diff --git a/java/test/org/broadinstitute/sting/BaseTest.java b/java/test/org/broadinstitute/sting/BaseTest.java index 0aa21ca6c..b6c206522 100755 --- a/java/test/org/broadinstitute/sting/BaseTest.java +++ b/java/test/org/broadinstitute/sting/BaseTest.java @@ -42,9 +42,8 @@ public abstract class BaseTest { /** our log, which we want to capture anything from org.broadinstitute.sting */ public static Logger logger = Logger.getRootLogger(); - protected static String seqLocation = "/seq/"; - protected static String oneKGLocation = "/broad/1KG/"; protected static String hg18Reference = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"; + protected static String hg19Reference = "/seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.fasta"; protected static String b36KGReference = "/broad/1KG/reference/human_b36_both.fasta"; protected static String GATKDataLocation = "/humgen/gsa-hpprojects/GATK/data/"; protected static String validationDataLocation = GATKDataLocation + "Validation_Data/"; @@ -76,59 +75,12 @@ public abstract class BaseTest { logger.setLevel(Level.WARN); // find our file sources - try { - findFileLocations(); - } catch (IOException e) { - logger.fatal("We can't locate the base /seq and /broad/1KG directories, for the following reason: " + e.getMessage()); - throw new RuntimeException("BaseTest setup failed: findFileLocations emited exception",e); + if (!fileExist(hg18Reference) || !fileExist(hg19Reference) || !fileExist(b36KGReference)) { + logger.fatal("We can't locate the reference directories. Aborting!"); + throw new RuntimeException("BaseTest setup failed: unable to locate the reference directories"); } } } - - 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")) { - throw new IOException("Unable to find both data directories or your test.conf, make sure it's placed in the base Sting directory"); - } - - BufferedReader inputStream = new BufferedReader(new FileReader("test.conf")); - - String line = ""; - while ((line = inputStream.readLine()) != null) { - String[] array = line.split("="); - - // check the length - if (array.length != 2) { - throw new IOException("Line : " + line + ", split != 2"); - } - // clean up the right side - if (array[1].contains("\n")) { - array[1] = array[1].substring(0, array[1].indexOf("\n") - 1); - } - // check to see if the right side exists - if (!fileExist(array[1])) { - throw new IOException("Line : " + line + ", right side doesn't exist"); - } - // check to see what type it is - if (array[0].equals("seq")) { - 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"); - } - } - - } - - } /** * test if the file exists @@ -139,7 +91,6 @@ public abstract class BaseTest { public static boolean fileExist(String file) { File temp = new File(file); return temp.exists(); - } /** @@ -192,14 +143,14 @@ public abstract class BaseTest { } catch (NoSuchAlgorithmException e) { throw new StingException("Unable to find MD5 digest"); } - InputStream is = null; + InputStream is; try { is = new FileInputStream(file); } catch (FileNotFoundException e) { throw new StingException("Unable to open file " + file); } byte[] buffer = new byte[8192]; - int read = 0; + int read; try { while ((read = is.read(buffer)) > 0) { digest.update(buffer, 0, read); diff --git a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java index 2b28989ad..5035053c3 100755 --- a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java @@ -10,7 +10,7 @@ import java.util.Arrays; public class VariantContextIntegrationTest extends WalkerTest { private static String cmdRoot = "-T TestVariantContext" + - " -R " + oneKGLocation + "reference/human_b36_both.fasta"; + " -R " + b36KGReference; private static String root = cmdRoot + " -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + diff --git a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUnitTest.java b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUnitTest.java index e565e9124..e789eeed8 100755 --- a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUnitTest.java @@ -29,7 +29,7 @@ public class VariantContextUnitTest extends BaseTest { @BeforeClass public static void init() throws FileNotFoundException { // sequence - seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")); + seq = new IndexedFastaSequenceFile(new File(hg18Reference)); GenomeLocParser.setupRefContigOrdering(seq); } diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java index 06fc52397..8a2066235 100755 --- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java @@ -46,7 +46,7 @@ public class ReferenceOrderedViewUnitTest extends BaseTest { @BeforeClass public static void init() throws FileNotFoundException { // sequence - seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")); + seq = new IndexedFastaSequenceFile(new File(hg18Reference)); GenomeLocParser.setupRefContigOrdering(seq); } diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java index 5d5cb9424..a8de32a2e 100755 --- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java @@ -42,7 +42,7 @@ public abstract class ReferenceViewTemplate extends BaseTest { */ @BeforeClass public static void initialize() throws FileNotFoundException { - sequenceFile = new IndexedFastaSequenceFile( new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta") ); + sequenceFile = new IndexedFastaSequenceFile( new File(hg18Reference) ); GenomeLocParser.setupRefContigOrdering(sequenceFile); } diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java index bb16fd3ea..a9c866bed 100755 --- a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolUnitTest.java @@ -45,7 +45,7 @@ public class ReferenceOrderedDataPoolUnitTest extends BaseTest { @BeforeClass public static void init() throws FileNotFoundException { - File sequenceFile = new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"); + File sequenceFile = new File(hg18Reference); GenomeLocParser.setupRefContigOrdering(new IndexedFastaSequenceFile(sequenceFile)); TabularROD.setDelimiter(TabularROD.DEFAULT_DELIMITER, TabularROD.DEFAULT_DELIMITER_REGEX); } diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java index d5a612b76..95376deeb 100755 --- a/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java @@ -62,7 +62,7 @@ public class SAMBAMDataSourceUnitTest extends BaseTest { fl = new ArrayList(); // sequence - seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")); + seq = new IndexedFastaSequenceFile(new File(hg18Reference)); GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary()); } diff --git a/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java b/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java index 64f851eba..07a4baa44 100755 --- a/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java @@ -73,7 +73,7 @@ public class BoundedReadIteratorUnitTest extends BaseTest { fl = new ArrayList(); // sequence - seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")); + seq = new IndexedFastaSequenceFile(new File(hg18Reference)); GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary()); } diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodUnitTest.java index a8e9d369a..ec9c47258 100755 --- a/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/PlinkRodUnitTest.java @@ -32,7 +32,7 @@ public class PlinkRodUnitTest extends BaseTest { @BeforeClass public static void beforeTests() { try { - seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); + seq = new IndexedFastaSequenceFile(new File(b36KGReference)); } catch (FileNotFoundException e) { throw new StingException("unable to load the sequence dictionary"); } diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/TabularRODUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/TabularRODUnitTest.java index 05ad1f13f..d4af0eebc 100755 --- a/java/test/org/broadinstitute/sting/gatk/refdata/TabularRODUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/TabularRODUnitTest.java @@ -37,7 +37,7 @@ public class TabularRODUnitTest extends BaseTest { @BeforeClass public static void init() throws FileNotFoundException { // sequence - seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")); + seq = new IndexedFastaSequenceFile(new File(hg18Reference)); GenomeLocParser.setupRefContigOrdering(seq); } diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptorsUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptorsUnitTest.java index 07139898b..59fd7bd7c 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptorsUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptorsUnitTest.java @@ -40,7 +40,7 @@ public class VariantContextAdaptorsUnitTest extends BaseTest { @BeforeClass public static void beforeClass() { - seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "/reference/human_b36_both.fasta")); // TODO: make human reference use BaseTest + seq = new IndexedFastaSequenceFile(new File(b36KGReference)); GenomeLocParser.setupRefContigOrdering(seq); } diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java index 1b5b15a31..090ae961a 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java @@ -36,7 +36,7 @@ public class VCF4UnitTest extends BaseTest { @BeforeClass public static void setupContig() { IndexedFastaSequenceFile seq; - seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); + seq = new IndexedFastaSequenceFile(new File(b36KGReference)); GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary()); } diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java index a0ba235e4..74a84cf9c 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java @@ -34,7 +34,6 @@ import org.junit.Before; import org.junit.Test; import java.io.File; -import java.io.FileNotFoundException; import java.io.IOException; import java.util.ArrayList; import java.util.Iterator; @@ -100,7 +99,7 @@ public class RMDTrackManagerUnitTest extends BaseTest { // @Test used only to determine how fast queries are, don't uncomment! (unless you know what you're doing). public void testSpeedOfRealQuery() { IndexedFastaSequenceFile file = null; - file = new IndexedFastaSequenceFile(new File("/broad/1KG/reference/human_b36_both.fasta")); + file = new IndexedFastaSequenceFile(new File(b36KGReference)); final int intervalSize = 10000000; GenomeLocParser.setupRefContigOrdering(file.getSequenceDictionary()); RMDTrackManager manager = new RMDTrackManager(); diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java index c988dae57..b8a7d4e73 100644 --- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java +++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java @@ -52,7 +52,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest { @Before public void setup() { builder = new TribbleRMDTrackBuilder(); - IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); + IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(b36KGReference)); GenomeLocParser.setupRefContigOrdering(seq); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java index 517d6563e..1dc166193 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java @@ -17,7 +17,7 @@ public class PileupWalkerIntegrationTest extends WalkerTest { @Test public void testGnarleyFHSPileup() { String gatk_args = "-T Pileup -I " + validationDataLocation + "FHS_Pileup_Test.bam " - + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -L chr15:46,347,148 -o %s"; String expected_md5 = "052187dd2bf2516a027578c8775856a8"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5)); @@ -27,7 +27,7 @@ public class PileupWalkerIntegrationTest extends WalkerTest { @Test public void testExtendedEventPileup() { String gatk_args = "-T Pileup -I " + validationDataLocation + "OV-0930.normal.chunk.bam " - + "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -show_indels -o %s"; String expected_md5="06eedc2e7927650961d99d703f4301a4"; WalkerTestSpec spec = new WalkerTestSpec(gatk_args,1,Arrays.asList(expected_md5)); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java index 1ff248f1f..a87813aa0 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java @@ -23,7 +23,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { md5.add("b4f98bee580508637c88c421064936fc"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -B variant,GeliText," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" + " -T VariantsToVCF" + " -L 1:10,000,000-11,000,000" + @@ -40,7 +40,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { md5.add("0f310612c8609cba3dcf9cc97b2c1195"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -B variant,GeliText," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" + " -T VariantsToVCF" + " -L 1:10,000,000-11,000,000" + @@ -57,7 +57,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { md5.add("28728ad3a6af20a1e1aaaf185ffbff2b"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -B variant,HapMap," + validationDataLocation + "rawHapMap.yri.chr1.txt" + " -T VariantsToVCF" + " -L 1:1-1,000,000" + @@ -73,7 +73,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest { md5.add("19371e6cfea5f29fb75d5a2be7fccd34"); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -B variant,VCF," + validationDataLocation + "complexExample.vcf4" + " -T VariantsToVCF" + " -o %s", 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 a5330df18..922dc7c9a 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -8,7 +8,7 @@ import java.util.Arrays; public class VariantAnnotatorIntegrationTest extends WalkerTest { public static String baseTestString() { - return "-T VariantAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta -o %s"; + return "-T VariantAnnotator -R " + b36KGReference + " -o %s"; } @Test diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java index f28bf2e94..f175aa24f 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java @@ -18,8 +18,6 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { private boolean RUN_TESTS = true; private String root = "-T DepthOfCoverage "; - private String hg18 = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"; - private String b36 = "/broad/1KG/reference/human_b36_both.fasta"; private String buildRootCmd(String ref, List bams, List intervals) { StringBuilder bamBuilder = new StringBuilder(); @@ -59,7 +57,7 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest { String[] intervals = {"1:10,000,000-10,002,000","1:10,003,000-10,004,000"}; String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam"}; - String cmd = buildRootCmd(b36,new ArrayList(Arrays.asList(bams)), new ArrayList(Arrays.asList(intervals))) + " --maxMappingQuality 0"; + String cmd = buildRootCmd(b36KGReference,new ArrayList(Arrays.asList(bams)), new ArrayList(Arrays.asList(intervals))) + " --maxMappingQuality 0"; WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList()); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java index 2bc90ed85..f027109f1 100644 --- a/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java @@ -18,8 +18,6 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { private boolean RUN_TESTS = true; private String root = "-T DepthOfCoverage "; - private String hg18 = "/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"; - private String b36 = "/broad/1KG/reference/human_b36_both.fasta"; private String buildRootCmd(String ref, List bams, List intervals) { StringBuilder bamBuilder = new StringBuilder(); @@ -53,7 +51,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"}; String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"}; - String cmd = buildRootCmd(hg18,new ArrayList(Arrays.asList(bams)),new ArrayList(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv -ct 10 -ct 15 -ct 20 -ct 25"; + String cmd = buildRootCmd(hg18Reference,new ArrayList(Arrays.asList(bams)),new ArrayList(Arrays.asList(intervals))) + " -mmq 0 -mbq 0 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv -ct 10 -ct 15 -ct 20 -ct 25"; WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList()); // now add the expected files that get generated @@ -88,7 +86,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest { String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"}; String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"}; - String cmd = buildRootCmd(hg18,new ArrayList(Arrays.asList(bams)),new ArrayList(Arrays.asList(intervals))) + " -mmq 0 -mbq 5 --maxBaseQuality 4 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv"; + String cmd = buildRootCmd(hg18Reference,new ArrayList(Arrays.asList(bams)),new ArrayList(Arrays.asList(intervals))) + " -mmq 0 -mbq 5 --maxBaseQuality 4 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv"; WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList()); spec.addAuxFile("d570c27d82a80ebd2852e9d34aff4e87",baseOutputFile); 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 541ad7250..48c0215cc 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 " + 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", + "-T BamToFastq -R " + b36KGReference + " -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("49431d567524d6fd32a569504b25f212")); executeTest("testBamToFasta", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( - "-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", + "-T BamToFastq -reverse -R " + b36KGReference + " -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("f3a4a39d36270136c12bb1315fdb7dff")); 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 0ac220f8b..92829806c 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 " + 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", + "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -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 " + oneKGLocation + "reference/human_b36_both.fasta -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -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 " + b36KGReference + " -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -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 " + oneKGLocation + "reference/human_b36_both.fasta -B snps,GeliText," + 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", + "-T FastaAlternateReferenceMaker -R " + b36KGReference + " -B snps,GeliText," + 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 8c9ba85f3..af7ca0991 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java @@ -8,7 +8,7 @@ import java.util.Arrays; public class VariantFiltrationIntegrationTest extends WalkerTest { public static String baseTestString() { - return "-T VariantFiltration -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta"; + return "-T VariantFiltration -o %s -R " + b36KGReference; } 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 18de01950..2e4bb0529 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 testPooled1() { // WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( -// "-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, +// "-T UnifiedGenotyper -R " + b36KGReference + " -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("c91f44a198cd7222520118726ea806ca")); // executeTest("testPooled1", spec); // } @@ -34,7 +34,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testMultiSamplePilot1Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-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", 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000", 1, Arrays.asList("3a402233264e21a84d421e3a4ea64768")); executeTest("testMultiSamplePilot1 - Joint Estimate", spec); } @@ -42,7 +42,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testMultiSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-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", 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000", 1, Arrays.asList("79736b3e955a16b30f827b2786fc08b1")); executeTest("testMultiSamplePilot2 - Joint Estimate", spec); } @@ -50,7 +50,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testSingleSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-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", 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000", 1, Arrays.asList("b8d93c6fcb4b17d454cdcbfc4b43f076")); executeTest("testSingleSamplePilot2 - Joint Estimate", spec); } @@ -66,17 +66,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { String md5 = "098802639cfab1b777c96d38376f118a"; WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000", 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000", 1, Arrays.asList(md5)); executeTest("test parallelization (single thread)", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 2", 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 2", 1, Arrays.asList(md5)); executeTest("test parallelization (2 threads)", spec2); WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - "-T UnifiedGenotyper -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 4", 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,075,000 -nt 4", 1, Arrays.asList(md5)); executeTest("test parallelization (4 threads)", spec3); } @@ -98,7 +98,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-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 " + entry.getKey(), 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 " + entry.getKey(), 1, Arrays.asList(entry.getValue())); executeTest(String.format("testParameter[%s]", entry.getKey()), spec); } @@ -107,12 +107,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testConfidence() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( - "-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 -stand_call_conf 10 ", 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1, Arrays.asList("4937bab94b0bae1aa61cdf3a06cb49e8")); executeTest("testConfidence1", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - "-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 -stand_emit_conf 10 ", 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,010,000 -stand_emit_conf 10 ", 1, Arrays.asList("f8b722dad5c4868a4bba246eef83f96d")); executeTest("testConfidence2", spec2); } @@ -131,7 +131,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-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 -vf " + entry.getKey(), 1, + "-T UnifiedGenotyper -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -vf " + entry.getKey(), 1, Arrays.asList(entry.getValue())); executeTest(String.format("testOtherFormat[%s]", entry.getKey()), spec); } @@ -154,7 +154,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-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 --heterozygosity " + entry.getKey(), 1, + "-T UnifiedGenotyper -vf GELI -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 --heterozygosity " + entry.getKey(), 1, Arrays.asList(entry.getValue())); executeTest(String.format("testHeterozyosity[%s]", entry.getKey()), spec); } @@ -174,7 +174,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { for ( Map.Entry entry : e.entrySet() ) { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-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 " + entry.getKey(), 1, + "-T UnifiedGenotyper -vf GELI -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm " + entry.getKey(), 1, Arrays.asList(entry.getValue())); executeTest(String.format("testOtherBaseCallModel[%s]", entry.getKey()), spec); } @@ -189,7 +189,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiTechnologies() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper" + - " -R " + oneKGLocation + "reference/human_b36_both.fasta" + + " -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" + " -varout %s" + " -L 1:10,000,000-10,100,000" + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java index ac84a8ac7..756416d5c 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java @@ -10,7 +10,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { @Test public void testUnifiedGenotyperWholeGenome() { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T UnifiedGenotyper" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -L chr1:1-50,000,000" + @@ -24,7 +24,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { @Test public void testUnifiedGenotyperWholeExome() { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T UnifiedGenotyper" + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + @@ -38,7 +38,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { @Test public void testUnifiedGenotyperWGParallel() { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T UnifiedGenotyper" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -L chr1:1-50,000,000" + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index 57f4866f2..eea1a4ca2 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -11,7 +11,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { public void testRealignerLod5() { String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "18fca887d1eb7dc300e717ae03b9da62"}; WalkerTestSpec spec = new WalkerTestSpec( - "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", + "-T IndelRealigner -noPG -LOD 5 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", 2, Arrays.asList(md5s)); executeTest("test realigner lod5", spec); @@ -21,7 +21,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { public void testRealignerLod50() { String[] md5s = {"9247b1437ec3b9bc96590524f245220c", "9537e4f195ce5840136f60fb61201369"}; WalkerTestSpec spec = new WalkerTestSpec( - "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", + "-T IndelRealigner -noPG -LOD 50 -maxConsensuses 100 -greedy 100 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10030000 -compress 1 -targetIntervals " + validationDataLocation + "cleaner.test.intervals -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe", 2, Arrays.asList(md5s)); executeTest("test realigner lod50", spec); @@ -31,7 +31,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest { public void testRealignerKnownsOnly() { String[] md5s = {"7084d4e543bc756730ab306768028530", "1091436c40d5ba557d85662999cc0c1d"}; WalkerTestSpec spec = new WalkerTestSpec( - "-T IndelRealigner -noPG -LOD 1.0 -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf4 -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly", + "-T IndelRealigner -noPG -LOD 1.0 -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.chrom1.SLX.SRP000032.2009_06.bam -L 1:10023000-10076000 -compress 1 -targetIntervals " + validationDataLocation + "NA12878.indels.intervals -B knownIndels,VCF," + validationDataLocation + "NA12878.indels.vcf4 -O %s -stats %s --sortInCoordinateOrderEvenThoughItIsHighlyUnsafe -knownsOnly", 2, Arrays.asList(md5s)); executeTest("test realigner known indels only", spec); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java index 215e0e784..44ff3b0f9 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java @@ -10,7 +10,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest { public void testRealigner() { WalkerTestSpec spec1 = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T IndelRealigner" + " -LOD 5" + " -maxConsensuses 100" + @@ -25,7 +25,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest { executeTest("testIndelRealignerWholeGenome", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T IndelRealigner" + " -LOD 5" + " -maxConsensuses 100" + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java index 230a25736..44fc13b13 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java @@ -11,19 +11,19 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest { public void testIntervals() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( - "-T RealignerTargetCreator -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates", + "-T RealignerTargetCreator -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates", 1, Arrays.asList("d21e83a8b0d3f63acd9ca3b0b636e515")); executeTest("test standard", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - "-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -R " + oneKGLocation + "reference/human_b36_both.fasta -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates", + "-T RealignerTargetCreator -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_b36.rod -R " + b36KGReference + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000 -o %s --realignReadsWithBadMates", 1, Arrays.asList("bfccfa50f62d10ee2fe8cfa68fb70002")); executeTest("test dbsnp", spec2); WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec( - "-T RealignerTargetCreator -R " + oneKGLocation + "reference/human_b36_both.fasta -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s", + "-T RealignerTargetCreator -R " + b36KGReference + " -B indels,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4 -BTI indels -o %s", 1, Arrays.asList("1a11cfc9cc713617c82bdec503ebe02a")); //TODO -- Guillermo, re-enable this when the VCF->VC conversion works with indels diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java index 21aa83a3b..63b9ee969 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java @@ -10,7 +10,7 @@ public class RealignerTargetCreatorPerformanceTest extends WalkerTest { public void testRealignerTargetCreator() { WalkerTestSpec spec1 = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T RealignerTargetCreator" + " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + @@ -21,7 +21,7 @@ public class RealignerTargetCreatorPerformanceTest extends WalkerTest { executeTest("testRealignerTargetCreatorWholeGenome", spec1); WalkerTestSpec spec2 = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T RealignerTargetCreator" + " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + 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 b906cdd4e..05db302b2 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java @@ -28,7 +28,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -T CountCovariates" + " -I " + bam + @@ -64,7 +64,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); if ( paramsFile != null ) { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -T TableRecalibration" + " -I " + bam + ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) @@ -90,7 +90,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -T CountCovariates" + " -I " + bam + " -L 1:1-1,000" + @@ -115,7 +115,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); if ( paramsFile != null ) { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -T TableRecalibration" + " -I " + bam + ( bam.equals( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" ) @@ -144,7 +144,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -T CountCovariates" + " -I " + bam + @@ -172,7 +172,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); if ( paramsFile != null ) { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -T TableRecalibration" + " -I " + bam + " -outputBam %s" + @@ -201,7 +201,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -B dbsnp,VCF," + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + @@ -225,7 +225,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -B anyNameABCD,VCF," + validationDataLocation + "vcfexample3.vcf" + " -T CountCovariates" + " -I " + bam + @@ -253,7 +253,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -T CountCovariates" + " -I " + bam + @@ -285,7 +285,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); if ( paramsFile != null ) { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -T TableRecalibration" + " -I " + bam + " -L 1:10,100,000-10,300,000" + @@ -312,7 +312,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -T CountCovariates" + " -I " + bam + @@ -340,7 +340,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest { System.out.printf("PARAMS FOR %s is %s%n", bam, paramsFile); if ( paramsFile != null ) { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " -T TableRecalibration" + " -I " + bam + " -outputBam %s" + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java index 0f7243ef0..3a77ce7e6 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java @@ -10,7 +10,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { private void testCountCovariatesWholeGenomeRunner(String moreArgs) { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T CountCovariates" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -L chr1:1-50,000,000" + @@ -24,7 +24,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { private void testCountCovariatesWholeExomeRunner(String moreArgs) { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T CountCovariates" + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + @@ -49,7 +49,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { @Test public void testTableRecalibratorWholeGenome() { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T TableRecalibration" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -L chr1:1-50,000,000" + @@ -64,7 +64,7 @@ public class RecalibrationWalkersPerformanceTest extends WalkerTest { @Test public void testTableRecalibratorWholeExome() { WalkerTestSpec spec = new WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T TableRecalibration" + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java index 000328a35..25861c632 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java @@ -9,7 +9,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest { @Test public void testProbes() { String testVCF = validationDataLocation + "complexExample.vcf4"; - String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T PickSequenomProbes -L 1:10,000,000-11,000,000 -B input,VCF,"+testVCF+" -o %s"; + String testArgs = "-R " + b36KGReference + " -T PickSequenomProbes -L 1:10,000,000-11,000,000 -B input,VCF,"+testVCF+" -o %s"; WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, Arrays.asList("71e717e1813791575231f884b51c0aa3")); executeTest("Test probes", spec); @@ -19,7 +19,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest { public void testProbesUsingDbSNPMask() { String testVCF = validationDataLocation + "pickSeqIntegrationTest.vcf"; String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R " - + oneKGLocation + "reference/human_b36_both.fasta -omitWindow -nameConvention " + + b36KGReference + " -omitWindow -nameConvention " + "-project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation + "pickSeqIntegrationTest.interval_list -B input,VCF,"+testVCF+" -o %s"; WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, @@ -33,7 +33,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest { public void testProbesUsingDbSNPMaskWithNMW1() { String testVCF = validationDataLocation + "pickSeqIntegrationTest.vcf"; String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R " - + oneKGLocation + "reference/human_b36_both.fasta -omitWindow -nameConvention " + + b36KGReference + " -omitWindow -nameConvention " + "-nmw 1 -project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation + "pickSeqIntegrationTest.interval_list -B input,VCF,"+testVCF+" -o %s"; WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java index 49652dbc6..54109d1a2 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java @@ -9,7 +9,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest { @Test public void testSNPs() { String testPedFile = validationDataLocation + "Sequenom_Test_File.txt"; - String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s"; + String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s"; WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, Arrays.asList("2dab4630f40b76c0762de83fcbb60d09")); executeTest("Test SNPs", spec); @@ -19,7 +19,7 @@ public class SequenomValidationConverterIntegrationTest extends WalkerTest { // TODO- need to be reenabled when PED reader tracks gets updated to read indels correctly public void testIndels() { String testPedFile = validationDataLocation + "pilot2_indel_validation.renamed.ped"; - String testArgs = "-R "+oneKGLocation+"reference/human_b36_both.fasta -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s"; + String testArgs = "-R "+b36KGReference + " -T SequenomValidationConverter -B sequenom,Plink,"+testPedFile+" -o %s"; WalkerTest.WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1, Arrays.asList("fad2dd71550dec064d458c4aa83e4de9")); executeTest("Test Indels", spec); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java index cb346e567..ad0e36298 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java @@ -10,7 +10,7 @@ import java.util.Map; public class VariantEvalIntegrationTest extends WalkerTest { private static String cmdRoot = "-T VariantEval" + - " -R " + oneKGLocation + "reference/human_b36_both.fasta"; + " -R " + b36KGReference; private static String root = cmdRoot + " -D " + GATKDataLocation + "dbsnp_129_b36.rod" + @@ -99,13 +99,13 @@ public class @Test public void testVEGenomicallyAnnotated() { - String vecmd = "-T VariantEval " + - "-R " + oneKGLocation + "reference/human_b36_both.fasta " + - "-L 21 " + - "-D " + GATKDataLocation + "dbsnp_129_b36.rod " + - "-E CountFunctionalClasses -noStandard " + - "-B eval,VCF," + validationDataLocation + "test.filtered.maf_annotated.vcf " + - "-o %s"; + String vecmd = "-T VariantEval" + + " -R " + b36KGReference + + " -L 21" + + " -D " + GATKDataLocation + "dbsnp_129_b36.rod" + + " -E CountFunctionalClasses -noStandard" + + " -B eval,VCF," + validationDataLocation + "test.filtered.maf_annotated.vcf" + + " -o %s"; String md5 = "d41d8cd98f00b204e9800998ecf8427e"; WalkerTestSpec spec = new WalkerTestSpec(vecmd, 1, Arrays.asList(md5)); diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java index cc08accbe..1fc5df0c1 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java @@ -19,7 +19,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { String md5 = entry.getValue(); WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -T GenerateVariantClusters" + " -B input,VCF," + vcf + @@ -47,7 +47,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest { if ( paramsFile != null ) { File file = createTempFile("cluster",".vcf"); WalkerTestSpec spec = new WalkerTestSpec( - "-R " + oneKGLocation + "reference/human_b36_both.fasta" + + "-R " + b36KGReference + " --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" + " -T VariantRecalibrator" + " -B input,VCF," + vcf + diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java index 13a483eca..96570a6a6 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java @@ -36,7 +36,7 @@ import java.util.Arrays; public class CombineVariantsIntegrationTest extends WalkerTest { public static String baseTestString(String args) { - return "-T CombineVariants -L 1:1-50,000,000 -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta" + args; + return "-T CombineVariants -L 1:1-50,000,000 -o %s -R " + b36KGReference + args; } public void test1InOut(String file, String md5) { diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java index 713ca4129..4f3fe5349 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java @@ -38,7 +38,7 @@ public class LiftoverVariantsIntegrationTest extends WalkerTest { @Test public void testb36Tohg19() { WalkerTestSpec spec = new WalkerTestSpec( - "-T LiftoverVariants -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta -B variant,vcf," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict " + oneKGLocation + "reference/human_g1k_v37.dict", + "-T LiftoverVariants -o %s -R " + b36KGReference + " -B variant,vcf," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -chain " + validationDataLocation + "b36ToHg19.broad.over.chain -dict /seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.dict", 1, Arrays.asList("1637877892a019061e74eb3d9a9d100f")); executeTest("test b36 to hg19", spec); diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java index ab2f70cb4..3b0758da2 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java @@ -36,7 +36,7 @@ public class BeagleIntegrationTest extends WalkerTest { @Test public void testBeagleOutput() { WalkerTestSpec spec = new WalkerTestSpec( - "-T BeagleOutputToVCF -R " + oneKGLocation + "reference/human_g1k_v37.fasta " + + "-T BeagleOutputToVCF -R " + hg19Reference + " " + "-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " + "-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " + "-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " + @@ -48,7 +48,7 @@ public class BeagleIntegrationTest extends WalkerTest { @Test public void testBeagleInput() { WalkerTestSpec spec = new WalkerTestSpec( - "-T ProduceBeagleInput -R " + oneKGLocation + "reference/human_g1k_v37.fasta " + + "-T ProduceBeagleInput -R " + hg19Reference + " " + "-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " + "-beagle %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e")); executeTest("test BeagleInput", spec); 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 3c62437cf..32bf7bb2f 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java @@ -10,8 +10,8 @@ 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 " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + - "-T ClipReads " + + "-R " + hg18Reference + + " -T ClipReads " + "-I " + validationDataLocation + "clippingReadsTest.bam " + "-o %s " + "-ob %s " + args, @@ -43,7 +43,7 @@ public class ClipReadsWalkersIntegrationTest extends WalkerTest { @Test public void testUseOriginalQuals() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - "-R " + seqLocation + "references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta" + + "-R " + hg18Reference + " -T ClipReads" + " -I " + validationDataLocation + "originalQuals.chr1.1-1K.bam" + " -L chr1:1-1,000" + diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java index e9f337fde..95b2ddcd0 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java @@ -38,7 +38,7 @@ public class HLACallerIntegrationTest extends WalkerTest { @Test public void testFindClosestHLA() { WalkerTestSpec spec = new WalkerTestSpec( - "-T FindClosestHLA -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -PolymorphicSites " + validationDataLocation + "HLA_POLYMORPHIC_SITES.txt -o %s", 1, + "-T FindClosestHLA -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + b36KGReference + " -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -PolymorphicSites " + validationDataLocation + "HLA_POLYMORPHIC_SITES.txt -o %s", 1, Arrays.asList("a49b6f54a4585d1dd958c55a5523427d")); executeTest("test FindClosestHLA", spec); } @@ -46,7 +46,7 @@ public class HLACallerIntegrationTest extends WalkerTest { @Test public void testCalculateBaseLikelihoods() { WalkerTestSpec spec = new WalkerTestSpec( - "-T CalculateBaseLikelihoods -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 0 -o %s", 1, + "-T CalculateBaseLikelihoods -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + b36KGReference + " -L " + intervals + " -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 0 -o %s", 1, Arrays.asList("98e64882f93bf7550457bee4182caab6")); executeTest("test CalculateBaseLikelihoods", spec); } @@ -54,7 +54,7 @@ public class HLACallerIntegrationTest extends WalkerTest { @Test public void testHLACaller() { WalkerTestSpec spec = new WalkerTestSpec( - "-T HLACaller -noVerbose -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + oneKGLocation + "reference/human_b36_both.fasta -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 5 -HLAfrequencies " + validationDataLocation + "HLA_FREQUENCIES.txt -bl " + validationDataLocation + "HLA_HISEQ.baselikelihoods -o %s", 1, + "-T HLACaller -noVerbose -I " + validationDataLocation + "NA12878.HISEQ.HLA.bam -R " + b36KGReference + " -L " + intervals + " -useInterval " + intervals + " -HLAdictionary " + validationDataLocation + "HLA_DICTIONARY.txt -filter " + validationDataLocation + "HLA_HISEQ.filter -maxAllowedMismatches 6 -minRequiredMatches 5 -HLAfrequencies " + validationDataLocation + "HLA_FREQUENCIES.txt -bl " + validationDataLocation + "HLA_HISEQ.baselikelihoods -o %s", 1, Arrays.asList("f9931b378bde213e71fca6ecaa24b48b")); executeTest("test HLACaller", spec); } diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/HapmapPoolAllelicInfoIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/HapmapPoolAllelicInfoIntegrationTest.java deleted file mode 100755 index c806265cd..000000000 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/HapmapPoolAllelicInfoIntegrationTest.java +++ /dev/null @@ -1,58 +0,0 @@ -package org.broadinstitute.sting.playground.gatk.walkers; - -import org.broadinstitute.sting.WalkerTest; -import org.junit.Test; - -import java.util.Arrays; - -/** - * Created by IntelliJ IDEA. - * User: chartl - * Date: Nov 18, 2009 - * Time: 9:29:31 AM - * To change this template use File | Settings | File Templates. - * -public class HapmapPoolAllelicInfoIntegrationTest extends WalkerTest { - - @Test - public void testFHSPool3() { - String test_args = "-T HapmapPoolAllelicInfo -samples /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_samples.txt " - + "-B /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_sample_paths.txt " - + "-B calls,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_raw_calls.geli " - + "-I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHSP_pool3_test.bam " - + "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -of %s " - + "-ps 40 -L /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_test_intervals.interval_list -q 0"; - String md5ForThisTest = "da1222d7514f247eae066134d8e3cde3"; - WalkerTestSpec spec = new WalkerTestSpec(test_args, 1, Arrays.asList(md5ForThisTest)); - executeTest("Pool 3 of FHS Pilot on testbed intervals", spec); - } - - @Test - public void testFHSPool3NoIntervals() { - String test_args = "-T HapmapPoolAllelicInfo -samples /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_samples.txt " - + "-B /humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_sample_paths.txt " - + "-B calls,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/FHS_pilot_pool3_raw_calls.geli " - + "-I /humgen/gsa-scr1/GATK_Data/Validation_Data/FHSP_pool3_test.bam " - + "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -of %s " - + "-ps 40 -q 0"; - String md5ForThisTest = "9ee3f390657c32c9c4fbe654bcd3cdf9"; - WalkerTestSpec spec = new WalkerTestSpec(test_args, 1, Arrays.asList(md5ForThisTest)); - executeTest("Testing hapmap sites without reads at them (no testbed intervals)", spec); - } - - @Test - public void testSmallPool() { - - String test_args = "-T HapmapPoolAllelicInfo -samples /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878_NA12891_samples.txt " - +"-B NA12878,GFF,/humgen/gsa-scr1/andrewk/hapmap_1kg/gffs/NA12878.gff " - +"-B NA12891,GFF,/humgen/gsa-scr1/andrewk/hapmap_1kg/gffs/NA12891.gff " - +"-I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12891.a2b.recal.annotation_subset.bam " - +"-L chr1:14000000-18000000 -B calls,Variants,/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12891.a2b.ssg1b.geli.calls " - +"-of %s -R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta -ps 2 -q 0"; - String md5ForThisTest = "cc81a9d8279e7b6ad50f9dc1f19a7419"; - WalkerTestSpec spec = new WalkerTestSpec(test_args, 1, Arrays.asList(md5ForThisTest)); - executeTest("Test on pool of two individuals -- CEU father+daughter chips against subset of the father's calls; power at lod 3", spec); - - } -} -*/ diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java index e3de2ddfc..1cf80f966 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java @@ -14,7 +14,7 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest { TODO put this test back in once it gets faster. String[] md5 = {"d19d6d1eb52fb09e7493653dc645d92a"}; WalkerTestSpec spec = new WalkerTestSpec( - "-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " + + "-T GenomicAnnotator -R " + b36KGReference + " " + "-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " + "-B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt " + "-m " + //generate many records from one input record if necessary @@ -28,13 +28,13 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest { String[] md5WithDashSArg = {"94edacdaee0dd58508d35d4d6040e31b"}; WalkerTestSpec specWithSArg = new WalkerTestSpec( - "-T GenomicAnnotator -R " + oneKGLocation + "reference/human_b36_both.fasta " + - "-B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf " + - "-B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt " + - "-m " + //generate many records from one input record if necessary - "-vcf %s " + - "-BTI variant " + - "-s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet", + "-T GenomicAnnotator -R " + b36KGReference + + " -B variant,vcf,/humgen/gsa-hpprojects/GATK/data/Annotations/examples/CEU_hapmap_nogt_23_subset.vcf" + + " -B dbsnp,AnnotatorInputTable,/humgen/gsa-hpprojects/GATK/data/Annotations/dbsnp/b130/snp130-b36-only-the-SNPs.txt" + + " -m" + //generate many records from one input record if necessary + " -vcf %s" + + " -BTI variant" + + " -s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet", 1, Arrays.asList(md5WithDashSArg)); executeTest("test with dbSNP and -s arg", specWithSArg); diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java index d637ae4f5..62f53c29a 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java @@ -10,10 +10,10 @@ import java.util.List; public class DuplicatesWalkersIntegrationTest extends WalkerTest { public void testCounter(String name, String args, String md5) { WalkerTestSpec spec = new WalkerTestSpec( - "-T CountDuplicates " + - "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + - "-I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam " + - "-o %s " + args, + "-T CountDuplicates" + + " -R " + hg18Reference + + " -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam" + + " -o %s " + args, 1, // just one output file Arrays.asList("tmp"), Arrays.asList(md5)); @@ -25,10 +25,10 @@ public class DuplicatesWalkersIntegrationTest extends WalkerTest { public void testCombiner(String name, String args, String md51, String md52) { WalkerTestSpec spec = new WalkerTestSpec( - "-T CombineDuplicates " + - "-R /seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta " + - "-I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam " + - "-o %s --outputBAM %s " + args, + "-T CombineDuplicates" + + " -R " + hg18Reference + + " -I /humgen/gsa-hpprojects/GATK/data/Validation_Data/TCGA-06-0188.aligned.duplicates_marked.bam" + + " -o %s --outputBAM %s " + args, 2, // just one output file Arrays.asList("tmp", "bam"), Arrays.asList(md51, md52)); diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java index 9a6438cfb..e6a7a61f4 100644 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java @@ -11,7 +11,7 @@ import java.util.Arrays; public class RodSystemValidationIntegrationTest extends WalkerTest { public static String baseTestString1KG() { - return "-T RodSystemValidation -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta"; + return "-T RodSystemValidation -o %s -R " + b36KGReference; } diff --git a/java/test/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelectIntegrationTest.java b/java/test/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelectIntegrationTest.java index e4f6ee26e..edefa76f2 100755 --- a/java/test/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelectIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelectIntegrationTest.java @@ -33,7 +33,7 @@ import java.util.Arrays; public class VariantSelectIntegrationTest extends WalkerTest { public static String baseTestString() { - return "-T VariantSelect -o %s -R " + oneKGLocation + "reference/human_b36_both.fasta"; + return "-T VariantSelect -o %s -R " + b36KGReference; } diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java index d4ec57808..08c0d92a2 100644 --- a/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java @@ -24,7 +24,7 @@ public class GenomeLocUnitTest extends BaseTest { @BeforeClass public static void init() throws FileNotFoundException { // sequence - seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")); + seq = new IndexedFastaSequenceFile(new File(hg18Reference)); GenomeLocParser.setupRefContigOrdering(seq); } diff --git a/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java b/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java index 0ca87e0fe..eb21be98a 100644 --- a/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java @@ -23,7 +23,7 @@ public class BedParserUnitTest extends BaseTest { @BeforeClass public static void beforeTests() { - seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); + seq = new IndexedFastaSequenceFile(new File(b36KGReference)); GenomeLocParser.setupRefContigOrdering(seq); } diff --git a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java index ab7416f1b..30a77a276 100755 --- a/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterUnitTest.java @@ -66,7 +66,7 @@ public class GLFWriterUnitTest extends BaseTest { @BeforeClass public static void beforeTests() { IndexedFastaSequenceFile seq; - seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta")); + seq = new IndexedFastaSequenceFile(new File(b36KGReference)); GenomeLocParser.setupRefContigOrdering(seq); } diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java index fb8ff61bb..5451c5cce 100644 --- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java +++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java @@ -37,7 +37,7 @@ public class VCFWriterUnitTest extends BaseTest { @BeforeClass public static void beforeTests() { - IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")); + IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(hg18Reference)); GenomeLocParser.setupRefContigOrdering(seq); }