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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
This commit is contained in:
aaron 2009-12-29 07:40:48 +00:00
parent 9d263b2565
commit a34c2442c0
34 changed files with 145 additions and 147 deletions
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18
java/test/org/broadinstitute/sting/BaseTest.java
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@ -34,14 +34,16 @@ import java.util.Enumeration;
* Class BaseTest
* <p/>
* 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");
}

2
java/test/org/broadinstitute/sting/alignment/AlignerIntegrationTest.java
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@ -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));

2
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java
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@ -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 {

2
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByIntervalTest.java
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@ -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);
}

2
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java
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@ -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);
}

2
java/test/org/broadinstitute/sting/gatk/iterators/IntervalOverlapIteratorTest.java
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@ -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;

2
java/test/org/broadinstitute/sting/gatk/iterators/PlusOneFixIteratorTest.java
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@ -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;

6
java/test/org/broadinstitute/sting/gatk/refdata/ReferenceOrderedDataTest.java
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@ -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<String> lst = new ArrayList<String>();
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<String> lst = new ArrayList<String>();
ReferenceOrderedData.extractRodsFromFile(lst,file);
ReferenceOrderedData.extractRodsFromFile(lst,file2);

4
java/test/org/broadinstitute/sting/gatk/refdata/RodGLFTest.java
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@ -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;

4
java/test/org/broadinstitute/sting/gatk/refdata/RodVCFTest.java
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@ -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");
}

2
java/test/org/broadinstitute/sting/gatk/refdata/rodDbSNPTest.java
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@ -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");
}

4
java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java
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@ -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<File> bamList;
private Walker countReadWalker;
private File output;

4
java/test/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageIntegrationTest.java
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@ -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<String, String> expectations = new HashMap<String, String>();
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);

4
java/test/org/broadinstitute/sting/gatk/walkers/PileupWalkerIntegrationTest.java
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@ -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));

22
java/test/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkewIntegrationTest.java
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@ -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));

22
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
View File

@ -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);
}

10
java/test/org/broadinstitute/sting/gatk/walkers/concordance/CallsetConcordanceIntegrationTest.java
View File

@ -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);
}

4
java/test/org/broadinstitute/sting/gatk/walkers/fasta/BamToFastqIntegrationTest.java
View File

@ -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);

6
java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
View File

@ -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);

12
java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -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);
}

26
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -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<String, String> 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<String, String> 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<Double, String> 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<String, String> 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" +

6
java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
View File

@ -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);

6
java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalsIntegrationTest.java
View File

@ -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);

46
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -16,21 +16,21 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariates1() {
HashMap<String, String> e = new HashMap<String, String>();
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<String, String> 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<String, String> e = new HashMap<String, String>();
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<String, String> 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<String, String> e = new HashMap<String, String>();
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<String, String> 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<String, String> e = new HashMap<String, String>();
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<String, String> 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<String, String> e = new HashMap<String, String>();
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<String, String> 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<String, String> e = new HashMap<String, String>();
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<String, String> 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<String, String> e = new HashMap<String, String>();
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<String, String> 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" +

8
java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java
View File

@ -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"); }

24
java/test/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalkerIntegrationTest.java
View File

@ -36,8 +36,8 @@ public class VariantEvalWalkerIntegrationTest extends WalkerTest {
*/
for ( Map.Entry<String, String> 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<String> md5 = new ArrayList<String>();
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 " +

8
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCFIntegrationTest.java
View File

@ -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",

4
java/test/org/broadinstitute/sting/utils/GenotypeUtilsTest.java
View File

@ -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");
}

10
java/test/org/broadinstitute/sting/utils/bed/BedParserTest.java
View File

@ -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");
}

2
java/test/org/broadinstitute/sting/utils/fasta/FastaSequenceIndexTest.java
View File

@ -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

2
java/test/org/broadinstitute/sting/utils/genotype/glf/GLFReaderTest.java
View File

@ -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;

2
java/test/org/broadinstitute/sting/utils/genotype/glf/GLFWriterTest.java
View File

@ -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");
}

2
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFIntegrationTest.java
View File

@ -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);
}

12
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFReaderTest.java
View File

@ -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");