From 195b4ea7b4f4deb0a2c64b25b18bd83f137c8e88 Mon Sep 17 00:00:00 2001 From: aaron Date: Thu, 11 Jun 2009 17:46:06 +0000 Subject: [PATCH] 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 --- .../sting/utils/genotype/Genotype.java | 39 +++++++++++++++++++ .../utils/{ => genotype}/glf/GLFRecord.java | 2 +- .../utils/{ => genotype}/glf/GLFWriter.java | 4 +- .../{ => genotype}/glf/LikelihoodObject.java | 2 +- .../{ => genotype}/glf/SinglePointCall.java | 2 +- .../glf/VariableLengthCall.java | 2 +- .../sam/ArtificialPatternedSAMIterator.java | 6 +-- .../utils/sam/ArtificialReadsTraversal.java | 7 +--- .../utils/sam/ArtificialSAMIterator.java | 4 +- ...lSamUtils.java => ArtificialSAMUtils.java} | 2 +- .../shards/IntervalShardStrategyTest.java | 4 +- .../dataSources/shards/IntervalShardTest.java | 4 +- .../shards/LinearLocusShardStrategyTest.java | 5 +-- .../shards/ShardStrategyFactoryTest.java | 4 +- .../simpleDataSources/SAMByReadsTest.java | 10 ++--- .../gatk/walkers/PrintReadsWalkerTest.java | 11 +++--- .../sting/utils/GenomeLocSortedSetTest.java | 4 +- .../{ => genotype}/glf/GLFWriterTest.java | 8 ++-- .../glf/LikelihoodObjectTest.java | 2 +- .../ArtificialPatternedSAMIteratorTest.java | 4 +- .../sam/ArtificialSAMFileWriterTest.java | 6 +-- .../sam/ArtificialSAMQueryIteratorTest.java | 13 +++---- ...sTest.java => ArtificialSAMUtilsTest.java} | 12 +++--- 23 files changed, 92 insertions(+), 65 deletions(-) create mode 100644 java/src/org/broadinstitute/sting/utils/genotype/Genotype.java rename java/src/org/broadinstitute/sting/utils/{ => genotype}/glf/GLFRecord.java (99%) mode change 100644 => 100755 rename java/src/org/broadinstitute/sting/utils/{ => genotype}/glf/GLFWriter.java (98%) rename java/src/org/broadinstitute/sting/utils/{ => genotype}/glf/LikelihoodObject.java (98%) rename java/src/org/broadinstitute/sting/utils/{ => genotype}/glf/SinglePointCall.java (98%) rename java/src/org/broadinstitute/sting/utils/{ => genotype}/glf/VariableLengthCall.java (98%) rename java/src/org/broadinstitute/sting/utils/sam/{ArtificialSamUtils.java => ArtificialSAMUtils.java} (99%) rename java/test/org/broadinstitute/sting/utils/{ => genotype}/glf/GLFWriterTest.java (93%) rename java/test/org/broadinstitute/sting/utils/{ => genotype}/glf/LikelihoodObjectTest.java (98%) rename java/test/org/broadinstitute/sting/utils/sam/{ArtificialSamUtilsTest.java => ArtificialSAMUtilsTest.java} (89%) diff --git a/java/src/org/broadinstitute/sting/utils/genotype/Genotype.java b/java/src/org/broadinstitute/sting/utils/genotype/Genotype.java new file mode 100644 index 000000000..8759c0468 --- /dev/null +++ b/java/src/org/broadinstitute/sting/utils/genotype/Genotype.java @@ -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 { + +} diff --git a/java/src/org/broadinstitute/sting/utils/glf/GLFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java old mode 100644 new mode 100755 similarity index 99% rename from java/src/org/broadinstitute/sting/utils/glf/GLFRecord.java rename to java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java index 00afe3f72..14a574337 --- a/java/src/org/broadinstitute/sting/utils/glf/GLFRecord.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.glf; +package org.broadinstitute.sting.utils.genotype.glf; import net.sf.samtools.util.BinaryCodec; diff --git a/java/src/org/broadinstitute/sting/utils/glf/GLFWriter.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java similarity index 98% rename from java/src/org/broadinstitute/sting/utils/glf/GLFWriter.java rename to java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java index 05acf6497..f54b5bf1f 100755 --- a/java/src/org/broadinstitute/sting/utils/glf/GLFWriter.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFWriter.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/utils/glf/LikelihoodObject.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/LikelihoodObject.java similarity index 98% rename from java/src/org/broadinstitute/sting/utils/glf/LikelihoodObject.java rename to java/src/org/broadinstitute/sting/utils/genotype/glf/LikelihoodObject.java index 8c82baa7a..7d52cf871 100755 --- a/java/src/org/broadinstitute/sting/utils/glf/LikelihoodObject.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/LikelihoodObject.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.glf; +package org.broadinstitute.sting.utils.genotype.glf; import java.util.HashMap; diff --git a/java/src/org/broadinstitute/sting/utils/glf/SinglePointCall.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/SinglePointCall.java similarity index 98% rename from java/src/org/broadinstitute/sting/utils/glf/SinglePointCall.java rename to java/src/org/broadinstitute/sting/utils/genotype/glf/SinglePointCall.java index 8f13344c9..bf941153d 100644 --- a/java/src/org/broadinstitute/sting/utils/glf/SinglePointCall.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/SinglePointCall.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.glf; +package org.broadinstitute.sting.utils.genotype.glf; import net.sf.samtools.util.BinaryCodec; diff --git a/java/src/org/broadinstitute/sting/utils/glf/VariableLengthCall.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/VariableLengthCall.java similarity index 98% rename from java/src/org/broadinstitute/sting/utils/glf/VariableLengthCall.java rename to java/src/org/broadinstitute/sting/utils/genotype/glf/VariableLengthCall.java index a98d837d7..63d3617b1 100644 --- a/java/src/org/broadinstitute/sting/utils/glf/VariableLengthCall.java +++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/VariableLengthCall.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.utils.glf; +package org.broadinstitute.sting.utils.genotype.glf; import net.sf.samtools.util.BinaryCodec; diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java index 02599839f..cbb8a1e02 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIterator.java @@ -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); } } diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java index 1ce907565..1fb3a41bd 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialReadsTraversal.java @@ -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 readWalker = (ReadWalker) 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, diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java index f727581c4..3254a1332 100644 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMIterator.java @@ -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; } diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSamUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java similarity index 99% rename from java/src/org/broadinstitute/sting/utils/sam/ArtificialSamUtils.java rename to java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java index 953862ab9..37320f54d 100755 --- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSamUtils.java +++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java @@ -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; /** diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategyTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategyTest.java index 2b6a49ad4..1f0bc2932 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategyTest.java +++ b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardStrategyTest.java @@ -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; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardTest.java index d727661b7..a703e7c4a 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardTest.java +++ b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/IntervalShardTest.java @@ -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; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategyTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategyTest.java index 6af3fd925..23d6da164 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategyTest.java +++ b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/LinearLocusShardStrategyTest.java @@ -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; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java index 8141a4660..85ca15add 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java +++ b/java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java @@ -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; diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java index 053d22cb3..f10ef2b27 100755 --- a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java +++ b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java @@ -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.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()); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java index b8e39f5e5..53dc5a3d7 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerTest.java @@ -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); diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetTest.java index 641ee0bd8..79d591673 100755 --- a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetTest.java +++ b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetTest.java @@ -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; diff --git a/java/test/org/broadinstitute/sting/utils/glf/GLFWriterTest.java b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java similarity index 93% rename from java/test/org/broadinstitute/sting/utils/glf/GLFWriterTest.java rename to java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java index 928a17620..feedf1184 100755 --- a/java/test/org/broadinstitute/sting/utils/glf/GLFWriterTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java @@ -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; /* diff --git a/java/test/org/broadinstitute/sting/utils/glf/LikelihoodObjectTest.java b/java/test/org/broadinstitute/sting/utils/genotype/glf/LikelihoodObjectTest.java similarity index 98% rename from java/test/org/broadinstitute/sting/utils/glf/LikelihoodObjectTest.java rename to java/test/org/broadinstitute/sting/utils/genotype/glf/LikelihoodObjectTest.java index 61a17dce9..a6d106b84 100755 --- a/java/test/org/broadinstitute/sting/utils/glf/LikelihoodObjectTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/glf/LikelihoodObjectTest.java @@ -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; diff --git a/java/test/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorTest.java b/java/test/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorTest.java index 46ddb30bc..f0b9a0761 100644 --- a/java/test/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorTest.java +++ b/java/test/org/broadinstitute/sting/utils/sam/ArtificialPatternedSAMIteratorTest.java @@ -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 diff --git a/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterTest.java b/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterTest.java index ff7a44a0a..006d4e12a 100644 --- a/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterTest.java +++ b/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMFileWriterTest.java @@ -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()); diff --git a/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorTest.java b/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorTest.java index 8ad9c15ba..ed04d19a1 100644 --- a/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorTest.java +++ b/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIteratorTest.java @@ -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); } } diff --git a/java/test/org/broadinstitute/sting/utils/sam/ArtificialSamUtilsTest.java b/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsTest.java similarity index 89% rename from java/test/org/broadinstitute/sting/utils/sam/ArtificialSamUtilsTest.java rename to java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsTest.java index 558c47b74..9768d9258 100644 --- a/java/test/org/broadinstitute/sting/utils/sam/ArtificialSamUtilsTest.java +++ b/java/test/org/broadinstitute/sting/utils/sam/ArtificialSAMUtilsTest.java @@ -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();