WTF - I thought we had disabled the randomized dithering of rank sum tests for integration tests?!
Well, it wasn't done so I went ahead and did so. Lots of MD5 changes accordingly.
This commit is contained in:
Eric Banks
parent
ba2c3b57ed
commit
021adf4220
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@ -183,6 +183,6 @@ public abstract class RankSumTest extends InfoFieldAnnotation implements ActiveR
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* @param headerLines
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*/
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public void initialize ( AnnotatorCompatible walker, GenomeAnalysisEngine toolkit, Set<VCFHeaderLine> headerLines ) {
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useDithering = ! toolkit.getArguments().disableRandomization;
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useDithering = ! toolkit.getArguments().disableDithering;
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}
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}
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@ -56,8 +56,8 @@ import java.util.List;
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public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
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private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132;
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private final static String baseCommandIndels = "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
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private final static String baseCommandIndelsb37 = "-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -mbq 20 --dbsnp " + b37dbSNP132;
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// --------------------------------------------------------------------------------------------------------------
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//
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@ -73,7 +73,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("118ed5b54fc9ce1cde89f06a20afebef"));
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Arrays.asList("d8b0c5be39ec6b239641c2f2646d2bc3"));
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executeTest(String.format("test indel caller in SLX"), spec);
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}
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@ -88,7 +88,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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" -minIndelCnt 1" +
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" -L 1:10,000,000-10,100,000",
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1,
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Arrays.asList("6ef59013331bc031ea37807b325d7d2c"));
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Arrays.asList("d9572a227ccb13a6baa6dc4fb65bc1e5"));
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executeTest(String.format("test indel caller in SLX with low min allele count"), spec);
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}
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@ -101,7 +101,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,500,000",
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1,
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Arrays.asList("dd3ee4675377191e34aaf67335e0219a"));
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Arrays.asList("54e13f696f56eb742bf449ad11d0dc5f"));
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executeTest(String.format("test indel calling, multiple technologies"), spec);
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}
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@ -111,7 +111,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
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"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
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Arrays.asList("bb06ef8262f91664b7d2fe7e1e5df195"));
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Arrays.asList("16d975480ff1e689113171805b916b62"));
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executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
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}
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@ -121,7 +121,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles "
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+ privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation +
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"pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1,
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Arrays.asList("0a2a8cc2d1a79e84624836a31de5491c"));
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Arrays.asList("60ed3f8d5bc3f765e6ce3fa698b68bb7"));
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executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec);
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}
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@ -136,7 +136,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
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"low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1,
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Arrays.asList("939f80c6d2dfb592956aed3bdeaf319d"));
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Arrays.asList("e87f5c76661527ef7aa44e528fe19573"));
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executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
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}
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@ -176,7 +176,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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public void testMinIndelFraction0() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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assessMinIndelFraction + " -minIndelFrac 0.0", 1,
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Arrays.asList("fc937f92e59dfe07b894411b5dfc166a"));
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Arrays.asList("264325878b988acc11d8e5d9d2ba0b7f"));
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executeTest("test minIndelFraction 0.0", spec);
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}
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@ -184,7 +184,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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public void testMinIndelFraction25() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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assessMinIndelFraction + " -minIndelFrac 0.25", 1,
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Arrays.asList("41ad9e0edca4b9987390ba5c07f39e4a"));
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Arrays.asList("98abcfb0a008050eba8b9c285a25b2a0"));
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executeTest("test minIndelFraction 0.25", spec);
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}
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@ -200,7 +200,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest {
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@Test
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public void testHaplotype0Length() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -I " + privateTestDir + "haplotype0.bam -L 20:47507681 -R " + b37KGReference + " -baq CALCULATE_AS_NECESSARY -glm BOTH -o /dev/null",
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"-T UnifiedGenotyper --disableDithering -I " + privateTestDir + "haplotype0.bam -L 20:47507681 -R " + b37KGReference + " -baq CALCULATE_AS_NECESSARY -glm BOTH -o /dev/null",
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0,
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Collections.<String>emptyList());
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executeTest("testHaplotype0Length", spec);
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@ -60,8 +60,8 @@ import java.util.Collections;
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public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
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private final static String baseCommandNoCmdLineHeaderStdout = "-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam";
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private final static String baseCommand = "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
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private final static String baseCommandNoCmdLineHeaderStdout = "-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam";
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// --------------------------------------------------------------------------------------------------------------
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//
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@ -73,15 +73,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMinBaseQualityScore() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --min_base_quality_score 26", 1,
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Arrays.asList("6ee6537e9ebc1bfc7c6cf8f04b1582ff"));
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Arrays.asList("30be17df00acc8a92223f51fe7c1bdf7"));
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executeTest("test min_base_quality_score 26", spec);
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}
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@Test
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public void testSLOD() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("55760482335497086458b09e415ecf54"));
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"-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --computeSLOD --no_cmdline_in_header -glm BOTH --dbsnp " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("4aa226c00a242047cf427d0919003048"));
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executeTest("test SLOD", spec);
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}
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@ -89,15 +89,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testNDA() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " --annotateNDA -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("938e888a40182878be4c3cc4859adb69"));
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Arrays.asList("17f65eca1e6c1f06919a58f230b6d8d3"));
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executeTest("test NDA", spec);
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}
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@Test
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public void testCompTrack() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("7dc186d420487e4e156a24ec8dea0951"));
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"-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -comp:FOO " + b36dbSNP129 + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000", 1,
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Arrays.asList("50937942e3d228614d2531c3be237709"));
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executeTest("test using comp track", spec);
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}
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@ -111,17 +111,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testOutputParameterSitesOnly() {
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testOutputParameters("-sites_only", "f99c7471127a6fb6f72e136bc873b2c9");
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testOutputParameters("-sites_only", "48cd40d3994911a6f2609bfd375e1d2d");
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}
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@Test
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public void testOutputParameterAllConfident() {
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testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "5649f72de04e1391e0f2bb86843d3d72");
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testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "28f40ce47651f504158fc4e5bb58df4b");
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}
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@Test
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public void testOutputParameterAllSites() {
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testOutputParameters("--output_mode EMIT_ALL_SITES", "cb151bb9e90680b12714d481091ed209");
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testOutputParameters("--output_mode EMIT_ALL_SITES", "5259dafaa1b57d9489003b16a48e35f8");
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}
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private void testOutputParameters(final String args, final String md5) {
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@ -135,7 +135,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testConfidence() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 ", 1,
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Arrays.asList("4af83a883ecc03a23b0aa6dd4b8f1ceb"));
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Arrays.asList("918109938ef355d759dafc3ebb47d8a5"));
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executeTest("test confidence 1", spec1);
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}
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@ -143,7 +143,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testNoPrior() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -stand_call_conf 10 -noPrior", 1,
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Arrays.asList("422656266117f8d01e17e5c491c49a24"));
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Arrays.asList("7ac60bdc355d97c0939e644b58de47d7"));
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executeTest("test no prior 1", spec1);
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}
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@ -155,12 +155,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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// --------------------------------------------------------------------------------------------------------------
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@Test
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public void testHeterozyosity1() {
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testHeterozosity( 0.01, "ffc1f83a045dc09360e11de7a8efd159" );
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testHeterozosity( 0.01, "3b66f82dbb746875638e076bf51a1583" );
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}
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@Test
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public void testHeterozyosity2() {
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testHeterozosity( 1.0 / 1850, "5426a98df9f5fd70aef295d889c4e4f1" );
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testHeterozosity( 1.0 / 1850, "714c1795334c7c62c046a75479381ae6" );
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}
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private void testHeterozosity(final double arg, final String md5) {
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@ -176,7 +176,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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//
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// --------------------------------------------------------------------------------------------------------------
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private final static String COMPRESSED_OUTPUT_MD5 = "d5a7326fdcf6d441b73c381912ad3a2a";
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private final static String COMPRESSED_OUTPUT_MD5 = "6f79205f7ed8006470f056f6805db6c8";
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@Test
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public void testCompressedOutput() {
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@ -232,7 +232,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -o %s" +
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" -L 1:10,000,000-10,100,000",
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1,
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Arrays.asList("0a4a78da876bfa3d42170249a94357b4"));
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Arrays.asList("d995b76adc3766889f7c2c88da14055c"));
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executeTest(String.format("test multiple technologies"), spec);
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}
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@ -251,7 +251,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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" -L 1:10,000,000-10,100,000" +
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" -baq CALCULATE_AS_NECESSARY",
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1,
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Arrays.asList("89182fd4d9532ab4b2a0a84bfb557089"));
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Arrays.asList("9669e1643d22d5ad047b3941aeefd6db"));
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executeTest(String.format("test calling with BAQ"), spec);
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}
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@ -281,8 +281,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testNsInCigar() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "testWithNs.bam -o %s -L 8:141813600-141813700 -out_mode EMIT_ALL_SITES", 1,
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Arrays.asList("4d36969d4f8f1094f1fb6e7e085c19f6"));
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"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "testWithNs.bam -o %s -L 8:141813600-141813700 -out_mode EMIT_ALL_SITES", 1,
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Arrays.asList("2ae3fd39c53a6954d32faed8703adfe8"));
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executeTest("test calling on reads with Ns in CIGAR", spec);
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}
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}
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@ -53,7 +53,7 @@ import java.util.Arrays;
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public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
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private final static String baseCommand = "-T UnifiedGenotyper --disableDithering -R " + b36KGReference + " --no_cmdline_in_header -glm BOTH -minIndelFrac 0.0 --dbsnp " + b36dbSNP129;
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// --------------------------------------------------------------------------------------------------------------
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//
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@ -64,7 +64,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testMultiSamplePilot1() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
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Arrays.asList("52b6086f4597da5b35ab902bea4066fc"));
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Arrays.asList("e3efd1917192ea743ac1e9958aa0a98f"));
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executeTest("test MultiSample Pilot1", spec);
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}
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@ -72,7 +72,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testWithAllelesPassedIn1() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
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Arrays.asList("5b31b811072a4df04524e13604015f9b"));
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Arrays.asList("ebfcc3dd8c1788929cb50050c5d456df"));
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executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
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}
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@ -80,7 +80,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testWithAllelesPassedIn2() {
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WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
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baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "allelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,025,000", 1,
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Arrays.asList("d9992e55381afb43742cc9b30fcd7538"));
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Arrays.asList("698e54aeae3130779d246b9480a4052c"));
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executeTest("test MultiSample Pilot2 with alleles passed in and emitting all sites", spec2);
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}
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@ -88,22 +88,22 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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|||
public void testSingleSamplePilot2() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1,
|
||||
Arrays.asList("33ab66c2f062cfa1f7fcc077165f778c"));
|
||||
Arrays.asList("aaadb2a355d87344eabb6ac4495a11e4"));
|
||||
executeTest("test SingleSample Pilot2", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testMultipleSNPAlleles() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
|
||||
Arrays.asList("28bfbff3da3af43d6a1eff673e5cb0f8"));
|
||||
"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
|
||||
Arrays.asList("09a1a4d4bf0289bcc5e8a958f783a989"));
|
||||
executeTest("test Multiple SNP alleles", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testBadRead() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
|
||||
"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
|
||||
Arrays.asList("d915535c1458733f09f82670092fcab6"));
|
||||
executeTest("test bad read", spec);
|
||||
}
|
||||
|
|
@ -111,16 +111,16 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
|
|||
@Test
|
||||
public void testReverseTrim() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
|
||||
Arrays.asList("a9edd04374ee9c42970291f39a50c191"));
|
||||
"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
|
||||
Arrays.asList("57a1bb44967988f2b7ae7779127990ae"));
|
||||
executeTest("test reverse trim", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testMismatchedPLs() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
|
||||
Arrays.asList("6fc32ca9de769060f3c2a3d94f8f2f91"));
|
||||
"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
|
||||
Arrays.asList("3011c20165951ca43c8a4e86a5835dbd"));
|
||||
executeTest("test mismatched PLs", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -62,25 +62,25 @@ public class UnifiedGenotyperReducedReadsIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testReducedBam() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
|
||||
Arrays.asList("f82389f2bc6d3f932a36be65b60af648"));
|
||||
"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
|
||||
Arrays.asList("da3fd775c8add1f7962baabf06b7d372"));
|
||||
executeTest("test calling on a ReducedRead BAM", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testReducedBamSNPs() {
|
||||
testReducedCalling("SNP", "c87f89af948a554cc66bc3afa5251c3b");
|
||||
testReducedCalling("SNP", "76244ab1be60814f1412e6cd09e546cc");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testReducedBamINDELs() {
|
||||
testReducedCalling("INDEL", "ed4ddc42447ec037c1e14757b6cf0515");
|
||||
testReducedCalling("INDEL", "9a986b98ed014576ce923e07452447f4");
|
||||
}
|
||||
|
||||
|
||||
private void testReducedCalling(final String model, final String md5) {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s -L 20:10,000,000-10,500,000 -glm " + model, 1,
|
||||
"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "NA12878.HiSeq.b37.chr20.10_11mb.reduced.bam -o %s -L 20:10,000,000-10,500,000 -glm " + model, 1,
|
||||
Arrays.asList(md5));
|
||||
executeTest("test calling on a ReducedRead BAM with " + model, spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -57,7 +57,7 @@ import static org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCal
|
|||
public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends WalkerTest {
|
||||
|
||||
private void HCTestComplexVariants(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 4";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, bam) + " -L 20:10028767-10028967 -L 20:10431524-10431924 -L 20:10723661-10724061 -L 20:10903555-10903955 --no_cmdline_in_header -o %s -minPruning 4";
|
||||
final WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCallerComplexVariants: args=" + args, spec);
|
||||
}
|
||||
|
|
@ -68,7 +68,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
|
|||
}
|
||||
|
||||
private void HCTestSymbolicVariants(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:5947969-5948369 -L 20:61091236-61091636 --no_cmdline_in_header -o %s -minPruning 1";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, bam) + " -L 20:5947969-5948369 -L 20:61091236-61091636 --no_cmdline_in_header -o %s -minPruning 1";
|
||||
final WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCallerSymbolicVariants: args=" + args, spec);
|
||||
}
|
||||
|
|
@ -80,7 +80,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
|
|||
}
|
||||
|
||||
private void HCTestComplexGGA(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " --no_cmdline_in_header -o %s -minPruning 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, bam) + " --no_cmdline_in_header -o %s -minPruning 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCallerComplexGGA: args=" + args, spec);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -73,7 +73,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
final static String INTERVALS_FILE = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.test.intervals";
|
||||
|
||||
private void HCTest(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s -L %s", REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s -L %s", REF, bam, INTERVALS_FILE) + " --no_cmdline_in_header -o %s -minPruning 3";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCaller: args=" + args, spec);
|
||||
}
|
||||
|
|
@ -105,7 +105,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
}
|
||||
|
||||
private void HCTestIndelQualityScores(String bam, String args, String md5) {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10,005,000-10,025,000 --no_cmdline_in_header -o %s -minPruning 2";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, bam) + " -L 20:10,005,000-10,025,000 --no_cmdline_in_header -o %s -minPruning 2";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
executeTest("testHaplotypeCallerIndelQualityScores: args=" + args, spec);
|
||||
}
|
||||
|
|
@ -120,7 +120,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
final IndexedFastaSequenceFile fasta = new IndexedFastaSequenceFile(new File(b37KGReference));
|
||||
final GenomeLocParser parser = new GenomeLocParser(fasta.getSequenceDictionary());
|
||||
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, bam) + " -L 20:10,001,603-10,001,642 -L 20:10,001,653-10,001,742 --no_cmdline_in_header -o %s";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, bam) + " -L 20:10,001,603-10,001,642 -L 20:10,001,653-10,001,742 --no_cmdline_in_header -o %s";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base + " " + args, Arrays.asList(md5));
|
||||
for( final File vcf : executeTest("testHaplotypeCallerNearbySmallIntervals: args=" + args, spec).getFirst() ) {
|
||||
if( containsDuplicateRecord(vcf, parser) ) {
|
||||
|
|
@ -158,14 +158,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
// any of the calls in that region because it is so messy.
|
||||
@Test
|
||||
public void HCTestProblematicReadsModifiedInActiveRegions() {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("0689d2c202849fd05617648eaf429b9a"));
|
||||
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void HCTestStructuralIndels() {
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("cb190c935541ebb9f660f713a882b922"));
|
||||
executeTest("HCTestStructuralIndels: ", spec);
|
||||
}
|
||||
|
|
@ -173,7 +173,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestDoesNotFailOnBadRefBase() {
|
||||
// don't care about the output - just want to make sure it doesn't fail
|
||||
final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o /dev/null -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2 -stand_emit_conf 2";
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "NA12878.readsOverBadBase.chr3.bam") + " --no_cmdline_in_header -o /dev/null -L 3:60830000-60840000 --minPruning 3 -stand_call_conf 2 -stand_emit_conf 2";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Collections.<String>emptyList());
|
||||
executeTest("HCTestDoesNotFailOnBadRefBase: ", spec);
|
||||
}
|
||||
|
|
@ -187,7 +187,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestReducedBam() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
|
||||
"-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
|
||||
Arrays.asList("3c87eb93ffe3a0166aca753050b981e1"));
|
||||
executeTest("HC calling on a ReducedRead BAM", spec);
|
||||
}
|
||||
|
|
@ -195,7 +195,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testReducedBamWithReadsNotFullySpanningDeletion() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
|
||||
"-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
|
||||
Arrays.asList("8adfa8a27a312760dab50787da595c57"));
|
||||
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue