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gatk-3.8
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Moved fasta support files into their own package. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@408 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-04-14 18:13:23 +00:00
parent 7a4a5a17c0
commit 0629f79049
15 changed files with 17 additions and 15 deletions
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2
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisTK.java
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@ -21,10 +21,10 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.traversals.*;
import org.broadinstitute.sting.gatk.executive.MicroManager;
import org.broadinstitute.sting.utils.FastaSequenceFile2;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import java.io.File;
import java.io.PrintStream;

2
java/src/org/broadinstitute/sting/gatk/dataSources/ReadDataSource.java
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@ -8,7 +8,7 @@ import java.io.File;
import org.broadinstitute.sting.gatk.iterators.VerifyingSamIterator;
import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
import org.broadinstitute.sting.utils.FastaSequenceFile2;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
/**
* User: aaron

2
java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/ReferenceDataSource.java
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@ -2,8 +2,8 @@ package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
import org.broadinstitute.sting.gatk.iterators.BoundedReferenceIterator;
import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
import org.broadinstitute.sting.utils.FastaSequenceFile2;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import java.io.File;

2
java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.executive;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.FastaSequenceFile2;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.gatk.walkers.LocusWalker;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;

2
java/src/org/broadinstitute/sting/gatk/iterators/BoundedReferenceIterator.java
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@ -1,7 +1,7 @@
package org.broadinstitute.sting.gatk.iterators;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.FastaSequenceFile2;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import java.util.Iterator;

2
java/src/org/broadinstitute/sting/gatk/iterators/ReferenceIterator.java
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@ -4,8 +4,8 @@ import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.samtools.util.RuntimeIOException;
import net.sf.samtools.util.StringUtil;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.FastaSequenceFile2;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import java.util.Iterator;
import java.util.NoSuchElementException;

1
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -17,6 +17,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.Walker;
import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import java.io.*;
import java.util.*;

2
java/src/org/broadinstitute/sting/gatk/traversals/TraverseByReads.java
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@ -8,7 +8,7 @@ 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.FastaSequenceFile2;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import java.util.List;
import java.util.Arrays;

4
java/src/org/broadinstitute/sting/utils/FastaSequenceFile2.java → java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils;
package org.broadinstitute.sting.utils.fasta;
import edu.mit.broad.picard.PicardException;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
@ -469,4 +469,4 @@ public class FastaSequenceFile2 implements ReferenceSequenceFile {
public String toString() {
return this.file.getAbsolutePath();
}
}
}

4
java/src/org/broadinstitute/sting/utils/FastaSequenceIndex.java → java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils;
package org.broadinstitute.sting.utils.fasta;
import edu.mit.broad.picard.PicardException;
@ -145,4 +145,4 @@ class FastaSequenceIndexEntry {
basesPerLine,
bytesPerLine );
}
}
}

2
java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java
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@ -5,8 +5,8 @@ import static junit.framework.Assert.fail;
import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.FastaSequenceFile2;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import org.junit.*;
import java.io.File;

2
java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
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@ -7,8 +7,8 @@ import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory;
import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2;
import org.broadinstitute.sting.utils.FastaSequenceFile2;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;

1
java/test/org/broadinstitute/sting/utils/GenomeLocTest.java
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@ -8,6 +8,7 @@ import org.junit.*;
import static org.junit.Assert.*;
import org.apache.commons.cli.ParseException;
import org.broadinstitute.sting.utils.cmdLine.ArgumentParser;
import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
import java.util.ArrayList;
import java.io.File;

2
java/test/org/broadinstitute/sting/utils/FastaSequenceFile2Test.java → java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceFile2Test.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils;
package org.broadinstitute.sting.utils.fasta;
import edu.mit.broad.picard.reference.ReferenceSequence;
import net.sf.samtools.util.StringUtil;

2
java/test/org/broadinstitute/sting/utils/FastaSequenceIndexTest.java → java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils;
package org.broadinstitute.sting.utils.fasta;
import org.junit.BeforeClass;
import org.junit.Before;