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a rename for consistancy of Sam to SAM, creating a genotype utils dir, and moving the GLF code into it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@984 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-06-11 17:46:06 +00:00
parent 599ceeddd8
commit 195b4ea7b4
23 changed files with 92 additions and 65 deletions
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39
java/src/org/broadinstitute/sting/utils/genotype/Genotype.java 100644
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@ -0,0 +1,39 @@
package org.broadinstitute.sting.utils.genotype;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
/**
*
* @author aaron
*
* Class Genotype
*
* The interface for making genotype calls.
*/
public interface Genotype {
}

2
java/src/org/broadinstitute/sting/utils/glf/GLFRecord.java → java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java 100644 → 100755
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils.glf;
package org.broadinstitute.sting.utils.genotype.glf;
import net.sf.samtools.util.BinaryCodec;

4
java/src/org/broadinstitute/sting/utils/glf/GLFWriter.java → java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java
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@ -1,10 +1,8 @@
package org.broadinstitute.sting.utils.glf;
package org.broadinstitute.sting.utils.genotype.glf;
import net.sf.samtools.util.BinaryCodec;
import net.sf.samtools.util.BlockCompressedOutputStream;
import java.util.ArrayList;
import java.util.List;
import java.io.File;
import java.io.DataOutputStream;

2
java/src/org/broadinstitute/sting/utils/glf/LikelihoodObject.java → java/src/org/broadinstitute/sting/utils/genotype/glf/LikelihoodObject.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils.glf;
package org.broadinstitute.sting.utils.genotype.glf;
import java.util.HashMap;

2
java/src/org/broadinstitute/sting/utils/glf/SinglePointCall.java → java/src/org/broadinstitute/sting/utils/genotype/glf/SinglePointCall.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils.glf;
package org.broadinstitute.sting.utils.genotype.glf;
import net.sf.samtools.util.BinaryCodec;

2
java/src/org/broadinstitute/sting/utils/glf/VariableLengthCall.java → java/src/org/broadinstitute/sting/utils/genotype/glf/VariableLengthCall.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils.glf;
package org.broadinstitute.sting.utils.genotype.glf;
import net.sf.samtools.util.BinaryCodec;

6
java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java
View File

@ -113,7 +113,7 @@ public class ArtificialPatternedSAMIterator extends ArtificialSAMIterator {
return false;
} else {
++totalReadCount;
this.next = ArtificialSamUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), -1, -1, 50);
this.next = ArtificialSAMUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), -1, -1, 50);
--uMappedReadCount;
return true;
}
@ -135,9 +135,9 @@ public class ArtificialPatternedSAMIterator extends ArtificialSAMIterator {
*/
private SAMRecord getNextRecord( int read ) {
if (read > this.readCount) {
return ArtificialSamUtils.createArtificialRead(this.header, String.valueOf(reads[readCount - 1]), currentChromo, reads[readCount - 1], 50);
return ArtificialSAMUtils.createArtificialRead(this.header, String.valueOf(reads[readCount - 1]), currentChromo, reads[readCount - 1], 50);
}
return ArtificialSamUtils.createArtificialRead(this.header, String.valueOf(reads[read]), currentChromo, reads[read], 50);
return ArtificialSAMUtils.createArtificialRead(this.header, String.valueOf(reads[read]), currentChromo, reads[read], 50);
}
}

7
java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java
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@ -7,11 +7,8 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.apache.log4j.Logger;
import java.util.Arrays;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileHeader;
@ -52,7 +49,7 @@ public class ArtificialReadsTraversal extends TraversalEngine {
public int endingChr = 5;
public int readsPerChr = 100;
public int unMappedReads = 1000;
private int DEFAULT_READ_LENGTH = ArtificialSamUtils.DEFAULT_READ_LENGTH;
private int DEFAULT_READ_LENGTH = ArtificialSAMUtils.DEFAULT_READ_LENGTH;
private ArtificialPatternedSAMIterator iter;
/** our log, which we want to capture anything from this class */
protected static Logger logger = Logger.getLogger(ArtificialReadsTraversal.class);
@ -96,7 +93,7 @@ public class ArtificialReadsTraversal extends TraversalEngine {
throw new IllegalArgumentException("Walker isn't a read walker!");
ReadWalker<M, T> readWalker = (ReadWalker<M, T>) walker;
SAMFileHeader header = ArtificialSamUtils.createArtificialSamHeader(( endingChr - startingChr ) + 1, startingChr, readsPerChr + DEFAULT_READ_LENGTH);
SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(( endingChr - startingChr ) + 1, startingChr, readsPerChr + DEFAULT_READ_LENGTH);
iter = new ArtificialPatternedSAMIterator(this.startingChr,
this.endingChr,
this.readsPerChr,

4
java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java
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@ -121,13 +121,13 @@ public class ArtificialSAMIterator implements PeekingStingIterator {
return false;
} else {
++totalReadCount;
this.next = ArtificialSamUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), -1, -1, 50);
this.next = ArtificialSAMUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), -1, -1, 50);
--uMappedReadCount;
return true;
}
}
++totalReadCount;
this.next = ArtificialSamUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), currentChromo, currentRead, 50);
this.next = ArtificialSAMUtils.createArtificialRead(this.header, String.valueOf(totalReadCount), currentChromo, currentRead, 50);
++currentRead;
return true;
}

2
java/src/org/broadinstitute/sting/utils/sam/ArtificialSamUtils.java → java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
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@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.Reads;
* @author aaron
* @version 1.0
*/
public class ArtificialSamUtils {
public class ArtificialSAMUtils {
public static final int DEFAULT_READ_LENGTH = 50;
/**

4
java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategyTest.java
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@ -7,7 +7,7 @@ import static org.junit.Assert.assertTrue;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.sam.ArtificialSamUtils;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.BaseTest;
import net.sf.samtools.SAMFileHeader;
@ -53,7 +53,7 @@ import net.sf.samtools.SAMFileHeader;
public class IntervalShardStrategyTest extends BaseTest {
private GenomeLocSortedSet mSortedSet = null;
private SAMFileHeader header = ArtificialSamUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private static final int NUMBER_OF_CHROMOSOMES = 5;
private static final int STARTING_CHROMOSOME = 1;
private static final int CHROMOSOME_SIZE = 1000;

4
java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardTest.java
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@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.dataSources.shards;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.sam.ArtificialSamUtils;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.junit.Before;
import org.junit.Test;
import static org.junit.Assert.assertTrue;
@ -44,7 +44,7 @@ import net.sf.samtools.SAMFileHeader;
public class IntervalShardTest extends BaseTest {
private IntervalShard intervalShard = null;
private SAMFileHeader header = ArtificialSamUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private static final int NUMBER_OF_CHROMOSOMES = 5;
private static final int STARTING_CHROMOSOME = 1;
private static final int CHROMOSOME_SIZE = 1000;

5
java/test/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategyTest.java
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@ -2,13 +2,12 @@ package org.broadinstitute.sting.gatk.dataSources.shards;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.sam.ArtificialSamUtils;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.BaseTest;
import org.junit.Before;
import org.junit.Test;
import static org.junit.Assert.assertTrue;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceDictionary;
/*
@ -46,7 +45,7 @@ import net.sf.samtools.SAMSequenceDictionary;
public class LinearLocusShardStrategyTest extends BaseTest {
private GenomeLocSortedSet mSortedSet = null;
private SAMFileHeader header = ArtificialSamUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private static final int NUMBER_OF_CHROMOSOMES = 5;
private static final int STARTING_CHROMOSOME = 1;
private static final int CHROMOSOME_SIZE = 1000;

4
java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java
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@ -6,7 +6,7 @@ import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.sam.ArtificialSamUtils;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.junit.*;
import static org.junit.Assert.assertTrue;
@ -33,7 +33,7 @@ import static org.junit.Assert.assertTrue;
*/
public class ShardStrategyFactoryTest extends BaseTest {
private SAMFileHeader header = ArtificialSamUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private static final int NUMBER_OF_CHROMOSOMES = 5;
private static final int STARTING_CHROMOSOME = 1;
private static final int CHROMOSOME_SIZE = 1000;

10
java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java
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@ -1,10 +1,8 @@
package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
import static junit.framework.Assert.fail;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory;
@ -12,7 +10,7 @@ import org.broadinstitute.sting.gatk.iterators.BoundedReadIterator;
import org.broadinstitute.sting.gatk.iterators.*;
import org.broadinstitute.sting.gatk.Reads;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.sam.ArtificialSamUtils;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.ArtificialSAMQueryIterator;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@ -85,7 +83,7 @@ public class SAMByReadsTest extends BaseTest {
SAMDataSource data = new SAMDataSource(reads,true);
for (int x = 0; x < 10; x++) {
++iterations;
PeekingStingIterator iter = ArtificialSamUtils.unmappedReadIterator(1, 100, 10, 1000);
PeekingStingIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 10, 1000);
BoundedReadIterator ret = data.toUnmappedReads(100, iter);
// count the reads we've gotten back
if (ret == null) {
@ -223,13 +221,13 @@ class ArtificialResourcePool extends SAMIteratorPool {
public ArtificialResourcePool( int startingChr, int endingChr, int readCount, int readSize) {
super( new Reads(Collections.<File>emptyList()),true );
header = ArtificialSamUtils.createArtificialSamHeader(( endingChr - startingChr ) + 1, startingChr, readCount + readSize);
header = ArtificialSAMUtils.createArtificialSamHeader(( endingChr - startingChr ) + 1, startingChr, readCount + readSize);
}
@Override
public StingSAMIterator iterator( GenomeLoc loc ) {
ArtificialSAMQueryIterator iter = ArtificialSamUtils.queryReadIterator(1, 10, 100, 1000);
ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 10, 100, 1000);
if (loc != null) {
iter.queryContained(loc.getContig(), (int)loc.getStart(), (int)loc.getStop());
}

11
java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java
View File

@ -1,12 +1,11 @@
package org.broadinstitute.sting.gatk.walkers;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.executive.Accumulator;
import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
import org.broadinstitute.sting.gatk.dataSources.providers.ShardDataProvider;
import org.broadinstitute.sting.utils.sam.ArtificialReadsTraversal;
import org.broadinstitute.sting.utils.sam.ArtificialSAMFileWriter;
import org.broadinstitute.sting.utils.sam.ArtificialSamUtils;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.junit.Before;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
@ -85,8 +84,8 @@ public class PrintReadsWalkerTest extends BaseTest {
@Test
public void testReturnRead() {
PrintReadsWalker walker = new PrintReadsWalker();
SAMFileHeader head = ArtificialSamUtils.createArtificialSamHeader(3,1,1000);
SAMRecord rec = ArtificialSamUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
SAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
SAMRecord ret = walker.map(bases, rec);
assertTrue(ret == rec);
assertTrue(ret.getReadName().equals(rec.getReadName()));
@ -96,8 +95,8 @@ public class PrintReadsWalkerTest extends BaseTest {
@Test
public void testReducingRead() {
PrintReadsWalker walker = new PrintReadsWalker();
SAMFileHeader head = ArtificialSamUtils.createArtificialSamHeader(3,1,1000);
SAMRecord rec = ArtificialSamUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
SAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
ArtificialSAMFileWriter writer = new ArtificialSAMFileWriter();
SAMRecord ret = walker.map(bases, null);
walker.reduce(ret,writer);

4
java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetTest.java
View File

@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.sam.ArtificialSamUtils;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import static org.junit.Assert.assertTrue;
import org.junit.Before;
import org.junit.Test;
@ -37,7 +37,7 @@ import java.util.Iterator;
public class GenomeLocSortedSetTest extends BaseTest {
private GenomeLocSortedSet mSortedSet = null;
private SAMFileHeader header = ArtificialSamUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(NUMBER_OF_CHROMOSOMES, STARTING_CHROMOSOME, CHROMOSOME_SIZE);
private static final int NUMBER_OF_CHROMOSOMES = 5;
private static final int STARTING_CHROMOSOME = 1;
private static final int CHROMOSOME_SIZE = 1000;

8
java/test/org/broadinstitute/sting/utils/glf/GLFWriterTest.java → java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java
View File

@ -1,14 +1,12 @@
package org.broadinstitute.sting.utils.glf;
package org.broadinstitute.sting.utils.genotype.glf;
import org.junit.Test;
import org.junit.Before;
import org.broadinstitute.sting.BaseTest;
import net.sf.samtools.util.BinaryCodec;
import net.sf.samtools.util.BlockCompressedOutputStream;
import org.broadinstitute.sting.utils.genotype.glf.GLFWriter;
import org.broadinstitute.sting.utils.genotype.glf.LikelihoodObject;
import java.io.File;
import java.io.DataOutputStream;
import java.io.IOException;
/*

2
java/test/org/broadinstitute/sting/utils/glf/LikelihoodObjectTest.java → java/test/org/broadinstitute/sting/utils/genotype/glf/LikelihoodObjectTest.java
View File

@ -1,4 +1,4 @@
package org.broadinstitute.sting.utils.glf;
package org.broadinstitute.sting.utils.genotype.glf;
import org.junit.Before;
import org.junit.Test;

4
java/test/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorTest.java
View File

@ -51,12 +51,12 @@ public class ArtificialPatternedSAMIteratorTest extends BaseTest {
private int startingChr = 1;
private int endingChr = 2;
private int readCount = 100;
private int DEFAULT_READ_LENGTH = ArtificialSamUtils.DEFAULT_READ_LENGTH;
private int DEFAULT_READ_LENGTH = ArtificialSAMUtils.DEFAULT_READ_LENGTH;
SAMFileHeader header;
@Before
public void before() {
header = ArtificialSamUtils.createArtificialSamHeader(( endingChr - startingChr ) + 1, startingChr, readCount + DEFAULT_READ_LENGTH);
header = ArtificialSAMUtils.createArtificialSamHeader(( endingChr - startingChr ) + 1, startingChr, readCount + DEFAULT_READ_LENGTH);
}
@Test

6
java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterTest.java
View File

@ -56,13 +56,13 @@ public class ArtificialSAMFileWriterTest extends BaseTest {
@Before
public void before() {
writer = new ArtificialSAMFileWriter();
header = ArtificialSamUtils.createArtificialSamHeader(numChr, startChr, chrSize);
header = ArtificialSAMUtils.createArtificialSamHeader(numChr, startChr, chrSize);
}
@Test
public void testBasicCount() {
for (int x = 0; x < 100; x++) {
SAMRecord rec = ArtificialSamUtils.createArtificialRead(header, String.valueOf(x), 1, x, ArtificialSamUtils.DEFAULT_READ_LENGTH);
SAMRecord rec = ArtificialSAMUtils.createArtificialRead(header, String.valueOf(x), 1, x, ArtificialSAMUtils.DEFAULT_READ_LENGTH);
writer.addAlignment(rec);
}
assertEquals(100, writer.getRecords().size());
@ -75,7 +75,7 @@ public class ArtificialSAMFileWriterTest extends BaseTest {
for (int x = 0; x < 100; x++) {
names.add(String.valueOf(x));
SAMRecord rec = ArtificialSamUtils.createArtificialRead(header, String.valueOf(x), 1, x, ArtificialSamUtils.DEFAULT_READ_LENGTH);
SAMRecord rec = ArtificialSAMUtils.createArtificialRead(header, String.valueOf(x), 1, x, ArtificialSAMUtils.DEFAULT_READ_LENGTH);
writer.addAlignment(rec);
}
assertEquals(100, writer.getRecords().size());

13
java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorTest.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.utils.sam;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.iterators.PeekingStingIterator;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
import net.sf.samtools.SAMRecord;
@ -44,7 +43,7 @@ public class ArtificialSAMQueryIteratorTest extends BaseTest {
@Test
public void testWholeChromosomeQuery() {
ArtificialSAMQueryIterator iter = ArtificialSamUtils.queryReadIterator(1, 2, 100);
ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
iter.queryContained("chr1", 1, -1);
int count = 0;
while (iter.hasNext()) {
@ -57,7 +56,7 @@ public class ArtificialSAMQueryIteratorTest extends BaseTest {
@Test
public void testContainedQueryStart() {
ArtificialSAMQueryIterator iter = ArtificialSamUtils.queryReadIterator(1, 2, 100);
ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
iter.queryContained("chr1", 1, 50);
int count = 0;
while (iter.hasNext()) {
@ -70,7 +69,7 @@ public class ArtificialSAMQueryIteratorTest extends BaseTest {
@Test
public void testOverlappingQueryStart() {
ArtificialSAMQueryIterator iter = ArtificialSamUtils.queryReadIterator(1, 2, 100);
ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
iter.queryOverlapping("chr1", 1, 50);
int count = 0;
while (iter.hasNext()) {
@ -83,7 +82,7 @@ public class ArtificialSAMQueryIteratorTest extends BaseTest {
@Test
public void testContainedQueryMiddle() {
ArtificialSAMQueryIterator iter = ArtificialSamUtils.queryReadIterator(1, 2, 100);
ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
iter.queryContained("chr1", 25, 74);
int count = 0;
while (iter.hasNext()) {
@ -96,7 +95,7 @@ public class ArtificialSAMQueryIteratorTest extends BaseTest {
@Test
public void testOverlappingQueryMiddle() {
ArtificialSAMQueryIterator iter = ArtificialSamUtils.queryReadIterator(1, 2, 100);
ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
iter.queryOverlapping("chr1", 25, 74);
int count = 0;
while (iter.hasNext()) {
@ -109,7 +108,7 @@ public class ArtificialSAMQueryIteratorTest extends BaseTest {
@Test(expected = IllegalArgumentException.class)
public void testUnknownChromosome() {
ArtificialSAMQueryIterator iter = ArtificialSamUtils.queryReadIterator(1, 2, 100);
ArtificialSAMQueryIterator iter = ArtificialSAMUtils.queryReadIterator(1, 2, 100);
iter.queryOverlapping("chr621", 25, 74);
}
}

12
java/test/org/broadinstitute/sting/utils/sam/ArtificialSamUtilsTest.java → java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsTest.java
View File

@ -16,12 +16,12 @@ import net.sf.samtools.SAMRecord;
* Time: 3:09:34 AM
* To change this template use File | Settings | File Templates.
*/
public class ArtificialSamUtilsTest extends BaseTest {
public class ArtificialSAMUtilsTest extends BaseTest {
@Test
public void basicReadIteratorTest() {
StingSAMIterator iter = ArtificialSamUtils.unmappedReadIterator(1, 100, 100);
StingSAMIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 100);
int count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
@ -32,7 +32,7 @@ public class ArtificialSamUtilsTest extends BaseTest {
@Test
public void tenPerChromosome() {
StingSAMIterator iter = ArtificialSamUtils.unmappedReadIterator(1, 100, 10);
StingSAMIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 10);
int count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
@ -45,7 +45,7 @@ public class ArtificialSamUtilsTest extends BaseTest {
@Test
public void onePerChromosome() {
StingSAMIterator iter = ArtificialSamUtils.unmappedReadIterator(1, 100, 1);
StingSAMIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 1);
int count = 0;
while (iter.hasNext()) {
SAMRecord rec = iter.next();
@ -58,7 +58,7 @@ public class ArtificialSamUtilsTest extends BaseTest {
@Test
public void basicUnmappedIteratorTest() {
StingSAMIterator iter = ArtificialSamUtils.unmappedReadIterator(1, 100, 100, 1000);
StingSAMIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 100, 1000);
int count = 0;
for (int x = 0; x < (100* 100); x++ ) {
if (!iter.hasNext()) {
@ -82,7 +82,7 @@ public class ArtificialSamUtilsTest extends BaseTest {
@Test
public void testPeeking() {
PeekingStingIterator iter = ArtificialSamUtils.unmappedReadIterator(1, 100, 100);
PeekingStingIterator iter = ArtificialSAMUtils.unmappedReadIterator(1, 100, 100);
int count = 0;
while (iter.hasNext()) {
int readCnt = ((ArtificialSAMIterator)(iter)).readsTaken();