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Update integration tests to use the new ROD syntax. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4112 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-08-25 18:13:30 +00:00
parent 14198b74d5
commit bf0b6bd486
21 changed files with 73 additions and 73 deletions
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2
java/src/org/broadinstitute/sting/commandline/ArgumentMatches.java
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@ -204,6 +204,6 @@ public class ArgumentMatches implements Iterable<ArgumentMatch> {
* @return A unique set of matches.
*/
private Set<ArgumentMatch> getUniqueMatches() {
return new HashSet<ArgumentMatch>( argumentMatches.values() );
return new LinkedHashSet<ArgumentMatch>( argumentMatches.values() );
}
}

4
java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java
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@ -14,7 +14,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
private static String root = cmdRoot +
" -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +
" -B vcf,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
" -B:vcf,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf";
static HashMap<String, String> expectations = new HashMap<String, String>();
static {
@ -46,7 +46,7 @@ public class VariantContextIntegrationTest extends WalkerTest {
public void testToVCF() {
// this really just tests that we are seeing the same number of objects over all of chr1
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -B vcf,VCF," + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
WalkerTestSpec spec = new WalkerTestSpec( cmdRoot + " -B:vcf,VCF " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.500.vcf -L 1:1-1000000 -o %s --outputVCF %s",
2, // just one output file
Arrays.asList("e3c35d0c4b5d4935c84a270f9df0951f", "f4db5f7346792b1155693722bc190f63"));
executeTest("testToVCF", spec);

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

@ -24,7 +24,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B variant,GeliText," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.variants.geli.calls" +
" -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" +
" -sample NA123AB" +
@ -41,7 +41,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B variant,GeliText," + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.lod5.genotypes.geli.calls" +
" -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" +
" -sample NA123AB" +
@ -58,7 +58,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B variant,HapMap," + validationDataLocation + "rawHapMap.yri.chr1.txt" +
" -B:variant,HapMap " + validationDataLocation + "rawHapMap.yri.chr1.txt" +
" -T VariantsToVCF" +
" -L 1:1-1,000,000" +
" -o %s",
@ -74,7 +74,7 @@ public class VariantsToVCFIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B variant,VCF," + validationDataLocation + "complexExample.vcf4" +
" -B:variant,VCF " + validationDataLocation + "complexExample.vcf4" +
" -T VariantsToVCF" +
" -o %s",
1, // just one output file

24
java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java
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@ -14,7 +14,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testHasAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
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,
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("89b846266a0c565b9d2a7dbe793546aa"));
executeTest("test file has annotations, not asking for annotations, #1", spec);
}
@ -22,7 +22,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testHasAnnotsNotAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
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,
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("14e546fa7e819faeda3227c842fa92e7"));
executeTest("test file has annotations, not asking for annotations, #2", spec);
}
@ -30,7 +30,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testHasAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"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,
baseTestString() + " -G \"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("b48199f9dc6f91c61418536151afa8fd"));
executeTest("test file has annotations, asking for annotations, #1", spec);
}
@ -38,7 +38,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testHasAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"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,
baseTestString() + " -G \"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("dcc7c522c4178b4fd9a0e5439bcdaebc"));
executeTest("test file has annotations, asking for annotations, #2", spec);
}
@ -46,7 +46,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoAnnotsNotAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
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,
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("34d2831e7d843093a2cf47c1f4e5f0f0"));
executeTest("test file doesn't have annotations, not asking for annotations, #1", spec);
}
@ -54,7 +54,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoAnnotsNotAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
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,
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("20b946924fffdf6700cd029424fb72b5"));
executeTest("test file doesn't have annotations, not asking for annotations, #2", spec);
}
@ -62,7 +62,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoAnnotsAsking1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"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,
baseTestString() + " -G \"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("133275d150a8100ba4dc756d17b23ef1"));
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
}
@ -70,7 +70,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoAnnotsAsking2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"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,
baseTestString() + " -G \"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("120fc0d4af1d370f1b306700258464b9"));
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
}
@ -78,7 +78,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testOverwritingHeader() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
Arrays.asList("10c31f8ab903843538a7604ed1e5405c"));
executeTest("test overwriting header", spec);
}
@ -86,7 +86,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testNoReads() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
baseTestString() + " -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("a6ec667a656e7ba368de9dbae781eef3"));
executeTest("not passing it any reads", spec);
}
@ -94,7 +94,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testDBTagWithDbsnp() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
baseTestString() + " -D " + GATKDataLocation + "dbsnp_129_b36.rod -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("8b4c309fe4900b5c8ae720c649715c7d"));
executeTest("getting DB tag with dbSNP", spec);
}
@ -102,7 +102,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
@Test
public void testDBTagWithHapMap() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B compH3,VCF," + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B variant,VCF," + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
baseTestString() + " -B:compH3,VCF " + validationDataLocation + "fakeHM3.vcf -G \"Standard\" -B:variant,VCF " + validationDataLocation + "vcfexample3empty.vcf -BTI variant", 1,
Arrays.asList("ff6b3468f21b262de671e823349cbb3c"));
executeTest("getting DB tag with HM3", spec);
}

2
java/test/org/broadinstitute/sting/gatk/walkers/coverage/CompareCallableLociWalkerIntegrationTest.java
View File

@ -30,7 +30,7 @@ import org.junit.Test;
import java.util.Arrays;
public class CompareCallableLociWalkerIntegrationTest extends WalkerTest {
final static String commonArgs = "-R " + hg18Reference + " -T CompareCallableLoci -B comp1,Bed," + validationDataLocation + "1kg_slx.chr1_10mb.callable -B comp2,Bed," + validationDataLocation + "ga2_slx.chr1_10mb.callable -o %s";
final static String commonArgs = "-R " + hg18Reference + " -T CompareCallableLoci -B:comp1,Bed " + validationDataLocation + "1kg_slx.chr1_10mb.callable -B:comp2,Bed " + validationDataLocation + "ga2_slx.chr1_10mb.callable -o %s";
@Test
public void testCompareCallableLociWalker1() {

4
java/test/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceIntegrationTest.java
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@ -16,13 +16,13 @@ public class FastaAlternateReferenceIntegrationTest extends WalkerTest {
executeTest("testFastaReference", spec1);
WalkerTestSpec spec2 = new WalkerTestSpec(
"-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",
"-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 " + 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",
"-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);

16
java/test/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationIntegrationTest.java
View File

@ -15,7 +15,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testNoAction() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -B variant,VCF," + validationDataLocation + "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("89b846266a0c565b9d2a7dbe793546aa"));
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," + validationDataLocation + "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("46877eb3ec258e6b70d8fcacca1acb25"));
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," + validationDataLocation + "vcfexample2.vcf -B variant,VCF," + validationDataLocation + "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("650504a58af863d9cef699087a7961aa"));
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," + validationDataLocation + "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("b0b9110aeff967dd87cd0ec273d20791"));
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," + validationDataLocation + "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("8405a7ef69792c239d903d13832a1ea7"));
executeTest("test filter #2", spec);
}
@ -55,7 +55,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testFilterWithSeparateNames() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " --filterName ABF -filter 'AlleleBalance < 70.0' --filterName FSF -filter 'FisherStrand == 1.4' -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("8266b9eb2ba35d77ab1cecb395322f31"));
executeTest("test filter with separate names #2", spec);
}
@ -63,7 +63,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testGenotypeFilter1() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -G_filter 'GQ == 0.60' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("99d8a47623cba215ee7d803c514ef116"));
executeTest("test genotype filter #1", spec);
}
@ -71,7 +71,7 @@ public class VariantFiltrationIntegrationTest extends WalkerTest {
@Test
public void testGenotypeFilter2() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B variant,VCF," + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
baseTestString() + " -G_filter 'AF == 0.04 && isHomVar == 1' -G_filterName foo -B:variant,VCF " + validationDataLocation + "vcfexample2.vcf -L 1:10,020,000-10,021,000", 1,
Arrays.asList("c58ea74c32290c9b4e8ae3dd1d0250e1"));
executeTest("test genotype filter #2", spec);
}

2
java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -31,7 +31,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
public void testRealignerKnownsOnly() {
String[] md5s = {"7084d4e543bc756730ab306768028530", "74652bd8240291293ec921f8ecfa1622"};
WalkerTestSpec spec = new WalkerTestSpec(
"-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",
"-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);

2
java/test/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreatorIntegrationTest.java
View File

@ -23,7 +23,7 @@ public class RealignerTargetCreatorIntegrationTest extends WalkerTest {
executeTest("test dbsnp", spec2);
WalkerTest.WalkerTestSpec spec3 = new WalkerTest.WalkerTestSpec(
"-T RealignerTargetCreator -R " + b36KGReference + " -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("5206cee6c01b299417bf2feeb8b3dc96"));
executeTest("test rods only", spec3);

2
java/test/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupIntegrationTest.java
View File

@ -18,7 +18,7 @@ public class ValidatingPileupIntegrationTest extends WalkerTest {
"-T ValidatingPileup" +
" -I " + validationDataLocation + "MV1994.selected.bam" +
" -R " + validationDataLocation + "Escherichia_coli_K12_MG1655.fasta" +
" -B pileup,SAMPileup,"+ validationDataLocation + "MV1994.selected.pileup" +
" -B:pileup,SAMPileup "+ validationDataLocation + "MV1994.selected.pileup" +
" -S SILENT -nt 8",0, Collections.<String>emptyList());
executeTest("testEcoliThreaded",spec);
}

4
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -202,7 +202,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B dbsnp,VCF," + validationDataLocation + "vcfexample3.vcf" +
" -B:dbsnp,VCF " + validationDataLocation + "vcfexample3.vcf" +
" -T CountCovariates" +
" -I " + bam +
" -L 1:10,000,000-10,200,000" +
@ -226,7 +226,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-R " + b36KGReference +
" -B anyNameABCD,VCF," + validationDataLocation + "vcfexample3.vcf" +
" -B:anyNameABCD,VCF " + validationDataLocation + "vcfexample3.vcf" +
" -T CountCovariates" +
" -I " + bam +
" --DBSNP /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod" +

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 " + b36KGReference + " -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);
@ -21,7 +21,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R "
+ b36KGReference + " -omitWindow -nameConvention "
+ "-project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation +
"pickSeqIntegrationTest.interval_list -B input,VCF,"+testVCF+" -o %s";
"pickSeqIntegrationTest.interval_list -B:input,VCF "+testVCF+" -o %s";
WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("0ab37fe4db3fef345815c56e57e75cec"));
executeTest("Test probes", spec);
@ -35,7 +35,7 @@ public class PickSequenomProbesIntegrationTest extends WalkerTest {
String testArgs = "-snp_mask " + GATKDataLocation + "/dbsnp_130_b36.rod -R "
+ b36KGReference + " -omitWindow -nameConvention "
+ "-nmw 1 -project_id 1kgp3_s4_lf -T PickSequenomProbes -L " + validationDataLocation +
"pickSeqIntegrationTest.interval_list -B input,VCF,"+testVCF+" -o %s";
"pickSeqIntegrationTest.interval_list -B:input,VCF "+testVCF+" -o %s";
WalkerTestSpec spec = new WalkerTestSpec(testArgs, 1,
Arrays.asList("8f0bc8954069c659c203cbb53d4dbad2"));
executeTest("Test probes", spec);

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 "+b36KGReference + " -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 "+b36KGReference + " -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);

6
java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -24,7 +24,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
"-R " + b36KGReference +
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -T GenerateVariantClusters" +
" -B input,VCF," + vcf +
" -B:input,VCF " + vcf +
" -L 1:1-100,000,000" +
" --ignore_filter GATK_STANDARD" +
" -an QD -an HRun -an SB" +
@ -51,7 +51,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
"-R " + b36KGReference +
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -T VariantRecalibrator" +
" -B input,VCF," + vcf +
" -B:input,VCF " + vcf +
" -L 1:40,000,000-100,000,000" +
" --ignore_filter GATK_STANDARD" +
" --ignore_filter HARD_TO_VALIDATE" +
@ -89,7 +89,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" --DBSNP " + GATKDataLocation + "dbsnp_129_b36.rod" +
" -T ApplyVariantCuts" +
" -L 1:40,000,000-100,000,000" +
" -B input,VCF," + inputVCFFile +
" -B:input,VCF " + inputVCFFile +
" -o %s" +
" -tranchesFile " + tranchesFile,
1, // just one output file

12
java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
View File

@ -45,7 +45,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
public void test1InOut(String file, String md5, String args) {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -priority v1 -B v1,VCF," + validationDataLocation + file + args),
baseTestString(" -priority v1 -B:v1,VCF " + validationDataLocation + file + args),
1,
Arrays.asList(md5));
executeTest("testInOut1--" + file, spec);
@ -53,7 +53,7 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
public void combine2(String file1, String file2, String args, String md5) {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -priority v1,v2 -B v1,VCF," + validationDataLocation + file1 + " -B v2,VCF," + validationDataLocation + file2 + args),
baseTestString(" -priority v1,v2 -B:v1,VCF " + validationDataLocation + file1 + " -B:v2,VCF " + validationDataLocation + file2 + args),
1,
Arrays.asList(md5));
executeTest("combine2 1:" + new File(file1).getName() + " 2:" + new File(file2).getName(), spec);
@ -78,10 +78,10 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
@Test public void threeWayWithRefs() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -B NA19240_BGI,VCF,"+validationDataLocation+"NA19240.BGI.RG.vcf" +
" -B NA19240_ILLUMINA,VCF,"+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
" -B NA19240_WUGSC,VCF,"+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
" -B denovoInfo,VCF,"+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
baseTestString(" -B:NA19240_BGI,VCF "+validationDataLocation+"NA19240.BGI.RG.vcf" +
" -B:NA19240_ILLUMINA,VCF "+validationDataLocation+"NA19240.ILLUMINA.RG.vcf" +
" -B:NA19240_WUGSC,VCF "+validationDataLocation+"NA19240.WUGSC.RG.vcf" +
" -B:denovoInfo,VCF "+validationDataLocation+"yri_merged_validation_data_240610.annotated.b36.vcf" +
" -setKey centerSet" +
" -variantMergeOptions UNION" +
" -priority NA19240_BGI,NA19240_ILLUMINA,NA19240_WUGSC,denovoInfo" +

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 " + 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",
"-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);

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

@ -16,7 +16,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
String samplesFile = validationDataLocation + "SelectVariants.samples.txt";
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'AF < 0.2' -B variant,VCF," + testfile),
baseTestString(" -sn A -sn '[CDH]' -sn " + samplesFile + " -env -ef -select 'AF < 0.2' -B:variant,VCF " + testfile),
1,
Arrays.asList("3a15628b5980031c629c0c33e7e60b40")
);

4
java/test/org/broadinstitute/sting/oneoffprojects/walkers/ValidateRODForReadsIntegrationTest.java
View File

@ -21,7 +21,7 @@ public class ValidateRODForReadsIntegrationTest extends WalkerTest {
@Test
public void testSimpleVCFPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B vcf,vcf," + vcfFile, 1,
baseTestString1KG() + " -B:vcf,vcf " + vcfFile, 1,
Arrays.asList("f7919e9dc156fb5d3ad0541666864ea5"));
executeTest("testSimpleVCFPileup", spec);
}
@ -29,7 +29,7 @@ public class ValidateRODForReadsIntegrationTest extends WalkerTest {
@Test
public void testSimpleDbSNPPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B dbsnp,dbsnp," + dbSNPFile, 1,
baseTestString1KG() + " -B:dbsnp,dbsnp " + dbSNPFile, 1,
Arrays.asList("c63b8ef9291a450f0519c73ac9cae189"));
executeTest("testSimpleDbSNPPileup", spec);
}

10
java/test/org/broadinstitute/sting/playground/gatk/walkers/BeagleIntegrationTest.java
View File

@ -37,10 +37,10 @@ public class BeagleIntegrationTest extends WalkerTest {
public void testBeagleOutput() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T BeagleOutputToVCF -R " + hg19Reference + " " +
"-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
"-B beagleR2,BEAGLE," + beagleValidationDataLocation + "inttestbgl.r2 " +
"-B beagleProbs,BEAGLE," + beagleValidationDataLocation + "inttestbgl.gprobs " +
"-B beaglePhased,BEAGLE," + beagleValidationDataLocation + "inttestbgl.phased " +
"-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " +
"-B:beagleR2,BEAGLE " + beagleValidationDataLocation + "inttestbgl.r2 " +
"-B:beagleProbs,BEAGLE " + beagleValidationDataLocation + "inttestbgl.gprobs " +
"-B:beaglePhased,BEAGLE " + beagleValidationDataLocation + "inttestbgl.phased " +
"-o %s", 1, Arrays.asList("e7b9aac20246f26ffcc599850f6cb2a0"));
executeTest("test BeagleOutputToVCF", spec);
}
@ -49,7 +49,7 @@ public class BeagleIntegrationTest extends WalkerTest {
public void testBeagleInput() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T ProduceBeagleInput -R " + hg19Reference + " " +
"-B variant,VCF," + beagleValidationDataLocation + "inttestbgl.input.vcf " +
"-B:variant,VCF " + beagleValidationDataLocation + "inttestbgl.input.vcf " +
"-beagle %s", 1, Arrays.asList("c0d30e5dbe903874f8422a0e63a5118e"));
executeTest("test BeagleInput", spec);
}

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

@ -15,8 +15,8 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
String[] md5 = {"d19d6d1eb52fb09e7493653dc645d92a"};
WalkerTestSpec spec = new WalkerTestSpec(
"-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 " +
"-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
"-o %s " +
"-BTI variant",
@ -29,8 +29,8 @@ public class GenomicAnnotatorIntegrationTest extends WalkerTest {
String[] md5WithDashSArg = {"94edacdaee0dd58508d35d4d6040e31b"};
WalkerTestSpec specWithSArg = new WalkerTestSpec(
"-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" +
" -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
" -o %s" +
" -BTI variant" +

22
java/test/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationIntegrationTest.java
View File

@ -18,7 +18,7 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
@Test
public void testSimpleGeliPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B eval,GeliText," + validationDataLocation + "ROD_validation/chr1.geli", 1,
baseTestString1KG() + " -B:eval,GeliText " + validationDataLocation + "ROD_validation/chr1.geli", 1,
Arrays.asList("832efb29a6d4e8dbae374d3eeee17d9d"));
executeTest("testSimpleGeliPileup", spec);
}
@ -26,7 +26,7 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
@Test
public void testSimpleVCFPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf", 1,
baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf", 1,
Arrays.asList("5d84c75746738833b6c9441d9d614553"));
executeTest("testSimpleVCFPileup", spec);
}
@ -34,8 +34,8 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
@Test
public void testComplexVCFPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf" +
" -B eval2,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4"
baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf" +
" -B:eval2,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4"
, 1,
Arrays.asList("8d97cbc29f73a0027267858f961e6fe5"));
executeTest("testComplexVCFPileup", spec);
@ -44,8 +44,8 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
@Test
public void testBTIWithROD() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf" +
" -B eval2,VCF," + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4" + " -BTI eval"
baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf" +
" -B:eval2,VCF " + validationDataLocation + "NA12878.chr1_10mb_11mb.slx.indels.vcf4" + " -BTI eval"
, 1,
Arrays.asList("ccfc0389a3c614f7892dbe972543f0ec"));
executeTest("testBTIWithROD", spec);
@ -54,9 +54,9 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
@Test
public void testLargeComplexVCFPileup() {
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B eval,VCF," + validationDataLocation + "MultiSample.vcf" +
" -B eval2,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
" -B eval3,VCF," + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
baseTestString1KG() + " -B:eval,VCF " + validationDataLocation + "MultiSample.vcf" +
" -B:eval2,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
" -B:eval3,VCF " + validationDataLocation + "CEU_hapmap_nogt_23.vcf" +
" -L 1 -L 2 -L 20"
, 1,
Arrays.asList("8805912af2c38ec8d1cbc8d82532725e"));
@ -67,8 +67,8 @@ public class RodSystemValidationIntegrationTest extends WalkerTest {
public void testBlockZippedVrsUnzippedVCF1() {
final String vcfName = validationDataLocation + "bgzipped_vcfs/vcfexample.vcf";
WalkerTestSpec spec = new WalkerTestSpec(
baseTestString1KG() + " -B eval,VCF," + vcfName +
" -B eval2,VCF," + vcfName + ".gz" +
baseTestString1KG() + " -B:eval,VCF " + vcfName +
" -B:eval2,VCF " + vcfName + ".gz" +
" --PerLocusEqual"
, 1,
Arrays.asList("ab3da32eae65e8c15a9f4a787a190a37"));