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Removed hard-coded pointers to references 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3934 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-04 17:59:37 +00:00
parent a47824d680
commit 340bd0e2c1
48 changed files with 125 additions and 237 deletions
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61
java/test/org/broadinstitute/sting/BaseTest.java
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@ -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);

2
java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java
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@ -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" +

2
java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUnitTest.java
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@ -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);
}

2
java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewUnitTest.java
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@ -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);
}

2
java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java
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@ -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);
}

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

2
java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceUnitTest.java
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@ -62,7 +62,7 @@ public class SAMBAMDataSourceUnitTest extends BaseTest {
fl = new ArrayList<File>();
// 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());
}

2
java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorUnitTest.java
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@ -73,7 +73,7 @@ public class BoundedReadIteratorUnitTest extends BaseTest {
fl = new ArrayList<File>();
// 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());
}

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

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

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

2
java/test/org/broadinstitute/sting/gatk/refdata/features/vcf4/VCF4UnitTest.java
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@ -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());
}

3
java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java
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@ -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();

2
java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java
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@ -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);
}

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

8
java/test/org/broadinstitute/sting/gatk/walkers/VariantsToVCFIntegrationTest.java
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@ -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",

2
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -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

4
java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java
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@ -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<String> bams, List<String> 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<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals))) + " --maxMappingQuality 0";
String cmd = buildRootCmd(b36KGReference,new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals))) + " --maxMappingQuality 0";
WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList<String>());

6
java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java
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@ -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<String> bams, List<String> 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<String>(Arrays.asList(bams)),new ArrayList<String>(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<String>(Arrays.asList(bams)),new ArrayList<String>(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<String>());
// 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<String>(Arrays.asList(bams)),new ArrayList<String>(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<String>(Arrays.asList(bams)),new ArrayList<String>(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<String>());
spec.addAuxFile("d570c27d82a80ebd2852e9d34aff4e87",baseOutputFile);

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 " + 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);

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 " + 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);

2
java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -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;
}

28
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

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

6
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java
View File

@ -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" +

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

@ -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);

4
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java
View File

@ -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" +

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

@ -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

4
java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorPerformanceTest.java
View File

@ -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" +

24
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -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" +

8
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersPerformanceTest.java
View File

@ -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" +

6
java/test/org/broadinstitute/sting/gatk/walkers/sequenom/PickSequenomProbesIntegrationTest.java
View File

@ -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,

4
java/test/org/broadinstitute/sting/gatk/walkers/sequenom/SequenomValidationConverterIntegrationTest.java
View File

@ -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);

16
java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalIntegrationTest.java
View File

@ -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));

4
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -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 +

2
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -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) {

2
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariantsIntegrationTest.java
View File

@ -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);

4
java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
View File

@ -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);

6
java/test/org/broadinstitute/sting/playground/gatk/walkers/ClipReadsWalkersIntegrationTest.java
View File

@ -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" +

6
java/test/org/broadinstitute/sting/playground/gatk/walkers/HLAcaller/HLACallerIntegrationTest.java
View File

@ -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);
}

58
java/test/org/broadinstitute/sting/playground/gatk/walkers/HapmapPoolAllelicInfoIntegrationTest.java
View File

@ -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);
}
}
*/

16
java/test/org/broadinstitute/sting/playground/gatk/walkers/annotator/GenomicAnnotatorIntegrationTest.java
View File

@ -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);

16
java/test/org/broadinstitute/sting/playground/gatk/walkers/duplicates/DuplicatesWalkersIntegrationTest.java
View File

@ -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));

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java
View File

@ -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;
}

2
java/test/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VariantSelectIntegrationTest.java
View File

@ -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;
}

2
java/test/org/broadinstitute/sting/utils/GenomeLocUnitTest.java
View File

@ -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);
}

2
java/test/org/broadinstitute/sting/utils/bed/BedParserUnitTest.java
View File

@ -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);
}

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

@ -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);
}

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

@ -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);
}