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Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Mauricio Carneiro 2011-06-29 18:09:58 -04:00
parent 231845ab2f ef51429b66
commit 9e5d0d8155
7 changed files with 19 additions and 19 deletions
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2
public/java/test/org/broadinstitute/sting/BaseTest.java
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@ -83,7 +83,7 @@ public abstract class BaseTest {
*/ */
public static final String MD5_FILE_DB_SUBDIR = "integrationtests"; public static final String MD5_FILE_DB_SUBDIR = "integrationtests";
public static final String testDir = "testdata/"; public static final String testDir = "public/testdata/";
/** before the class starts up */ /** before the class starts up */
static { static {

14
public/java/test/org/broadinstitute/sting/gatk/GenomeAnalysisEngineUnitTest.java
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@ -60,8 +60,8 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine(); GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>(); Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags())); samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags())); samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
testEngine.setSAMFileIDs(samFiles); testEngine.setSAMFileIDs(samFiles);
testEngine.checkForDuplicateSamFiles(); testEngine.checkForDuplicateSamFiles();
@ -72,10 +72,10 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine(); GenomeAnalysisEngine testEngine = new GenomeAnalysisEngine();
Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>(); Collection<SAMReaderID> samFiles = new ArrayList<SAMReaderID>();
samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags())); samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
samFiles.add(new SAMReaderID(new File("testdata/exampleNORG.bam"), new Tags())); samFiles.add(new SAMReaderID(new File("public/testdata/exampleNORG.bam"), new Tags()));
samFiles.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags())); samFiles.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
samFiles.add(new SAMReaderID(new File("testdata/exampleNORG.bam"), new Tags())); samFiles.add(new SAMReaderID(new File("public/testdata/exampleNORG.bam"), new Tags()));
testEngine.setSAMFileIDs(samFiles); testEngine.setSAMFileIDs(samFiles);
testEngine.checkForDuplicateSamFiles(); testEngine.checkForDuplicateSamFiles();
@ -97,7 +97,7 @@ public class GenomeAnalysisEngineUnitTest extends BaseTest {
GATKArgumentCollection argCollection = new GATKArgumentCollection(); GATKArgumentCollection argCollection = new GATKArgumentCollection();
testEngine.setArguments(argCollection); testEngine.setArguments(argCollection);
File fastaFile = new File("testdata/exampleFASTA.fasta"); File fastaFile = new File("public/testdata/exampleFASTA.fasta");
GenomeLocParser genomeLocParser = new GenomeLocParser(new IndexedFastaSequenceFile(fastaFile)); GenomeLocParser genomeLocParser = new GenomeLocParser(new IndexedFastaSequenceFile(fastaFile));
testEngine.setGenomeLocParser(genomeLocParser); testEngine.setGenomeLocParser(genomeLocParser);

2
public/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java
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@ -21,7 +21,7 @@ public class BedParserUnitTest extends BaseTest {
private static IndexedFastaSequenceFile seq; private static IndexedFastaSequenceFile seq;
private GenomeLocParser genomeLocParser; private GenomeLocParser genomeLocParser;
private File bedFile = new File("testdata/sampleBedFile.bed"); private File bedFile = new File("public/testdata/sampleBedFile.bed");
@BeforeClass @BeforeClass
public void beforeTests() { public void beforeTests() {

2
public/java/test/org/broadinstitute/sting/utils/codecs/hapmap/HapMapUnitTest.java
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@ -39,7 +39,7 @@ import java.io.IOException;
*/ */
public class HapMapUnitTest { public class HapMapUnitTest {
// our sample hapmap file // our sample hapmap file
private final static File hapMapFile = new File("testdata/genotypes_chr1_ASW_phase3.3_first500.hapmap"); private final static File hapMapFile = new File("public/testdata/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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@ -17,8 +17,8 @@ import java.util.*;
*/ */
public class IndexFactoryUnitTest { public class IndexFactoryUnitTest {
File inputFile = new File("testdata/HiSeq.10000.vcf"); File inputFile = new File("public/testdata/HiSeq.10000.vcf");
File outputFile = new File("testdata/onTheFlyOutputTest.vcf"); File outputFile = new File("public/testdata/onTheFlyOutputTest.vcf");
File outputFileIndex = Tribble.indexFile(outputFile); File outputFileIndex = Tribble.indexFile(outputFile);
/** /**

12
public/java/test/org/broadinstitute/sting/utils/text/ListFileUtilsUnitTest.java
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@ -49,12 +49,12 @@ public class ListFileUtilsUnitTest extends BaseTest {
public void testIgnoreBlankLinesInBAMListFiles() throws Exception { public void testIgnoreBlankLinesInBAMListFiles() throws Exception {
File tempListFile = createTempListFile("testIgnoreBlankLines", File tempListFile = createTempListFile("testIgnoreBlankLines",
"", "",
"testdata/exampleBAM.bam", "public/testdata/exampleBAM.bam",
" " " "
); );
List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>(); List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags())); expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking); performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
} }
@ -63,13 +63,13 @@ public class ListFileUtilsUnitTest extends BaseTest {
public void testCommentSupportInBAMListFiles() throws Exception { public void testCommentSupportInBAMListFiles() throws Exception {
File tempListFile = createTempListFile("testCommentSupport", File tempListFile = createTempListFile("testCommentSupport",
"#", "#",
"testdata/exampleBAM.bam", "public/testdata/exampleBAM.bam",
"#testdata/foo.bam", "#public/testdata/foo.bam",
" # testdata/bar.bam" " # public/testdata/bar.bam"
); );
List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>(); List<SAMReaderID> expectedBAMFileListAfterUnpacking = new ArrayList<SAMReaderID>();
expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("testdata/exampleBAM.bam"), new Tags())); expectedBAMFileListAfterUnpacking.add(new SAMReaderID(new File("public/testdata/exampleBAM.bam"), new Tags()));
performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking); performBAMListFileUnpackingTest(tempListFile, expectedBAMFileListAfterUnpacking);
} }

2
public/java/test/org/broadinstitute/sting/utils/threading/GenomeLocProcessingTrackerUnitTest.java
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@ -29,7 +29,7 @@ public class GenomeLocProcessingTrackerUnitTest extends BaseTest {
IndexedFastaSequenceFile fasta = null; IndexedFastaSequenceFile fasta = null;
GenomeLocParser genomeLocParser = null; GenomeLocParser genomeLocParser = null;
String chr1 = null; String chr1 = null;
private final static String FILE_ROOT = "testdata/GLPTFile"; private final static String FILE_ROOT = "public/testdata/GLPTFile";
@BeforeTest @BeforeTest
public void before() { public void before() {