From a34c2442c0f8a4dd0ff74546f849bb052573413f Mon Sep 17 00:00:00 2001 From: aaron Date: Tue, 29 Dec 2009 07:40:48 +0000 Subject: [PATCH] moved hard-coded file paths to the oneKGLocation, validationDataLocation, and seqLocation variables setup in the BaseTest. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2460 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/BaseTest.java | 18 +++++--- .../alignment/AlignerIntegrationTest.java | 2 +- .../SAMBAMDataSourceTest.java | 2 +- .../simpleDataSources/SAMByIntervalTest.java | 2 +- .../simpleDataSources/SAMByReadsTest.java | 2 +- .../IntervalOverlapIteratorTest.java | 2 +- .../iterators/PlusOneFixIteratorTest.java | 2 +- .../refdata/ReferenceOrderedDataTest.java | 6 +-- .../sting/gatk/refdata/RodGLFTest.java | 4 +- .../sting/gatk/refdata/RodVCFTest.java | 4 +- .../sting/gatk/refdata/rodDbSNPTest.java | 2 +- .../gatk/traversals/TraverseReadsTest.java | 4 +- .../DepthOfCoverageIntegrationTest.java | 4 +- .../walkers/PileupWalkerIntegrationTest.java | 4 +- .../SecondBaseSkewIntegrationTest.java | 22 ++++----- .../VariantAnnotatorIntegrationTest.java | 22 ++++----- .../CallsetConcordanceIntegrationTest.java | 10 ++-- .../fasta/BamToFastqIntegrationTest.java | 4 +- ...astaAlternateReferenceIntegrationTest.java | 6 +-- .../VariantFiltrationIntegrationTest.java | 12 ++--- .../UnifiedGenotyperIntegrationTest.java | 26 +++++------ .../IntervalCleanerIntegrationTest.java | 6 +-- .../indels/IntervalsIntegrationTest.java | 6 +-- .../RecalibrationWalkersIntegrationTest.java | 46 +++++++++---------- .../ClipReadsWalkersIntegrationTest.java | 8 ++-- .../VariantEvalWalkerIntegrationTest.java | 24 +++++----- .../VariantsToVCFIntegrationTest.java | 8 ++-- .../sting/utils/GenotypeUtilsTest.java | 4 +- .../sting/utils/bed/BedParserTest.java | 10 +--- .../utils/fasta/FastaSequenceIndexTest.java | 2 +- .../utils/genotype/glf/GLFReaderTest.java | 2 +- .../utils/genotype/glf/GLFWriterTest.java | 2 +- .../genotype/vcf/VCFIntegrationTest.java | 2 +- .../utils/genotype/vcf/VCFReaderTest.java | 12 ++--- 34 files changed, 145 insertions(+), 147 deletions(-) diff --git a/java/test/org/broadinstitute/sting/BaseTest.java b/java/test/org/broadinstitute/sting/BaseTest.java index 58c41ca47..d7fb209c6 100755 --- a/java/test/org/broadinstitute/sting/BaseTest.java +++ b/java/test/org/broadinstitute/sting/BaseTest.java @@ -34,14 +34,16 @@ import java.util.Enumeration; * Class BaseTest *

* This is the base test class for all of our test cases. All test cases should extend from this - * class, since it sets up the logger, and resolves any data directories that we rely on. + * class; it sets up the logger, and resolves the location of directories that we rely on. */ public abstract class BaseTest { /** our log, which we want to capture anything from org.broadinstitute.sting */ - public static Logger logger = Logger.getRootLogger();// .getLogger(CommandLineProgram.class); + public static Logger logger = Logger.getRootLogger(); + + protected static String seqLocation = "/seq/"; + protected static String oneKGLocation = "/broad/1KG/"; + protected static String validationDataLocation = "/humgen/gsa-scr1/GATK_Data/Validation_Data/"; - protected static String seqLocation = "/seq"; - protected static String oneKGLocation = "/broad/1KG"; protected static String testDir = "testdata/"; protected static boolean alreadySetup = false; @@ -72,8 +74,7 @@ public abstract class BaseTest { findFileLocations(); } catch (IOException e) { logger.fatal("We can't locate the base /seq and /broad/1KG directories, for the following reason: " + e.getMessage()); - e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. - throw new RuntimeException("BaseTest setup failed: findFileLocations emited exception with a reason: " + e.getMessage()); + throw new RuntimeException("BaseTest setup failed: findFileLocations emited exception",e); } } } @@ -81,6 +82,8 @@ public abstract class BaseTest { public static void findFileLocations() throws IOException { // if either doesn't exist if (!fileExist(seqLocation) || !fileExist(oneKGLocation)) { + + // get the working directory String workDir = System.getProperty("user.dir"); if (!fileExist("test.conf")) { @@ -110,7 +113,8 @@ public abstract class BaseTest { seqLocation = array[1]; } else if (array[0].equals("1KG")) { oneKGLocation = array[1]; - + } else if (array[0].equals("validation")) { + validationDataLocation = array[1]; } else { throw new IOException("Line : " + line + ", unknown left side"); } diff --git a/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java b/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java index 1ccd0db0d..9eccd3d71 100644 --- a/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java @@ -20,7 +20,7 @@ public class AlignerIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-R /humgen/gsa-scr1/GATK_Data/bwa/human_b36_both.fasta" + " -T Align" + - " -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878_Pilot1_20.trimmed.unmapped.bam" + + " -I " + validationDataLocation + "NA12878_Pilot1_20.trimmed.unmapped.bam" + " -ob %s", 1, // just one output file Arrays.asList(md5)); diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java index a4eab30ad..81b28eca2 100755 --- a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java @@ -86,7 +86,7 @@ public class SAMBAMDataSourceTest extends BaseTest { int count = 0; // setup the data - fl.add(new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam")); + fl.add(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam")); Reads reads = new Reads(fl); try { diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalTest.java index ff86c771f..00880492b 100644 --- a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalTest.java @@ -87,7 +87,7 @@ public class SAMByIntervalTest extends BaseTest { //GenomeLoc.setupRefContigOrdering(seq.getSequenceDictionary()); // setup the test files - fl.add(new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/index_test.bam")); + fl.add(new File(validationDataLocation + "index_test.bam")); reads = new Reads(fl); } 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 c2a356f5e..a3a726883 100755 --- a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java @@ -61,7 +61,7 @@ public class SAMByReadsTest extends BaseTest { //GenomeLoc.setupRefContigOrdering(seq.getSequenceDictionary()); // setup the test files - fl.add(new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/index_test.bam")); + fl.add(new File(validationDataLocation + "index_test.bam")); reads = new Reads(fl); } diff --git a/java/test/org/broadinstitute/sting/gatk/iterators/IntervalOverlapIteratorTest.java b/java/test/org/broadinstitute/sting/gatk/iterators/IntervalOverlapIteratorTest.java index b691c331c..69e863f7d 100644 --- a/java/test/org/broadinstitute/sting/gatk/iterators/IntervalOverlapIteratorTest.java +++ b/java/test/org/broadinstitute/sting/gatk/iterators/IntervalOverlapIteratorTest.java @@ -24,7 +24,7 @@ import java.util.Iterator; * test the DuplicateDetectorIterator class. */ public class IntervalOverlapIteratorTest extends BaseTest { - private final File bam = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/index_test.bam"); + private final File bam = new File(validationDataLocation + "index_test.bam"); private static IndexedFastaSequenceFile seq; private int chromosomeOneReadCount = 885; diff --git a/java/test/org/broadinstitute/sting/gatk/iterators/PlusOneFixIteratorTest.java b/java/test/org/broadinstitute/sting/gatk/iterators/PlusOneFixIteratorTest.java index c32d67885..934dfffa9 100644 --- a/java/test/org/broadinstitute/sting/gatk/iterators/PlusOneFixIteratorTest.java +++ b/java/test/org/broadinstitute/sting/gatk/iterators/PlusOneFixIteratorTest.java @@ -23,7 +23,7 @@ import net.sf.samtools.SAMRecord; * Time: 11:02:24 PM */ public class PlusOneFixIteratorTest extends BaseTest { - private final File bam = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/index_test.bam"); + private final File bam = new File(validationDataLocation + "index_test.bam"); private static IndexedFastaSequenceFile seq; private int chromosomeOneReadCount = 885; diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDataTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDataTest.java index 810de7be1..a3ff0a209 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDataTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDataTest.java @@ -20,7 +20,7 @@ import java.util.List; public class ReferenceOrderedDataTest extends BaseTest { @Test public void extractRodsFromFileTest() { - String file = "/humgen/gsa-scr1/GATK_Data/Validation_Data/testRODFileImpl.csv"; + String file = validationDataLocation + "testRODFileImpl.csv"; List lst = new ArrayList(); ReferenceOrderedData.extractRodsFromFile(lst,file); Assert.assertEquals(6,lst.size()); @@ -32,8 +32,8 @@ public class ReferenceOrderedDataTest extends BaseTest { } @Test public void extractRodsFromMultiFileTest() { - String file = "/humgen/gsa-scr1/GATK_Data/Validation_Data/testRODFileImpl.csv"; - String file2 = "/humgen/gsa-scr1/GATK_Data/Validation_Data/testRODFileImpl2.csv"; + String file = validationDataLocation + "testRODFileImpl.csv"; + String file2 = validationDataLocation + "testRODFileImpl2.csv"; List lst = new ArrayList(); ReferenceOrderedData.extractRodsFromFile(lst,file); ReferenceOrderedData.extractRodsFromFile(lst,file2); diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java index 8cee6f584..b7c2b4313 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java @@ -27,10 +27,10 @@ import java.io.File; * You'll notice that the first is a hom ref, and the other two are hom alt SNP's */ public class RodGLFTest extends BaseTest { - static final File glfFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/glfTestFile.glf"); + static final File glfFile = new File(validationDataLocation + "glfTestFile.glf"); static final int finalRecordCount = 100; // the number of records in the above file static final int contigCount = 1; - static final String ref = "/broad/1KG/reference/human_b36_both.fasta"; + static final String ref = oneKGLocation + "reference/human_b36_both.fasta"; static ReferenceSequenceFile r; private RodGLF iter = null; diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java index 278860b0d..8faa7e1e0 100755 --- a/java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java @@ -32,12 +32,12 @@ import java.util.List; public class RodVCFTest extends BaseTest { private static IndexedFastaSequenceFile seq; - private static File vcfFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample.vcf"); + private static File vcfFile = new File(validationDataLocation + "vcfexample.vcf"); private VCFHeader mHeader; @BeforeClass public static void beforeTests() { try { - seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta")); + seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); } catch (FileNotFoundException e) { throw new StingException("unable to load the sequence dictionary"); } diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/rodDbSNPTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/rodDbSNPTest.java index a179ad2f6..55a1ef393 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/rodDbSNPTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/rodDbSNPTest.java @@ -24,7 +24,7 @@ public class rodDbSNPTest extends BaseTest { @BeforeClass public static void beforeTests() { try { - seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta")); + seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); } catch (FileNotFoundException e) { throw new StingException("unable to load the sequence dictionary"); } diff --git a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java index f9e1cb715..e26630af5 100755 --- a/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java +++ b/java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java @@ -53,8 +53,8 @@ import java.util.List; public class TraverseReadsTest extends BaseTest { private ReferenceSequenceFile seq; - private File bam = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/index_test.bam"); // TCGA-06-0188.aligned.duplicates_marked.bam"); - private File refFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/Homo_sapiens_assembly17.fasta"); + private File bam = new File(validationDataLocation + "index_test.bam"); // TCGA-06-0188.aligned.duplicates_marked.bam"); + private File refFile = new File(validationDataLocation + "Homo_sapiens_assembly17.fasta"); private List bamList; private Walker countReadWalker; private File output; diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java index 13ff007cd..f9b2edc69 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java @@ -10,7 +10,7 @@ import java.util.List; import java.io.File; public class DepthOfCoverageIntegrationTest extends WalkerTest { - private static String root = "-L 1:10,164,500-10,164,520 -R /broad/1KG/reference/human_b36_both.fasta -T DepthOfCoverage -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam"; + private static String root = "-L 1:10,164,500-10,164,520 -R " + oneKGLocation + "reference/human_b36_both.fasta -T DepthOfCoverage -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam"; static HashMap expectations = new HashMap(); static { expectations.put("-minMAPQ 1", "8b73fad5cce4620907d5da2a985219d5"); @@ -41,7 +41,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { @Test public void testDepthOfCoverage454() { WalkerTestSpec spec = new WalkerTestSpec( - "-T DepthOfCoverage -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam -L 1:10,001,890-10,001,895 -o %s", + "-T DepthOfCoverage -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam -L 1:10,001,890-10,001,895 -o %s", 1, // just one output file Arrays.asList("a332d1539b29dff615b198818a3d4dd1")); executeTest("testDepthOfCoverage454", spec); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java index e6c0b4719..70692c597 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java @@ -16,8 +16,8 @@ public class PileupWalkerIntegrationTest extends WalkerTest { @Test public void testGnarleyFHSPileup() { - String gatk_args = "-T Pileup -I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_Pileup_Test.bam " - + "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + String gatk_args = "-T Pileup -I " + validationDataLocation + "FHS_Pileup_Test.bam " + + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + " -L chr15:46,347,148 -o %s"; String expected_md5 = "d23032d10111755ccb1c1b01e6e097a7"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5)); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java index 38731d918..2e768b272 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java @@ -28,10 +28,10 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { @Test public void testOnE2File() { String test_args = "-T VariantAnnotator -A SecondBaseSkew " - +"-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " - +"-I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHSP_pool3_2bannot.bam " - +"-B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_raw_calls.geli " - +"-vcf %s -sample variant -L /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_test_intervals.interval_list"; + +"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + +"-I " + validationDataLocation + "FHSP_pool3_2bannot.bam " + +"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli " + +"-vcf %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; String md5_for_this_test = "4bd8a28bcbad107b102fc796918d5932"; @@ -44,10 +44,10 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { @Test public void testOnUnannotatedFile() { String test_args = "-T VariantAnnotator -A SecondBaseSkew " - +"-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " - +"-I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHSP_pool3_test.bam " - +"-B variant,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_raw_calls.geli " - +"-vcf %s -sample variant -L /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_test_intervals.interval_list"; + +"-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + +"-I " + validationDataLocation + "FHSP_pool3_test.bam " + +"-B variant,Variants," + validationDataLocation + "FHS_pilot_pool3_raw_calls.geli " + +"-vcf %s -sample variant -L " + validationDataLocation + "FHS_test_intervals.interval_list"; String md5_for_this_test = "3eee411119888fc4633870a91ed2093d"; @@ -57,9 +57,9 @@ public class SecondBaseSkewIntegrationTest extends WalkerTest { @Test public void testOnIndels() { - String test_args = "-T VariantAnnotator -I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_Pileup_Test.bam" - + " -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A SecondBaseSkew" - + " -sample variant -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pileup_test_chr15.vcf" + String test_args = "-T VariantAnnotator -I " + validationDataLocation + "FHS_Pileup_Test.bam" + + " -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -A SecondBaseSkew" + + " -sample variant -B variant,VCF," + validationDataLocation + "FHS_pileup_test_chr15.vcf" + " -vcf %s -L chr15:46347148"; String expected_md5 = "c70dfb30c3caa9184604f88bc7f62a07"; WalkerTestSpec spec = new WalkerTestSpec(test_args,1,Arrays.asList(expected_md5)); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 949f6778d..32b36054f 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -9,11 +9,11 @@ import java.util.Arrays; public class VariantAnnotatorIntegrationTest extends WalkerTest { public static String secondBaseTestString() { - return "-T VariantAnnotator -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -vcf %s -A SecondBaseSkew"; + return "-T VariantAnnotator -R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -vcf %s -A SecondBaseSkew"; } public static String validationDataPath() { - return "/humgen/gsa-scr1/GATK_Data/Validation_Data/"; + return validationDataLocation + ""; } public static String secondBaseTestFile( int testNo ) { @@ -41,7 +41,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { } public static String baseTestString() { - return "-T VariantAnnotator -R /broad/1KG/reference/human_b36_both.fasta -vcf %s"; + return "-T VariantAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta -vcf %s"; } @@ -49,7 +49,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, Arrays.asList("fecfec68226bbd9b458ede55d48e0762")); executeTest("test file has annotations, not asking for annotations, #1", spec); } @@ -57,7 +57,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsNotAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, Arrays.asList("59845ada9dc5bc66e0042cfefdf8f16f")); executeTest("test file has annotations, not asking for annotations, #2", spec); } @@ -65,7 +65,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, Arrays.asList("b0012ffce509196885bfdf1612086263")); executeTest("test file has annotations, asking for annotations, #1", spec); } @@ -73,7 +73,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, Arrays.asList("7e00e94a046e82ac41f6fd298a64cc74")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -81,7 +81,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoAnnotsNotAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, Arrays.asList("c70cc6bb6b83748ec8d968dc3bf879c4")); executeTest("test file doesn't have annotations, not asking for annotations, #1", spec); } @@ -89,7 +89,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoAnnotsNotAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, Arrays.asList("e7c8900ff9a18f2c8a033ae741e7143b")); executeTest("test file doesn't have annotations, not asking for annotations, #2", spec); } @@ -97,7 +97,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, Arrays.asList("a6630eec84161a089dde204e09744c45")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @@ -105,7 +105,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + baseTestString() + " -standard -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, Arrays.asList("130658564083f650981b28728b813917")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java index 6f334920c..a8ab8b157 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java @@ -7,13 +7,13 @@ import java.util.Arrays; public class CallsetConcordanceIntegrationTest extends WalkerTest { public static String baseTestString() { - return "-T CallsetConcordance -R /broad/1KG/reference/human_b36_both.fasta -L 1:1-8000 -CO %s"; + return "-T CallsetConcordance -R " + oneKGLocation + "reference/human_b36_both.fasta -L 1:1-8000 -CO %s"; } @Test public void testSimpleVenn() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SimpleVenn", 1, + baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn", 1, Arrays.asList("5c8e4757d2ce46bc50991a171f988327")); executeTest("testSimpleVenn", spec); } @@ -21,7 +21,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { @Test public void testSNPConcordance() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1, + baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SNPGenotypeConcordance:qscore=5", 1, Arrays.asList("b4904813cdfd37f0a092aa6cadcd3f71")); executeTest("testSNPConcordance", spec); } @@ -29,7 +29,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { @Test public void testNWayVenn() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -B set3,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/CEU.sample.vcf -CT NWayVenn", 1, + baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -B set3,VCF," + validationDataLocation + "CEU.sample.vcf -CT NWayVenn", 1, Arrays.asList("cf915dc9762d6a44a7bdadc0d7eae9b8")); executeTest("testNWayVenn", spec); } @@ -37,7 +37,7 @@ public class CallsetConcordanceIntegrationTest extends WalkerTest { @Test public void testMulti() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B set1,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example1.vcf -B set2,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.example2.vcf -CT SimpleVenn -CT NWayVenn -CT SNPGenotypeConcordance:qscore=5", 1, + baseTestString() + " -B set1,VCF," + validationDataLocation + "NA12878.example1.vcf -B set2,VCF," + validationDataLocation + "NA12878.example2.vcf -CT SimpleVenn -CT NWayVenn -CT SNPGenotypeConcordance:qscore=5", 1, Arrays.asList("d046599a2fef386fa0ad5dfc9671c3a9")); executeTest("testMulti", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java index 1d4ef2fad..02692acac 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java @@ -10,13 +10,13 @@ public class BamToFastqIntegrationTest extends WalkerTest { public void testIntervals() { WalkerTestSpec spec1 = new WalkerTestSpec( - "-T BamToFastq -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s", + "-T BamToFastq -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s", 1, Arrays.asList("2ec2ff5ac405099bf48186d2c7e5fabd")); executeTest("testBamToFasta", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( - "-T BamToFastq -reverse -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s", + "-T BamToFastq -reverse -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s", 1, Arrays.asList("5a79484da43925b0e0461be28fdad07c")); executeTest("testBamToFastaReverse", spec2); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java index a38082192..e0af6fbfd 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java @@ -10,19 +10,19 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest { public void testIntervals() { WalkerTestSpec spec1 = new WalkerTestSpec( - "-T FastaAlternateReferenceMaker -R /broad/1KG/reference/human_b36_both.fasta -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s", + "-T FastaAlternateReferenceMaker -R " + oneKGLocation + "reference/human_b36_both.fasta -L 1:10,000,100-10,000,500;1:10,100,000-10,101,000;1:10,900,000-10,900,001 -o %s", 1, Arrays.asList("328d2d52cedfdc52da7d1abff487633d")); executeTest("testFastaReference", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( - "-T FastaAlternateReferenceMaker -R /broad/1KG/reference/human_b36_both.fasta -B indels,PointIndel,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.indels -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s", + "-T FastaAlternateReferenceMaker -R " + oneKGLocation + "reference/human_b36_both.fasta -B indels,PointIndel," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,075,000-10,075,380;1:10,093,447-10,093,847;1:10,271,252-10,271,452 -o %s", 1, Arrays.asList("3a48986c3832a768b478c3e95f994b0f")); executeTest("testFastaAlternateReferenceIndels", spec2); WalkerTestSpec spec4 = new WalkerTestSpec( - "-T FastaAlternateReferenceMaker -R /broad/1KG/reference/human_b36_both.fasta -B snps,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chr1_10mb_11mb.slx.geli.calls -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s", + "-T FastaAlternateReferenceMaker -R " + oneKGLocation + "reference/human_b36_both.fasta -B snps,Variants," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.geli.calls -B snpmask,dbsnp,/humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -L 1:10,023,400-10,023,500;1:10,029,200-10,029,500 -o %s", 1, Arrays.asList("82705a88f6fc25880dd2331183531d9a")); executeTest("testFastaAlternateReferenceSnps", spec4); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java index 6283c52a3..da75a7b70 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java @@ -8,14 +8,14 @@ import java.util.Arrays; public class VariantFiltrationIntegrationTest extends WalkerTest { public static String baseTestString() { - return "-T VariantFiltration -o %s -R /broad/1KG/reference/human_b36_both.fasta"; + return "-T VariantFiltration -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta"; } @Test public void testNoAction() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("340e3a09d0571dc969557cc979a132b3")); executeTest("test no action", spec); } @@ -23,7 +23,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testClusteredSnps() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -window 10 -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -window 10 -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("53e2c4645bab58a4f039ff51d5bffb7e")); executeTest("test clustered SNPs", spec); } @@ -31,7 +31,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testMask() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -mask foo -B mask,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -mask foo -B mask,VCF," + validationDataLocation + "vcfexample2.vcf -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("27dacba4bcc6beaac608a7b34b7206f0")); executeTest("test mask", spec); } @@ -39,7 +39,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testFilter1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -filter 'DoC < 20 || FisherStrand > 20.0' -filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("e1a17255db9aa17016457ce2d81c6fff")); executeTest("test filter #1", spec); } @@ -47,7 +47,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest { @Test public void testFilter2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, + baseTestString() + " -filter 'AlleleBalance < 70.0 && FisherStrand == 1.4' -filterName bar -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1, Arrays.asList("18ef67575a76c2be74af8bd8b9fdf86e")); executeTest("test filter #2", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index 49c9a175d..e51a535e1 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -21,7 +21,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testMultiSamplePilot1PointEM() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, + "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, Arrays.asList("caeb030b47503e9d79cf1e18b86e8bc9")); executeTest("testMultiSamplePilot1 - Point Estimate EM", spec); } @@ -29,7 +29,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testMultiSamplePilot2PointEM() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, + "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, Arrays.asList("f87c182b694a7baeab886d8f75c91e28")); executeTest("testMultiSamplePilot2 - Point Estimate EM", spec); } @@ -42,7 +42,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testPooled1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1, + "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1, Arrays.asList("acf8006174a460247fabbc650802c29b")); executeTest("testPooled1", spec); } @@ -55,7 +55,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testMultiSamplePilot1Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, + "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, Arrays.asList("92b32599938bc60d6d636b425c5e0a6c")); executeTest("testMultiSamplePilot1 - Joint Estimate", spec); } @@ -63,7 +63,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testMultiSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, + "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, Arrays.asList("cc90c3dd5d30dd4ac0fceb748283ddb9")); executeTest("testMultiSamplePilot2 - Joint Estimate", spec); } @@ -71,7 +71,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testSingleSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, + "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, Arrays.asList("d04c02cdbf1e1adbdf84540c861a64f7")); executeTest("testSingleSamplePilot2 - Joint Estimate", spec); } @@ -93,7 +93,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 " + entry.getKey(), 1, + "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 " + entry.getKey(), 1, Arrays.asList(entry.getValue())); executeTest(String.format("testParameter[%s]", entry.getKey()), spec); } @@ -102,7 +102,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testConfidence() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1, + "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -bm empirical -gm JOINT_ESTIMATE -confidence 10 ", 1, Arrays.asList("c8c4a463ab23585d8373f3e8a7fbec22")); executeTest("testConfidence", spec); } @@ -121,7 +121,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -vf " + entry.getKey(), 1, + "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 -vf " + entry.getKey(), 1, Arrays.asList(entry.getValue())); executeTest(String.format("testOtherFormat[%s]", entry.getKey()), spec); } @@ -144,7 +144,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -vf GELI -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 --heterozygosity " + entry.getKey(), 1, + "-T UnifiedGenotyper -vf GELI -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30 --heterozygosity " + entry.getKey(), 1, Arrays.asList(entry.getValue())); executeTest(String.format("testHeterozyosity[%s]", entry.getKey()), spec); } @@ -164,7 +164,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -vf GELI -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -gm JOINT_ESTIMATE -confidence 30 -bm " + entry.getKey(), 1, + "-T UnifiedGenotyper -vf GELI -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -gm JOINT_ESTIMATE -confidence 30 -bm " + entry.getKey(), 1, Arrays.asList(entry.getValue())); executeTest(String.format("testOtherBaseCallModel[%s]", entry.getKey()), spec); } @@ -179,8 +179,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiTechnologies() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper" + - " -R /broad/1KG/reference/human_b36_both.fasta" + - " -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" + + " -R " + oneKGLocation + "reference/human_b36_both.fasta" + + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" + " -varout %s" + " -L 1:10,000,000-10,100,000" + " -bm empirical" + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java index 0118d9b5b..00488a97a 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java @@ -11,21 +11,21 @@ public class IntervalCleanerIntegrationTest extends WalkerTest { String[] md5lod5 = {"4a440cbb39a8093f28f6ce66d8b9a104", "460631e8d98644dcf53b3045ca40f02a"}; WalkerTestSpec spec1 = new WalkerTestSpec( - "-T IntervalCleaner -LOD 5 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s", + "-T IntervalCleaner -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L " + validationDataLocation + "cleaner.test.intervals --OutputCleaned %s -snps %s", 2, Arrays.asList(md5lod5)); executeTest("testLod5", spec1); String[] md5lod200 = {"32401cef2134d973ff0037df27f1dcca", "6137bf0c25c7972b07b0d3fc6979cf5b"}; WalkerTestSpec spec2 = new WalkerTestSpec( - "-T IntervalCleaner -LOD 200 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s", + "-T IntervalCleaner -LOD 200 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L " + validationDataLocation + "cleaner.test.intervals --OutputCleaned %s -snps %s", 2, Arrays.asList(md5lod200)); executeTest("testLod200", spec2); String[] md5cleanedOnly = {"7b5a6dcc0ee770f4c8e5d0d9f36a5c34", "460631e8d98644dcf53b3045ca40f02a"}; WalkerTestSpec spec3 = new WalkerTestSpec( - "-T IntervalCleaner -LOD 5 -cleanedOnly -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s", + "-T IntervalCleaner -LOD 5 -cleanedOnly -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L " + validationDataLocation + "cleaner.test.intervals --OutputCleaned %s -snps %s", 2, Arrays.asList(md5cleanedOnly)); executeTest("testCleanedOnly", spec3); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsIntegrationTest.java index 559176b37..52067b1b8 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsIntegrationTest.java @@ -10,19 +10,19 @@ public class IntervalsIntegrationTest extends WalkerTest { public void testIntervals() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( - "-T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -o %s", + "-T IndelIntervals -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -o %s", 1, Arrays.asList("76f97b91921f427ab639b6b8228ac4dc")); executeTest("testIndelIntervals", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - "-T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -o %s", + "-T MismatchIntervals -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -o %s", 1, Arrays.asList("31e8b5d4c42f2c63c08b8f6b8e10ac99")); executeTest("testMismatchIntervals", spec2); WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - "-T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -intervals /humgen/gsa-scr1/GATK_Data/Validation_Data/indelIntervals.test -intervals /humgen/gsa-scr1/GATK_Data/Validation_Data/mismatchIntervals.test -o %s", + "-T IntervalMerger -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-11,000,000 -intervals " + validationDataLocation + "indelIntervals.test -intervals " + validationDataLocation + "mismatchIntervals.test -o %s", 1, Arrays.asList("bf1f23667ef0065bbcb9754f50c2d664")); executeTest("testMergeIntervals", spec3); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java index e6b0c317c..add0a3df5 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -16,21 +16,21 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariates1() { HashMap e = new HashMap(); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "c1b54d4221fb4fa88e0231a74310708e" ); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "337ea30c4dcc2fe6a9adc442ffd0706b"); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "ffbfd38b1720cfb67ba1bb63d4308552" ); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "60e227ea8c3409fa85b92cae7ea6574f" ); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "c1b54d4221fb4fa88e0231a74310708e" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "337ea30c4dcc2fe6a9adc442ffd0706b"); + e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "ffbfd38b1720cfb67ba1bb63d4308552" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "60e227ea8c3409fa85b92cae7ea6574f" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -T CountCovariates" + " -I " + bam + - ( bam.equals( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) + ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) ? " -L 1:10,800,000-10,810,000" : " -L 1:10,000,000-10,200,000" ) + " -cov ReadGroupCovariate" + " -cov QualityScoreCovariate" + @@ -49,10 +49,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibrator1() { HashMap e = new HashMap(); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "f7749792ffffbb86aec66e92a3bddf7f" ); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "f1780e3c3e12f07527e0468149312f10"); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "c54a67a1687a4139a8ae19762217987f" ); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "d9ddbacdafc621d830a1db637973d795" ); + e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "f7749792ffffbb86aec66e92a3bddf7f" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "f1780e3c3e12f07527e0468149312f10"); + e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "c54a67a1687a4139a8ae19762217987f" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "d9ddbacdafc621d830a1db637973d795" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -61,10 +61,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); if ( paramsFile != null ) { WalkerTestSpec spec = new WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + " -T TableRecalibration" + " -I " + bam + - ( bam.equals( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) + ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) ? " -L 1:10,800,000-10,810,000" : " -L 1:10,100,000-10,300,000" ) + " -outputBam %s" + " --no_pg_tag" + @@ -80,15 +80,15 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesVCF() { HashMap e = new HashMap(); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "3ee0e811682c0f29951128204765ece9"); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "3ee0e811682c0f29951128204765ece9"); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + - " -B dbsnp,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3.vcf" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + " -B dbsnp,VCF," + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + " -L 1:10,000,000-10,200,000" + @@ -108,14 +108,14 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesNoReadGroups() { HashMap e = new HashMap(); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "f49bc79225bffbf8b64590b65a4b4305" ); + e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "f49bc79225bffbf8b64590b65a4b4305" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -T CountCovariates" + " -I " + bam + @@ -138,7 +138,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorNoReadGroups() { HashMap e = new HashMap(); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "62413fdbfe99cd6e24992de4234de5bc" ); + e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "62413fdbfe99cd6e24992de4234de5bc" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -147,7 +147,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); if ( paramsFile != null ) { WalkerTestSpec spec = new WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + " -T TableRecalibration" + " -I " + bam + " -L 1:10,100,000-10,300,000" + @@ -166,14 +166,14 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testCountCovariatesNoIndex() { HashMap e = new HashMap(); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "906e5a08401722cc9a5528d2fd20ea6a" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "906e5a08401722cc9a5528d2fd20ea6a" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -T CountCovariates" + " -I " + bam + @@ -193,7 +193,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { @Test public void testTableRecalibratorNoIndex() { HashMap e = new HashMap(); - e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "aa38b04c6b58badabb6b09d590284a2a" ); + e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "aa38b04c6b58badabb6b09d590284a2a" ); for ( Map.Entry entry : e.entrySet() ) { String bam = entry.getKey(); @@ -202,7 +202,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); if ( paramsFile != null ) { WalkerTestSpec spec = new WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + " -T TableRecalibration" + " -I " + bam + " -outputBam %s" + diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java index 49bb1578c..0f7ea2753 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java @@ -10,9 +10,9 @@ import java.util.List; public class ClipReadsWalkersIntegrationTest extends WalkerTest { public void testClipper(String name, String args, String md51, String md52) { WalkerTestSpec spec = new WalkerTestSpec( - "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + "-T ClipReads " + - "-I /humgen/gsa-scr1/GATK_Data/Validation_Data/clippingReadsTest.bam " + + "-I " + validationDataLocation + "clippingReadsTest.bam " + "-o %s " + "-ob %s " + args, 2, // just one output file @@ -32,9 +32,9 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { @Test public void testClipRange2() { testClipper("clipRange2", "-CT 1-5,11-15", "be4fcad5b666a5540028b774169cbad7", "f05ab5fe821b77cd5b066212ff56f8ff"); } @Test public void testClipSeq() { testClipper("clipSeqX", "-X CCCCC", "db199bd06561c9f2122f6ffb07941fbc", "c218c0649838423a06f3296430f65c4f"); } - @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF /humgen/gsa-scr1/GATK_Data/Validation_Data/seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "1151e10833da794203df2ba7cc76d5c5"); } + @Test public void testClipSeqFile() { testClipper("clipSeqXF", "-XF " + validationDataLocation + "seqsToClip.fasta", "d011a3152b31822475afbe0281491f8d", "1151e10833da794203df2ba7cc76d5c5"); } - @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF /humgen/gsa-scr1/GATK_Data/Validation_Data/seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "4a1153d6f0600cf53ff7959a043e57cc"); } + @Test public void testClipMulti() { testClipper("clipSeqMulti", "-QT 10 -CT 1-5 -XF " + validationDataLocation + "seqsToClip.fasta -X CCCCC", "a23187bd9bfb06557f799706d98441de", "4a1153d6f0600cf53ff7959a043e57cc"); } @Test public void testClipNs() { testClipper("testClipNs", "-QT 10 -CR WRITE_NS", Q10ClipOutput, "fb77d3122df468a71e03ca92b69493f4"); } @Test public void testClipQ0s() { testClipper("testClipQs", "-QT 10 -CR WRITE_Q0S", Q10ClipOutput, "24053a87b00c0bc2ddf420975e9fea4d"); } diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java index dfef017c2..e0905295c 100644 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java @@ -36,8 +36,8 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { */ for ( Map.Entry e : md5.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + - " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + " --rodBind eval,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" + " -T VariantEval" + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -L 1:10,000,000-11,000,000" + @@ -68,8 +68,8 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { * -minConfidenceScore 6 */ WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + - " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + " --rodBind eval,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" + " -T VariantEval" + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -L 1:10,000,000-11,000,000" + @@ -100,8 +100,8 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { * --includeViolations */ WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + - " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + " --rodBind eval,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" + " -T VariantEval" + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -L 1:10,000,000-11,000,000" + @@ -133,8 +133,8 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { */ WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + - " --rodBind eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + " --rodBind eval,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" + " -T VariantEval" + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -L 1:10,000,000-11,000,000" + @@ -162,8 +162,8 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { */ WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T VariantEval -R /broad/1KG/reference/human_b36_both.fasta " + - "-B eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/UMichVsBroad.venn.set1Only.calls " + + "-T VariantEval -R " + oneKGLocation + "reference/human_b36_both.fasta " + + "-B eval,Variants," + validationDataLocation + "UMichVsBroad.venn.set1Only.calls " + "-D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod -hc /humgen/gsa-scr1/GATK_Data/1KG_gffs/NA12878.1kg.gff " + "-G " + "--supressDateInformation " + @@ -179,8 +179,8 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest { List md5 = new ArrayList(); md5.add(""); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-T VariantEval -R /broad/1KG/reference/human_b36_both.fasta " + - "-B eval,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.pilot_3.all.geli.calls " + + "-T VariantEval -R " + oneKGLocation + "reference/human_b36_both.fasta " + + "-B eval,Variants," + validationDataLocation + "NA12878.pilot_3.all.geli.calls " + "-D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod " + "--supressDateInformation " + "-L /humgen/gsa-scr1/GATK_Data/thousand_genomes_alpha_redesign.targets.b36.interval_list " + diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCFIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCFIntegrationTest.java index 89cb7ff5c..d19e51c87 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCFIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCFIntegrationTest.java @@ -37,8 +37,8 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { * */ WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + - " --rodBind NA123AB,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + " --rodBind NA123AB,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" + " -T VariantsToVCF" + " -L 1:10,000,000-11,000,000" + " --vcfout %s", @@ -66,8 +66,8 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { * */ WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R /broad/1KG/reference/human_b36_both.fasta" + - " --rodBind NA123AB,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" + + "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + " --rodBind NA123AB,Variants," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" + " -T VariantsToVCF" + " -L 1:10,000,000-11,000,000" + " --vcfout %s", diff --git a/java/test/org/broadinstitute/sting/utils/GenotypeUtilsTest.java b/java/test/org/broadinstitute/sting/utils/GenotypeUtilsTest.java index 02f43826d..dd018a5d7 100644 --- a/java/test/org/broadinstitute/sting/utils/GenotypeUtilsTest.java +++ b/java/test/org/broadinstitute/sting/utils/GenotypeUtilsTest.java @@ -22,12 +22,12 @@ import java.io.FileNotFoundException; public class GenotypeUtilsTest extends BaseTest { private static IndexedFastaSequenceFile seq; - private static File vcfFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample.vcf"); + private static File vcfFile = new File(validationDataLocation + "vcfexample.vcf"); @BeforeClass public static void beforeTests() { try { - seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta")); + seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); } catch (FileNotFoundException e) { throw new StingException("unable to load the sequence dictionary"); } diff --git a/java/test/org/broadinstitute/sting/utils/bed/BedParserTest.java b/java/test/org/broadinstitute/sting/utils/bed/BedParserTest.java index b95657f91..ef3d17b9b 100644 --- a/java/test/org/broadinstitute/sting/utils/bed/BedParserTest.java +++ b/java/test/org/broadinstitute/sting/utils/bed/BedParserTest.java @@ -15,13 +15,7 @@ import java.io.FileNotFoundException; import java.util.ArrayList; import java.util.List; -/** - * Created by IntelliJ IDEA. - * User: aaron - * Date: Oct 5, 2009 - * Time: 9:09:42 PM - * To change this template use File | Settings | File Templates. - */ + public class BedParserTest extends BaseTest { private static IndexedFastaSequenceFile seq; @@ -30,7 +24,7 @@ public class BedParserTest extends BaseTest { @BeforeClass public static void beforeTests() { try { - seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta")); + seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); } catch (FileNotFoundException e) { throw new StingException("unable to load the sequence dictionary"); } diff --git a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java index 78704da6a..d4ab9de78 100755 --- a/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java +++ b/java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java @@ -27,7 +27,7 @@ public class FastaSequenceIndexTest extends BaseTest { @BeforeClass public static void initialize() { sequenceIndexName = seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta.fai"; - sequenceIndexColonSemiColonTestName = "/humgen/gsa-scr1/GATK_Data/Validation_Data/testing.fai"; + sequenceIndexColonSemiColonTestName = validationDataLocation + "testing.fai"; } @Before diff --git a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFReaderTest.java b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFReaderTest.java index bd06631c6..3b5723317 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFReaderTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFReaderTest.java @@ -20,7 +20,7 @@ public class GLFReaderTest extends BaseTest { // our test file - static final File glfFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/index_test_likelihoods.glf"); + static final File glfFile = new File(validationDataLocation + "index_test_likelihoods.glf"); //static final File glfFile = new File("CALLS.glf"); static final int finalRecordCount = 484140; // the number of records in the above file static final int contigCount = 25; diff --git a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java index ac6206684..0f3b9f5d3 100755 --- a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java @@ -68,7 +68,7 @@ public class GLFWriterTest extends BaseTest { @BeforeClass public static void beforeTests() { try { - seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta")); + seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); } catch (FileNotFoundException e) { throw new StingException("unable to load the sequence dictionary"); } diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFIntegrationTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFIntegrationTest.java index 46cc91051..cd502631b 100755 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFIntegrationTest.java @@ -11,7 +11,7 @@ public class VCFIntegrationTest extends WalkerTest { public void test1() { // Read in and then emit each record WalkerTestSpec spec = new WalkerTestSpec( - "-T PrintRODs -R /broad/1KG/reference/human_b36_both.fasta -L 1:10,000,000-10,050,000 -o %s -B vcf,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/complexExample.vcf", 1, + "-T PrintRODs -R " + oneKGLocation + "reference/human_b36_both.fasta -L 1:10,000,000-10,050,000 -o %s -B vcf,VCF," + validationDataLocation + "complexExample.vcf", 1, Arrays.asList("26ad7a663d0f247ac26ce5490edd7ec0")); executeTest("test vcf", spec); } diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java index a38092dd4..6def7d60b 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java @@ -15,17 +15,17 @@ import java.util.*; /** test the VCFReader class test */ public class VCFReaderTest extends BaseTest { - private static final File vcfFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample.vcf"); - private static final File multiSampleVCF = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/MultiSample.vcf"); - private static final String VCF_MIXUP_FILE = "/humgen/gsa-scr1/GATK_Data/Validation_Data/mixedup.v2.vcf"; - private static final File complexFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/complexExample.vcf"); - private static final File headerNoRecordsFile = new File("/humgen/gsa-scr1/GATK_Data/Validation_Data/headerNoRecords.vcf"); + private static final File vcfFile = new File(validationDataLocation + "vcfexample.vcf"); + private static final File multiSampleVCF = new File(validationDataLocation + "MultiSample.vcf"); + private static final String VCF_MIXUP_FILE = validationDataLocation + "mixedup.v2.vcf"; + private static final File complexFile = new File(validationDataLocation + "complexExample.vcf"); + private static final File headerNoRecordsFile = new File(validationDataLocation + "headerNoRecords.vcf"); @BeforeClass public static void beforeTests() { try { - IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta")); + IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); GenomeLocParser.setupRefContigOrdering(seq); } catch (FileNotFoundException e) { throw new StingException("unable to load the sequence dictionary");