zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fix build problems with tests

This commit is contained in:
Mark DePristo 2012-08-31 11:56:40 -04:00
parent 817ece37a2
commit cf91d894e4
4 changed files with 31 additions and 43 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/java/src/org/broadinstitute/sting/utils/baq/ReadTransformingIterator.java
View File

@ -19,7 +19,7 @@ public class ReadTransformingIterator implements StingSAMIterator {
/**
* Creates a new ReadTransforming iterator
*/
@Requires({"it != null", "engine != null", "transformer != null", "transformer.isInitialized()"})
@Requires({"it != null", "transformer != null", "transformer.isInitialized()"})
public ReadTransformingIterator(final StingSAMIterator it, final ReadTransformer transformer) {
if ( ! transformer.isInitialized() )
throw new IllegalStateException("Creating a read transformer stream for an uninitialized read transformer: " + transformer);

23
public/java/test/org/broadinstitute/sting/gatk/datasources/reads/DownsamplerBenchmark.java
View File

@ -36,8 +36,8 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.filters.UnmappedReadFilter;
import org.broadinstitute.sting.gatk.iterators.LocusIteratorByState;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.baq.BAQ;
import java.util.Collections;
import java.util.Iterator;
@ -69,18 +69,15 @@ public class DownsamplerBenchmark extends ReadProcessingBenchmark {
for(int i = 0; i < reps; i++) {
SAMFileReader reader = new SAMFileReader(inputFile);
ReadProperties readProperties = new ReadProperties(Collections.<SAMReaderID>singletonList(new SAMReaderID(inputFile,new Tags())),
reader.getFileHeader(),
false,
SAMFileReader.ValidationStringency.SILENT,
downsampling.create(),
new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
Collections.<ReadFilter>emptyList(),
false,
BAQ.CalculationMode.OFF,
BAQ.QualityMode.DONT_MODIFY,
null, // no BAQ
null, // no BQSR
(byte)0);
reader.getFileHeader(),
false,
SAMFileReader.ValidationStringency.SILENT,
downsampling.create(),
new ValidationExclusion(Collections.singletonList(ValidationExclusion.TYPE.ALL)),
Collections.<ReadFilter>emptyList(),
Collections.<ReadTransformer>emptyList(),
false,
(byte)0);
GenomeLocParser genomeLocParser = new GenomeLocParser(reader.getFileHeader().getSequenceDictionary());
// Filter unmapped reads. TODO: is this always strictly necessary? Who in the GATK normally filters these out?

24
public/java/test/org/broadinstitute/sting/gatk/datasources/reads/SAMDataSourceUnitTest.java
View File

@ -24,9 +24,6 @@
package org.broadinstitute.sting.gatk.datasources.reads;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.Assert.fail;
import net.sf.picard.reference.IndexedFastaSequenceFile;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMProgramRecord;
@ -35,24 +32,25 @@ import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.commandline.Tags;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
import org.broadinstitute.sting.gatk.resourcemanagement.ThreadAllocation;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.Collections;
import java.util.List;
import static org.testng.Assert.*;
/**
* @author aaron
* @version 1.0
@ -183,11 +181,8 @@ public class SAMDataSourceUnitTest extends BaseTest {
null,
new ValidationExclusion(),
new ArrayList<ReadFilter>(),
Collections.<ReadTransformer>emptyList(),
false,
BAQ.CalculationMode.OFF,
BAQ.QualityMode.DONT_MODIFY,
null, // no BAQ
null, // no BQSR
(byte) -1,
removeProgramRecords);
@ -205,11 +200,8 @@ public class SAMDataSourceUnitTest extends BaseTest {
null,
new ValidationExclusion(),
new ArrayList<ReadFilter>(),
Collections.<ReadTransformer>emptyList(),
false,
BAQ.CalculationMode.OFF,
BAQ.QualityMode.DONT_MODIFY,
null, // no BAQ
null, // no BQSR
(byte) -1,
removeProgramRecords);

25
public/java/test/org/broadinstitute/sting/gatk/iterators/LocusIteratorByStateUnitTest.java
View File

@ -4,25 +4,27 @@ import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMFileReader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.util.CloseableIterator;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.Assert;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.ReadProperties;
import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.datasources.reads.SAMReaderID;
import org.broadinstitute.sting.gatk.filters.ReadFilter;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.baq.BAQ;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.*;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
/**
* testing of the LocusIteratorByState
@ -349,11 +351,8 @@ public class LocusIteratorByStateUnitTest extends BaseTest {
null,
new ValidationExclusion(),
Collections.<ReadFilter>emptyList(),
Collections.<ReadTransformer>emptyList(),
false,
BAQ.CalculationMode.OFF,
BAQ.QualityMode.DONT_MODIFY,
null, // no BAQ
null, // no BQSR
(byte) -1
);
}