diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java index 39dc944f9..6869cd1cb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java @@ -39,6 +39,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper; import org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotatorEngine; 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.*; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; @@ -47,6 +48,7 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecordFilter; import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broad.tribble.vcf.VCFConstants; +import java.io.FileNotFoundException; import java.io.PrintStream; import java.util.*; @@ -133,7 +135,12 @@ public class UnifiedGenotyperEngine { filter.add(LOW_QUAL_FILTER_NAME); - referenceReader = new CachingIndexedFastaSequenceFile(toolkit.getArguments().referenceFile); + try { + referenceReader = new CachingIndexedFastaSequenceFile(toolkit.getArguments().referenceFile); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(toolkit.getArguments().referenceFile,ex); + } } /** 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 899288762..091831c82 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -58,6 +58,7 @@ import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.collections.Pair; import java.io.File; +import java.io.FileNotFoundException; import java.io.FileWriter; import java.io.IOException; import java.util.*; @@ -217,8 +218,13 @@ public class IndelRealigner extends ReadWalker { if ( MISMATCH_THRESHOLD <= 0.0 || MISMATCH_THRESHOLD > 1.0 ) throw new RuntimeException("Entropy threshold must be a fraction between 0 and 1"); - referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile); - + try { + referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile,ex); + } + if ( !TARGET_NOT_SORTED ) { NwayIntervalMergingIterator merger = new NwayIntervalMergingIterator(IntervalMergingRule.OVERLAPPING_ONLY); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java index 981b89355..8acece2ed 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java @@ -35,10 +35,12 @@ import org.broad.tribble.vcf.VCFWriter; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.MathUtils; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import java.io.File; +import java.io.FileNotFoundException; import java.util.*; // Streams in VariantContext objects and streams out VariantContexts produced by merging phased segregating polymorphisms into MNP VariantContexts @@ -73,7 +75,12 @@ public class MergeSegregatingAlternateAllelesVCFWriter implements VCFWriter { public MergeSegregatingAlternateAllelesVCFWriter(VCFWriter innerWriter, GenomeLocParser genomeLocParser, File referenceFile, VariantContextMergeRule vcMergeRule, VariantContextUtils.AlleleMergeRule alleleMergeRule, String singleSample, boolean emitOnlyMergedRecords, Logger logger, boolean takeOwnershipOfInner, boolean trackAltAlleleStats) { this.innerWriter = innerWriter; this.genomeLocParser = genomeLocParser; - this.referenceFileForMNPmerging = new CachingIndexedFastaSequenceFile(referenceFile); + try { + this.referenceFileForMNPmerging = new CachingIndexedFastaSequenceFile(referenceFile); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(referenceFile,ex); + } this.vcMergeRule = vcMergeRule; this.alleleMergeRule = alleleMergeRule; this.useSingleSample = singleSample; diff --git a/java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java b/java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java index d16c50fac..631c69b8c 100644 --- a/java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java +++ b/java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java @@ -116,7 +116,7 @@ public class RemapAlignments extends CommandLineProgram { SAMFileHeader h = new SAMFileHeader(); - for ( Entry attr : oldHeader.getAttributes() ) h.setAttribute(attr.getKey(), attr.getValue()); + for ( Entry attr : oldHeader.getAttributes() ) h.setAttribute(attr.getKey(), attr.getValue()); h.setGroupOrder(oldHeader.getGroupOrder()); h.setProgramRecords(oldHeader.getProgramRecords()); h.setReadGroups(oldHeader.getReadGroups()); diff --git a/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java b/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java index 9b2550bfd..bda52dd4e 100644 --- a/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java +++ b/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java @@ -29,6 +29,7 @@ import net.sf.picard.reference.*; import net.sf.samtools.SAMSequenceRecord; import java.io.File; +import java.io.FileNotFoundException; import java.util.Arrays; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -111,11 +112,11 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile { * Open the given indexed fasta sequence file. Throw an exception if the file cannot be opened. * @param file The file to open. */ - public CachingIndexedFastaSequenceFile(final File file) { + public CachingIndexedFastaSequenceFile(final File file) throws FileNotFoundException { this(file, DEFAULT_CACHE_SIZE); } - public CachingIndexedFastaSequenceFile(final File file, long cacheSize ) { + public CachingIndexedFastaSequenceFile(final File file, long cacheSize ) throws FileNotFoundException { super(file); setCacheSize(cacheSize); } diff --git a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index a48369bae..d689af645 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -50,7 +50,7 @@ public class ReadUtils { copy.setReadGroups(toCopy.getReadGroups()); copy.setSequenceDictionary(toCopy.getSequenceDictionary()); - for (Map.Entry e : toCopy.getAttributes()) + for (Map.Entry e : toCopy.getAttributes()) copy.setAttribute(e.getKey(), e.getValue()); return copy; diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java index 461042713..50c52cd99 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilderUnitTest.java @@ -30,6 +30,7 @@ import org.broad.tribble.Tribble; import org.broad.tribble.index.Index; import org.broad.tribble.vcf.VCFCodec; import org.broadinstitute.sting.gatk.arguments.ValidationExclusion; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLocParser; @@ -59,7 +60,13 @@ public class RMDTrackBuilderUnitTest extends BaseTest { @BeforeMethod public void setup() { - seq = new CachingIndexedFastaSequenceFile(new File(b36KGReference)); + File referenceFile = new File(b36KGReference); + try { + seq = new CachingIndexedFastaSequenceFile(referenceFile); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(referenceFile,ex); + } genomeLocParser = new GenomeLocParser(seq); builder = new RMDTrackBuilder(seq.getSequenceDictionary(),genomeLocParser,null); } diff --git a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java index a56fc146a..72c9fd76c 100755 --- a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsUnitTest.java @@ -15,6 +15,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID; import org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.utils.GenomeLocParser; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile; import static org.testng.Assert.fail; @@ -74,7 +75,12 @@ public class TraverseReadsUnitTest extends BaseTest { @BeforeClass public void doOnce() { - ref = new CachingIndexedFastaSequenceFile(refFile); + try { + ref = new CachingIndexedFastaSequenceFile(refFile); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(refFile,ex); + } genomeLocParser = new GenomeLocParser(ref); engine = new GenomeAnalysisEngine(); diff --git a/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java b/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java index 177797c07..08be4f742 100644 --- a/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/baq/BAQUnitTest.java @@ -5,6 +5,7 @@ package org.broadinstitute.sting.utils.baq; // the imports for unit testing. +import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.testng.annotations.Test; import org.testng.annotations.DataProvider; @@ -17,6 +18,7 @@ import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.Utils; import java.io.File; +import java.io.FileNotFoundException; import java.util.Arrays; import java.util.List; import java.util.ArrayList; @@ -38,7 +40,13 @@ public class BAQUnitTest extends BaseTest { @BeforeMethod public void before() { header = ArtificialSAMUtils.createArtificialSamHeader(numChr, startChr, chrSize); - fasta = new IndexedFastaSequenceFile(new File(hg18Reference)); + File referenceFile = new File(hg18Reference); + try { + fasta = new IndexedFastaSequenceFile(referenceFile); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(referenceFile,ex); + } } private class BAQTest { diff --git a/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java b/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java index 3167e41c7..e592c99b9 100644 --- a/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.utils.bed; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLocParser; @@ -10,6 +11,7 @@ import org.testng.annotations.Test; import java.io.File; +import java.io.FileNotFoundException; import java.util.List; import net.sf.picard.reference.IndexedFastaSequenceFile; @@ -23,7 +25,14 @@ public class BedParserUnitTest extends BaseTest { @BeforeClass public void beforeTests() { - seq = new CachingIndexedFastaSequenceFile(new File(b36KGReference)); + File referenceFile = new File(b36KGReference); + try { + seq = new CachingIndexedFastaSequenceFile(referenceFile); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(referenceFile,ex); + } + genomeLocParser = new GenomeLocParser(seq); } diff --git a/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java b/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java index 1fbe745aa..a60f1b0fe 100644 --- a/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java @@ -5,6 +5,7 @@ package org.broadinstitute.sting.utils.fasta; // the imports for unit testing. +import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.testng.annotations.Test; import org.testng.annotations.DataProvider; @@ -13,6 +14,7 @@ import org.testng.annotations.BeforeMethod; import org.broadinstitute.sting.BaseTest; import java.io.File; +import java.io.FileNotFoundException; import java.util.Arrays; import java.util.List; import java.util.ArrayList; @@ -53,8 +55,14 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest { @Test(dataProvider = "fastas", enabled = true) public void testCachingIndexedFastaReaderSequential1(File fasta, int cacheSize, int querySize) { - IndexedFastaSequenceFile caching = cacheSize == -1 ? new CachingIndexedFastaSequenceFile(fasta) : new CachingIndexedFastaSequenceFile(fasta, cacheSize); - IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta); + IndexedFastaSequenceFile caching, uncached; + try { + caching = cacheSize == -1 ? new CachingIndexedFastaSequenceFile(fasta) : new CachingIndexedFastaSequenceFile(fasta, cacheSize); + uncached = new IndexedFastaSequenceFile(fasta); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(fasta,ex); + } SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0); logger.warn(String.format("Checking contig %s length %d with cache size %d and query size %d", @@ -76,8 +84,14 @@ public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest { // Tests grabbing sequences around a middle cached value. @Test(dataProvider = "fastas", enabled = true) public void testCachingIndexedFastaReaderTwoStage(File fasta, int cacheSize, int querySize) { - IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta); - IndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, cacheSize); + IndexedFastaSequenceFile caching, uncached; + try { + uncached = new IndexedFastaSequenceFile(fasta); + caching = new CachingIndexedFastaSequenceFile(fasta, cacheSize); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(fasta,ex); + } SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0); diff --git a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java index 36c0336d8..d0b5158e9 100755 --- a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java @@ -1,5 +1,6 @@ package org.broadinstitute.sting.utils.genotype.glf; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.GenomeLoc; @@ -13,6 +14,7 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; import java.io.File; +import java.io.FileNotFoundException; import net.sf.samtools.SAMSequenceRecord; import net.sf.picard.reference.IndexedFastaSequenceFile; @@ -69,7 +71,13 @@ public class GLFWriterUnitTest extends BaseTest { @BeforeClass public void beforeTests() { - seq = new CachingIndexedFastaSequenceFile(new File(b36KGReference)); + File referenceFile = new File(b36KGReference); + try { + seq = new CachingIndexedFastaSequenceFile(referenceFile); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(referenceFile,ex); + } genomeLocParser = new GenomeLocParser(seq); } 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 61e31825c..3552af037 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java @@ -6,6 +6,7 @@ import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.vcf.*; +import org.broadinstitute.sting.utils.exceptions.UserException; import org.testng.Assert; import org.broadinstitute.sting.BaseTest; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; @@ -40,8 +41,14 @@ public class VCFWriterUnitTest extends BaseTest { @BeforeClass public void beforeTests() { - IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference)); - genomeLocParser = new GenomeLocParser(seq); + File referenceFile = new File(hg18Reference); + try { + IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(referenceFile); + genomeLocParser = new GenomeLocParser(seq); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(referenceFile,ex); + } } /** test, using the writer and reader, that we can output and input a VCF file without problems */ diff --git a/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java b/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java index dc170a4d7..8e7eb6c89 100644 --- a/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/interval/IntervalUtilsUnitTest.java @@ -13,6 +13,7 @@ import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; import java.io.File; +import java.io.FileNotFoundException; import java.io.IOException; import java.util.ArrayList; import java.util.Arrays; @@ -28,8 +29,13 @@ public class IntervalUtilsUnitTest extends BaseTest { @BeforeClass public void init() { - ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(reference); - genomeLocParser = new GenomeLocParser(seq); + try { + ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(reference); + genomeLocParser = new GenomeLocParser(seq); + } + catch(FileNotFoundException ex) { + throw new UserException.CouldNotReadInputFile(reference,ex); + } } @Test(expectedExceptions=UserException.class) diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1562.jar b/settings/repository/edu.mit.broad/picard-private-parts-1702.jar similarity index 53% rename from settings/repository/edu.mit.broad/picard-private-parts-1562.jar rename to settings/repository/edu.mit.broad/picard-private-parts-1702.jar index 25c7e8ae6..1f8a5c047 100644 Binary files a/settings/repository/edu.mit.broad/picard-private-parts-1562.jar and b/settings/repository/edu.mit.broad/picard-private-parts-1702.jar differ diff --git a/settings/repository/edu.mit.broad/picard-private-parts-1562.xml b/settings/repository/edu.mit.broad/picard-private-parts-1702.xml similarity index 58% rename from settings/repository/edu.mit.broad/picard-private-parts-1562.xml rename to settings/repository/edu.mit.broad/picard-private-parts-1702.xml index 81a03fd6f..87daf0c38 100644 --- a/settings/repository/edu.mit.broad/picard-private-parts-1562.xml +++ b/settings/repository/edu.mit.broad/picard-private-parts-1702.xml @@ -1,3 +1,3 @@ - + diff --git a/settings/repository/net.sf/picard-1.29.571.xml b/settings/repository/net.sf/picard-1.29.571.xml deleted file mode 100644 index fd00ca0c2..000000000 --- a/settings/repository/net.sf/picard-1.29.571.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/picard-1.29.571.jar b/settings/repository/net.sf/picard-1.37.686.jar similarity index 59% rename from settings/repository/net.sf/picard-1.29.571.jar rename to settings/repository/net.sf/picard-1.37.686.jar index 32350c90e..7ae927cb2 100644 Binary files a/settings/repository/net.sf/picard-1.29.571.jar and b/settings/repository/net.sf/picard-1.37.686.jar differ diff --git a/settings/repository/net.sf/picard-1.37.686.xml b/settings/repository/net.sf/picard-1.37.686.xml new file mode 100644 index 000000000..174345540 --- /dev/null +++ b/settings/repository/net.sf/picard-1.37.686.xml @@ -0,0 +1,3 @@ + + + diff --git a/settings/repository/net.sf/sam-1.29.571.xml b/settings/repository/net.sf/sam-1.29.571.xml deleted file mode 100644 index adee85dfa..000000000 --- a/settings/repository/net.sf/sam-1.29.571.xml +++ /dev/null @@ -1,3 +0,0 @@ - - - diff --git a/settings/repository/net.sf/sam-1.29.571.jar b/settings/repository/net.sf/sam-1.37.686.jar similarity index 76% rename from settings/repository/net.sf/sam-1.29.571.jar rename to settings/repository/net.sf/sam-1.37.686.jar index f75d0ed17..44a4ac383 100644 Binary files a/settings/repository/net.sf/sam-1.29.571.jar and b/settings/repository/net.sf/sam-1.37.686.jar differ diff --git a/settings/repository/net.sf/sam-1.37.686.xml b/settings/repository/net.sf/sam-1.37.686.xml new file mode 100644 index 000000000..df9147198 --- /dev/null +++ b/settings/repository/net.sf/sam-1.37.686.xml @@ -0,0 +1,3 @@ + + +