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A few misc. residual errors in last commit

This commit is contained in:
Mark DePristo 2012-06-21 16:04:25 -04:00
parent 734756d6b2
commit d17369e0ac
3 changed files with 6 additions and 5 deletions
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5
public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
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@ -27,6 +27,7 @@ package org.broadinstitute.sting.utils.codecs.hapmap;
import org.broad.tribble.annotation.Strand; import org.broad.tribble.annotation.Strand;
import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.AsciiLineReader;
import org.broad.tribble.readers.PositionalBufferedStream; import org.broad.tribble.readers.PositionalBufferedStream;
import org.broadinstitute.sting.BaseTest;
import org.testng.Assert; import org.testng.Assert;
import org.testng.annotations.Test; import org.testng.annotations.Test;
@ -38,9 +39,9 @@ import java.io.IOException;
/** /**
* Unit tests for the HapMap codec * Unit tests for the HapMap codec
*/ */
public class HapMapUnitTest { public class HapMapUnitTest extends BaseTest {
// our sample hapmap file // our sample hapmap file
private final static File hapMapFile = new File("public/testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap"); private final static File hapMapFile = new File(privateTestDir + "genotypes_chr1_ASW_phase3.3_first500.hapmap");
private final static String knownLine = "rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_r" + private final static String knownLine = "rs2185539 C/T chr1 556738 + ncbi_b36 bbs urn:lsid:bbs.hapmap.org:Protocol:Phase3.r3:1 urn:lsid:bbs.hapmap.org:Assay:Phase3.r3_r" +
"s2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC TC TT CT CC CC CC CC CC CC CC CC CC"; "s2185539:1 urn:lsid:dcc.hapmap.org:Panel:US_African-30-trios:4 QC+ CC TC TT CT CC CC CC CC CC CC CC CC CC";
/** /**

4
public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
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@ -27,8 +27,8 @@ import java.util.EnumSet;
*/ */
public class IndexFactoryUnitTest extends BaseTest { public class IndexFactoryUnitTest extends BaseTest {
File inputFile = new File("public/testdata/HiSeq.10000.vcf"); File inputFile = new File(privateTestDir + "HiSeq.10000.vcf");
File outputFile = new File("public/testdata/onTheFlyOutputTest.vcf"); File outputFile = new File(privateTestDir + "onTheFlyOutputTest.vcf");
File outputFileIndex = Tribble.indexFile(outputFile); File outputFileIndex = Tribble.indexFile(outputFile);
private SAMSequenceDictionary dict; private SAMSequenceDictionary dict;

2
public/java/test/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFileUnitTest.java
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@ -25,7 +25,7 @@ import net.sf.samtools.SAMSequenceRecord;
* Basic unit test for GenomeLoc * Basic unit test for GenomeLoc
*/ */
public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest { public class CachingIndexedFastaSequenceFileUnitTest extends BaseTest {
private File simpleFasta = new File(privateTestDir + "/exampleFASTA.fasta"); private File simpleFasta = new File(publicTestDir + "/exampleFASTA.fasta");
private static final int STEP_SIZE = 1; private static final int STEP_SIZE = 1;
//private static final List<Integer> QUERY_SIZES = Arrays.asList(1); //private static final List<Integer> QUERY_SIZES = Arrays.asList(1);