From 7880863eb7d0d79b2df34df05103c604a85e7124 Mon Sep 17 00:00:00 2001 From: depristo Date: Sun, 12 Sep 2010 15:07:38 +0000 Subject: [PATCH] Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4267 348d0f76-0448-11de-a6fe-93d51630548a --- .../reference/FastaSequenceIndexBuilder.java | 4 +-- .../sting/alignment/Alignment.java | 4 +-- .../alignment/AlignmentValidationWalker.java | 4 +-- .../sting/alignment/bwa/BWTFiles.java | 12 +++---- .../sting/alignment/bwa/c/BWACAligner.java | 28 ++++++++-------- .../bwa/java/AlignerTestHarness.java | 4 +-- .../bwa/java/AlignmentMatchSequence.java | 8 ++--- .../alignment/bwa/java/BWAAlignment.java | 4 +-- .../sting/alignment/reference/bwt/BWT.java | 4 +-- .../alignment/reference/bwt/BWTReader.java | 8 ++--- .../alignment/reference/bwt/BWTWriter.java | 8 ++--- .../sting/alignment/reference/bwt/Bases.java | 4 +-- .../sting/alignment/reference/bwt/Counts.java | 4 +-- .../reference/bwt/CreateBWTFromReference.java | 6 ++-- .../alignment/reference/bwt/SuffixArray.java | 6 ++-- .../reference/bwt/SuffixArrayReader.java | 8 ++--- .../reference/bwt/SuffixArrayWriter.java | 8 ++--- .../packing/BasePackedInputStream.java | 4 +-- .../packing/BasePackedOutputStream.java | 4 +-- .../reference/packing/PackUtils.java | 12 +++---- .../commandline/ArgumentDefinitionGroup.java | 4 +-- .../commandline/ArgumentDefinitions.java | 6 ++-- .../sting/commandline/ArgumentIOType.java | 4 +-- .../sting/commandline/ArgumentSource.java | 4 +-- .../commandline/ArgumentTypeDescriptor.java | 32 +++++++++---------- .../sting/commandline/CommandLineUtils.java | 4 +-- .../sting/commandline/ParsingEngine.java | 6 ++-- .../sting/gatk/GenomeAnalysisEngine.java | 8 ++--- .../sting/gatk/ReadMetrics.java | 4 +-- .../sting/gatk/WalkerManager.java | 6 ++-- .../arguments/GATKArgumentCollection.java | 10 +++--- .../sting/gatk/contexts/AlignmentContext.java | 12 +++---- .../sting/gatk/contexts/ReferenceContext.java | 4 +-- .../contexts/StratifiedAlignmentContext.java | 8 ++--- .../variantcontext/VariantContextUtils.java | 14 ++++---- .../DataSourceGenerationException.java | 4 +-- .../providers/LocusReferenceView.java | 8 ++--- .../datasources/providers/ReferenceView.java | 4 +-- .../providers/ShardDataProvider.java | 6 ++-- .../datasources/shards/IntervalSharder.java | 8 ++--- .../datasources/shards/MonolithicShard.java | 4 +-- .../shards/ShardStrategyFactory.java | 6 ++-- .../ReferenceDataSource.java | 16 +++++----- .../ReferenceOrderedDataSource.java | 6 ++-- .../simpleDataSources/ResourcePool.java | 6 ++-- .../simpleDataSources/SAMDataSource.java | 14 ++++---- .../SimpleDataSourceLoadException.java | 4 +-- .../SimpleDataSourceSplitException.java | 4 +-- .../datasources/utilities/BAMFileStat.java | 6 ++-- .../sting/gatk/executive/Accumulator.java | 4 +-- .../executive/HierarchicalMicroScheduler.java | 10 +++--- .../sting/gatk/executive/ShardTraverser.java | 6 ++-- .../sting/gatk/executive/TreeReducer.java | 6 ++-- .../sting/gatk/io/OutputTracker.java | 4 +-- .../gatk/io/storage/OutputStreamStorage.java | 4 +-- .../sting/gatk/io/storage/StorageFactory.java | 4 +-- .../gatk/io/storage/VCFWriterStorage.java | 4 +-- .../gatk/io/stubs/SAMFileWriterStub.java | 10 +++--- .../gatk/iterators/BufferingReadIterator.java | 4 +-- .../sting/gatk/phonehome/GATKRunReport.java | 6 ++-- .../sting/gatk/refdata/IntervalRod.java | 4 +-- .../sting/gatk/refdata/PlinkRod.java | 24 +++++++------- .../sting/gatk/refdata/RODRecordIterator.java | 4 +-- .../sting/gatk/refdata/RODRecordListImpl.java | 8 ++--- .../gatk/refdata/RefMetaDataTracker.java | 4 +-- .../gatk/refdata/SeekableRODIterator.java | 12 +++---- .../features/refseq/RefSeqFeature.java | 4 +-- .../tracks/RMDTrackCreationException.java | 4 +-- .../gatk/refdata/tracks/TribbleTrack.java | 4 +-- .../builders/TribbleRMDTrackBuilder.java | 6 ++-- .../analyzeannotations/AnnotationDatum.java | 4 +-- .../walkers/annotator/HaplotypeScore.java | 4 +-- .../annotator/VariantAnnotatorEngine.java | 4 +-- .../annotator/genomicannotator/JoinTable.java | 6 ++-- .../genomicannotator/JoinTableParser.java | 4 +-- .../TranscriptToGenomicInfo.java | 4 +-- .../gatk/walkers/coverage/CoverageUtils.java | 6 ++-- .../coverage/DepthOfCoverageWalker.java | 8 ++--- .../gatk/walkers/fasta/FastaSequence.java | 4 +-- .../filters/FiltrationContextWindow.java | 6 ++-- .../DiploidGenotypeCalculationModel.java | 6 ++-- .../SimpleIndelCalculationModel.java | 4 +-- .../gatk/walkers/indels/IndelRealigner.java | 4 +-- .../gatk/walkers/qc/CycleQualityWalker.java | 4 +-- .../gatk/walkers/qc/ReadValidationWalker.java | 4 +-- .../walkers/qc/ValidatingPileupWalker.java | 4 +-- .../recalibration/RecalDataManager.java | 8 ++--- .../walkers/varianteval/CountVariants.java | 6 ++-- .../varianteval/GenotypeConcordance.java | 6 ++-- .../varianteval/IndelLengthHistogram.java | 6 ++-- .../MendelianViolationEvaluator.java | 4 +-- .../varianteval/SimpleMetricsByAC.java | 4 +-- .../varianteval/VariantEvalWalker.java | 6 ++-- .../VariantGaussianMixtureModel.java | 8 ++--- .../walkers/BeagleOutputByDepthWalker.java | 8 ++--- .../walkers/DesignFileGeneratorWalker.java | 4 +-- .../walkers/DownsamplingValidationWalker.java | 8 ++--- .../walkers/MendelianViolationClassifier.java | 6 ++-- .../walkers/QualityScoreByStrandWalker.java | 4 +-- .../walkers/TestReadFishingWalker.java | 4 +-- .../walkers/VCF4WriterTestWalker.java | 4 +-- .../AnalyzeConcordance.java | 6 ++-- .../examples/SampleXmlMarshaller.java | 4 +-- .../gatk/walkers/LocusMismatchWalker.java | 4 +-- .../gatk/walkers/ReadBackedPhasingWalker.java | 12 +++---- .../CoverageAcrossBaitsWalker.java | 4 +-- .../gatk/walkers/phasing/Biallele.java | 4 +-- .../gatk/walkers/phasing/BialleleSNP.java | 8 ++--- .../validation/RodSystemValidationWalker.java | 4 +-- .../sting/playground/utils/GenomicMap.java | 14 ++++---- .../sting/playground/utils/ProcessUtils.java | 4 +-- .../utils/report/AnalysisModuleScanner.java | 4 +-- .../utils/report/ReportMarshaller.java | 4 +-- .../gatk/GATKExtensionsGenerator.java | 4 +-- .../sting/utils/CardinalityCounter.java | 4 +-- .../broadinstitute/sting/utils/GenomeLoc.java | 10 +++--- .../sting/utils/GenomeLocParser.java | 26 +++++++-------- .../sting/utils/GenomeLocSortedSet.java | 6 ++-- .../sting/utils/HeapSizeMonitor.java | 6 ++-- .../utils/MalformedGenomeLocException.java | 4 +-- .../broadinstitute/sting/utils/PathUtils.java | 4 +-- .../sting/utils/ReservoirDownsampler.java | 4 +-- .../sting/utils/SequenceDictionaryUtils.java | 4 +-- .../sting/utils/WilcoxonRankSum.java | 6 ++-- .../sting/utils/classloader/JVMUtils.java | 6 ++-- .../sting/utils/classloader/PackageUtils.java | 4 +-- .../utils/classloader/PluginManager.java | 4 +-- .../utils/collections/CircularArray.java | 6 ++-- .../utils/collections/MergingIterator.java | 6 ++-- .../sting/utils/duplicates/DupUtils.java | 4 +-- ...ption.java => ReviewedStingException.java} | 12 +++---- .../sting/utils/exceptions/UserException.java | 2 +- .../utils/fasta/ArtificialFastaUtils.java | 8 ++--- .../sting/utils/file/FSLockWithShared.java | 4 +-- .../utils/genotype/LikelihoodObject.java | 8 ++--- .../sting/utils/genotype/glf/GLFReader.java | 4 +-- .../sting/utils/genotype/glf/GLFRecord.java | 4 +-- .../sting/utils/help/ApplicationDetails.java | 4 +-- .../help/ResourceBundleExtractorDoclet.java | 4 +-- .../sting/utils/instrumentation/Sizeof.java | 8 ++--- .../pileup/AbstractReadBackedPileup.java | 20 ++++++------ .../ReadBackedExtendedEventPileupImpl.java | 6 ++-- .../sting/utils/sam/AlignmentUtils.java | 8 ++--- .../utils/sam/ArtificialSAMFileReader.java | 4 +-- .../utils/sam/ArtificialSAMQueryIterator.java | 8 ++--- .../sting/utils/sam/ArtificialSAMUtils.java | 8 ++--- .../sting/utils/sam/SAMFileReaderBuilder.java | 6 ++-- .../sting/utils/text/TextFormattingUtils.java | 4 +-- .../sting/utils/wiggle/WiggleWriter.java | 4 +-- .../org/broadinstitute/sting/BaseTest.java | 10 +++--- .../org/broadinstitute/sting/WalkerTest.java | 10 +++--- .../commandline/ParsingEngineUnitTest.java | 8 ++--- .../providers/ShardDataProviderUnitTest.java | 6 ++-- .../ReadGroupBlackListFilterUnitTest.java | 8 ++--- .../tracks/RMDTrackManagerUnitTest.java | 6 ++-- .../sting/utils/GenomeLocParserUnitTest.java | 14 ++++---- .../utils/GenomeLocSortedSetUnitTest.java | 4 +-- .../sting/utils/PathUtilsUnitTest.java | 4 +-- .../utils/genotype/vcf/VCFWriterUnitTest.java | 6 ++-- .../IntervalFileMergingIteratorUnitTest.java | 4 +-- 160 files changed, 525 insertions(+), 525 deletions(-) rename java/src/org/broadinstitute/sting/utils/exceptions/{GATKException.java => ReviewedStingException.java} (74%) diff --git a/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java b/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java index 0244434b4..45b190537 100644 --- a/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java +++ b/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java @@ -26,7 +26,7 @@ package net.sf.picard.reference; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSourceProgressListener; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*; @@ -215,7 +215,7 @@ public class FastaSequenceIndexBuilder { throw new UserException.CouldNotReadInputFile(fastaFile, String.format("Could not read fasta file"), e); } catch (Exception e) { - throw new GATKException(e.getMessage(), e); + throw new ReviewedStingException(e.getMessage(), e); } } diff --git a/java/src/org/broadinstitute/sting/alignment/Alignment.java b/java/src/org/broadinstitute/sting/alignment/Alignment.java index 98a8ed9c1..a70be0006 100644 --- a/java/src/org/broadinstitute/sting/alignment/Alignment.java +++ b/java/src/org/broadinstitute/sting/alignment/Alignment.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.alignment; import net.sf.samtools.*; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.utils.Utils; @@ -189,7 +189,7 @@ public class Alignment { read = (SAMRecord)unmappedRead.clone(); } catch(CloneNotSupportedException ex) { - throw new GATKException("Unable to create aligned read from template."); + throw new ReviewedStingException("Unable to create aligned read from template."); } if(newSAMHeader != null) diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java index f6a40ec9d..16e713bf6 100644 --- a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java +++ b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java @@ -29,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.alignment.bwa.c.BWACAligner; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; @@ -120,7 +120,7 @@ public class AlignmentValidationWalker extends ReadWalker { logger.error(String.format(" Mapping quality: %s%n", alignmentsByScore[i].getMappingQuality())); } } - throw new GATKException(String.format("Read %s mismatches!", read.getReadName())); + throw new ReviewedStingException(String.format("Read %s mismatches!", read.getReadName())); } return 1; diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java b/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java index 0dacfb460..cd7800900 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.bwa; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; import org.broadinstitute.sting.alignment.reference.bwt.BWT; @@ -75,7 +75,7 @@ public class BWTFiles { */ public BWTFiles(String prefix) { if(prefix == null) - throw new GATKException("Prefix must not be null."); + throw new ReviewedStingException("Prefix must not be null."); annFile = new File(prefix + ".ann"); ambFile = new File(prefix + ".amb"); pacFile = new File(prefix + ".pac"); @@ -134,7 +134,7 @@ public class BWTFiles { success &= reverseSAFile.delete(); if(!success) - throw new GATKException("Unable to clean up autogenerated representation"); + throw new ReviewedStingException("Unable to clean up autogenerated representation"); } } @@ -182,7 +182,7 @@ public class BWTFiles { writeEncodedReferenceSequence(reverseReferenceSequence,rpacFile,rbwtFile,rsaFile); } catch(IOException ex) { - throw new GATKException("Unable to write autogenerated reference sequence to temporary files"); + throw new ReviewedStingException("Unable to write autogenerated reference sequence to temporary files"); } // Make sure that, at the very least, all temporary files are deleted on exit. @@ -228,13 +228,13 @@ public class BWTFiles { * Convert the given reference sequence into a form suitable for building into * on-the-fly sequences. * @param referenceSequence The reference sequence to normalize. - * @throws GATKException if normalized sequence cannot be generated. + * @throws org.broadinstitute.sting.utils.exceptions.ReviewedStingException if normalized sequence cannot be generated. */ private static void normalizeReferenceSequence(byte[] referenceSequence) { StringUtil.toUpperCase(referenceSequence); for(byte base: referenceSequence) { if(base != 'A' && base != 'C' && base != 'G' && base != 'T') - throw new GATKException(String.format("Base type %c is not supported when building references on-the-fly",(char)base)); + throw new ReviewedStingException(String.format("Base type %c is not supported when building references on-the-fly",(char)base)); } } } diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java index 8c9fba53e..322dd01b6 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.c; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMFileHeader; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.alignment.bwa.BWAConfiguration; import org.broadinstitute.sting.alignment.bwa.BWTFiles; @@ -29,15 +29,15 @@ public class BWACAligner extends BWAAligner { public BWACAligner(BWTFiles bwtFiles, BWAConfiguration configuration) { super(bwtFiles,configuration); if(thunkPointer != 0) - throw new GATKException("BWA/C attempting to reinitialize."); + throw new ReviewedStingException("BWA/C attempting to reinitialize."); - if(!bwtFiles.annFile.exists()) throw new GATKException("ANN 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 GATKException("PAC 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 GATKException("Forward SA 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 GATKException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.annFile.exists()) throw new ReviewedStingException("ANN file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.ambFile.exists()) throw new ReviewedStingException("AMB file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.pacFile.exists()) throw new ReviewedStingException("PAC file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.forwardBWTFile.exists()) throw new ReviewedStingException("Forward BWT file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.forwardSAFile.exists()) throw new ReviewedStingException("Forward SA file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.reverseBWTFile.exists()) throw new ReviewedStingException("Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it."); + if(!bwtFiles.reverseSAFile.exists()) throw new ReviewedStingException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it."); thunkPointer = create(bwtFiles,configuration); } @@ -60,7 +60,7 @@ public class BWACAligner extends BWAAligner { @Override public void updateConfiguration(BWAConfiguration configuration) { if(thunkPointer != 0) - throw new GATKException("BWA/C: attempting to update configuration of uninitialized aligner."); + throw new ReviewedStingException("BWA/C: attempting to update configuration of uninitialized aligner."); updateConfiguration(thunkPointer,configuration); } @@ -70,7 +70,7 @@ public class BWACAligner extends BWAAligner { @Override public void close() { if(thunkPointer == 0) - throw new GATKException("BWA/C close attempted, but BWA/C is not properly initialized."); + throw new ReviewedStingException("BWA/C close attempted, but BWA/C is not properly initialized."); destroy(thunkPointer); } @@ -82,7 +82,7 @@ public class BWACAligner extends BWAAligner { @Override public Alignment getBestAlignment(final byte[] bases) { if(thunkPointer == 0) - throw new GATKException("BWA/C getBestAlignment attempted, but BWA/C is not properly initialized."); + throw new ReviewedStingException("BWA/C getBestAlignment attempted, but BWA/C is not properly initialized."); return getBestAlignment(thunkPointer,bases); } @@ -193,7 +193,7 @@ public class BWACAligner extends BWAAligner { */ public BWAPath[] getPaths(byte[] bases) { if(thunkPointer == 0) - throw new GATKException("BWA/C getPaths attempted, but BWA/C is not properly initialized."); + throw new ReviewedStingException("BWA/C getPaths attempted, but BWA/C is not properly initialized."); return getPaths(thunkPointer,bases); } @@ -226,7 +226,7 @@ public class BWACAligner extends BWAAligner { */ protected Alignment[] convertPathsToAlignments(byte[] bases, BWAPath[] paths) { if(thunkPointer == 0) - throw new GATKException("BWA/C convertPathsToAlignments attempted, but BWA/C is not properly initialized."); + throw new ReviewedStingException("BWA/C convertPathsToAlignments attempted, but BWA/C is not properly initialized."); return convertPathsToAlignments(thunkPointer,bases,paths); } diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java index 633d281a6..ae6e22221 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java @@ -2,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.BaseUtils; import java.io.File; @@ -61,7 +61,7 @@ public class AlignerTestHarness { alignmentCleaned = (SAMRecord)read.clone(); } catch( CloneNotSupportedException ex ) { - throw new GATKException("SAMRecord clone not supported", ex); + throw new ReviewedStingException("SAMRecord clone not supported", ex); } if( alignmentCleaned.getReadNegativeStrandFlag() ) diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java index 503b406a6..879ecb5fb 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.bwa.java; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.Deque; import java.util.ArrayDeque; @@ -32,7 +32,7 @@ public class AlignmentMatchSequence implements Cloneable { copy = (AlignmentMatchSequence)super.clone(); } catch( CloneNotSupportedException ex ) { - throw new GATKException("Unable to clone AlignmentMatchSequence."); + throw new ReviewedStingException("Unable to clone AlignmentMatchSequence."); } copy.entries = new ArrayDeque(); @@ -52,7 +52,7 @@ 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 GATKException("convertToCigar: cannot process state: " + entry.getAlignmentState()); + default: throw new ReviewedStingException("convertToCigar: cannot process state: " + entry.getAlignmentState()); } cigar.add( new CigarElement(entry.count,operator) ); } @@ -128,7 +128,7 @@ public class AlignmentMatchSequence implements Cloneable { return (AlignmentMatchSequenceEntry)super.clone(); } catch( CloneNotSupportedException ex ) { - throw new GATKException("Unable to clone AlignmentMatchSequenceEntry."); + throw new ReviewedStingException("Unable to clone AlignmentMatchSequenceEntry."); } } diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java index e86ea858e..c59546bbb 100644 --- a/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java +++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.alignment.bwa.java; import org.broadinstitute.sting.alignment.Alignment; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import net.sf.samtools.Cigar; /** @@ -148,7 +148,7 @@ public class BWAAlignment extends Alignment implements Cloneable { newAlignment = (BWAAlignment)super.clone(); } catch( CloneNotSupportedException ex ) { - throw new GATKException("Unable to clone BWAAlignment."); + throw new ReviewedStingException("Unable to clone BWAAlignment."); } newAlignment.creationNumber = numCreated++; newAlignment.alignmentMatchSequence = alignmentMatchSequence.clone(); diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java index 96ec794ce..7f8c48253 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.alignment.reference.bwt; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * Represents the Burrows-Wheeler Transform of a reference sequence. @@ -124,7 +124,7 @@ public class BWT { */ protected byte getBase(long index) { if(index == inverseSA0) - throw new GATKException(String.format("Base at index %d does not have a text representation",index)); + throw new ReviewedStingException(String.format("Base at index %d does not have a text representation",index)); SequenceBlock block = getSequenceBlock(index); int position = getSequencePosition(index); diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java index b4e095433..64a595419 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream; import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; @@ -28,7 +28,7 @@ public class BWTReader { this.inputStream = new FileInputStream(inputFile); } catch( FileNotFoundException ex ) { - throw new GATKException("Unable to open input file", ex); + throw new ReviewedStingException("Unable to open input file", ex); } } @@ -66,7 +66,7 @@ public class BWTReader { } } catch( IOException ex ) { - throw new GATKException("Unable to read BWT from input stream.", ex); + throw new ReviewedStingException("Unable to read BWT from input stream.", ex); } return new BWT(inverseSA0, new Counts(count,true), sequenceBlocks); @@ -80,7 +80,7 @@ public class BWTReader { inputStream.close(); } catch( IOException ex ) { - throw new GATKException("Unable to close input file", ex); + throw new ReviewedStingException("Unable to close input file", ex); } } } diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java index f8f7782ac..b3867ebfe 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream; import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream; @@ -28,7 +28,7 @@ public class BWTWriter { this.outputStream = new BufferedOutputStream(new FileOutputStream(outputFile)); } catch( FileNotFoundException ex ) { - throw new GATKException("Unable to open output file", ex); + throw new ReviewedStingException("Unable to open output file", ex); } } @@ -53,7 +53,7 @@ public class BWTWriter { intPackedOutputStream.write(bwt.counts.toArray(false)); } catch( IOException ex ) { - throw new GATKException("Unable to read BWT from input stream.", ex); + throw new ReviewedStingException("Unable to read BWT from input stream.", ex); } } @@ -65,7 +65,7 @@ public class BWTWriter { outputStream.close(); } catch( IOException ex ) { - throw new GATKException("Unable to close input file", ex); + throw new ReviewedStingException("Unable to close input file", ex); } } } diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java index 1a1e5e3ca..bc0a5b63d 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.*; @@ -87,7 +87,7 @@ public class Bases implements Iterable if( entry.getValue().equals(ascii) ) return entry.getKey(); } - throw new GATKException(String.format("Base %c is an invalid base to pack", (char)ascii)); + throw new ReviewedStingException(String.format("Base %c is an invalid base to pack", (char)ascii)); } /** diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java index fc06f4136..268b11ac4 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.HashMap; import java.util.Map; @@ -96,7 +96,7 @@ public class Counts implements Cloneable { other = (Counts)super.clone(); } catch(CloneNotSupportedException ex) { - throw new GATKException("Unable to clone counts object", ex); + throw new ReviewedStingException("Unable to clone counts object", ex); } other.counts = new HashMap(counts); other.cumulativeCounts = new HashMap(cumulativeCounts); diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java index a78e8633b..92bb713f0 100755 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java @@ -31,7 +31,7 @@ import net.sf.picard.reference.ReferenceSequence; import java.io.*; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; /** @@ -182,7 +182,7 @@ public class CreateBWTFromReference { for( int i = 0; i < bwt.length(); i++ ) { if( bwtSequence[i] != existingBWTSequence[i] ) - throw new GATKException("BWT mismatch at " + i); + throw new ReviewedStingException("BWT mismatch at " + i); } File existingSAFile = new File(inputFileName+".sa"); @@ -193,7 +193,7 @@ 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 GATKException(String.format("Suffix array mismatch at %d; SA is %d; should be %d",i,existingSuffixArray.get(i),suffixArray.get(i))); + throw new ReviewedStingException(String.format("Suffix array mismatch at %d; SA is %d; should be %d",i,existingSuffixArray.get(i),suffixArray.get(i))); } } diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java index 48868895d..dba3633d1 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.Comparator; import java.util.TreeSet; @@ -53,7 +53,7 @@ public class SuffixArray { this.bwt = bwt; if(sequenceInterval != 1 && bwt == null) - throw new GATKException("A BWT must be provided if the sequence interval is not 1"); + throw new ReviewedStingException("A BWT must be provided if the sequence interval is not 1"); } /** @@ -118,7 +118,7 @@ public class SuffixArray { inverseSA0 = i; } if(inverseSA0 < 0) - throw new GATKException("Unable to find first inverse SA entry in generated suffix array."); + throw new ReviewedStingException("Unable to find first inverse SA entry in generated suffix array."); return new SuffixArray(inverseSA0,occurrences,suffixArray); } diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java index 4fb983a5b..c10984145 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream; import org.broadinstitute.sting.alignment.reference.packing.PackUtils; @@ -35,7 +35,7 @@ public class SuffixArrayReader { this.bwt = bwt; } catch( FileNotFoundException ex ) { - throw new GATKException("Unable to open input file", ex); + throw new ReviewedStingException("Unable to open input file", ex); } } @@ -61,7 +61,7 @@ public class SuffixArrayReader { uintPackedInputStream.read(suffixArray); } catch( IOException ex ) { - throw new GATKException("Unable to read BWT from input stream.", ex); + throw new ReviewedStingException("Unable to read BWT from input stream.", ex); } return new SuffixArray(inverseSA0, new Counts(occurrences,true), suffixArray, suffixArrayInterval, bwt); @@ -76,7 +76,7 @@ public class SuffixArrayReader { inputStream.close(); } catch( IOException ex ) { - throw new GATKException("Unable to close input file", ex); + throw new ReviewedStingException("Unable to close input file", ex); } } } diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java index febb87f8f..972fc2a15 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.bwt; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream; import java.io.*; @@ -27,7 +27,7 @@ public class SuffixArrayWriter { this.outputStream = new BufferedOutputStream(new FileOutputStream(outputFile)); } catch( FileNotFoundException ex ) { - throw new GATKException("Unable to open input file", ex); + throw new ReviewedStingException("Unable to open input file", ex); } } @@ -48,7 +48,7 @@ public class SuffixArrayWriter { uintPackedOutputStream.write(suffixArray.sequence,1,suffixArray.sequence.length-1); } catch( IOException ex ) { - throw new GATKException("Unable to read BWT from input stream.", ex); + throw new ReviewedStingException("Unable to read BWT from input stream.", ex); } } @@ -61,7 +61,7 @@ public class SuffixArrayWriter { outputStream.close(); } catch( IOException ex ) { - throw new GATKException("Unable to close input file", ex); + throw new ReviewedStingException("Unable to close input file", ex); } } } diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java index c3291774e..6681e37ec 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.packing; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.*; import java.nio.ByteOrder; @@ -51,7 +51,7 @@ public class BasePackedInputStream { public BasePackedInputStream( Class type, FileInputStream inputStream, ByteOrder byteOrder ) { if( type != Integer.class ) - throw new GATKException("Only bases packed into 32-bit words are currently supported by this input stream. Type specified: " + type.getName()); + throw new ReviewedStingException("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(); diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java index cfdb10949..c62f40e51 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.packing; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.*; import java.nio.ByteBuffer; @@ -134,7 +134,7 @@ public class BasePackedOutputStream { else if( type == Byte.class ) buffer.put((byte)packedBases); else - throw new GATKException("Cannot pack bases into type " + type.getName()); + throw new ReviewedStingException("Cannot pack bases into type " + type.getName()); targetOutputStream.write(buffer.array()); } } diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java index 3ab0b7589..beed21b49 100644 --- a/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java +++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.alignment.reference.packing; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; import java.io.IOException; @@ -58,14 +58,14 @@ 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 GATKException("Cannot determine number of bits available in type: " + type.getName()); + throw new ReviewedStingException("Cannot determine number of bits available in type: " + type.getName()); return (int)(Math.log(typeSize)/Math.log(2)); } catch( NoSuchFieldException ex ) { - throw new GATKException("Cannot determine number of bits available in type: " + type.getName(),ex); + throw new ReviewedStingException("Cannot determine number of bits available in type: " + type.getName(),ex); } catch( IllegalAccessException ex ) { - throw new GATKException("Cannot determine number of bits available in type: " + type.getName(),ex); + throw new ReviewedStingException("Cannot determine number of bits available in type: " + type.getName(),ex); } } @@ -85,7 +85,7 @@ public class PackUtils { case 'T': return 3; default: - throw new GATKException("Unknown base type: " + base); + throw new ReviewedStingException("Unknown base type: " + base); } } @@ -105,7 +105,7 @@ public class PackUtils { case 3: return 'T'; default: - throw new GATKException("Unknown pack type: " + pack); + throw new ReviewedStingException("Unknown pack type: " + pack); } } diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java index 6ae6bc053..c36a8e04f 100644 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.List; import java.util.Collections; @@ -69,7 +69,7 @@ public class ArgumentDefinitionGroup implements Iterable { */ public ArgumentDefinitionGroup merge( ArgumentDefinitionGroup other ) { if( !groupNameMatches(other) ) - throw new GATKException("Unable to merge two argument groups with differing names."); + throw new ReviewedStingException("Unable to merge two argument groups with differing names."); // Create a merged definition group. List mergedDefinitions = new ArrayList(); diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java index 88503eacd..39e698ca3 100755 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.Set; import java.util.HashSet; @@ -56,9 +56,9 @@ public class ArgumentDefinitions implements Iterable { if( definition.fullName.length() == 0 ) throw new IllegalArgumentException( "Argument cannot have 0-length fullname." ); if( hasArgumentDefinition( definition.fullName, FullNameDefinitionMatcher ) ) - throw new GATKException("Duplicate definition of argument with full name: " + definition.fullName); + throw new ReviewedStingException("Duplicate definition of argument with full name: " + definition.fullName); if( definition.shortName != null && hasArgumentDefinition( definition.shortName, ShortNameDefinitionMatcher ) ) - throw new GATKException("Duplicate definition of argument with short name: " + definition.shortName); + throw new ReviewedStingException("Duplicate definition of argument with short name: " + definition.shortName); argumentDefinitions.add( definition ); } diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java b/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java index 9b21def56..fe33ab382 100644 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java @@ -24,7 +24,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.annotation.Annotation; @@ -46,6 +46,6 @@ public enum ArgumentIOType { for (ArgumentIOType ioType: ArgumentIOType.values()) if (ioType.annotationClass.isAssignableFrom(annotation.getClass())) return ioType; - throw new GATKException("Unknown annotation type: " + annotation); + throw new ReviewedStingException("Unknown annotation type: " + annotation); } } diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java index fedbe815c..937c9549a 100644 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.reflect.Field; import java.util.Arrays; @@ -208,7 +208,7 @@ public class ArgumentSource { */ public MultiplexArgumentTypeDescriptor createDependentTypeDescriptor(Object containingObject) { if(!isDependent()) - throw new GATKException("Field " + field.getName() + " is independent; no dependent type descriptor can be derived."); + throw new ReviewedStingException("Field " + field.getName() + " is independent; no dependent type descriptor can be derived."); return ((MultiplexArgumentTypeDescriptor)typeDescriptor).createCustomTypeDescriptor(this,containingObject); } diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java index 8eea131e1..a7090f299 100644 --- a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java +++ b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.gatk.walkers.Multiplex; import org.broadinstitute.sting.gatk.walkers.Multiplexer; @@ -83,7 +83,7 @@ public abstract class ArgumentTypeDescriptor { if( descriptor.supports(type) ) return descriptor; } - throw new GATKException("Can't process command-line arguments of type: " + type.getName()); + throw new ReviewedStingException("Can't process command-line arguments of type: " + type.getName()); } /** @@ -265,7 +265,7 @@ public abstract class ArgumentTypeDescriptor { for (Class annotation: ARGUMENT_ANNOTATIONS) if (source.field.isAnnotationPresent(annotation)) return source.field.getAnnotation(annotation); - throw new GATKException("ArgumentAnnotation is not present for the argument field: " + source.field.getName()); + throw new ReviewedStingException("ArgumentAnnotation is not present for the argument field: " + source.field.getName()); } /** @@ -333,7 +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 GATKException("parsing " + type.toString() + "doesn't contain the field " + val.toString()); } + catch (NoSuchFieldException e) { throw new ReviewedStingException("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) @@ -349,7 +349,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor { result = ctor.newInstance(value); } } catch (InvocationTargetException e) { - throw new GATKException("constructFromString:InvocationTargetException: Failed conversion - this is most likely caused by using an incorrect data type (e.g. a double when an int is required)"); + throw new ReviewedStingException("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 (Exception e) { throw new DynamicClassResolutionException(String.class, e); } @@ -416,11 +416,11 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor { } catch (InstantiationException e) { logger.fatal("ArgumentParser: InstantiationException: cannot convert field " + source.field.getName()); - throw new GATKException("constructFromString:InstantiationException: Failed conversion " + e.getMessage()); + throw new ReviewedStingException("constructFromString:InstantiationException: Failed conversion " + e.getMessage()); } catch (IllegalAccessException e) { logger.fatal("ArgumentParser: IllegalAccessException: cannot convert field " + source.field.getName()); - throw new GATKException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage()); + throw new ReviewedStingException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage()); } for( ArgumentMatch match: matches ) { @@ -452,7 +452,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor { } } else - throw new GATKException("Unsupported compound argument type: " + type); + throw new ReviewedStingException("Unsupported compound argument type: " + type); // WARNING: Side effect! parsingEngine.addTags(result,tags); @@ -520,7 +520,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor { @Override public Object createTypeDefault(ArgumentSource source,Class type) { if(multiplexer == null || multiplexedIds == null) - throw new GATKException("No multiplexed ids available"); + throw new ReviewedStingException("No multiplexed ids available"); Map multiplexedMapping = new HashMap(); Class componentType = getCollectionComponentType(source.field); @@ -539,7 +539,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor { @Override public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) { if(multiplexedIds == null) - throw new GATKException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first."); + throw new ReviewedStingException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first."); Map multiplexedMapping = new HashMap(); @@ -570,14 +570,14 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor { if(!source.field.getName().equals(sourceField)) continue; if(source.field.isAnnotationPresent(Multiplex.class)) - throw new GATKException("Command-line arguments can only depend on independent fields"); + throw new ReviewedStingException("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 GATKException(String.format("Unable to find source field %s, referred to by dependent field %s",sourceField,dependentArgument.field.getName())); + throw new ReviewedStingException(String.format("Unable to find source field %s, referred to by dependent field %s",sourceField,dependentArgument.field.getName())); } Class multiplexerType = dependentArgument.field.getAnnotation(Multiplex.class).value(); @@ -587,7 +587,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor { multiplexerConstructor.setAccessible(true); } catch(NoSuchMethodException ex) { - throw new GATKException(String.format("Unable to find constructor for class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex); + throw new ReviewedStingException(String.format("Unable to find constructor for class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex); } Multiplexer multiplexer = null; @@ -595,13 +595,13 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor { multiplexer = multiplexerConstructor.newInstance(sourceValues); } catch(IllegalAccessException ex) { - throw new GATKException(String.format("Constructor for class %s with parameters %s is inaccessible",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex); + throw new ReviewedStingException(String.format("Constructor for class %s with parameters %s is inaccessible",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex); } catch(InstantiationException ex) { - throw new GATKException(String.format("Can't create class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex); + throw new ReviewedStingException(String.format("Can't create class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex); } catch(InvocationTargetException ex) { - throw new GATKException(String.format("Can't invoke constructor of class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex); + throw new ReviewedStingException(String.format("Can't invoke constructor of class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex); } return new MultiplexArgumentTypeDescriptor(multiplexer,multiplexer.multiplex()); diff --git a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java index 0fdeda438..9048cd200 100644 --- a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java +++ b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.walkers.Walker; @@ -123,7 +123,7 @@ public class CommandLineUtils { try { return annotation.getClass().getMethod(method).invoke(annotation); } catch (Exception e) { - throw new GATKException("Unable to access method " + method + " on annotation " + annotation.getClass(), e); + throw new ReviewedStingException("Unable to access method " + method + " on annotation " + annotation.getClass(), e); } } } diff --git a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java index 9b8e6ad23..261197ec8 100755 --- a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java +++ b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.commandline; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.Utils; @@ -294,7 +294,7 @@ public class ParsingEngine { // Grab the first argument definition and report that one as the failure. Theoretically, we should notify of all failures. List definitions = argumentSource.createArgumentDefinitions(); if(definitions.size() < 1) - throw new GATKException("Internal error. Argument source creates no definitions."); + throw new ReviewedStingException("Internal error. Argument source creates no definitions."); ArgumentDefinition definition = definitions.get(0); throw new UserException.DeprecatedArgument(definition.fullName,definition.doc); } @@ -315,7 +315,7 @@ public class ParsingEngine { // Abort if no home is found for the object. if( targets.size() == 0 ) - throw new GATKException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches); + throw new ReviewedStingException("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(); diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 2bcc58aac..725bc3727 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -31,7 +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.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; @@ -156,12 +156,12 @@ public class GenomeAnalysisEngine { // validate our parameters if (args == null) { - throw new GATKException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null."); + throw new ReviewedStingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null."); } // validate our parameters if (my_walker == null) - throw new GATKException("The walker passed to GenomeAnalysisEngine can not be null."); + throw new ReviewedStingException("The walker passed to GenomeAnalysisEngine can not be null."); // save our argument parameter this.argCollection = args; @@ -808,7 +808,7 @@ public class GenomeAnalysisEngine { drivingDataSource.getSequenceDictionary(), SHARD_SIZE); } else - throw new GATKException("Unable to support walker of type" + walker.getClass().getName()); + throw new ReviewedStingException("Unable to support walker of type" + walker.getClass().getName()); return shardStrategy; } diff --git a/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java b/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java index fdc2cb459..27a86ab3f 100755 --- a/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java +++ b/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java @@ -30,7 +30,7 @@ import java.util.Map; import java.util.HashMap; import java.util.Collections; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * Holds a bunch of basic information about the traversal. @@ -78,7 +78,7 @@ public class ReadMetrics implements Cloneable { newMetrics = (ReadMetrics)super.clone(); } catch(CloneNotSupportedException ex) { - throw new GATKException("Unable to clone runtime metrics",ex); + throw new ReviewedStingException("Unable to clone runtime metrics",ex); } newMetrics.nRecords = nRecords; newMetrics.nReads = nReads; diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java index 18bf662eb..45675092c 100755 --- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java +++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java @@ -30,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.text.TextFormattingUtils; import org.broadinstitute.sting.utils.help.DescriptionTaglet; @@ -168,7 +168,7 @@ public class WalkerManager extends PluginManager { public static DataSource getWalkerDataSource(Class walkerClass) { By byDataSource = walkerClass.getAnnotation(By.class); if( byDataSource == null ) - throw new GATKException("Unable to find By annotation for walker class " + walkerClass.getName()); + throw new ReviewedStingException("Unable to find By annotation for walker class " + walkerClass.getName()); return byDataSource.value(); } @@ -397,7 +397,7 @@ public class WalkerManager extends PluginManager { private static Requires getWalkerRequirements(Class walkerClass) { Requires requiresDataSource = walkerClass.getAnnotation(Requires.class); if( requiresDataSource == null ) - throw new GATKException( "Unable to find data types required by walker class " + walkerClass.getName()); + throw new ReviewedStingException( "Unable to find data types required by walker class " + walkerClass.getName()); return requiresDataSource; } diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index d80e95462..6abd8c209 100755 --- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -27,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Input; @@ -191,7 +191,7 @@ public class GATKArgumentCollection { try { serializer.write(collection, result); } catch (Exception e) { - throw new GATKException("Failed to marshal the data to the file " + outputFile, e); + throw new ReviewedStingException("Failed to marshal the data to the file " + outputFile, e); } } @@ -206,7 +206,7 @@ public class GATKArgumentCollection { try { serializer.write(collection, outputFile); } catch (Exception e) { - throw new GATKException("Failed to marshal the data to the file " + outputFile, e); + throw new ReviewedStingException("Failed to marshal the data to the file " + outputFile, e); } } @@ -222,7 +222,7 @@ public class GATKArgumentCollection { GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, source); return example; } catch (Exception e) { - throw new GATKException("Failed to marshal the data from file " + filename, e); + throw new ReviewedStingException("Failed to marshal the data from file " + filename, e); } } @@ -237,7 +237,7 @@ public class GATKArgumentCollection { GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, file); return example; } catch (Exception e) { - throw new GATKException("Failed to marshal the data from file " + file.toString(), e); + throw new ReviewedStingException("Failed to marshal the data from file " + file.toString(), e); } } diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java index 29867a7f4..255945619 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.contexts; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup; @@ -66,9 +66,9 @@ public class AlignmentContext { } public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, long skippedBases,boolean hasPileupBeenDownsampled ) { - if ( loc == null ) throw new GATKException("BUG: GenomeLoc in Alignment context is null"); - if ( basePileup == null ) throw new GATKException("BUG: ReadBackedPileup in Alignment context is null"); - if ( skippedBases < 0 ) throw new GATKException("BUG: skippedBases is -1 in Alignment context"); + if ( loc == null ) throw new ReviewedStingException("BUG: GenomeLoc in Alignment context is null"); + if ( basePileup == null ) throw new ReviewedStingException("BUG: ReadBackedPileup in Alignment context is null"); + if ( skippedBases < 0 ) throw new ReviewedStingException("BUG: skippedBases is -1 in Alignment context"); this.loc = loc; this.basePileup = basePileup; @@ -89,7 +89,7 @@ public class AlignmentContext { */ public ReadBackedPileup getBasePileup() { if(!hasBasePileup()) - throw new GATKException("No base pileup is available. Please check for a base pileup with hasBasePileup() before attempting to retrieve a pileup."); + throw new ReviewedStingException("No base pileup is available. Please check for a base pileup with hasBasePileup() before attempting to retrieve a pileup."); return basePileup; } @@ -99,7 +99,7 @@ public class AlignmentContext { */ public ReadBackedExtendedEventPileup getExtendedEventPileup() { if(!hasExtendedEventPileup()) - throw new GATKException("No extended event pileup is present."); + throw new ReviewedStingException("No extended event pileup is present."); return (ReadBackedExtendedEventPileup)basePileup; } diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java index 0221ef3db..96d49fc2e 100644 --- a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.contexts; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.BaseUtils; import net.sf.samtools.util.StringUtil; @@ -191,7 +191,7 @@ public class ReferenceContext { byte[] b = new byte[stop-start]; if ( stop > bases.length ) - throw new GATKException("Bases beyond the current window requested: window="+window+", requested="+n); + throw new ReviewedStingException("Bases beyond the current window requested: window="+window+", requested="+n); int i = 0; for ( int j = start ; j < stop ; j++) b[i++]=bases[j]; diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java index 2be1dea28..f42ab6a66 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.contexts; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.*; @@ -72,7 +72,7 @@ public class StratifiedAlignmentContext { case REVERSE: return new AlignmentContext(loc,basePileup.getNegativeStrandPileup()); default: - throw new GATKException("Unable to get alignment context for type = " + type); + throw new ReviewedStingException("Unable to get alignment context for type = " + type); } } @@ -144,9 +144,9 @@ public class StratifiedAlignmentContext { boolean isExtended = contexts.iterator().next().basePileup instanceof ReadBackedExtendedEventPileup; for(StratifiedAlignmentContext context: contexts) { if(!loc.equals(context.getLocation())) - throw new GATKException("Illegal attempt to join contexts from different genomic locations"); + throw new ReviewedStingException("Illegal attempt to join contexts from different genomic locations"); if(isExtended != (context.basePileup instanceof ReadBackedExtendedEventPileup)) - throw new GATKException("Illegal attempt to join simple and extended contexts"); + throw new ReviewedStingException("Illegal attempt to join simple and extended contexts"); } AlignmentContext jointContext; diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java index eb037cf09..522366289 100755 --- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java @@ -30,7 +30,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation; import org.broad.tribble.util.variantcontext.*; import org.broadinstitute.sting.utils.*; import org.broad.tribble.vcf.VCFConstants; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; public class VariantContextUtils { @@ -111,7 +111,7 @@ public class VariantContextUtils { */ public static List initializeMatchExps(String[] names, String[] exps) { if ( names == null || exps == null ) - throw new GATKException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) ); + throw new ReviewedStingException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) ); if ( names.length != exps.length ) throw new UserException("Inconsistent number of provided filter names and expressions: names=" + Arrays.toString(names) + " exps=" + Arrays.toString(exps)); @@ -323,7 +323,7 @@ public class VariantContextUtils { for ( VariantContext vc : VCs ) { if ( loc.getStart() != vc.getStart() ) // || !first.getReference().equals(vc.getReference()) ) - throw new GATKException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString()); + throw new ReviewedStingException("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 @@ -450,7 +450,7 @@ public class VariantContextUtils { if ( ref == null || ref.length() < myRef.length() ) ref = myRef; else if ( ref.length() == myRef.length() && ! ref.equals(myRef) ) - throw new GATKException("BUG: equal length references with difference bases: "+ ref + " " + myRef); + throw new ReviewedStingException("BUG: equal length references with difference bases: "+ ref + " " + myRef); } return ref; @@ -472,7 +472,7 @@ public class VariantContextUtils { // Allele myRef = vc.getReference(); - if ( refAllele.length() <= myRef.length() ) throw new GATKException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele); + if ( refAllele.length() <= myRef.length() ) throw new ReviewedStingException("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); @@ -577,7 +577,7 @@ public class VariantContextUtils { padVC = false; else if (refAllele.length() == locLength-1) padVC = true; - else throw new GATKException("Badly formed variant context, reference length must be at most one base shorter than location size"); + else throw new ReviewedStingException("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 @@ -591,7 +591,7 @@ 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 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"); + throw new ReviewedStingException("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 alleles = new ArrayList(); Map genotypes = new TreeMap(); diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java index d1c2b2b76..7e6cab6c8 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * User: aaron @@ -20,7 +20,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException; * This exception is throw when we're unable to generate a data source, * most likely due to an incomplete input source list */ -public class DataSourceGenerationException extends GATKException { +public class DataSourceGenerationException extends ReviewedStingException { public DataSourceGenerationException(String message) { super(message); } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java index 83fefe700..eff273d0e 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.gatk.walkers.Walker; @@ -85,8 +85,8 @@ 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 GATKException( "Reference window starts after current locus" ); - if( window.stop() < 0 ) throw new GATKException( "Reference window ends before current locus" ); + if( window.start() > 0 ) throw new ReviewedStingException( "Reference window starts after current locus" ); + if( window.stop() < 0 ) throw new ReviewedStingException( "Reference window ends before current locus" ); windowStart = window.start(); windowStop = window.stop(); @@ -121,7 +121,7 @@ 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 GATKException("Illegal attempt to expand reference view bounds to accommodate location on a different contig."); + throw new ReviewedStingException("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()), diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java index ee4997164..385de4e5f 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java @@ -10,7 +10,7 @@ import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMRecord; import net.sf.picard.reference.ReferenceSequence; import net.sf.picard.reference.IndexedFastaSequenceFile; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * User: hanna * Date: May 22, 2009 @@ -80,7 +80,7 @@ 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 GATKException("Insufficient buffer size for Xs overhanging genome -- expand BUFFER"); + throw new ReviewedStingException("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); diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java index f4ca0b05c..cb912ccf9 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java @@ -2,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; import java.util.List; @@ -110,7 +110,7 @@ public abstract class ShardDataProvider { Collection> conflicts = registeredView.getConflictingViews(); for( Class conflict: conflicts ) { if( conflict.isInstance(view) ) - throw new GATKException(String.format("Tried to register two conflicting views: %s and %s", + throw new ReviewedStingException(String.format("Tried to register two conflicting views: %s and %s", registeredView.getClass().getSimpleName(), view.getClass().getSimpleName())); } @@ -120,7 +120,7 @@ public abstract class ShardDataProvider { for( Class conflict: view.getConflictingViews() ) { for( View registeredView: registeredViews ) { if( conflict.isInstance(registeredView) ) - throw new GATKException(String.format("Tried to register two conflicting views: %s and %s", + throw new ReviewedStingException(String.format("Tried to register two conflicting views: %s and %s", registeredView.getClass().getSimpleName(), view.getClass().getSimpleName())); } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java index 5f9bdb958..0c4c08480 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java @@ -35,7 +35,7 @@ import java.util.*; import net.sf.samtools.*; import net.sf.picard.util.PeekableIterator; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * Shard intervals based on position within the BAM file. @@ -124,7 +124,7 @@ public class IntervalSharder { for(GenomeLoc location: loci) { if(!location.getContig().equals(contig)) - throw new GATKException("Location outside bounds of contig"); + throw new ReviewedStingException("Location outside bounds of contig"); if(!binIterator.hasNext()) break; @@ -191,7 +191,7 @@ public class IntervalSharder { } else { if(lastFilePointer == null) - throw new GATKException("Illegal state: initializer failed to create cached file pointer."); + throw new ReviewedStingException("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); @@ -475,7 +475,7 @@ class BinQueueState implements Comparable { // 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 GATKException("Sharding mechanism error - bin->locus cache is invalid."); + throw new ReviewedStingException("Sharding mechanism error - bin->locus cache is invalid."); } // Straight integer subtraction works here because lhsStart, rhsStart always positive. diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java index 2af2caf68..98df7b7b1 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.shards; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.gatk.ReadMetrics; import org.broadinstitute.sting.gatk.ReadProperties; @@ -42,7 +42,7 @@ public class MonolithicShard implements Shard { public MonolithicShard(SAMDataSource readsDataSource, ShardType shardType, List locs) { this.readsDataSource = readsDataSource; if(shardType != ShardType.LOCUS && shardType != ShardType.READ) - throw new GATKException("Invalid shard type for monolithic shard: " + shardType); + throw new ReviewedStingException("Invalid shard type for monolithic shard: " + shardType); this.shardType = shardType; this.locs = locs; } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java index 74ee8361e..2bc7a3207 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java @@ -2,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLocSortedSet; import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource; @@ -71,7 +71,7 @@ public class ShardStrategyFactory { case READS_EXPERIMENTAL: return new ReadShardStrategy(readsDataSource,null); default: - throw new GATKException("Strategy: " + strat + " isn't implemented for this type of shatter request"); + throw new ReviewedStingException("Strategy: " + strat + " isn't implemented for this type of shatter request"); } } @@ -109,7 +109,7 @@ public class ShardStrategyFactory { case READS_EXPERIMENTAL: return new ReadShardStrategy(readsDataSource,lst); default: - throw new GATKException("Strategy: " + strat + " isn't implemented"); + throw new ReviewedStingException("Strategy: " + strat + " isn't implemented"); } } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java index 83d4ad469..825131962 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import net.sf.picard.reference.FastaSequenceIndexBuilder; import net.sf.picard.sam.CreateSequenceDictionary; import net.sf.picard.reference.IndexedFastaSequenceFile; @@ -68,7 +68,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener try { // get exclusive lock if (!indexLock.exclusiveLock()) - throw new GATKException("Index file could not be written because a lock could not be obtained." + + throw new ReviewedStingException("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 +82,7 @@ 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 GATKException("Index file does not exist and could not be created because " + e.getMessage(), e); + throw new ReviewedStingException("Index file does not exist and could not be created because " + e.getMessage(), e); } finally { indexLock.unlock(); @@ -108,7 +108,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener try { // get shared lock on dict file so nobody else can start creating it if (!dictLock.exclusiveLock()) - throw new GATKException("Dictionary file could not be written because a lock could not be obtained." + + throw new ReviewedStingException("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 +121,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener new CreateSequenceDictionary().instanceMain(args); if (!tempFile.renameTo(dictFile)) - throw new GATKException("Error transferring temp file " + tempFile + " to dict file " + dictFile); + throw new ReviewedStingException("Error transferring temp file " + tempFile + " to dict file " + dictFile); } catch(FileSystemInabilityToLockException ex) { logger.info("Unable to create write lock: " + ex.getMessage()); @@ -130,7 +130,7 @@ 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 GATKException("Dictionary file does not exist and could not be created because " + e.getMessage(), e); + throw new ReviewedStingException("Dictionary file does not exist and could not be created because " + e.getMessage(), e); } finally { dictLock.unlock(); @@ -149,7 +149,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener try { try { if (!dictLock.sharedLock()) { - throw new GATKException("Could not open dictionary file because a lock could not be obtained."); + throw new ReviewedStingException("Could not open dictionary file because a lock could not be obtained."); } } catch(FileSystemInabilityToLockException ex) { @@ -159,7 +159,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener try { if (!indexLock.sharedLock()) { - throw new GATKException("Could not open index file because a lock could not be obtained."); + throw new ReviewedStingException("Could not open index file because a lock could not be obtained."); } } catch(FileSystemInabilityToLockException ex) { diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java index 1aaee0bb2..f67ed96f6 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java @@ -11,7 +11,7 @@ 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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -156,7 +156,7 @@ class ReferenceOrderedDataPool extends ResourcePool { // make sure we actually removed the assignment if (obj == null) - throw new GATKException("Failed to remove resource assignment; target key had no associated value in the resource assignment map"); + throw new ReviewedStingException("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 GATKException("Iterator does not belong to the given pool."); + throw new ReviewedStingException("Iterator does not belong to the given pool."); availableResources.add(resource); } } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java index 69d43b92a..149468cb5 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java @@ -41,7 +41,7 @@ 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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; @@ -294,7 +294,7 @@ public class SAMDataSource implements SimpleDataSource { */ public void fillShard(BAMFormatAwareShard shard) { if(!shard.buffersReads()) - throw new GATKException("Attempting to fill a non-buffering shard."); + throw new ReviewedStingException("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. @@ -326,7 +326,7 @@ public class SAMDataSource implements SimpleDataSource { return seekMonolithic(shard); if(!(shard instanceof BAMFormatAwareShard)) - throw new GATKException("BlockDrivenSAMDataSource cannot operate on shards of type: " + shard.getClass()); + throw new ReviewedStingException("BlockDrivenSAMDataSource cannot operate on shards of type: " + shard.getClass()); BAMFormatAwareShard bamAwareShard = (BAMFormatAwareShard)shard; if(bamAwareShard.buffersReads()) { @@ -349,7 +349,7 @@ public class SAMDataSource implements SimpleDataSource { if(readers.getReader(id) == read.getFileSource().getReader()) return id; } - throw new GATKException("Unable to find id for reader associated with read " + read.getReadName()); + throw new ReviewedStingException("Unable to find id for reader associated with read " + read.getReadName()); } /** @@ -508,7 +508,7 @@ public class SAMDataSource implements SimpleDataSource { public synchronized void releaseReaders(SAMReaders readers) { if(!allResources.contains(readers)) - throw new GATKException("Tried to return readers from the pool that didn't originate in the pool."); + throw new ReviewedStingException("Tried to return readers from the pool that didn't originate in the pool."); availableResources.add(readers); } @@ -523,12 +523,12 @@ public class SAMDataSource implements SimpleDataSource { if(id != null) return id; } - throw new GATKException("No such reader id is available"); + throw new ReviewedStingException("No such reader id is available"); } private synchronized void createNewResource() { if(allResources.size() > maxEntries) - throw new GATKException("Cannot create a new resource pool. All resources are in use."); + throw new ReviewedStingException("Cannot create a new resource pool. All resources are in use."); SAMReaders readers = new SAMReaders(readProperties); allResources.add(readers); availableResources.add(readers); diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java index 7dc2b51fa..e890e6d3a 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * @@ -28,7 +28,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException; *

* Generate this on a simple data source load exception */ -public class SimpleDataSourceLoadException extends GATKException { +public class SimpleDataSourceLoadException extends ReviewedStingException { public SimpleDataSourceLoadException(String msg) { super(msg); } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java index 040327bc3..d83bb4ce9 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /* @@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException; *

* an exception that get's thrown if we can't split up a data source appropriately */ -public class SimpleDataSourceSplitException extends GATKException { +public class SimpleDataSourceSplitException extends ReviewedStingException { public SimpleDataSourceSplitException(String msg) { super(msg); } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java b/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java index 1cadb1252..327c747f3 100644 --- a/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java @@ -27,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.instrumentation.Sizeof; import java.io.File; @@ -58,7 +58,7 @@ public class BAMFileStat extends CommandLineProgram { public int execute() { switch(command) { case ShowBlocks: - throw new GATKException("The BAM block inspector has been disabled."); + throw new ReviewedStingException("The BAM block inspector has been disabled."); case ShowIndex: showIndexBins(new File(bamFileName),range); break; @@ -171,7 +171,7 @@ public class BAMFileStat extends CommandLineProgram { } } catch(IllegalAccessException ex) { - throw new GATKException("Unable to examine cached index",ex); + throw new ReviewedStingException("Unable to examine cached index",ex); } System.out.printf("%nOverall: %d bins, %d chunks, %d linear index entries",numBins,numChunks,numLinearIndexEntries); diff --git a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java index 6d2a25565..3cdcaddcf 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java @@ -29,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.GenomeLocSortedSet; @@ -184,7 +184,7 @@ public abstract class Accumulator { */ public void accumulate( ShardDataProvider provider, Object result ) { if(!(provider instanceof LocusShardDataProvider)) - throw new GATKException("Unable to reduce by interval on reads traversals at this time."); + throw new ReviewedStingException("Unable to reduce by interval on reads traversals at this time."); GenomeLoc location = ((LocusShardDataProvider)provider).getLocus(); diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java index 477d522a1..feae86587 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java @@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource; import org.broadinstitute.sting.gatk.io.*; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor; import javax.management.MBeanServer; @@ -109,7 +109,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar mbs.registerMBean(this, name); } catch (JMException ex) { - throw new GATKException("Unable to register microscheduler with JMX", ex); + throw new ReviewedStingException("Unable to register microscheduler with JMX", ex); } } @@ -129,7 +129,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar while (isShardTraversePending() || isTreeReducePending()) { // Check for errors during execution. if(hasTraversalErrorOccurred()) - throw new GATKException("An error has occurred during the traversal.",getTraversalError()); + throw new ReviewedStingException("An error has occurred during the traversal.",getTraversalError()); // Too many files sitting around taking up space? Merge them. if (isMergeLimitExceeded()) @@ -158,7 +158,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar notifyTraversalDone(walker,result); } catch (Exception ex) { - throw new GATKException("Unable to retrieve result", ex); + throw new ReviewedStingException("Unable to retrieve result", ex); } outputTracker.close(); @@ -358,7 +358,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar private synchronized Throwable getTraversalError() { if(!hasTraversalErrorOccurred()) - throw new GATKException("User has attempted to retrieve a traversal error when none exists"); + throw new ReviewedStingException("User has attempted to retrieve a traversal error when none exists"); return error; } diff --git a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java index 661a99fd6..62788737c 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java @@ -8,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.concurrent.Callable; /** @@ -83,7 +83,7 @@ public class ShardTraverser implements Callable { catch(Throwable t) { // Notify that an exception has occurred and rethrow it. microScheduler.notifyOfTraversalError(t); - throw new GATKException("An error has occurred during traversal",t); + throw new ReviewedStingException("An error has occurred during traversal",t); } finally { synchronized(this) { @@ -115,7 +115,7 @@ public class ShardTraverser implements Callable { } } catch( InterruptedException ex ) { - throw new GATKException("Interrupted while waiting for more output to be finalized.",ex); + throw new ReviewedStingException("Interrupted while waiting for more output to be finalized.",ex); } } diff --git a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java index 8485eafd5..8fb4adb5d 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.executive; import org.broadinstitute.sting.gatk.walkers.TreeReducible; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.concurrent.Callable; import java.util.concurrent.Future; @@ -90,11 +90,11 @@ public class TreeReducer implements Callable { } catch( InterruptedException ex ) { microScheduler.notifyOfTraversalError(ex); - throw new GATKException("Hierarchical reduce interrupted", ex); + throw new ReviewedStingException("Hierarchical reduce interrupted", ex); } catch( ExecutionException ex ) { microScheduler.notifyOfTraversalError(ex); - throw new GATKException("Hierarchical reduce failed", ex); + throw new ReviewedStingException("Hierarchical reduce failed", ex); } long endTime = System.currentTimeMillis(); diff --git a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java index 92bf8327b..5acf579e7 100755 --- a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java +++ b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.io; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.commandline.ArgumentSource; import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder; @@ -139,7 +139,7 @@ public abstract class OutputTracker { */ protected T getTargetStream( Stub stub ) { if( !outputs.containsKey(stub) ) - throw new GATKException("OutputTracker was not notified that this stub exists: " + stub); + throw new ReviewedStingException("OutputTracker was not notified that this stub exists: " + stub); Storage storage = outputs.get(stub); if( storage == null ) { storage = StorageFactory.createStorage(stub); diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java index 541a46b3b..4dc976289 100644 --- a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java +++ b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.gatk.io.storage; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -59,7 +59,7 @@ public class OutputStreamStorage extends OutputStream implements Storage, VCFWriter { this.stream = stub.getOutputStream(); } else - throw new GATKException("Unable to create target to which to write; storage was provided with neither a file nor a stream."); + throw new ReviewedStingException("Unable to create target to which to write; storage was provided with neither a file nor a stream."); writer = new StandardVCFWriter(stream); } diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java index 2b5cc7917..ca73ac29d 100644 --- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java +++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java @@ -35,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; /** @@ -156,7 +156,7 @@ public class SAMFileWriterStub implements Stub, StingSAMFileWrite */ public void setCompressionLevel( Integer compressionLevel ) { if(writeStarted) - throw new GATKException("Attempted to change the compression level of a file with alignments already in it."); + throw new ReviewedStingException("Attempted to change the compression level of a file with alignments already in it."); this.compressionLevel = compressionLevel; } @@ -192,7 +192,7 @@ public class SAMFileWriterStub implements Stub, StingSAMFileWrite */ public void setPresorted(boolean presorted) { if(writeStarted) - throw new GATKException("Attempted to change the presorted state of a file with alignments already in it."); + throw new ReviewedStingException("Attempted to change the presorted state of a file with alignments already in it."); this.presorted = presorted; } @@ -210,7 +210,7 @@ public class SAMFileWriterStub implements Stub, StingSAMFileWrite */ public void setMaxRecordsInRam(int maxRecordsInRam) { if(writeStarted) - throw new GATKException("Attempted to change the max records in RAM of a file with alignments already in it."); + throw new ReviewedStingException("Attempted to change the max records in RAM of a file with alignments already in it."); this.maxRecordsInRam = maxRecordsInRam; } @@ -228,7 +228,7 @@ public class SAMFileWriterStub implements Stub, StingSAMFileWrite */ public void writeHeader(SAMFileHeader header) { if(writeStarted) - throw new GATKException("Attempted to change the header of a file with alignments already in it."); + throw new ReviewedStingException("Attempted to change the header of a file with alignments already in it."); this.headerOverride = header; } diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java index f913f9464..f3a060be1 100644 --- a/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java +++ b/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java @@ -31,7 +31,7 @@ import java.util.Queue; import java.util.LinkedList; import java.util.NoSuchElementException; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * Buffers access to a large stream of reads, replenishing the buffer only when the reads @@ -66,7 +66,7 @@ public class BufferingReadIterator implements CloseableIterator { } public void remove() { - throw new GATKException("Unable to remove from a BufferingReadIterator"); + throw new ReviewedStingException("Unable to remove from a BufferingReadIterator"); } /** diff --git a/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java index 6cab3a353..9d67fdf05 100644 --- a/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java +++ b/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java @@ -30,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.Utils; import org.simpleframework.xml.Element; import org.simpleframework.xml.ElementList; @@ -169,7 +169,7 @@ public class GATKRunReport { */ public GATKRunReport(Walker walker, Exception e, GenomeAnalysisEngine engine, PhoneHomeOption type) { if ( type == PhoneHomeOption.NO_ET ) - throw new GATKException("Trying to create a run report when type is NO_ET!"); + throw new ReviewedStingException("Trying to create a run report when type is NO_ET!"); mGATKHeader = CommandLineGATK.createApplicationHeader(); currentPath = System.getProperty("user.dir"); @@ -245,7 +245,7 @@ public class GATKRunReport { serializer.write(this, stream); //throw new StingException("test"); } catch (Exception e) { - throw new GATKException("Failed to marshal the data to the file " + stream, e); + throw new ReviewedStingException("Failed to marshal the data to the file " + stream, e); } } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java index 0b1c41857..63ee1a62b 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.refdata; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import java.io.File; @@ -28,7 +28,7 @@ public class IntervalRod extends BasicReferenceOrderedDatum { } public String repl() { - throw new GATKException("repl() is not implemented yet"); + throw new ReviewedStingException("repl() is not implemented yet"); } public String toSimpleString() { return loc.toString(); } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java index 215c09f55..3b879b232 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.refdata; import org.broad.tribble.util.variantcontext.Allele; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; @@ -65,7 +65,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator implements Ite named_constructor = type.getConstructor(String.class); } catch (java.lang.NoSuchMethodException e) { - throw new GATKException("ROD class "+type.getName()+" does not have constructor that accepts a single String argument (track name)"); + throw new ReviewedStingException("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 diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java index e5f0487d5..3a7b26753 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java @@ -2,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import java.util.*; @@ -47,10 +47,10 @@ public class RODRecordListImpl extends AbstractList implements Comp records.add(r); if ( r == null ) continue; if ( ! this.name.equals(r.getName() ) ) { - throw new GATKException("Attempt to add GATKFeature with non-matching name "+r.getName()+" to the track "+name); + throw new ReviewedStingException("Attempt to add GATKFeature with non-matching name "+r.getName()+" to the track "+name); } if ( location != null && ! location.overlapsP(r.getLocation()) ) { - throw new GATKException("Attempt to add GATKFeature that lies outside of specified interval "+location+"; offending GATKFeature:\n"+r.toString()); + throw new ReviewedStingException("Attempt to add GATKFeature that lies outside of specified interval "+location+"; offending GATKFeature:\n"+r.toString()); } } } @@ -72,7 +72,7 @@ public class RODRecordListImpl extends AbstractList implements Comp public void add(GATKFeature record, boolean allowNameMismatch) { if ( record != null ) { if ( ! allowNameMismatch && ! name.equals(record.getName() ) ) - throw new GATKException("Attempt to add GATKFeature with non-matching name "+record.getName()+" to the track "+name); + throw new ReviewedStingException("Attempt to add GATKFeature with non-matching name "+record.getName()+" to the track "+name); } records.add(record); } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java index a9d82a112..6bb6d19dc 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java @@ -5,7 +5,7 @@ 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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -290,7 +290,7 @@ public class RefMetaDataTracker { Collection contexts = getVariantContexts(ref, name, allowedTypes, curLocation, requireStartHere, false ); if ( contexts.size() > 1 ) - throw new GATKException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation); + throw new ReviewedStingException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation); else if ( contexts.size() == 0 ) return null; else diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java index f0180a4be..c995f53bc 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java @@ -5,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -131,7 +131,7 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator { */ public RODRecordList next() { if ( ! next_is_allowed ) - throw new GATKException("Illegal use of iterator: Can not advance iterator with next() after seek-forward query of length > 1"); + throw new ReviewedStingException("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 +178,7 @@ 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 GATKException("DEBUG: encountered contig that should have been loaded earlier"); // this should never happen + if ( stop < curr_position ) throw new ReviewedStingException("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 +257,14 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator { public RODRecordList seekForward(GenomeLoc interval) { if ( interval.getContigIndex() < curr_contig ) - throw new GATKException("Out of order query: query contig "+interval.getContig()+" is located before "+ + throw new ReviewedStingException("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 GATKException("Out of order query: query position "+interval +" is located before "+ + throw new ReviewedStingException("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 GATKException("Unsupported querying sequence: current query interval " + + throw new ReviewedStingException("Unsupported querying sequence: current query interval " + interval+" ends before the end of previous query interval ("+curr_query_end+")"); } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java index 6e9eb88de..af895b262 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java @@ -4,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; @@ -60,7 +60,7 @@ 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 GATKException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n); + if ( n >= exons.size() || n < 0 ) throw new ReviewedStingException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n); return exons.get(n); } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java index 484d90fdf..29aefacc6 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java @@ -23,7 +23,7 @@ package org.broadinstitute.sting.gatk.refdata.tracks; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** @@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException; * * if we fail for some reason to make a track, throw this exception */ -public class RMDTrackCreationException extends GATKException { +public class RMDTrackCreationException extends ReviewedStingException { public RMDTrackCreationException(String msg) { super(msg); } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java index 9694bcb24..4890bb9a0 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java @@ -30,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -115,7 +115,7 @@ public class TribbleTrack extends RMDTrack implements QueryableTrack { try { reader.close(); } catch (IOException e) { - throw new GATKException("Unable to close reader " + reader.toString(),e); + throw new ReviewedStingException("Unable to close reader " + reader.toString(),e); } reader = null; } diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java index 56cd44aa0..e0fc5dd52 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java @@ -36,7 +36,7 @@ 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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -227,7 +227,7 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen locked = lock.sharedLock(); } catch(FileSystemInabilityToLockException ex) { - throw new GATKException("Unexpected inability to lock exception", ex); + throw new ReviewedStingException("Unexpected inability to lock exception", ex); } Index idx; try { @@ -294,7 +294,7 @@ public class TribbleRMDTrackBuilder extends PluginManager implemen return index; } catch(FileSystemInabilityToLockException ex) { - throw new GATKException("Unexpected inability to lock exception", ex); + throw new ReviewedStingException("Unexpected inability to lock exception", ex); } finally { if (locked) lock.unlock(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java index 2995723e1..888eb7e6e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.walkers.analyzeannotations; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.Comparator; @@ -114,7 +114,7 @@ public class AnnotationDatum implements Comparator { final public float calcTiTv( final int INDEX ) { if( ti[INDEX] < 0 || tv[INDEX] < 0 ) { - throw new GATKException( "Integer overflow detected! There are too many variants piled up in one annotation bin." ); + throw new ReviewedStingException( "Integer overflow detected! There are too many variants piled up in one annotation bin." ); } if( tv[INDEX] == 0 ) { // Don't divide by zero diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java index bd5406137..bfa1c4db5 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*; import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.genotype.Haplotype; import org.broadinstitute.sting.utils.pileup.*; @@ -197,7 +197,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation { String b = haplotypeB.toString(); if (a.length() != b.length()) - throw new GATKException("Haplotypes a and b must be of same length"); + throw new ReviewedStingException("Haplotypes a and b must be of same length"); char chA, chB; char wc = REGEXP_WILDCARD.charAt(0); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java index 3e49fac4a..1b7527416 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java @@ -49,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.classloader.PackageUtils; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -168,7 +168,7 @@ public class VariantAnnotatorEngine { Collection results = this.annotateContext(tracker, ref, EMPTY_STRATIFIED_ALIGNMENT_CONTEXT, vc); if ( results.size() != 1 ) - throw new GATKException("BUG: annotateContext call requires 1 resulting annotated VC, but got " + results); + throw new ReviewedStingException("BUG: annotateContext call requires 1 resulting annotated VC, but got " + results); return results.iterator().next(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java index fa67bf888..1b2c85b3e 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java @@ -33,7 +33,7 @@ import java.util.ArrayList; import java.util.HashMap; import java.util.List; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; /** @@ -83,7 +83,7 @@ public class JoinTable */ public void parseFromFile(String filename, String localBindingName, String localColumnName, String externalBindingName, String externalColumnName) { if(parsedFromFile) { - throw new GATKException("parseFromFile(" + filename +", ..) called more than once"); + throw new ReviewedStingException("parseFromFile(" + filename +", ..) called more than once"); } parsedFromFile = true; @@ -135,7 +135,7 @@ public class JoinTable br.close(); } } catch(IOException e) { - throw new GATKException("Unable to close file: " + filename, e); + throw new ReviewedStingException("Unable to close file: " + filename, e); } } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java index c93c988a7..d3fcfd42a 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java @@ -31,7 +31,7 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -63,7 +63,7 @@ public class JoinTableParser public List readHeader(BufferedReader br) throws IOException { if(header != null) { - throw new GATKException("readHeader(..) called more than once. Header is currently set to: " + header); + throw new ReviewedStingException("readHeader(..) called more than once. Header is currently set to: " + header); } header = Collections.unmodifiableList(parseHeader(br)); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java index caf5f93ec..b0588b9e4 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java @@ -44,7 +44,7 @@ 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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; /** @@ -973,7 +973,7 @@ public class TranscriptToGenomicInfo extends RodWalker { */ public int computeInitialCodingCoord() { if(!isProteinCodingTranscript()) { - throw new GATKException("This method should only be called for protein-coding transcripts"); + throw new ReviewedStingException("This method should only be called for protein-coding transcripts"); } if(positiveStrand) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java index 7eec418f9..a58d71129 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java @@ -4,7 +4,7 @@ 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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.PileupElement; @@ -57,7 +57,7 @@ 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 GATKException("Invalid type ID sent to getTypeID. This is a BUG!"); + throw new ReviewedStingException("Invalid type ID sent to getTypeID. This is a BUG!"); } } @@ -119,7 +119,7 @@ public class CoverageUtils { try { counts[BaseUtils.simpleBaseToBaseIndex(e.getBase())]++; } catch (ArrayIndexOutOfBoundsException exc) { - throw new GATKException("Expected a simple base, but actually received"+(char)e.getBase()); + throw new ReviewedStingException("Expected a simple base, but actually received"+(char)e.getBase()); } } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java index 27a95f514..e93b579a6 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java @@ -40,7 +40,7 @@ import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.io.File; @@ -226,7 +226,7 @@ public class DepthOfCoverageWalker extends LocusWalker maxWindowElements() || elementsToRight > maxWindowElements() ) - throw new GATKException("Too large a window requested"); + throw new ReviewedStingException("Too large a window requested"); if ( elementsToLeft < 0 || elementsToRight < 0 ) - throw new GATKException("Window size cannot be negative"); + throw new ReviewedStingException("Window size cannot be negative"); FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1]; ListIterator iter = window.listIterator(currentContext - elementsToLeft); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java index 547ddde15..46a935f78 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java @@ -30,7 +30,7 @@ import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.vcf.VCFConstants; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.genotype.DiploidGenotype; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext; @@ -192,7 +192,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul public void incrementFrequency() { if ( frequency == 2 * N ) - throw new GATKException("Frequency was incremented past N; how is this possible?"); + throw new ReviewedStingException("Frequency was incremented past N; how is this possible?"); frequency++; double greedy = VALUE_NOT_CALCULATED; @@ -219,7 +219,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul // so we can ignore that case } if ( greedyIndex == -1 ) - throw new GATKException("There is no best choice for a new alternate allele; how is this possible?"); + throw new ReviewedStingException("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(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java index e3afe847b..25ba13061 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java @@ -5,7 +5,7 @@ import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.contexts.*; @@ -72,7 +72,7 @@ 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 GATKException("Internal error (probably a bug): event does not conform to expected format: "+ bestEvent); + throw new ReviewedStingException("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() /* genotypes */, diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index 74f025908..d785bf595 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -31,7 +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.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.interval.IntervalUtils; @@ -334,7 +334,7 @@ public class IndelRealigner extends ReadWalker { do { currentInterval = intervals.hasNext() ? intervals.next() : null; } while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) ); - } catch (GATKException e) { + } catch (ReviewedStingException e) { throw new UserException.MissortedFile(new File(intervalsFile), " *** Are you sure that your interval file is sorted? If not, you must use the --targetIntervalsAreNotSorted argument. ***", e); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java index e0b627d3d..7451565c8 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java @@ -30,7 +30,7 @@ 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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.collections.PrimitivePair; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.AlignmentUtils; @@ -81,7 +81,7 @@ public class CycleQualityWalker extends ReadWalker { private Map cyclesByLibraryMapOrig = null; public void initialize() { - if ( PREFIX == null ) throw new GATKException("Prefix for output file(s) must be specified"); + if ( PREFIX == null ) throw new ReviewedStingException("Prefix for output file(s) must be specified"); cyclesByLaneMap = new HashMap(); cyclesByLibraryMap = new HashMap(); cyclesByLaneMapOrig = new HashMap(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java index ec3a9b677..6ad0340a4 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java @@ -3,7 +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.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMFileWriter; @@ -58,7 +58,7 @@ public class ReadValidationWalker extends ReadWalker { try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { - throw new GATKException("Unable to get the MD5 algorithm. Get a more eXtreme version of JAVA!@!@!!"); + throw new ReviewedStingException("Unable to get the MD5 algorithm. Get a more eXtreme version of JAVA!@!@!!"); } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java index d06b2035d..72ba37830 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java @@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -140,7 +140,7 @@ public class ValidatingPileupWalker extends LocusWalker { if ( interesting != null ) interestingReasons.add(interesting); break; default: - throw new GATKException("BUG: Unexpected evaluation order " + evaluation); + throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation); } } } @@ -708,7 +708,7 @@ public class VariantEvalWalker extends RodWalker { for ( EvaluationContext group : contexts ) { String[] parts = group.getDisplayName().split(CONTEXT_SEPARATOR); if ( parts.length != N_CONTEXT_NAME_PARTS ) { - throw new GATKException("Unexpected number of eval name parts " + group.getDisplayName() + " length = " + parts.length + ", expected " + N_CONTEXT_NAME_PARTS); + throw new ReviewedStingException("Unexpected number of eval name parts " + group.getDisplayName() + " length = " + parts.length + ", expected " + N_CONTEXT_NAME_PARTS); } else { for ( int i = 0; i < parts.length; i++ ) nameSizes[i] = Math.max(nameSizes[i], parts[i].length()); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java index a7cce23ad..1a7152b49 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration; import org.apache.log4j.Logger; import org.broad.tribble.util.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.MathUtils; import org.broadinstitute.sting.utils.collections.ExpandingArrayList; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -699,7 +699,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel logger.warn("About to throw exception due to numerical instability. Try running with fewer annotations and then with fewer Gaussians. " + "It is best to only use the annotations which appear to be Gaussianly distributed for this Gaussian mixture model."); - throw new GATKException("Numerical Instability! Found NaN after performing log10: " + pVarInClusterLog10[kkk] + ", cluster = " + kkk + ", variant index = " + iii); + throw new ReviewedStingException("Numerical Instability! Found NaN after performing log10: " + pVarInClusterLog10[kkk] + ", cluster = " + kkk + ", variant index = " + iii); } } @@ -709,7 +709,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel if( Double.isNaN(pVarInCluster[kkk][iii]) ) { logger.warn("About to throw exception due to numerical instability. Try running with fewer annotations and then with fewer Gaussians. " + "It is best to only use the annotations which appear to be Gaussianly distributed for this Gaussian mixture model."); - throw new GATKException("Numerical Instability! Found NaN after rescaling log10 values: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii); + throw new ReviewedStingException("Numerical Instability! Found NaN after rescaling log10 values: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii); } } } @@ -775,7 +775,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel if( Double.isNaN(prob) ) { logger.warn("About to throw exception due to numerical instability. Try running with fewer annotations and then with fewer Gaussians. " + "It is best to only use the annotations which appear to be Gaussianly distributed for this Gaussian mixture model."); - throw new GATKException("Numerical Instability! Found NaN in M-step: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii); + throw new ReviewedStingException("Numerical Instability! Found NaN in M-step: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii); } sumProb += prob; for( int jjj = 0; jjj < numAnnotations; jjj++ ) { diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java index 762b64e87..a263008fc 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java @@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import java.io.PrintStream; @@ -156,7 +156,7 @@ public class BeagleOutputByDepthWalker extends RodWalker { else if (compGenotype.isHomVar()) hg = 2; else - throw new GATKException("Bug! invalid genotype!"); + throw new ReviewedStingException("Bug! invalid genotype!"); if (postbglGenotype.isNoCall()) bg = -1; @@ -167,7 +167,7 @@ public class BeagleOutputByDepthWalker extends RodWalker { else if (postbglGenotype.isHomVar()) bg = 2; else - throw new GATKException("Bug! invalid genotype!"); + throw new ReviewedStingException("Bug! invalid genotype!"); if (prebglGenotype.isNoCall()) @@ -179,7 +179,7 @@ public class BeagleOutputByDepthWalker extends RodWalker { else if (prebglGenotype.isHomVar()) pg = 2; else - throw new GATKException("Bug! invalid genotype!"); + throw new ReviewedStingException("Bug! invalid genotype!"); outputWriter.format("%d %d %d %d\n",dp, hg, pg, bg); diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java index ce24c5fc5..2c907ebd1 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java @@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.commandline.Output; @@ -196,7 +196,7 @@ class IntervalInfoBuilder { } } } else { - throw new GATKException("Attempting to update an IntervalInfoBuilder twice with the same (non-TCGA) gene: "+gene); + throw new ReviewedStingException("Attempting to update an IntervalInfoBuilder twice with the same (non-TCGA) gene: "+gene); } } else { diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java index bf5d96984..f50e33550 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java @@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.features.samread.SAMReadFeature; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; import org.broadinstitute.sting.gatk.contexts.AlignmentContext; import org.broadinstitute.sting.gatk.walkers.LocusWalker; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.commandline.Argument; @@ -71,7 +71,7 @@ public class DownsamplingValidationWalker extends LocusWalker { int matchingReadsFound = 0; if(unsampledReadsStartingAtThisLocus.isEmpty()) { if(!sampledReadsStartingAtThisLocus.isEmpty()) - throw new GATKException("Downsampler hallucinated a read starting at locus "+ref.getLocus()); + throw new ReviewedStingException("Downsampler hallucinated a read starting at locus "+ref.getLocus()); } else { boolean foundMatch = false; @@ -86,10 +86,10 @@ public class DownsamplingValidationWalker extends LocusWalker { } if(!foundMatch) - throw new GATKException("Downsampler failed to include any read starting at locus "+ref.getLocus()); + throw new ReviewedStingException("Downsampler failed to include any read starting at locus "+ref.getLocus()); if(matchingReadsFound > maxExpectedNumberOfReads) - throw new GATKException("Downsampler found too many reads starting at locus "+ref.getLocus()); + throw new ReviewedStingException("Downsampler found too many reads starting at locus "+ref.getLocus()); } return matchingReadsFound; diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java index 797a146c2..5401fa360 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java @@ -21,7 +21,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.vcf.VCFUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; @@ -420,7 +420,7 @@ public class MendelianViolationClassifier extends LocusWalker splitContext = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup()); diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java index 2ead0e1e0..7d0439eaf 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers; import java.io.File; import java.io.IOException; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.QualityUtils; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -210,7 +210,7 @@ class StrandedCounts { public void updateReadPair( int fQual, int rQual, int fOff, int rOff ) { // hehe f Off if ( rOff < 0 || fOff < 0 ) - throw new GATKException("Offset is negative. Should never happen."); + throw new ReviewedStingException("Offset is negative. Should never happen."); forwardCountsByOffset[fOff][fQual < 0 ? 0 : fQual > 40 ? 40 : fQual]++; reverseCountsByOffset[rOff][rQual < 0 ? 0 : rQual > 40 ? 40 : rQual]++; } diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java index 6c7ab7d59..2a10f1ad5 100644 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java @@ -34,7 +34,7 @@ import org.broadinstitute.sting.alignment.bwa.c.BWACAligner; import org.broadinstitute.sting.alignment.Alignment; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import net.sf.samtools.SAMRecord; @@ -128,7 +128,7 @@ public class TestReadFishingWalker extends ReadWalker { System.arraycopy(referenceSequence.getBases(),eventStart,revisedReference,eventStart+eventLength,bufferWidth); } else - throw new GATKException("Invalid indel type: " + type); + throw new ReviewedStingException("Invalid indel type: " + type); aligners.put(GenomeLocParser.createGenomeLoc(contig,start,stop),new BWACAligner(revisedReference,new BWAConfiguration())); if(++numAlignersCreated % 100 == 0) diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java index 34ab9fc64..d17bffcfc 100755 --- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java +++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java @@ -11,7 +11,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.walkers.RodWalker; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.vcf.VCFUtils; @@ -95,7 +95,7 @@ public class VCF4WriterTestWalker extends RodWalker { out.printf("Read %d header lines%n", header.getMetaData().size()); } catch (FileNotFoundException e ) { - throw new GATKException(e.getMessage()); + throw new ReviewedStingException(e.getMessage()); } final Set vcfSamples = header.getGenotypeSamples(); diff --git a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java index e1c977501..ddac5f58f 100644 --- a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java +++ b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.playground.analyzeconcordance; import org.broadinstitute.sting.commandline.CommandLineProgram; import org.broadinstitute.sting.commandline.Argument; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.text.XReadLines; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.utils.PathUtils; @@ -92,7 +92,7 @@ public class AnalyzeConcordance extends CommandLineProgram { generateHtmlReport(); logger.info("...Done!"); } catch (Exception e) { - throw new GATKException("Error analyzing concordance", e); + throw new ReviewedStingException("Error analyzing concordance", e); } return result; @@ -102,7 +102,7 @@ public class AnalyzeConcordance extends CommandLineProgram { // create the output directory where all the data tables and plots will go File outputDir = new File(this.outputDir); if (!outputDir.exists() && !outputDir.mkdirs()) { - throw new GATKException("Couldn't create directory: " + this.outputDir); + throw new ReviewedStingException("Couldn't create directory: " + this.outputDir); } } diff --git a/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java b/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java index 8468d87f5..c5f4c7efb 100755 --- a/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java +++ b/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.playground.examples; import org.apache.log4j.BasicConfigurator; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.simpleframework.xml.Element; import org.simpleframework.xml.Root; import org.simpleframework.xml.Serializer; @@ -121,7 +121,7 @@ public class SampleXmlMarshaller { SampleXmlMarshaller example = serializer.read(SampleXmlMarshaller.class, source); return example; } catch (Exception e) { - throw new GATKException("Failed to marshal the data to file " + filename,e); + throw new ReviewedStingException("Failed to marshal the data to file " + filename,e); } } } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java index 2aeff6db0..74329fd90 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java @@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine; import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext; import org.broadinstitute.sting.utils.BaseUtils; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.pileup.PileupElement; @@ -155,7 +155,7 @@ public class LocusMismatchWalker extends LocusWalker implements if ( g.isHomRef() ) return "HOM-REF"; else if ( g.isHet() ) return "HET"; else if ( g.isHom() ) return "HOM-NONREF"; - else throw new GATKException("Unexpected genotype in getGenotypeClass " + g); + else throw new ReviewedStingException("Unexpected genotype in getGenotypeClass " + g); } public boolean useRead( PileupElement e ) { diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java index 433f0aecf..c331596f7 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java @@ -38,7 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.commandline.Output; import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.vcf.VCFUtils; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; @@ -301,7 +301,7 @@ public class ReadBackedPhasingWalker extends RodWalker maxPhaseSites) { logger.warn("Trying to phase sample " + samp + " at locus " + VariantContextUtils.getLocation(vc) + " within a window of " + cacheWindow + " bases yields " + sampleWindowVaList.size() + " heterozygous sites to phase:\n" + toStringVRL(sampleWindowVaList)); @@ -433,7 +433,7 @@ public class ReadBackedPhasingWalker extends RodWalker 2!"); + throw new ReviewedStingException("LOGICAL ERROR: Only considering haplotypes of length > 2!"); byte prevBase = hap.getBase(0); // The 1st base in the haplotype byte curBase = hap.getBase(1); // The 2nd base in the haplotype @@ -746,7 +746,7 @@ public class ReadBackedPhasingWalker extends RodWalker { try { digest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { - throw new GATKException("Unable to find MD5 checksumer"); + throw new ReviewedStingException("Unable to find MD5 checksumer"); } out.println("Header:"); // enumerate the list of ROD's we've loaded diff --git a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java index f85f13da2..c22105ed5 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java +++ b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java @@ -49,7 +49,7 @@ import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.utils.*; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.collections.Pair; @@ -77,8 +77,8 @@ public class GenomicMap implements Iterable c) { - if ( name == null ) throw new GATKException("Custom contig name can not be null"); - if ( map.containsKey(name)) throw new GATKException("Custom contig "+name+" already exists"); + if ( name == null ) throw new ReviewedStingException("Custom contig name can not be null"); + if ( map.containsKey(name)) throw new ReviewedStingException("Custom contig "+name+" already exists"); map.put(name, c); } @@ -184,7 +184,7 @@ public class GenomicMap implements Iterable,Integer> seekForward(Collection segments,int position) { - if ( position < 1 ) throw new GATKException("Position "+position + " is outside of custom contig boundaries"); + if ( position < 1 ) throw new ReviewedStingException("Position "+position + " is outside of custom contig boundaries"); PushbackIterator iter = new PushbackIterator(segments.iterator()); @@ -392,7 +392,7 @@ public class GenomicMap implements Iterable segments) { diff --git a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java index d86934baa..781a6fc9c 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java +++ b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.playground.utils; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.text.XReadLines; import org.apache.log4j.Logger; @@ -60,7 +60,7 @@ public class ProcessUtils { return result; } catch (Exception e) { - throw new GATKException("Error running command:" + command, e); + throw new ReviewedStingException("Error running command:" + command, e); } } } diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java b/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java index 4308d93c3..46b23719d 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java +++ b/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.playground.utils.report; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; import org.broadinstitute.sting.playground.utils.report.tags.Param; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.annotation.Annotation; import java.lang.reflect.Field; @@ -73,7 +73,7 @@ public class AnalysisModuleScanner { /** scan the class and find all appropriate fields and tables */ public void scan() { if (cls == null || !cls.isAnnotationPresent(Analysis.class)) - throw new GATKException("The class passed in cannot be null, " + "" + + throw new ReviewedStingException("The class passed in cannot be null, " + "" + "and must contain the @Analysis annotation, class " + cls + " was the input"); // get the annotation off of the class diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java b/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java index 34314a4f7..1dc360797 100644 --- a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java +++ b/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.playground.utils.report; import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat; import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils; import org.broadinstitute.sting.playground.utils.report.utils.Node; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.*; import java.lang.reflect.Field; @@ -195,7 +195,7 @@ public class ReportMarshaller { else node.addAllChildren(nodes); } catch (IllegalAccessException e) { - throw new GATKException("Unable to access field " + f); + throw new ReviewedStingException("Unable to access field " + f); } } } diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java index d819c7502..92574d4ad 100644 --- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java +++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java @@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescripto import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager; import org.broadinstitute.sting.gatk.walkers.Walker; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; import java.io.IOException; @@ -94,7 +94,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram { protected int execute() { try { if (!outputDirectory.isDirectory() && !outputDirectory.mkdirs()) - throw new GATKException("Unable to create output directory: " + outputDirectory); + throw new ReviewedStingException("Unable to create output directory: " + outputDirectory); for (Class clp: clpManager.getValues()) { diff --git a/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java b/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java index 978920d81..50d5e8dda 100644 --- a/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java +++ b/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.Iterator; @@ -37,7 +37,7 @@ public class CardinalityCounter implements Iterator, Iterable { public int[] next() { if (!hasNext()) - throw new GATKException("CANNOT iterate past end!"); + throw new ReviewedStingException("CANNOT iterate past end!"); // Copy the assignment to be returned: int[] nextList = new int[valList.length]; diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java index 93537299f..9809bff0d 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMRecord; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.ArrayList; import java.util.List; @@ -163,9 +163,9 @@ public class GenomeLoc implements Comparable, Cloneable, Serializable return ! discontinuousP( that ); } - public GenomeLoc merge( GenomeLoc that ) throws GATKException { + public GenomeLoc merge( GenomeLoc that ) throws ReviewedStingException { if (!(this.contiguousP(that))) { - throw new GATKException("The two genome loc's need to be contigous"); + throw new ReviewedStingException("The two genome loc's need to be contigous"); } return new GenomeLoc(getContig(), this.contigIndex, @@ -173,9 +173,9 @@ public class GenomeLoc implements Comparable, Cloneable, Serializable Math.max( getStop(), that.getStop()) ); } - public GenomeLoc intersect( GenomeLoc that ) throws GATKException { + public GenomeLoc intersect( GenomeLoc that ) throws ReviewedStingException { if (!(this.overlapsP(that))) { - throw new GATKException("GenomeLoc::intersect(): The two genome loc's need to overlap"); + throw new ReviewedStingException("GenomeLoc::intersect(): The two genome loc's need to overlap"); } return new GenomeLoc(getContig(), this.contigIndex, diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java index d6530ade0..8f23ae6c7 100644 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java @@ -42,7 +42,7 @@ import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; import org.broadinstitute.sting.utils.bed.BedParser; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.interval.IntervalMergingRule; import org.broadinstitute.sting.utils.text.XReadLines; @@ -428,10 +428,10 @@ public class GenomeLocParser { public static GenomeLoc createGenomeLoc(int contigIndex, final long start, final long stop) { checkSetup(); if (start < 0) { - throw new GATKException("Bad start position " + start); + throw new ReviewedStingException("Bad start position " + start); } if (stop < -1) { - throw new GATKException("Bad stop position " + stop); + throw new ReviewedStingException("Bad stop position " + stop); } // a negative -1 indicates it's not a meaningful end position @@ -498,16 +498,16 @@ public class GenomeLocParser { */ private static GenomeLoc exceptionOnInvalidGenomeLoc(GenomeLoc toReturn) { if (toReturn.getStart() < 0) { - throw new GATKException("Parameters to GenomeLocParser are incorrect: the start position is less than 0"); + throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the start position is less than 0"); } if ((toReturn.getStop() != -1) && (toReturn.getStop() < 0)) { - throw new GATKException("Parameters to GenomeLocParser are incorrect: the stop position is less than 0"); + throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the stop position is less than 0"); } if (toReturn.getContigIndex() < 0) { - throw new GATKException("Parameters to GenomeLocParser are incorrect: the contig index is less than 0"); + throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the contig index is less than 0"); } if (toReturn.getContigIndex() >= contigInfo.getSequences().size()) { - throw new GATKException("Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count"); + throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count"); } return toReturn; @@ -528,11 +528,11 @@ public class GenomeLocParser { private static void exceptionOnInvalidGenomeLocBounds(GenomeLoc locus) { int contigSize = contigInfo.getSequence(locus.getContigIndex()).getSequenceLength(); if(locus.getStart() > contigSize) - throw new GATKException(String.format("GenomeLoc is invalid: locus start %d is after the end of contig %s",locus.getStart(),locus.getContig())); + throw new ReviewedStingException(String.format("GenomeLoc is invalid: locus start %d is after the end of contig %s",locus.getStart(),locus.getContig())); if(locus.getStop() > contigSize) - throw new GATKException(String.format("GenomeLoc is invalid: locus stop %d is after the end of contig %s",locus.getStop(),locus.getContig())); + throw new ReviewedStingException(String.format("GenomeLoc is invalid: locus stop %d is after the end of contig %s",locus.getStop(),locus.getContig())); if (locus.getStart() > locus.getStop()) { - throw new GATKException("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position"); + throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position"); } } @@ -624,7 +624,7 @@ public class GenomeLocParser { int index = -1; if ((index = contigInfo.getSequenceIndex(contig)) < 0) { - throw new GATKException("Contig name ( " + contig + " ) not in the set sequence dictionary."); + throw new ReviewedStingException("Contig name ( " + contig + " ) not in the set sequence dictionary."); } return exceptionOnInvalidGenomeLoc(new GenomeLoc(contig, index, loc.start, loc.getStop())); } @@ -637,7 +637,7 @@ public class GenomeLocParser { public static GenomeLoc setContigIndex(GenomeLoc loc, int contig) { checkSetup(); if ((contig >= GenomeLocParser.contigInfo.getSequences().size()) || (contig < 0)) { - throw new GATKException("Contig index ( " + contig + " ) is not in the sequence dictionary set."); + throw new ReviewedStingException("Contig index ( " + contig + " ) is not in the sequence dictionary set."); } return exceptionOnInvalidGenomeLoc(new GenomeLoc(GenomeLocParser.contigInfo.getSequence(contig).getSequenceName(), contig, loc.start, loc.getStop())); } @@ -710,7 +710,7 @@ public class GenomeLocParser { /** check to make sure that we've setup the contig information */ private static void checkSetup() { if (contigInfo == null) { - throw new GATKException("The GenomeLocParser hasn't been setup with a contig sequence yet"); + throw new ReviewedStingException("The GenomeLocParser hasn't been setup with a contig sequence yet"); } } diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java b/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java index 28b4aa98c..fcb73f1ce 100755 --- a/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java +++ b/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMSequenceDictionary; import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.*; @@ -110,7 +110,7 @@ public class GenomeLocSortedSet extends AbstractSet { } else { int loc = Collections.binarySearch(mArray,e); if (loc >= 0) { - throw new GATKException("Genome Loc Sorted Set already contains the GenomicLoc " + e.toString()); + throw new ReviewedStingException("Genome Loc Sorted Set already contains the GenomicLoc " + e.toString()); } else { mArray.add((loc+1) * -1,e); return true; @@ -194,7 +194,7 @@ public class GenomeLocSortedSet extends AbstractSet { } else if ( e.getStop() < p.getStart() ) { toExclude.pop(); // p starts after e stops, e is done } else { - throw new GATKException("BUG: unexpected condition: p=" + p + ", e=" + e); + throw new ReviewedStingException("BUG: unexpected condition: p=" + p + ", e=" + e); } if ( i++ % 10000 == 0 ) diff --git a/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java b/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java index e45e883cb..9cf1b8c06 100644 --- a/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java +++ b/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.management.ManagementFactory; import java.lang.management.MemoryMXBean; @@ -42,7 +42,7 @@ public class HeapSizeMonitor { monitorThread.join(); } catch(InterruptedException ex) { - throw new GATKException("Unable to connect to monitor thread"); + throw new ReviewedStingException("Unable to connect to monitor thread"); } monitorThread = null; } @@ -74,7 +74,7 @@ public class HeapSizeMonitor { Thread.sleep(monitorFrequencyMillis); } catch(InterruptedException ex) { - throw new GATKException("Unable to continue monitoring heap consumption",ex); + throw new ReviewedStingException("Unable to continue monitoring heap consumption",ex); } } } diff --git a/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java b/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java index a0d11d6c7..ce554397c 100644 --- a/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java +++ b/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * User: hanna * Date: Jun 2, 2009 @@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException; * bad sequence id out of bounds, etc. */ -public class MalformedGenomeLocException extends GATKException { +public class MalformedGenomeLocException extends ReviewedStingException { /** * Create a new MalformedGenomeLocException with the given message. Does not preserve the existing stack trace. * @param message The message. diff --git a/java/src/org/broadinstitute/sting/utils/PathUtils.java b/java/src/org/broadinstitute/sting/utils/PathUtils.java index 2feb14484..47466be20 100755 --- a/java/src/org/broadinstitute/sting/utils/PathUtils.java +++ b/java/src/org/broadinstitute/sting/utils/PathUtils.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.List; import java.util.ArrayList; @@ -114,7 +114,7 @@ public class PathUtils { } if (dir.listFiles() == null) { - throw new GATKException("The volume '" + dir.getAbsolutePath() + "' could not be accessed."); + throw new ReviewedStingException("The volume '" + dir.getAbsolutePath() + "' could not be accessed."); } } diff --git a/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java b/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java index b1a4e3c8d..1cfe4b25f 100644 --- a/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java +++ b/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.*; @@ -35,7 +35,7 @@ public class ReservoirDownsampler { */ public ReservoirDownsampler(final int maxElements) { if(maxElements < 0) - throw new GATKException("Unable to work with an negative size collection of elements"); + throw new ReviewedStingException("Unable to work with an negative size collection of elements"); this.reservoir = new ArrayList(maxElements); this.maxElements = maxElements; } diff --git a/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java b/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java index 4198bc9c3..fb3d6f6a2 100755 --- a/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java +++ b/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java @@ -29,7 +29,7 @@ import net.sf.samtools.SAMSequenceRecord; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import java.util.*; @@ -116,7 +116,7 @@ public class SequenceDictionaryUtils { case OUT_OF_ORDER: throw new UserException.IncompatibleSequenceDictionaries("Order of contigs differences, which is unsafe", name1, dict1, name2, dict2); default: - throw new GATKException("Unexpected SequenceDictionaryComparison type"); + throw new ReviewedStingException("Unexpected SequenceDictionaryComparison type"); } } diff --git a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java index e5819fb75..b9ea9d0bc 100755 --- a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java +++ b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java @@ -30,7 +30,7 @@ import cern.jet.random.Normal; import java.util.*; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; public class WilcoxonRankSum { static final String headerString = ("nA nB .005 .01 .025 .05 .10 .20"); @@ -186,7 +186,7 @@ public class WilcoxonRankSum { U = n1 < n2 ? U1 : U2; break; default: - throw new GATKException("Unexpected WILCOXON H0: " + h0); + throw new ReviewedStingException("Unexpected WILCOXON H0: " + h0); } // data is nA nB then @@ -233,7 +233,7 @@ public class WilcoxonRankSum { pvalue = NORMAL.cdf(z); break; default: - throw new GATKException("Unexpected WILCOXON H0: " + h0); + throw new ReviewedStingException("Unexpected WILCOXON H0: " + h0); } return pvalue; diff --git a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java index 905814304..9b7c2c4de 100755 --- a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.classloader; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.reflect.Modifier; import java.lang.reflect.Field; @@ -126,7 +126,7 @@ public class JVMUtils { field.set(instance, value); } catch( IllegalAccessException ex ) { - throw new GATKException(String.format("Could not set %s in instance %s to %s",field.getName(),instance.getClass().getName(),value.toString())); + throw new ReviewedStingException(String.format("Could not set %s in instance %s to %s",field.getName(),instance.getClass().getName(),value.toString())); } } @@ -142,7 +142,7 @@ public class JVMUtils { return field.get(instance); } catch( IllegalAccessException ex ) { - throw new GATKException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName())); + throw new ReviewedStingException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName())); } } diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java index b97dff22c..4f570aa7a 100755 --- a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.classloader; import ch.qos.logback.classic.Level; import ch.qos.logback.classic.Logger; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import org.reflections.Reflections; import org.reflections.scanners.SubTypesScanner; @@ -136,7 +136,7 @@ public class PackageUtils { method.invoke(ClassLoader.getSystemClassLoader(), url); resetReflections(); } catch (Exception e) { - throw new GATKException("Error adding url to the current classloader.", e); + throw new ReviewedStingException("Error adding url to the current classloader.", e); } } diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java index 4d59f9400..bc26a0609 100644 --- a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java +++ b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.classloader; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException; import java.util.HashMap; @@ -87,7 +87,7 @@ public abstract class PluginManager { Class plugin = pluginsByName.get(pluginName); try { if( plugin == null ) - throw new GATKException(String.format("Could not find %s with name: %s", pluginCategory,pluginName)); + throw new ReviewedStingException(String.format("Could not find %s with name: %s", pluginCategory,pluginName)); return plugin.newInstance(); } catch (Exception e) { throw new DynamicClassResolutionException(plugin, e); diff --git a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java index d107b85b2..5a669e65c 100644 --- a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java +++ b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.collections; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** This class, closely resembling a deque (except that it is not dynamically grown), @@ -69,7 +69,7 @@ public class CircularArray { /** Creates an array of fixed length */ public CircularArray(int length) { - if ( length <= 0 ) throw new GATKException("CircularArray length must be positive. Passed: "+length); + if ( length <= 0 ) throw new ReviewedStingException("CircularArray length must be positive. Passed: "+length); data = new Object[length]; offset = 0; } @@ -150,7 +150,7 @@ public class CircularArray { /** Creates an array of fixed length */ public Int(int length) { - if ( length <= 0 ) throw new GATKException("CircularArray length must be positive. Passed: "+length); + if ( length <= 0 ) throw new ReviewedStingException("CircularArray length must be positive. Passed: "+length); data = new int[length]; // automaticaly initialized to zeros offset = 0; } diff --git a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java index c6bf96f64..61b842c05 100644 --- a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java +++ b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java @@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.collections; import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator; import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import java.util.*; @@ -42,10 +42,10 @@ public class MergingIterator implements Iterator, Iterable it) { if ( it instanceof LocationAwareSeekableRODIterator) { this.it = (LocationAwareSeekableRODIterator)it; - if ( ! it.hasNext() ) throw new GATKException("Iterator is empty"); + if ( ! it.hasNext() ) throw new ReviewedStingException("Iterator is empty"); update(); } else { - throw new GATKException("Iterator passed to MergingIterator is not LocationAwareSeekableRODIterator"); + throw new ReviewedStingException("Iterator passed to MergingIterator is not LocationAwareSeekableRODIterator"); } } diff --git a/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java index 27d6619cd..d2baa46c1 100644 --- a/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java +++ b/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting.utils.duplicates; import net.sf.samtools.SAMRecord; import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.collections.Pair; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.PileupElement; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; @@ -41,7 +41,7 @@ public class DupUtils { try { return (SAMRecord)read.clone(); } catch ( CloneNotSupportedException e ) { - throw new GATKException("Unexpected Clone failure!"); + throw new ReviewedStingException("Unexpected Clone failure!"); } } diff --git a/java/src/org/broadinstitute/sting/utils/exceptions/GATKException.java b/java/src/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java similarity index 74% rename from java/src/org/broadinstitute/sting/utils/exceptions/GATKException.java rename to java/src/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java index a71cb85a8..e1ff72ca1 100644 --- a/java/src/org/broadinstitute/sting/utils/exceptions/GATKException.java +++ b/java/src/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java @@ -24,17 +24,17 @@ package org.broadinstitute.sting.utils.exceptions; -import org.broadinstitute.sting.utils.exceptions.StingException; - /** - * Temp class to track split from Sting exception to UserException + * A trivial extension around StingException to mark exceptions that have been reviewed for correctness, + * completeness, etc. By using this exception you are saying "this is the right error message". StingException + * is now just a catch all for lazy users. */ -public class GATKException extends StingException { - public GATKException(String msg) { +public class ReviewedStingException extends StingException { + public ReviewedStingException(String msg) { super(msg); } - public GATKException(String message, Throwable throwable) { + public ReviewedStingException(String message, Throwable throwable) { super(message, throwable); } } diff --git a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java index b7fe6655f..b5cd705db 100755 --- a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java +++ b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java @@ -41,7 +41,7 @@ import java.util.Arrays; * Date: Sep 3, 2010 * Time: 2:24:09 PM */ -public class UserException extends GATKException { +public class UserException extends ReviewedStingException { public UserException(String msg) { super(msg); } public UserException(String msg, Throwable e) { super(msg, e); } private UserException(Throwable e) { super("", e); } // cannot be called, private access diff --git a/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java b/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java index 8b1e85030..90f9fe5bd 100644 --- a/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java +++ b/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils.fasta; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.FileNotFoundException; import java.io.FileOutputStream; @@ -34,7 +34,7 @@ public class ArtificialFastaUtils { try { s = new PrintStream(new FileOutputStream(fileName)); } catch (FileNotFoundException e) { - throw new GATKException("Filename " + fileName + " passed to the ArtificialFastaUtils generated a FileNotFound exception", e); + throw new ReviewedStingException("Filename " + fileName + " passed to the ArtificialFastaUtils generated a FileNotFound exception", e); } generateFakeFasta(contigNames, contigSizes, pattern, s); } @@ -58,7 +58,7 @@ public class ArtificialFastaUtils { */ private static void generateFakeFasta(List contigNames, List contigSizes, BASE_PATTERN pattern, PrintStream s) { if (contigNames.size() != contigSizes.size()) { - throw new GATKException("ArtificialContig name and size arrays are not equal sizes"); + throw new ReviewedStingException("ArtificialContig name and size arrays are not equal sizes"); } for (int x = 0; x < contigNames.size(); x++) { ArtificialContig tig = new ArtificialContig(contigNames.get(x), contigSizes.get(x), pattern); @@ -122,7 +122,7 @@ class ArtificialContig { case ALL_G: return "G"; default: - throw new GATKException("Unknown base pattern"); + throw new ReviewedStingException("Unknown base pattern"); } } diff --git a/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java b/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java index 767a7aadf..965210bea 100644 --- a/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java +++ b/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils.file; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; import java.io.IOException; @@ -143,7 +143,7 @@ public class FSLockWithShared { channel.close(); } catch (Exception e) { - throw new GATKException("An error occurred while unlocking file", e); + throw new ReviewedStingException("An error occurred while unlocking file", e); } } } diff --git a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java index 334394a3e..f68523479 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils.genotype; import edu.mit.broad.picard.genotype.DiploidGenotype; import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods; import net.sf.samtools.SAMFileHeader; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.HashMap; @@ -234,15 +234,15 @@ public class LikelihoodObject { switch (mLikelihoodType) { case NEGATIVE_LOG: if (score < 0) - throw new GATKException("Likelikhood score of " + score + " is invalid, for NEGATIVE_LOG it must be greater than or equal to 0"); + throw new ReviewedStingException("Likelikhood score of " + score + " is invalid, for NEGATIVE_LOG it must be greater than or equal to 0"); break; case LOG: if (score > 0) - throw new GATKException("Likelikhood score of " + score + " is invalid, for LOG it must be less than or equal to 0"); + throw new ReviewedStingException("Likelikhood score of " + score + " is invalid, for LOG it must be less than or equal to 0"); break; case RAW: if (score < 0 || score > 1) - throw new GATKException("Likelikhood score of " + score + " is invalid, for RAW it must be [0,1]"); + throw new ReviewedStingException("Likelikhood score of " + score + " is invalid, for RAW it must be [0,1]"); break; } } diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java index bf5b15d02..86c53fe99 100644 --- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils.genotype.glf; import net.sf.samtools.util.BinaryCodec; import net.sf.samtools.util.BlockCompressedInputStream; import net.sf.samtools.util.RuntimeEOFException; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.genotype.LikelihoodObject; @@ -225,7 +225,7 @@ public class GLFReader implements Iterator { } public void remove() { - throw new GATKException("GLFReader doesn't support remove()"); + throw new ReviewedStingException("GLFReader doesn't support remove()"); } public void close() { diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java index 5d2b8e5cf..242d3a092 100755 --- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils.genotype.glf; import net.sf.samtools.util.BinaryCodec; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /* @@ -251,7 +251,7 @@ public abstract class GLFRecord { * @return the minimum value */ protected static double findMin(double vals[]) { - if (vals.length < 1) throw new GATKException("findMin: an array of size < 1 was passed in"); + if (vals.length < 1) throw new ReviewedStingException("findMin: an array of size < 1 was passed in"); double min = vals[0]; for (double d : vals) diff --git a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java index c2a5f8f77..b948b2eb5 100644 --- a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java +++ b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.help; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.commandline.CommandLineProgram; @@ -80,7 +80,7 @@ public class ApplicationDetails { runningInstructions = JVMUtils.getLocationFor( application ).getName(); } catch( IOException ex ) { - throw new GATKException("Unable to determine running instructions", ex); + throw new ReviewedStingException("Unable to determine running instructions", ex); } if( runningInstructions.endsWith(".jar") ) diff --git a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java index b044f779a..49a93148b 100644 --- a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java +++ b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java @@ -31,7 +31,7 @@ import java.util.*; import java.io.PrintStream; import java.io.IOException; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.classloader.JVMUtils; import org.broadinstitute.sting.utils.Utils; import org.broadinstitute.sting.gatk.walkers.Walker; @@ -181,7 +181,7 @@ public class ResourceBundleExtractorDoclet { for(Tag tag: element.tags()) { if(tag.name().equals("@"+DisplayNameTaglet.NAME)) { if(name != null) - throw new GATKException("Only one display name tag can be used per package / walker."); + throw new ReviewedStingException("Only one display name tag can be used per package / walker."); name = tag.text(); } else if(tag.name().equals("@"+VERSION_TAGLET_NAME)) diff --git a/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java b/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java index 2eaa07d89..d5c47bc07 100644 --- a/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java +++ b/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java @@ -24,7 +24,7 @@ package org.broadinstitute.sting.utils.instrumentation; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.lang.instrument.Instrumentation; import java.lang.reflect.Field; @@ -73,7 +73,7 @@ public class Sizeof { */ public static long getObjectSize(Object o) { if(!isEnabled()) - throw new GATKException("Sizeof operator is currently disabled! To enable, review the documentation in Sizeof.java"); + throw new ReviewedStingException("Sizeof operator is currently disabled! To enable, review the documentation in Sizeof.java"); return instrumentation.getObjectSize(o); } @@ -84,7 +84,7 @@ public class Sizeof { */ public static long getObjectGraphSize(Object o) { if(!isEnabled()) - throw new GATKException("Sizeof operator is currently disabled! To enable, review the documentation in Sizeof.java"); + throw new ReviewedStingException("Sizeof operator is currently disabled! To enable, review the documentation in Sizeof.java"); IdentityHashMap objectsSeen = new IdentityHashMap(); return getObjectGraphSize(o,objectsSeen); } @@ -134,7 +134,7 @@ public class Sizeof { fieldValue = field.get(o); } catch(IllegalAccessException ex) { - throw new GATKException("Unable to access field " + field.getName(),ex); + throw new ReviewedStingException("Unable to access field " + field.getName(),ex); } totalSize += getObjectGraphSize(fieldValue,objectsSeen); } diff --git a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java index 7b039608f..95f1e3073 100644 --- a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java +++ b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java @@ -24,7 +24,7 @@ package org.broadinstitute.sting.utils.pileup; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.BaseUtils; import org.broadinstitute.sting.gatk.iterators.IterableIterator; @@ -82,8 +82,8 @@ public abstract class AbstractReadBackedPileup pileup) { - if ( loc == null ) throw new GATKException("Illegal null genomeloc in ReadBackedPileup"); - if ( pileup == null ) throw new GATKException("Illegal null pileup in ReadBackedPileup"); + if ( loc == null ) throw new ReviewedStingException("Illegal null genomeloc in ReadBackedPileup"); + if ( pileup == null ) throw new ReviewedStingException("Illegal null pileup in ReadBackedPileup"); this.loc = loc; this.pileupElementTracker = new UnifiedPileupElementTracker(pileup); @@ -96,8 +96,8 @@ public abstract class AbstractReadBackedPileup pileup, int size, int nDeletions, int nMQ0Reads) { - if ( loc == null ) throw new GATKException("Illegal null genomeloc in UnifiedReadBackedPileup"); - if ( pileup == null ) throw new GATKException("Illegal null pileup in UnifiedReadBackedPileup"); + if ( loc == null ) throw new ReviewedStingException("Illegal null genomeloc in UnifiedReadBackedPileup"); + if ( pileup == null ) throw new ReviewedStingException("Illegal null pileup in UnifiedReadBackedPileup"); this.loc = loc; this.pileupElementTracker = new UnifiedPileupElementTracker(pileup); @@ -158,9 +158,9 @@ public abstract class AbstractReadBackedPileup readsOffsets2Pileup(List reads, List offsets ) { - if ( reads == null ) throw new GATKException("Illegal null read list in UnifiedReadBackedPileup"); - if ( offsets == null ) throw new GATKException("Illegal null offsets list in UnifiedReadBackedPileup"); - if ( reads.size() != offsets.size() ) throw new GATKException("Reads and offset lists have different sizes!"); + if ( reads == null ) throw new ReviewedStingException("Illegal null read list in UnifiedReadBackedPileup"); + if ( offsets == null ) throw new ReviewedStingException("Illegal null offsets list in UnifiedReadBackedPileup"); + if ( reads.size() != offsets.size() ) throw new ReviewedStingException("Reads and offset lists have different sizes!"); UnifiedPileupElementTracker pileup = new UnifiedPileupElementTracker(); for ( int i = 0; i < reads.size(); i++ ) { @@ -178,8 +178,8 @@ public abstract class AbstractReadBackedPileup readsOffsets2Pileup(List reads, int offset ) { - if ( reads == null ) throw new GATKException("Illegal null read list in UnifiedReadBackedPileup"); - if ( offset < 0 ) throw new GATKException("Illegal offset < 0 UnifiedReadBackedPileup"); + if ( reads == null ) throw new ReviewedStingException("Illegal null read list in UnifiedReadBackedPileup"); + if ( offset < 0 ) throw new ReviewedStingException("Illegal offset < 0 UnifiedReadBackedPileup"); UnifiedPileupElementTracker pileup = new UnifiedPileupElementTracker(); for ( int i = 0; i < reads.size(); i++ ) { diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java index 42718320e..b64ef8ce0 100644 --- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java +++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java @@ -23,7 +23,7 @@ */ package org.broadinstitute.sting.utils.pileup; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.collections.Pair; @@ -140,7 +140,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup< case INSERTION: v[i] = 'I'; break; case DELETION: v[i] = 'D'; break; case NOEVENT: v[i] = '.'; break; - default: throw new GATKException("Unknown event type encountered: "+e.getType()); + default: throw new ReviewedStingException("Unknown event type encountered: "+e.getType()); } i++; } @@ -190,7 +190,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup< indel = getDeletionString(e.getEventLength(),refBases); break; case NOEVENT: continue; - default: throw new GATKException("Unknown event type encountered: "+e.getType()); + default: throw new ReviewedStingException("Unknown event type encountered: "+e.getType()); } cnt = events.get(indel); diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java index 6683c89d2..c4f3338f0 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java @@ -31,7 +31,7 @@ import net.sf.samtools.Cigar; import net.sf.samtools.CigarElement; import net.sf.samtools.util.StringUtil; import org.broadinstitute.sting.gatk.contexts.ReferenceContext; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.pileup.*; import org.broadinstitute.sting.utils.Utils; @@ -146,7 +146,7 @@ public class AlignmentUtils { case H: case P: break; - default: throw new GATKException("The " + ce.getOperator() + " cigar element is not currently supported"); + default: throw new ReviewedStingException("The " + ce.getOperator() + " cigar element is not currently supported"); } } @@ -298,7 +298,7 @@ public class AlignmentUtils { case P: break; default: - throw new GATKException( "Unsupported cigar operator: " + ce.getOperator() ); + throw new ReviewedStingException( "Unsupported cigar operator: " + ce.getOperator() ); } } return alignment; @@ -337,7 +337,7 @@ public class AlignmentUtils { case P: break; default: - throw new GATKException( "Unsupported cigar operator: " + ce.getOperator() ); + throw new ReviewedStingException( "Unsupported cigar operator: " + ce.getOperator() ); } } return alignment; diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java index 5297e0345..16293ba62 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java @@ -10,7 +10,7 @@ import java.io.ByteArrayInputStream; import java.io.UnsupportedEncodingException; import java.util.*; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; /** @@ -93,7 +93,7 @@ public class ArtificialSAMFileReader extends SAMFileReader { return new ByteArrayInputStream(byteArray); } catch( UnsupportedEncodingException ex ) { - throw new GATKException("Unable to build empty input stream",ex); + throw new ReviewedStingException("Unable to build empty input stream",ex); } } } diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java index d98a6c6f1..4f5dcca61 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java @@ -6,7 +6,7 @@ import net.sf.samtools.SAMRecord; import java.util.List; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /* @@ -126,7 +126,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator { // sanity check that we have an actual matching read next SAMRecord rec = this.peek(); if (rec == null) { - throw new GATKException("The next read doesn't match"); + throw new ReviewedStingException("The next read doesn't match"); } // set the seeked variable to true seeked = true; @@ -165,7 +165,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator { super.next(); } if (!super.hasNext()) { - throw new GATKException("Unable to find the target chromosome"); + throw new ReviewedStingException("Unable to find the target chromosome"); } while (super.hasNext() && this.peek().getAlignmentStart() < start) { super.next(); @@ -173,7 +173,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator { // sanity check that we have an actual matching read next SAMRecord rec = this.peek(); if (!matches(rec)) { - throw new GATKException("The next read doesn't match"); + throw new ReviewedStingException("The next read doesn't match"); } // set the seeked variable to true seeked = true; diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java index b424c59a3..095fe3ab3 100755 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils.sam; import net.sf.samtools.*; import org.broadinstitute.sting.gatk.iterators.StingSAMIterator; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; import java.util.ArrayList; @@ -115,7 +115,7 @@ public class ArtificialSAMUtils { */ public static SAMFileHeader createEnumeratedReadGroups( SAMFileHeader header, List readGroupIDs, List sampleNames ) { if (readGroupIDs.size() != sampleNames.size()) { - throw new GATKException("read group count and sample name count must be the same"); + throw new ReviewedStingException("read group count and sample name count must be the same"); } List readGroups = new ArrayList(); @@ -145,7 +145,7 @@ public class ArtificialSAMUtils { public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, int length ) { if( (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) || (refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START) ) - throw new GATKException("Invalid alignment start for artificial read, start = " + alignmentStart); + throw new ReviewedStingException("Invalid alignment start for artificial read, start = " + alignmentStart); SAMRecord record = new SAMRecord(header); record.setReadName(name); record.setReferenceIndex(refIndex); @@ -183,7 +183,7 @@ public class ArtificialSAMUtils { */ public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual ) { if (bases.length != qual.length) { - throw new GATKException("Passed in read string is different length then the quality array"); + throw new ReviewedStingException("Passed in read string is different length then the quality array"); } SAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length); rec.setReadBases(bases); diff --git a/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java b/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java index ab22b4e19..f8a0ca6a7 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java +++ b/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java @@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileReader; import java.io.File; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; /** * Allows the user to steadily accumulate information about what @@ -72,9 +72,9 @@ public class SAMFileReaderBuilder { */ public SAMFileReader build() { if( samFile == null ) - throw new GATKException( "Filename for output sam file must be supplied."); + throw new ReviewedStingException( "Filename for output sam file must be supplied."); if( validationStringency == null ) - throw new GATKException( "Header for output sam file must be supplied."); + throw new ReviewedStingException( "Header for output sam file must be supplied."); SAMFileReader reader = new SAMFileReader( samFile ); reader.setValidationStringency( validationStringency ); diff --git a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java index 93cece9cd..803d6ac0f 100644 --- a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java +++ b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils.text; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.util.*; import java.util.regex.Pattern; @@ -110,7 +110,7 @@ public class TextFormattingUtils { bundle = new PropertyResourceBundle(new StringReader("")); } catch(IOException ioe) { - throw new GATKException("No resource bundle found, and unable to create an empty placeholder.",ioe); + throw new ReviewedStingException("No resource bundle found, and unable to create an empty placeholder.",ioe); } } return bundle; diff --git a/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java b/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java index 3c47d5a8b..ab91d0e2e 100755 --- a/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java +++ b/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.utils.wiggle; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.exceptions.UserException; @@ -76,7 +76,7 @@ public class WiggleWriter { write(wWriter,String.format("%d\t%s",loc.getStart(),dataPoint.toString())); } else { // todo -- maybe allow this to open a new file for the new chromosome? - throw new GATKException("Attempting to write multiple contigs into wiggle file, first contig was "+firstLoc.getContig()+" most recent "+loc.getContig()); + throw new ReviewedStingException("Attempting to write multiple contigs into wiggle file, first contig was "+firstLoc.getContig()+" most recent "+loc.getContig()); } } diff --git a/java/test/org/broadinstitute/sting/BaseTest.java b/java/test/org/broadinstitute/sting/BaseTest.java index 9f9f56676..1da296e42 100755 --- a/java/test/org/broadinstitute/sting/BaseTest.java +++ b/java/test/org/broadinstitute/sting/BaseTest.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting; import org.apache.log4j.*; import org.apache.log4j.spi.LoggingEvent; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.junit.*; import java.io.*; @@ -141,13 +141,13 @@ public abstract class BaseTest { try { digest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { - throw new GATKException("Unable to find MD5 digest"); + throw new ReviewedStingException("Unable to find MD5 digest"); } InputStream is; try { is = new FileInputStream(file); } catch (FileNotFoundException e) { - throw new GATKException("Unable to open file " + file); + throw new ReviewedStingException("Unable to open file " + file); } byte[] buffer = new byte[8192]; int read; @@ -161,14 +161,14 @@ public abstract class BaseTest { } catch (IOException e) { - throw new GATKException("Unable to process file for MD5", e); + throw new ReviewedStingException("Unable to process file for MD5", e); } finally { try { is.close(); } catch (IOException e) { - throw new GATKException("Unable to close input stream for MD5 calculation", e); + throw new ReviewedStingException("Unable to close input stream for MD5 calculation", e); } } } diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java index d82a9d76d..fcd9ac2f0 100755 --- a/java/test/org/broadinstitute/sting/WalkerTest.java +++ b/java/test/org/broadinstitute/sting/WalkerTest.java @@ -28,7 +28,7 @@ package org.broadinstitute.sting; import junit.framework.Assert; import org.broadinstitute.sting.gatk.CommandLineExecutable; import org.broadinstitute.sting.gatk.CommandLineGATK; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.Utils; import org.junit.Test; @@ -62,7 +62,7 @@ public class WalkerTest extends BaseTest { if ( ! dir.exists() ) { System.out.printf("##### Creating MD5 db %s%n", MD5_FILE_DB_SUBDIR); if ( ! dir.mkdir() ) { - throw new GATKException("Infrastructure failure: failed to create md5 directory " + MD5_FILE_DB_SUBDIR); + throw new ReviewedStingException("Infrastructure failure: failed to create md5 directory " + MD5_FILE_DB_SUBDIR); } } } @@ -81,7 +81,7 @@ public class WalkerTest extends BaseTest { try { FileUtils.copyFile(resultsFile, dbFile); } catch ( IOException e ) { - throw new GATKException(e.getMessage()); + throw new ReviewedStingException(e.getMessage()); } } else { System.out.printf("##### MD5 file is up to date: %s%n", dbFile.getPath()); @@ -213,7 +213,7 @@ public class WalkerTest extends BaseTest { } public Class getExpectedException() { - if ( ! expectsException() ) throw new GATKException("Tried to get expection for walker test that doesn't expect one"); + if ( ! expectsException() ) throw new ReviewedStingException("Tried to get expection for walker test that doesn't expect one"); return expectedException; } @@ -261,7 +261,7 @@ public class WalkerTest extends BaseTest { fl.deleteOnExit(); return fl; } catch (IOException ex) { - throw new GATKException("Cannot create temp file: " + ex.getMessage(), ex); + throw new ReviewedStingException("Cannot create temp file: " + ex.getMessage(), ex); } } diff --git a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java index c2650aad1..833e6cce4 100755 --- a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java +++ b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java @@ -26,7 +26,7 @@ package org.broadinstitute.sting.commandline; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.junit.Test; import org.junit.Before; import org.junit.Assert; @@ -355,7 +355,7 @@ public class ParsingEngineUnitTest extends BaseTest { parsingEngine.validate(); } - @Test(expected= GATKException.class) + @Test(expected= ReviewedStingException.class) public void duplicateLongNameTest() { parsingEngine.addArgumentSource( DuplicateLongNameProvider.class ); } @@ -368,7 +368,7 @@ public class ParsingEngineUnitTest extends BaseTest { public Integer bar; } - @Test(expected=GATKException.class) + @Test(expected= ReviewedStingException.class) public void duplicateShortNameTest() { parsingEngine.addArgumentSource( DuplicateShortNameProvider.class ); } @@ -593,7 +593,7 @@ public class ParsingEngineUnitTest extends BaseTest { RequiredArgProvider rap = new RequiredArgProvider(); } - @Test(expected=GATKException.class) + @Test(expected= ReviewedStingException.class) public void multipleArgumentCollectionTest() { parsingEngine.addArgumentSource( MultipleArgumentCollectionProvider.class ); } diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java index 23decfa06..691849959 100755 --- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java @@ -1,6 +1,6 @@ package org.broadinstitute.sting.gatk.datasources.providers; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.junit.Before; import org.junit.Assert; import org.junit.Test; @@ -66,7 +66,7 @@ public class ShardDataProviderUnitTest extends BaseTest { /** * Try adding a view which conflicts with some other view that's already been registered. */ - @Test(expected= GATKException.class) + @Test(expected= ReviewedStingException.class) public void testAddViewWithExistingConflict() { View initial = new ConflictingTestView( provider ); View conflictsWithInitial = new TestView( provider ); @@ -75,7 +75,7 @@ public class ShardDataProviderUnitTest extends BaseTest { /** * Try adding a view which has a conflict with a previously registered view. */ - @Test(expected=GATKException.class) + @Test(expected= ReviewedStingException.class) public void testAddViewWithNewConflict() { View conflictsWithInitial = new TestView( provider ); View initial = new ConflictingTestView( provider ); diff --git a/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java b/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java index fb2254e6d..0b86466dd 100644 --- a/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.gatk.filters; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.GenomeLocParser; import org.junit.BeforeClass; @@ -46,18 +46,18 @@ public class ReadGroupBlackListFilterUnitTest extends BaseTest { GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary()); } - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testBadFilter() { List badFilters = Collections.singletonList("bad"); new ReadGroupBlackListFilter(badFilters); } - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testBadFilterTag() { List badFilters = Collections.singletonList("bad:filter"); new ReadGroupBlackListFilter(badFilters); } - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testBadFilterFile() { List badFilters = Collections.singletonList("/foo/bar/rgbl.txt"); new ReadGroupBlackListFilter(badFilters); diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java index 98807fba0..8e81d83f0 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java @@ -27,7 +27,7 @@ import net.sf.samtools.SAMSequenceRecord; import net.sf.picard.reference.IndexedFastaSequenceFile; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLocParser; import org.junit.Assert; import org.junit.Before; @@ -72,7 +72,7 @@ public class RMDTrackManagerUnitTest extends BaseTest { try { fIter = ((TribbleTrack) t).query("1", 1, 5000); } catch (IOException e) { - throw new GATKException("blah I/O exception"); + throw new ReviewedStingException("blah I/O exception"); } while (fIter.hasNext()) { fIter.next(); @@ -123,7 +123,7 @@ public class RMDTrackManagerUnitTest extends BaseTest { try { fIter = ((TribbleTrack) t).query("1", x, x + intervalSize); } catch (IOException e) { - throw new GATKException("blah I/O exception"); + throw new ReviewedStingException("blah I/O exception"); } while (fIter.hasNext()) { fIter.next(); diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java index 46b2ed6f2..293c37cdd 100644 --- a/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java @@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import static org.junit.Assert.assertEquals; @@ -20,7 +20,7 @@ import org.junit.Test; * Test out the functionality of the new genome loc parser */ public class GenomeLocParserUnitTest extends BaseTest { - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testUnsetupException() { GenomeLocParser.contigInfo = null; GenomeLocParser.createGenomeLoc(0, 0, 0); @@ -66,7 +66,7 @@ public class GenomeLocParserUnitTest extends BaseTest { assertEquals("chr1".compareTo(GenomeLocParser.getContigInfo("chr1").getSequenceName()), 0); // should be in the reference } - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testParseBadString() { GenomeLocParser.parseGenomeLoc("Bad:0-1"); } @@ -144,7 +144,7 @@ public class GenomeLocParserUnitTest extends BaseTest { assertEquals(1, loc.getStart()); } - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testGenomeLocParseOnlyBadChrome() { GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr12"); assertEquals(0, loc.getContigIndex()); @@ -152,7 +152,7 @@ public class GenomeLocParserUnitTest extends BaseTest { assertEquals(1, loc.getStart()); } - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testGenomeLocBad() { GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1-"); assertEquals(0, loc.getContigIndex()); @@ -160,7 +160,7 @@ public class GenomeLocParserUnitTest extends BaseTest { assertEquals(1, loc.getStart()); } - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testGenomeLocBad2() { GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1-500-0"); assertEquals(0, loc.getContigIndex()); @@ -168,7 +168,7 @@ public class GenomeLocParserUnitTest extends BaseTest { assertEquals(1, loc.getStart()); } - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testGenomeLocBad3() { GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1--0"); assertEquals(0, loc.getContigIndex()); diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java index bbb11fc86..f722e1a42 100755 --- a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java @@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils; import net.sf.samtools.SAMFileHeader; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import static org.junit.Assert.assertTrue; import static org.junit.Assert.assertEquals; @@ -81,7 +81,7 @@ public class GenomeLocSortedSetUnitTest extends BaseTest { } - @Test(expected = GATKException.class) + @Test(expected = ReviewedStingException.class) public void testAddDupplicate() { assertTrue(mSortedSet.size() == 0); GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 0, 0); diff --git a/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java b/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java index f54944a05..88eea4604 100755 --- a/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java @@ -1,7 +1,7 @@ package org.broadinstitute.sting.utils; import org.broadinstitute.sting.BaseTest; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.junit.BeforeClass; import org.junit.Test; import org.junit.Assert; @@ -28,7 +28,7 @@ public class PathUtilsUnitTest extends BaseTest { try { PathUtils.refreshVolume(new File(filename)); - } catch (GATKException e) { + } catch (ReviewedStingException e) { result = false; } diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java index e22b5d18a..ab01ae5fc 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java @@ -7,7 +7,7 @@ import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.*; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLocParser; import org.junit.Assert; @@ -58,7 +58,7 @@ public class VCFWriterUnitTest extends BaseTest { headerFromFile = (VCFHeader)reader.readHeader(lineReader); } catch (FileNotFoundException e ) { - throw new GATKException(e.getMessage()); + throw new ReviewedStingException(e.getMessage()); } int counter = 0; @@ -80,7 +80,7 @@ public class VCFWriterUnitTest extends BaseTest { fakeVCFFile.delete(); } catch (IOException e ) { - throw new GATKException(e.getMessage()); + throw new ReviewedStingException(e.getMessage()); } } diff --git a/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java b/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java index 9f94659f6..8c2bfa224 100644 --- a/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java @@ -25,7 +25,7 @@ package org.broadinstitute.sting.utils.interval; -import org.broadinstitute.sting.utils.exceptions.GATKException; +import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.junit.BeforeClass; import org.junit.Test; import org.junit.Assert; @@ -101,7 +101,7 @@ public class IntervalFileMergingIteratorUnitTest extends BaseTest { GenomeLoc l_expected = check_it.next(); // System.out.println("int: "+l+" expected: "+l_expected) ; } - } catch ( GATKException e) { + } catch ( ReviewedStingException e) { Assert.assertEquals( e.getMessage(), "Interval chr5:7414 in the interval file is out of order."); } }