Update Picard / sam-jdk at Tim's request.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4925 348d0f76-0448-11de-a6fe-93d51630548a

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.*;
 
@@ -133,8 +135,13 @@ public class UnifiedGenotyperEngine {
 
         filter.add(LOW_QUAL_FILTER_NAME);
 
+        try {
             referenceReader = new CachingIndexedFastaSequenceFile(toolkit.getArguments().referenceFile);
         }
+        catch(FileNotFoundException ex) {
+            throw new UserException.CouldNotReadInputFile(toolkit.getArguments().referenceFile,ex);
+        }
+    }
 
     /**
      * Compute full calls at a given locus.

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.*;
@@ -217,7 +218,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         if ( MISMATCH_THRESHOLD <= 0.0 || MISMATCH_THRESHOLD > 1.0 )
             throw new RuntimeException("Entropy threshold must be a fraction between 0 and 1");
 
+        try {
             referenceReader = new CachingIndexedFastaSequenceFile(getToolkit().getArguments().referenceFile);
+        }
+        catch(FileNotFoundException ex) {
+            throw new UserException.CouldNotReadInputFile(getToolkit().getArguments().referenceFile,ex);
+        }
         
         if ( !TARGET_NOT_SORTED ) {
 

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;
+        try {
             this.referenceFileForMNPmerging = new CachingIndexedFastaSequenceFile(referenceFile);
+        }
+        catch(FileNotFoundException ex) {
+            throw new UserException.CouldNotReadInputFile(referenceFile,ex);
+        }        
         this.vcMergeRule = vcMergeRule;
         this.alleleMergeRule = alleleMergeRule;
         this.useSingleSample = singleSample;

java/src/org/broadinstitute/sting/playground/tools/RemapAlignments.java

@@ -116,7 +116,7 @@ public class RemapAlignments extends CommandLineProgram {
 		
 		SAMFileHeader h = new SAMFileHeader();
 		
-		for ( Entry<String, Object> attr : oldHeader.getAttributes() ) h.setAttribute(attr.getKey(), attr.getValue());
+		for ( Entry<String, String> attr : oldHeader.getAttributes() ) h.setAttribute(attr.getKey(), attr.getValue());
 		h.setGroupOrder(oldHeader.getGroupOrder());
 		h.setProgramRecords(oldHeader.getProgramRecords());
 		h.setReadGroups(oldHeader.getReadGroups());

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);
     }

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<String, Object> e : toCopy.getAttributes())
+        for (Map.Entry<String, String> e : toCopy.getAttributes())
             copy.setAttribute(e.getKey(), e.getValue());
 
         return copy;

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);
     }

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() {
+        try {
             ref = new CachingIndexedFastaSequenceFile(refFile);
+        }
+        catch(FileNotFoundException ex) {
+            throw new UserException.CouldNotReadInputFile(refFile,ex);
+        }
         genomeLocParser = new GenomeLocParser(ref);
 
         engine = new GenomeAnalysisEngine();

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 {

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);
     }
 

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 caching, uncached;
-        IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta);
+        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, uncached;
-        IndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, cacheSize);
+        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);
 

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);
 
     }

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;
@@ -40,9 +41,15 @@ public class VCFWriterUnitTest extends BaseTest {
 
     @BeforeClass
     public void beforeTests() {
-        IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(hg18Reference));
+        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 */
     @Test

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;
@@ -28,9 +29,14 @@ public class IntervalUtilsUnitTest extends BaseTest {
 
     @BeforeClass
     public void init() {
+        try {
             ReferenceSequenceFile seq = new CachingIndexedFastaSequenceFile(reference);
             genomeLocParser = new GenomeLocParser(seq);
         }
+        catch(FileNotFoundException ex) {
+            throw new UserException.CouldNotReadInputFile(reference,ex);
+        }
+    }
 
     @Test(expectedExceptions=UserException.class)
     public void testMergeListsBySetOperatorNoOverlap() {

settings/repository/edu.mit.broad/picard-private-parts-1702.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1562" status="integration" publication="20100902110200" />
+    <info organisation="edu.mit.broad" module="picard-private-parts" revision="1702" status="integration" publication="20110102175300" />
 </ivy-module>

settings/repository/net.sf/picard-1.29.571.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="picard" revision="1.29.571" status="release" />
-</ivy-module>

settings/repository/net.sf/picard-1.37.686.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="picard" revision="1.37.686" status="release" />
+</ivy-module>

settings/repository/net.sf/sam-1.29.571.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="net.sf" module="sam" revision="1.29.571" status="release" />
-</ivy-module>

settings/repository/net.sf/sam-1.37.686.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="net.sf" module="sam" revision="1.37.686" status="release" />
+</ivy-module>