@@ -615,7 +613,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
     private PrintStream getCorrectStream(DoCOutputType.Partition partition, DoCOutputType.Aggregation aggregation, DoCOutputType.FileType fileType) {
         DoCOutputType outputType = new DoCOutputType(partition,aggregation,fileType);
         if(!out.containsKey(outputType))
-            throw new StingException(String.format("Unable to find appropriate stream for partition = %s, aggregation = %s, file type = %s",partition,aggregation,fileType));
+            throw new UserError.CommandLineError(String.format("Unable to find appropriate stream for partition = %s, aggregation = %s, file type = %s",partition,aggregation,fileType));
         return out.get(outputType);
     }
 
@@ -767,7 +765,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
             int index = 0;
             for ( String s : namesInAg ) {
                 if ( ! s.equalsIgnoreCase(order.get(index)) ) {
-                    throw new StingException("IDs are out of order for type "+t+"! Aggregator has different ordering");
+                    throw new GATKException("IDs are out of order for type "+t+"! Aggregator has different ordering");
                 }
                 index++;
             }
@@ -776,7 +774,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
 
     public boolean checkType(DepthOfCoverageStats stats, DoCOutputType.Partition type ) {
         if ( stats.getHistograms().size() < 1 ) {
-            Utils.warnUser("The histogram per partition type "+type.toString()+" was empty\n"+
+            logger.warn("The histogram per partition type "+type.toString()+" was empty\n"+
                     "Do your read groups have this type? (Check your .bam header).");
             return false;
         } else {

java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java

@@ -1,5 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.io.PrintStream;
@@ -23,7 +24,7 @@ public class FastaSequence {
     }
 
     public void setName(String name) {
-        if ( printedHeader ) throw new StingException("Can not set name for FASTA record: header is already printed.");
+        if ( printedHeader ) throw new GATKException("Can not set name for FASTA record: header is already printed.");
         this.name = name;
     }
 

java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.filters;
 
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
@@ -80,9 +81,9 @@ public class FiltrationContextWindow {
      */
     public FiltrationContext[] getWindow(int elementsToLeft, int elementsToRight) {
         if ( elementsToLeft > maxWindowElements() || elementsToRight > maxWindowElements() )
-            throw new StingException("Too large a window requested");
+            throw new GATKException("Too large a window requested");
         if ( elementsToLeft < 0 || elementsToRight < 0 )
-            throw new StingException("Window size cannot be negative");        
+            throw new GATKException("Window size cannot be negative");        
 
         FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1];
         ListIterator<FiltrationContext> iter = window.listIterator(currentContext - elementsToLeft);

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java

@@ -191,7 +191,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
 
         public void incrementFrequency() {
             if ( frequency == 2 * N )
-                throw new StingException("Frequency was incremented past N; how is this possible?");
+                throw new GATKException("Frequency was incremented past N; how is this possible?");
             frequency++;
 
             double greedy = VALUE_NOT_CALCULATED;
@@ -218,7 +218,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
                 // so we can ignore that case
             }
             if ( greedyIndex == -1 )
-                throw new StingException("There is no best choice for a new alternate allele; how is this possible?");
+                throw new GATKException("There is no best choice for a new alternate allele; how is this possible?");
 
             if ( indexes[greedyIndex] == GenotypeType.HET.ordinal() )
                 indexes[greedyIndex] = GenotypeType.HOM.ordinal();

java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java

@@ -71,7 +71,7 @@ public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
                 alleles.add( Allele.create(bestEvent.substring(1), true ));
                 loc = GenomeLocParser.setStop(loc, loc.getStop() + bestEvent.length()-1);
             } else
-                throw new StingException("Internal error (probably a bug): event does not conform to expected format: "+ bestEvent);
+                throw new GATKException("Internal error (probably a bug): event does not conform to expected format: "+ bestEvent);
         }
 
         VariantContext vc = new VariantContext("UG_Indel_call", loc.getContig(), loc.getStart(), loc.getStop(), alleles, new HashMap<String, Genotype>() /* genotypes */,

java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java

@@ -25,10 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.indels;
 
-import net.sf.samtools.Cigar;
+import net.sf.samtools.*;
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMRecord;
 import org.broad.tribble.FeatureSource;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.VariantContext;
@@ -51,6 +48,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSource;
 import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.collections.CircularArray;
@@ -213,7 +211,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
 		normal_context = new WindowContext(0,WINDOW_SIZE);
 
         if ( bedOutput != null && output_file != null ) {
-            throw new StingException("-O option is deprecated and -bed option replaces it; you can not use both at the same time");
+            throw new UserError.DeprecatedArgument("-O", "-O option is deprecated and -bed option replaces it; you can not use both at the same time");
         }
 
 		if ( RefseqFileName != null ) {
@@ -225,7 +223,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
             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(new File(RefseqFileName), "Write failed", e);
             }
 		}
 
@@ -266,12 +264,12 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
             if ( bedOutput != null ) bedWriter = new FileWriter(bedOutput);
             if ( output_file != null ) bedWriter = new FileWriter(output_file);
         } catch (java.io.IOException e) {
-            throw new StingException("Failed to open BED file for writing. "+ e.getMessage());
+            throw new UserError.CouldNotReadInputFile(bedOutput, "Failed to open BED file for writing.", e);
         }
         try {
             if ( verboseOutput != null ) verboseWriter = new FileWriter(verboseOutput);
         } catch (java.io.IOException e) {
-            throw new StingException("Failed to open verbose file for writing. "+ e.getMessage());
+            throw new UserError.CouldNotReadInputFile(verboseOutput, "Failed to open BED file for writing.", e);
         }
 
         vcf_writer.writeHeader(new VCFHeader(getVCFHeaderInfo(), SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader()))) ;
@@ -301,7 +299,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
                 // we just jumped onto a new contig
                 if ( DEBUG ) System.out.println("DEBUG>>> Moved to contig "+read.getReferenceName());
                 if ( read.getReferenceIndex() < currentContigIndex ) // paranoidal
-                    throw new StingException("Read "+read.getReadName()+": contig is out of order; input BAM file is unsorted");
+                    throw new UserError.MissortedBAM(SAMFileHeader.SortOrder.coordinate, read, "Read "+read.getReadName()+": contig is out of order; input BAM file is unsorted");
 
                 // print remaining indels from the previous contig (if any);
                 if ( call_somatic ) emit_somatic(1000000000, true);
@@ -329,10 +327,10 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
             // tumor_context are synchronized exactly (windows are always shifted together by emit_somatic), so it's safe
 
             if ( read.getAlignmentStart() < currentPosition ) // oops, read out of order?
-                throw new StingException("Read "+read.getReadName() +" out of order on the contig\n"+
+                throw new UserError.MissortedBAM(SAMFileHeader.SortOrder.coordinate, read, "Read "+read.getReadName() +" out of order on the contig\n"+
-                                         "Read starts at "+refName+":"+read.getAlignmentStart()+"; last read seen started at "+refName+":"+currentPosition
+                        "Read starts at "+refName+":"+read.getAlignmentStart()+"; last read seen started at "+refName+":"+currentPosition
-					+"\nLast read was: "+lastRead.getReadName()+" RG="+lastRead.getAttribute("RG")+" at "+lastRead.getAlignmentStart()+"-"
+                        +"\nLast read was: "+lastRead.getReadName()+" RG="+lastRead.getAttribute("RG")+" at "+lastRead.getAlignmentStart()+"-"
-					+lastRead.getAlignmentEnd()+" cigar="+lastRead.getCigarString());
+                        +lastRead.getAlignmentEnd()+" cigar="+lastRead.getCigarString());
 
             currentPosition = read.getAlignmentStart();
             lastRead = read;
@@ -384,7 +382,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
                 // let's double check now that the read fits after the shift
                 if ( read.getAlignmentEnd() > normal_context.getStop()) {
                     // ooops, looks like the read does not fit into the window even after the latter was shifted!!
-                    throw new StingException("Read "+read.getReadName()+": out of coverage window bounds. Probably window is too small.\n"+
+                    throw new UserError.MissortedBAM(SAMFileHeader.SortOrder.coordinate, read, "Read "+read.getReadName()+": out of coverage window bounds. Probably window is too small.\n"+
                                              "Read length="+read.getReadLength()+"; cigar="+read.getCigarString()+"; start="+
                                              read.getAlignmentStart()+"; end="+read.getAlignmentEnd()+
                                              "; window start (after trying to accomodate the read)="+normal_context.getStart()+
@@ -395,14 +393,15 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
             if ( call_somatic ) {
 
                 String rg = (String)read.getAttribute("RG");
-                if ( rg == null ) throw new StingException("Read "+read.getReadName()+" has no read group in merged stream. RG is required for somatic calls.");
+                if ( rg == null )
+                    throw new UserError.MalformedBam(read, "Read "+read.getReadName()+" has no read group in merged stream. RG is required for somatic calls.");
 
                 if ( normalReadGroups.contains(rg) ) {
                     normal_context.add(read,ref.getBases());
                 } else if ( tumorReadGroups.contains(rg) ) {
                     tumor_context.add(read,ref.getBases());
                 } else {
-                    throw new StingException("Unrecognized read group in merged stream: "+rg);
+                    throw new UserError.MalformedBam(read, "Unrecognized read group in merged stream: "+rg);
                 }
                 if ( tumor_context.getReads().size() > MAX_READ_NUMBER ) {
                     System.out.println("WARNING: a count of "+MAX_READ_NUMBER+" reads reached in a window "+
@@ -504,7 +503,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
                             verboseWriter.write(fullRecord.toString());
                             verboseWriter.write('\n');
                         } catch (IOException e) {
-                            throw new StingException("Write failed (verbose writer). "+e.getMessage());
+                            throw new UserError.CouldNotCreateOutputFile(verboseOutput, "Write failed", e);
                         }
                     }
                 }
@@ -664,7 +663,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
                         verboseWriter.write(fullRecord + "\t"+ annotationString);
                         verboseWriter.write('\n');
                     } catch (IOException e) {
-                        throw new StingException("Write failed (verbose writer). "+e.getMessage());
+                        throw new UserError.CouldNotCreateOutputFile(verboseOutput, "Write failed", e);
                     }
                 }
             }
@@ -1223,7 +1222,7 @@ public class IndelGenotyperV2Walker extends ReadWalker<Integer,Integer> {
            try {
                 bed.write(message.toString()+"\n");
            } catch (IOException e) {
-                throw new StingException("Error encountered while writing into output BED file");
+               throw new UserError.CouldNotCreateOutputFile(bedOutput, "Error encountered while writing into output BED file", e);
            }
         }
 

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

@@ -31,6 +31,7 @@ import net.sf.samtools.util.SequenceUtil;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.*;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -333,7 +334,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 currentInterval = intervals.hasNext() ? intervals.next() : null;
             } while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) );
         } catch (StingException e) {
-            throw new StingException(e.getMessage() + " *** Are you sure that your interval file is sorted? If not, you must use the --targetIntervalsAreNotSorted argument. ***");
+            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);
         }
 
 
@@ -531,7 +532,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         statsOutput.write("\n");
                         statsOutput.flush();
                     } catch (Exception e) {
-                        throw new StingException(e.getMessage());
+                        throw new UserError.CouldNotCreateOutputFile("statsOutput", "Failed to write stats output file", e);
                     }
                 }
             } else {
@@ -558,7 +559,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         indelOutput.write(str.toString());
                         indelOutput.flush();
                     } catch (Exception e) {
-                        throw new StingException(e.getMessage());
+                        throw new UserError.CouldNotCreateOutputFile("indelOutput", "Failed to write indel output file", e);
                     }
                 }
                 if ( statsOutput != null ) {
@@ -572,7 +573,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         statsOutput.write("\n");
                         statsOutput.flush();
                     } catch (Exception e) {
-                        throw new StingException(e.getMessage());
+                        throw new UserError.CouldNotCreateOutputFile("statsOutput", "Failed to write stats output file", e);
                     }
                 }
 
@@ -607,7 +608,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                         currentInterval.toString(), improvement));
                 statsOutput.flush();
             } catch (Exception e) {
-                throw new StingException(e.getMessage());
+                throw new UserError.CouldNotCreateOutputFile("statsOutput", "Failed to write stats output file", e);
             }
         }
     }
@@ -1047,7 +1048,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 snpsOutput.write(sb.toString());
                 snpsOutput.flush();
             } catch (Exception e) {
-                throw new StingException(e.getMessage());                
+                throw new UserError.CouldNotCreateOutputFile("snpsOutput", "Failed to write SNPs output file", e);
             }
         }
         return reduces;

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

@@ -33,11 +33,13 @@ import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
 import org.broadinstitute.sting.gatk.filters.BadMateFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.pileup.ExtendedEventPileupElement;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
@@ -83,7 +85,7 @@ public class RealignerTargetCreator extends RodWalker<RealignerTargetCreator.Eve
 
     public void initialize() {
         if ( windowSize < 2 )
-            throw new StingException("Window Size must be an integer greater than 1");
+            throw new UserError.BadArgumentValue("windowSize", "Window Size must be an integer greater than 1");
     }
 
     public Event map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {

java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java

@@ -30,8 +30,10 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -80,7 +82,7 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
     private Map<String,CycleStats[]> cyclesByLibraryMapOrig = null;
 
     public void initialize() {
-        if ( PREFIX == null ) throw new StingException("Prefix for output file(s) must be specified");
+        if ( PREFIX == null ) throw new GATKException("Prefix for output file(s) must be specified");
         cyclesByLaneMap = new HashMap<String,CycleStats[]>();
         cyclesByLibraryMap = new HashMap<String,CycleStats[]>();
         cyclesByLaneMapOrig = new HashMap<String,CycleStats[]>();
@@ -94,23 +96,25 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
 
         SAMReadGroupRecord rg = read.getReadGroup();
 
-        if ( rg == null ) throw new StingException("Read "+read.getReadName()+" is not assigned to any read group");
+        if ( rg == null ) throw new UserError.ReadMissingReadGroup(read);
 
         String lane = read.getReadGroup().getPlatformUnit();
         String library = read.getReadGroup().getLibrary();
 
-        if ( lane == null ) throw new StingException("Read "+read.getReadName()+" has no platform unit information");
+        if ( lane == null ) throw new UserError.MalformedBam(read, "Read "+read.getReadName()+" has no platform unit information");
-        if ( library == null ) throw new StingException("Read "+read.getReadName()+" has no library information");
+        if ( library == null ) throw new UserError.MalformedBam(read, "Read "+read.getReadName()+" has no library information");
 
         int end = 0;
 
         if ( read.getReadPairedFlag() ) {
 
             if ( read.getFirstOfPairFlag() ) {
-                if ( read.getSecondOfPairFlag() ) throw new StingException("Read "+read.getReadName()+" has conflicting first/second in pair attributes");
+                if ( read.getSecondOfPairFlag() )
+                    throw new UserError.MalformedBam(read, "Read "+read.getReadName()+" has conflicting first/second in pair attributes");
                 end = 1;
             } else {
-                if ( ! read.getSecondOfPairFlag() ) throw new StingException("Read "+read.getReadName()+" has conflicting first/second in pair attributes");
+                if ( ! read.getSecondOfPairFlag() )
+                    throw new UserError.MalformedBam(read, "Read "+read.getReadName()+" has conflicting first/second in pair attributes");
                 end = 2;
             }
         }
@@ -357,7 +361,7 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
             }
 
         } catch (IOException ioe) {
-            throw new StingException("Failed to write report into the file "+f+":\n"+ioe.getMessage());
+            throw new UserError.CouldNotCreateOutputFile(f, "Failed to write report", ioe);
         }
     }
 
@@ -403,8 +407,8 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
         }
 
         public void add(byte[] quals) {
-            if ( quals.length > cycleQualsAv.length ) throw new StingException("A read of length "+quals.length+
+            if ( quals.length > cycleQualsAv.length )
-                    " encountered, which exceeds specified maximum read length");
+                throw new UserError("A read of length "+quals.length+" encountered, which exceeds specified maximum read length");
             if ( quals.length > maxL ) maxL = quals.length;
             if ( quals.length < minL ) minL = quals.length;
             readCount++;

java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadClippingStatsWalker.java

@@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
@@ -76,7 +77,7 @@ public class ReadClippingStatsWalker extends ReadWalker<ReadClippingStatsWalker.
         ReadClippingInfo info = new ReadClippingInfo();
         info.rg = read.getReadGroup();
 
-        if ( info.rg == null ) throw new StingException("Read "+read.getReadName()+" is not assigned to any read group");
+        if ( info.rg == null ) throw new UserError.ReadMissingReadGroup(read);
 
         for ( CigarElement elt : read.getCigar().getCigarElements() ) {
             if ( elt.getOperator() != CigarOperator.N )

java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileWriter;
@@ -58,7 +59,7 @@ public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
         try {
             m = MessageDigest.getInstance("MD5");
         } catch (NoSuchAlgorithmException e) {
-            throw new StingException("Unable to get the MD5 algorithm. Get a more eXtreme version of JAVA!@!@!!");
+            throw new GATKException("Unable to get the MD5 algorithm. Get a more eXtreme version of JAVA!@!@!!");
         }
     }
 

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

@@ -30,12 +30,10 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.features.sampileup.SAMPileupFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.Arrays;
@@ -61,8 +59,8 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
         if ( truePileup == null ) {
             out.printf("No truth pileup data available at %s%n", pileup.getPileupString(ref.getBaseAsChar()));
             if ( ! CONTINUE_AFTER_AN_ERROR ) {
-                Utils.scareUser(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools pileup data over all bases",
+                throw new UserError.CommandLineError(String.format("No pileup data available at %s given GATK's output of %s -- this walker requires samtools pileup data over all bases",
-                                context.getLocation(), new String(pileup.getBases())));
+                        context.getLocation(), new String(pileup.getBases())));
             }
         } else {
             String pileupDiff = pileupDiff(pileup, truePileup, true);
@@ -141,7 +139,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
         else if( pileup.hasIndelGenotype() )
             return pileup.getIndelGenotype();
         else
-            throw new StingException("Unsupported pileup type: " + pileup);
+            throw new GATKException("Unsupported pileup type: " + pileup);
     }
 }
 

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.UserError;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
@@ -186,7 +187,7 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
             }
         }
         if( !foundDBSNP && !RUN_WITHOUT_DBSNP ) {
-            throw new StingException("This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation.");
+            throw new UserError.CommandLineError("This calculation is critically dependent on being able to skip over known variant sites. Please provide a dbSNP ROD or a VCF file containing known sites of genetic variation.");
         }
 
         // Initialize the requested covariates by parsing the -cov argument
@@ -195,7 +196,7 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
             requestedCovariates.add( new ReadGroupCovariate() ); // Order is important here
             requestedCovariates.add( new QualityScoreCovariate() );
         } else {
-            throw new StingException("There are more required covariates than expected. The instantiation list needs to be updated with the new required covariate and in the correct order.");
+            throw new UserError.CommandLineError("There are more required covariates than expected. The instantiation list needs to be updated with the new required covariate and in the correct order.");
         }
         // Next add the standard covariates if -standard was specified by the user
         if( USE_STANDARD_COVARIATES ) {
@@ -213,9 +214,9 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
                             final Covariate covariate = (Covariate)covClass.newInstance();
                             requestedCovariates.add( covariate );
                         } catch ( InstantiationException e ) {
-                            throw new StingException( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
+                            throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
                         } catch ( IllegalAccessException e ) {
-                            throw new StingException( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
+                            throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
                         }
                     }
                 }
@@ -234,16 +235,16 @@ public class CovariateCounterWalker extends LocusWalker<CovariateCounterWalker.C
                                 final Covariate covariate = (Covariate)covClass.newInstance();
                                 requestedCovariates.add( covariate );
                             } catch ( InstantiationException e ) {
-                                throw new StingException( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
+                                throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
                             } catch ( IllegalAccessException e ) {
-                                throw new StingException( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
+                                throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
                             }
                         }
                     }
                 }
 
                 if( !foundClass ) {
-                    throw new StingException( "The requested covariate type (" + requestedCovariateString + ") isn't a valid covariate option. Use --list to see possible covariates." );
+                    throw new UserError.CommandLineError( "The requested covariate type (" + requestedCovariateString + ") isn't a valid covariate option. Use --list to see possible covariates." );
                 }
             }
         }

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

@@ -5,6 +5,7 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -52,7 +53,7 @@ public class CycleCovariate implements StandardCovariate {
                 RAC.DEFAULT_PLATFORM.contains( "454" ) || RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "SOLID" ) || RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "ABI_SOLID" ) ) {
                 // nothing to do
             } else {
-                throw new StingException( "The requested default platform (" + RAC.DEFAULT_PLATFORM +") is not a recognized platform. Implemented options are illumina, 454, and solid");
+                throw new UserError.CommandLineError("The requested default platform (" + RAC.DEFAULT_PLATFORM +") is not a recognized platform. Implemented options are illumina, 454, and solid");
             }
         }
     }

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

@@ -25,6 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
+import org.broadinstitute.sting.utils.exceptions.UserError;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.*;
@@ -233,7 +234,7 @@ public class RecalDataManager {
                 readGroup.setPlatform( RAC.DEFAULT_PLATFORM );
                 ((GATKSAMRecord)read).setReadGroup( readGroup );
             } else {
-                throw new StingException("The input .bam file contains reads with no read group. First observed at read with name = " + read.getReadName() +
+                throw new UserError.MalformedBam(read, "The input .bam file contains reads with no read group. First observed at read with name = " + read.getReadName() +
                                          " Users must set both the default read group using the --default_read_group <String> argument and the default platform using the --default_platform <String> argument." );
             }
         }
@@ -259,7 +260,7 @@ public class RecalDataManager {
                 }
                 readGroup.setPlatform( RAC.DEFAULT_PLATFORM );
             } else {
-                throw new StingException("The input .bam file contains reads with no platform information. First observed at read with name = " + read.getReadName() +
+                throw new UserError.MalformedBam(read, "The input .bam file contains reads with no platform information. First observed at read with name = " + read.getReadName() +
                                          " Users must set the default platform using the --default_platform <String> argument." );
             }
         }
@@ -292,14 +293,14 @@ public class RecalDataManager {
                     int iii;
                     byte prevBase = colorSpace[0]; // The sentinel
                     for( iii = 0; iii < readBases.length; iii++ ) {
-                        final byte thisBase = getNextBaseFromColor( prevBase, colorSpace[iii + 1] );
+                        final byte thisBase = getNextBaseFromColor( read, prevBase, colorSpace[iii + 1] );
                         inconsistency[iii] = (byte)( thisBase == readBases[iii] ? 0 : 1 );
                         prevBase = readBases[iii];
                     }
                     read.setAttribute( RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency );
 
                 } else {
-                    throw new StingException("Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() +
+                    throw new UserError.MalformedBam(read, "Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() +
                                             " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias.");
                 }
             }
@@ -324,7 +325,7 @@ 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 GATKException(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
@@ -338,7 +339,7 @@ public class RecalDataManager {
             final int[] inconsistency = new int[readBases.length];
             byte prevBase = colorSpace[0]; // The sentinel
             for( int iii = 0; iii < readBases.length; iii++ ) {
-                final byte thisBase = getNextBaseFromColor( prevBase, colorSpace[iii + 1] );
+                final byte thisBase = getNextBaseFromColor( read, prevBase, colorSpace[iii + 1] );
                 colorImpliedBases[iii] = thisBase;
                 inconsistency[iii] = ( thisBase == readBases[iii] ? 0 : 1 );
                 prevBase = readBases[iii];
@@ -356,8 +357,8 @@ public class RecalDataManager {
             }
 
         } else {
-            throw new StingException("Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() +
+            throw new UserError.MalformedBam(read, "Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() +
-                                    " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias.");
+                    " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias.");
         }
 
         return originalQualScores;
@@ -371,7 +372,7 @@ public class RecalDataManager {
                 if( attr instanceof String ) {
                     colorSpace = ((String)attr).substring(1).getBytes(); // trim off the Sentinel
                 } 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 GATKException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
                 }
 
                 for( byte color : colorSpace ) {
@@ -381,7 +382,7 @@ public class RecalDataManager {
                 }
 
             } else {
-                throw new StingException("Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() +
+                throw new UserError.MalformedBam(read, "Unable to find color space information in SOLiD read. First observed at read with name = " + read.getReadName() +
                                         " Unfortunately this .bam file can not be recalibrated without color space information because of potential reference bias.");
             }
         }
@@ -446,7 +447,7 @@ public class RecalDataManager {
                 colorSpaceQuals = x.getBytes();
                 SAMUtils.fastqToPhred(colorSpaceQuals);
             } else {
-                throw new StingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_QUAL_ATTRIBUTE_TAG, read.getReadName()));
+                throw new GATKException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_QUAL_ATTRIBUTE_TAG, read.getReadName()));
             }
 
             for( int iii = 1; iii < inconsistency.length - 1; iii++ ) {
@@ -491,7 +492,7 @@ public class RecalDataManager {
             }
             read.setReadBases( readBases );
         } else { // No color space quality tag in file
-            throw new StingException("REMOVE_REF_BIAS recal mode requires color space qualities but they can't be found for read: " + read.getReadName());
+            throw new UserError.MalformedBam(read, "REMOVE_REF_BIAS recal mode requires color space qualities but they can't be found for read: " + read.getReadName());
         }
     }
 
@@ -501,7 +502,7 @@ public class RecalDataManager {
      * @param color The color
      * @return The next base in the sequence
      */
-    private static byte getNextBaseFromColor( final byte prevBase, final byte color ) {
+    private static byte getNextBaseFromColor( SAMRecord read, final byte prevBase, final byte color ) {
         switch(color) {
             case '0':
                 return prevBase;
@@ -512,7 +513,7 @@ public class RecalDataManager {
             case '3':
                 return performColorThree( prevBase );
             default:
-                throw new StingException( "Unrecognized color space in SOLID read, color = " + (char)color +
+                throw new UserError.MalformedBam(read, "Unrecognized color space in SOLID read, color = " + (char)color +
                                           " Unfortunately this bam file can not be recalibrated without full color space information because of potential reference bias.");
         }
     }

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.UserError;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.text.XReadLines;
@@ -179,7 +180,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
                 // Read in the covariates that were used from the input file
                 else if( COVARIATE_PATTERN.matcher(line).matches() ) { // The line string is either specifying a covariate or is giving csv data
                     if( foundAllCovariates ) {
-                        throw new StingException( "Malformed input recalibration file. Found covariate names intermingled with data in file: " + RECAL_FILE );
+                        throw new UserError.MalformedFile( RECAL_FILE, "Malformed input recalibration file. Found covariate names intermingled with data in file: " + RECAL_FILE );
                     } else { // Found the covariate list in input file, loop through all of them and instantiate them
                         String[] vals = line.split(",");
                         for( int iii = 0; iii < vals.length - 3; iii++ ) { // There are n-3 covariates. The last three items are nObservations, nMismatch, and Qempirical
@@ -192,15 +193,15 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
                                         requestedCovariates.add( covariate );
 
                                     } catch ( InstantiationException e ) {
-                                        throw new StingException( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
+                                        throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must be concrete class.", covClass.getSimpleName()) );
                                     } catch ( IllegalAccessException e ) {
-                                        throw new StingException( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
+                                        throw new UserError.CommandLineError( String.format("Can not instantiate covariate class '%s': must have no-arg constructor.", covClass.getSimpleName()) );
                                     }
                                 }
                             }
 
                             if( !foundClass ) {
-                                throw new StingException( "Malformed input recalibration file. The requested covariate type (" + (vals[iii] + "Covariate") + ") isn't a valid covariate option." );
+                                throw new UserError.MalformedFile(RECAL_FILE, "Malformed input recalibration file. The requested covariate type (" + (vals[iii] + "Covariate") + ") isn't a valid covariate option." );
                             }
                         }
                     }
@@ -211,7 +212,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
 
                         // At this point all the covariates should have been found and initialized
                         if( requestedCovariates.size() < 2 ) {
-                            throw new StingException( "Malformed input recalibration csv file. Covariate names can't be found in file: " + RECAL_FILE );
+                            throw new UserError.MalformedFile(RECAL_FILE, "Malformed input recalibration csv file. Covariate names can't be found in file: " + RECAL_FILE );
                         }
 
                         final boolean createCollapsedTables = true;
@@ -224,21 +225,21 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
                         dataManager = new RecalDataManager( createCollapsedTables, requestedCovariates.size() );
 
                     }
-                    addCSVData(line); // Parse the line and add the data to the HashMap
+                    addCSVData(RECAL_FILE, line); // Parse the line and add the data to the HashMap
                 }
             }
 
         } catch ( FileNotFoundException e ) {
-            throw new StingException("Can not find input file: " + RECAL_FILE);
+            throw new UserError.CouldNotReadInputFile(RECAL_FILE, "Can not find input file", e);
         } catch ( NumberFormatException e ) {
-            throw new StingException("Error parsing recalibration data at line " + lineNumber + ". Perhaps your table was generated by an older version of CovariateCounterWalker.");
+            throw new UserError.MalformedFile(RECAL_FILE, "Error parsing recalibration data at line " + lineNumber + ". Perhaps your table was generated by an older version of CovariateCounterWalker.");
         }
         logger.info( "...done!" );
 
         if ( !sawEOF ) {
             final String errorMessage = "No EOF marker was present in the recal covariates table; this could mean that the file is corrupted or was generated with an old version of the CountCovariates tool.";
             if ( REQUIRE_EOF )
-                throw new StingException(errorMessage);
+                throw new UserError.MalformedFile(RECAL_FILE, errorMessage);
             logger.warn(errorMessage);
         }
 
@@ -248,7 +249,7 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
         }
 
         if( dataManager == null ) {
-            throw new StingException("Can't initialize the data manager. Perhaps the recal csv file contains no data?");
+            throw new UserError.MalformedFile(RECAL_FILE, "Can't initialize the data manager. Perhaps the recal csv file contains no data?");
         }
 
         // Create the tables of empirical quality scores that will be used in the sequential calculation
@@ -298,12 +299,12 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
      * For each covariate read in a value and parse it. Associate those values with the data itself (num observation and num mismatches)
      * @param line A line of CSV data read from the recalibration table data file
      */
-    private void addCSVData(final String line) {
+    private void addCSVData(final File file, final String line) {
         final String[] vals = line.split(",");
 
         // Check if the data line is malformed, for example if the read group string contains a comma then it won't be parsed correctly
         if( vals.length != requestedCovariates.size() + 3 ) { // +3 because of nObservations, nMismatch, and Qempirical
-            throw new StingException("Malformed input recalibration file. Found data line with too many fields: " + line +
+            throw new UserError.MalformedFile(file, "Malformed input recalibration file. Found data line with too many fields: " + line +
                     " --Perhaps the read group string contains a comma and isn't being parsed correctly.");
         }
 

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

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.recalibration;
 import org.broadinstitute.sting.utils.StingException;
 import net.sf.samtools.SAMRecord;
 import net.sf.picard.util.IlluminaUtil;
+import org.broadinstitute.sting.utils.exceptions.UserError;
 
 /**
  * @author alecw@broadinstitute.org
@@ -47,7 +48,7 @@ public class TileCovariate implements ExperimentalCovariate {
         Integer tile = IlluminaUtil.getTileFromReadName(read.getReadName());
         if (tile == null) {
             if( exceptionWhenNoTile ) {
-                throw new StingException( "Tile number not defined for read: " + read.getReadName() );
+                throw new UserError.MalformedBam(read, "Tile covariate specified but tile number not defined for read: " + read.getReadName() );
             } else {
                 return -1;
             }

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

@@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
+import org.broadinstitute.sting.utils.GATKException;
 import org.broadinstitute.sting.utils.StingException;
 
 
@@ -112,7 +113,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                 nComplex++;
                 break;
             default:
-                throw new StingException("Unexpected VariantContext type " + vc1.getType());
+                throw new GATKException("Unexpected VariantContext type " + vc1.getType());
         }
 
         for (Genotype g : vc1.getGenotypes().values()) {
@@ -130,7 +131,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     nHomVar++;
                     break;
                 default:
-                    throw new StingException("BUG: Unexpected genotype type: " + g);
+                    throw new GATKException("BUG: Unexpected genotype type: " + g);
             }
         }