diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java index 131d40bd6..0b73700fe 100644 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java @@ -8,6 +8,7 @@ import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.util.RuntimeIOException; import org.apache.log4j.Logger; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; +import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.rodDbSNP; import org.broadinstitute.sting.gatk.refdata.rodGFF; import org.broadinstitute.sting.gatk.refdata.HapMapAlleleFrequenciesROD; @@ -155,26 +156,24 @@ public class GenomeAnalysisTK extends CommandLineProgram { protected int execute() { final boolean TEST_ROD = false; - List rods = new ArrayList(); - - + List > rods = new ArrayList >(); if ( TEST_ROD ) { - ReferenceOrderedData gff = new ReferenceOrderedData(new File("trunk/data/gFFTest.gff"), rodGFF.class ); + ReferenceOrderedData gff = new ReferenceOrderedData(new File("trunk/data/gFFTest.gff"), rodGFF.class ); gff.testMe(); //ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("trunk/data/dbSNP_head.txt"), rodDbSNP.class ); - ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class ); + ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File("/Volumes/Users/mdepristo/broad/ATK/exampleSAMs/dbSNP_chr20.txt"), rodDbSNP.class ); //dbsnp.testMe(); rods.add(dbsnp); // { gff, dbsnp }; } else { if ( DBSNP_FILE != null ) { - ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File(DBSNP_FILE), rodDbSNP.class ); + ReferenceOrderedData dbsnp = new ReferenceOrderedData(new File(DBSNP_FILE), rodDbSNP.class ); //dbsnp.testMe(); rods.add(dbsnp); // { gff, dbsnp }; } if ( HAPMAP_FILE != null ) { - ReferenceOrderedData hapmap = new ReferenceOrderedData(new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class ); + ReferenceOrderedData hapmap = new ReferenceOrderedData(new File(HAPMAP_FILE), HapMapAlleleFrequenciesROD.class ); //dbsnp.testMe(); rods.add(hapmap); // { gff, dbsnp }; } @@ -182,7 +181,7 @@ public class GenomeAnalysisTK extends CommandLineProgram { initializeOutputStreams(); - Walker my_walker = null; + Walker my_walker = null; try { my_walker = walkerManager.createWalkerByName( Analysis_Name ); } diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index 65bd27e08..4fca25941 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -30,10 +30,10 @@ import java.util.*; public abstract class TraversalEngine { // list of reference ordered data objects - protected List rods = null; + protected List> rods = null; // Iterator over rods - List rodIters; + List.RODIterator> rodIters; // How strict should we be with SAM/BAM parsing? protected ValidationStringency strictness = ValidationStringency.STRICT; @@ -112,7 +112,7 @@ public abstract class TraversalEngine { * @param ref Reference file in FASTA format, assumes a .dict file is also available * @param rods Array of reference ordered data sets */ - public TraversalEngine(File reads, File ref, List rods) { + public TraversalEngine(File reads, File ref, List> rods) { readsFile = reads; refFileName = ref; this.rods = rods; @@ -411,10 +411,10 @@ public abstract class TraversalEngine { * * @return A list of ROD iterators for getting data from each ROD */ - protected List initializeRODs() { + protected List.RODIterator> initializeRODs() { // set up reference ordered data - rodIters = new ArrayList(); - for (ReferenceOrderedData data : rods) { + rodIters = new ArrayList.RODIterator>(); + for (ReferenceOrderedData data : rods) { rodIters.add(data.iterator()); } return rodIters; @@ -459,10 +459,10 @@ public abstract class TraversalEngine { * @param loc The location to get the rods at * @return A list of ReferenceOrderDatum at loc. ROD without a datum at loc will be null in the list */ - protected List getReferenceOrderedDataAtLocus(List rodIters, + protected List getReferenceOrderedDataAtLocus(List.RODIterator> rodIters, final GenomeLoc loc) { List data = new ArrayList(); - for (ReferenceOrderedData.RODIterator iter : rodIters) { + for (ReferenceOrderedData.RODIterator iter : rodIters) { data.add(iter.seekForward(loc)); } return data; diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java index 821c254f6..5b248ee9e 100644 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLoci.java @@ -31,14 +31,13 @@ import edu.mit.broad.picard.filter.FilteringIterator; */ public class TraverseByLoci extends TraversalEngine { - public TraverseByLoci(File reads, File ref, List rods) { + public TraverseByLoci(File reads, File ref, List> rods) { super(reads, ref, rods); } public T traverse(Walker walker, ArrayList locations) { if ( walker instanceof LocusWalker ) { - Walker x = walker; - LocusWalker locusWalker = (LocusWalker)x; + LocusWalker locusWalker = (LocusWalker)walker; return (T)this.traverseByLoci(locusWalker, locations); } else { throw new IllegalArgumentException("Walker isn't a loci walker!"); diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java index 324398eb3..dcd107957 100644 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLociByReference.java @@ -29,7 +29,7 @@ import edu.mit.broad.picard.filter.FilteringIterator; */ public class TraverseByLociByReference extends TraverseByLoci { - public TraverseByLociByReference(File reads, File ref, List rods) { + public TraverseByLociByReference(File reads, File ref, List> rods) { super(reads, ref, rods); } diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java index 639ad5407..8d09619c8 100644 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java @@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker; import org.broadinstitute.sting.gatk.walkers.Walker; import org.broadinstitute.sting.gatk.LocusContext; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData; +import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.iterators.ReferenceIterator; import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.Utils; @@ -26,7 +27,7 @@ import net.sf.samtools.SAMRecord; */ public class TraverseByReads extends TraversalEngine { - public TraverseByReads(File reads, File ref, List rods) { + public TraverseByReads(File reads, File ref, List> rods) { super(reads, ref, rods); } diff --git a/java/src/org/broadinstitute/sting/playground/ValidateSAM.java b/java/src/org/broadinstitute/sting/playground/ValidateSAM.java index 4d4344358..1f9230f02 100755 --- a/java/src/org/broadinstitute/sting/playground/ValidateSAM.java +++ b/java/src/org/broadinstitute/sting/playground/ValidateSAM.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.playground; +package org.broadinstitute.sting.playground; import net.sf.samtools.*; import net.sf.samtools.SAMFileReader.ValidationStringency; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java b/java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java index bf0aca249..2c1dc9e18 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java @@ -24,8 +24,8 @@ public class PrepareROD extends CommandLineProgram { @Option(shortName="RODNAME", doc="Name of the data") public String ROD_NAME = null; @Option(shortName="RODTYPE", doc="Referenced Ordered Data type") public String ROD_TYPE = null; - public static HashMap Types = new HashMap(); - public static void addModule(final String name, final Class rodType) { + public static HashMap> Types = new HashMap>(); + public static void addModule(final String name, final Class rodType) { System.out.printf("* Adding rod class %s%n", name); Types.put(name.toLowerCase(), rodType); } @@ -47,9 +47,9 @@ public class PrepareROD extends CommandLineProgram { final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG); GenomeLoc.setupRefContigOrdering(refFile); - Class rodClass = Types.get(ROD_TYPE.toLowerCase()); + Class rodClass = Types.get(ROD_TYPE.toLowerCase()); - ReferenceOrderedData rod = new ReferenceOrderedData(new File(ROD_FILE), rodClass ); + ReferenceOrderedData rod = new ReferenceOrderedData(new File(ROD_FILE), rodClass ); try { rod.validateFile(); } catch ( Exception e ) {