Remove AAL and update MD5s.
This commit is contained in:
Chris Hartl
parent
ab5526b372
commit
41bc416b65
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@ -55,36 +55,36 @@ public class UnifiedGenotyperGeneralPloidyIntegrationTest extends WalkerTest {
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@Test(enabled = true)
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public void testSNP_ACS_Pools() {
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PC_LSV_Test_short(" -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES","LSV_SNP_ACS","SNP","651469eeacdb3ab9e2690cfb71f6a634");
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PC_LSV_Test_short(" -maxAltAlleles 1 -ploidy 6 -out_mode EMIT_ALL_CONFIDENT_SITES","LSV_SNP_ACS","SNP","df0e67c975ef74d593f1c704daab1705");
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}
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@Test(enabled = true)
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public void testBOTH_GGA_Pools() {
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PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","be7dc20bdb5f200d189706bcf1aeb7ee");
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PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_BOTH_GGA","BOTH","d1c113a17e36762d27eb27fd12528e52");
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}
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@Test(enabled = true)
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public void testINDEL_GGA_Pools() {
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PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","25e5ea86d87b7d7ddaad834a6ed7481d");
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PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",LSV_ALLELES),"LSV_INDEL_GGA","INDEL","ab043eed87fadbe5761a55a4912b19ac");
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}
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@Test(enabled = true)
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public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
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PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","cdbf268d282e57189a88fb83f0e1fd72");
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PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","95d48e0680019d5406ff9adb8f2ff3ca");
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}
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@Test(enabled = true)
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public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
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PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","2ed40925cd112c1a45470d215b7ec4b3");
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PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1","LSV_INDEL_DISC_NOREF_p1","INDEL","8a4ddd64c4e9c42b4a8622582fcfa9c9");
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}
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@Test(enabled = true)
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public void testMT_SNP_DISCOVERY_sp4() {
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PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","33695a998bcc906cabcc758727004387");
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PC_MT_Test(CEUTRIO_BAM, " -maxAltAlleles 1 -ploidy 8", "MT_SNP_DISCOVERY_sp4","3fc6f4d458313616727c60e49c0e852b");
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}
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@Test(enabled = true)
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public void testMT_SNP_GGA_sp10() {
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PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "b2725242114bf9cc9bca14679705ba40");
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PC_MT_Test(CEUTRIO_BAM, String.format(" -maxAltAlleles 1 -ploidy 20 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s",NA12891_CALLS), "MT_SNP_GGA_sp10", "1bebbc0f28bff6fd64736ccca8839df8");
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}
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}
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@ -30,7 +30,7 @@ public class UnifiedGenotyperIntegrationTest 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("2ba9af34d2a4d55caf152265a30ead46"));
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Arrays.asList("847605f4efafef89529fe0e496315edd"));
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executeTest("test MultiSample Pilot1", spec);
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}
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@ -38,7 +38,7 @@ public class UnifiedGenotyperIntegrationTest 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("0630c35c070d7a7e0cf22b3cce797f22"));
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Arrays.asList("5b31b811072a4df04524e13604015f9b"));
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executeTest("test MultiSample Pilot2 with alleles passed in", spec1);
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}
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@ -46,7 +46,7 @@ public class UnifiedGenotyperIntegrationTest 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("5857dcb4e6a8422ae0813e42d433b122"));
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Arrays.asList("d9992e55381afb43742cc9b30fcd7538"));
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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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@ -54,7 +54,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testSingleSamplePilot2() {
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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 1:10,000,000-10,100,000", 1,
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Arrays.asList("489deda5d3276545364a06b7385f8bd9"));
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Arrays.asList("dff4412a074940d26994f9552476b209"));
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executeTest("test SingleSample Pilot2", spec);
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}
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@ -62,7 +62,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultipleSNPAlleles() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-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,
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Arrays.asList("595ba44c75d08dab98df222b8e61ab70"));
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Arrays.asList("b41b95aaa2c453c9b75b3b29a9c2718e"));
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executeTest("test Multiple SNP alleles", spec);
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}
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@ -70,7 +70,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testBadRead() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH -I " + privateTestDir + "badRead.test.bam -o %s -L 1:22753424-22753464", 1,
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Arrays.asList("360f9795facdaa14c0cb4b05207142e4"));
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Arrays.asList("d915535c1458733f09f82670092fcab6"));
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executeTest("test bad read", spec);
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}
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@ -78,7 +78,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testReverseTrim() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-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,
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Arrays.asList("4b4a62429f8eac1e2f27ba5e2edea9e5"));
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Arrays.asList("44e9f6cf11b4efecb454cd3de8de9877"));
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executeTest("test reverse trim", spec);
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}
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@ -86,7 +86,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMismatchedPLs() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + privateTestDir + "mismatchedPLs.bam -o %s -L 1:24020341", 1,
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Arrays.asList("cc892c91a93dbd8dbdf645803f35a0ee"));
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Arrays.asList("935ee705ffe8cc6bf1d9efcceea271c8"));
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executeTest("test mismatched PLs", spec);
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}
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@ -96,7 +96,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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//
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// --------------------------------------------------------------------------------------------------------------
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private final static String COMPRESSED_OUTPUT_MD5 = "3fc7d2681ff753e2d68605d7cf8b63e3";
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private final static String COMPRESSED_OUTPUT_MD5 = "e6e33f0ebabab027eabed51fe9a08da9";
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@Test
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public void testCompressedOutput() {
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@ -149,7 +149,7 @@ 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("04dc83d7dfb42b8cada91647bd9f32f1"));
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Arrays.asList("6ee6537e9ebc1bfc7c6cf8f04b1582ff"));
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executeTest("test min_base_quality_score 26", spec);
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}
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@ -157,7 +157,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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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("4429a665a1048f958db3c204297cdb9f"));
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Arrays.asList("55760482335497086458b09e415ecf54"));
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executeTest("test SLOD", spec);
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}
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@ -165,7 +165,7 @@ 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("f063e3573c513eaa9ce7d7df22143362"));
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Arrays.asList("938e888a40182878be4c3cc4859adb69"));
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executeTest("test NDA", spec);
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}
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@ -173,7 +173,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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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("d76e93e2676354dde832f08a508c6f88"));
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Arrays.asList("7dc186d420487e4e156a24ec8dea0951"));
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executeTest("test using comp track", spec);
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}
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@ -187,17 +187,17 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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@Test
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public void testOutputParameterSitesOnly() {
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testOutputParameters("-sites_only", "1a65172b9bd7a2023d48bc758747b34a");
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testOutputParameters("-sites_only", "f99c7471127a6fb6f72e136bc873b2c9");
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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", "3f1fa34d8440f6f21654ce60c0ba8f28");
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testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "9dbc9389db39cf9697e93e0bf529314f");
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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", "f240434b4d3c234f6f9e349e9ec05f4e");
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testOutputParameters("--output_mode EMIT_ALL_SITES", "8b26088a035e579c4afd3b46737291e4");
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}
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private void testOutputParameters(final String args, final String md5) {
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@ -211,7 +211,7 @@ 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("aec378bed312b3557c6dd7ec740c8091"));
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Arrays.asList("4af83a883ecc03a23b0aa6dd4b8f1ceb"));
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executeTest("test confidence 1", spec1);
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}
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@ -222,12 +222,12 @@ 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, "5da6b24033a6b02f466836443d49560e" );
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testHeterozosity( 0.01, "bdc8760d7ae1e01c0510b12c1e6fcfa3" );
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}
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@Test
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public void testHeterozyosity2() {
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testHeterozosity( 1.0 / 1850, "1f284c4af967a3c26687164f9441fb16" );
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testHeterozosity( 1.0 / 1850, "f508f06a47305e11e62776615cb14fe3" );
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}
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private void testHeterozosity(final double arg, final String md5) {
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@ -251,7 +251,7 @@ 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("cff553c53de970f64051ed5711407038"));
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Arrays.asList("13d91059f58fb50a07a6a34b9438a45b"));
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executeTest(String.format("test multiple technologies"), spec);
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}
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@ -270,7 +270,7 @@ 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("f960a91963e614a6c8d8cda57836df24"));
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Arrays.asList("07d8b77a5f6697f3a47a4f1efb0dcf50"));
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executeTest(String.format("test calling with BAQ"), spec);
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}
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@ -289,7 +289,7 @@ public class UnifiedGenotyperIntegrationTest 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("46a6d24c82ebb99d305462960fa09b7c"));
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Arrays.asList("0f026d2e568172cf32813cc54ea7ba23"));
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executeTest(String.format("test indel caller in SLX"), spec);
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}
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@ -304,7 +304,7 @@ public class UnifiedGenotyperIntegrationTest 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("2be25321bbc6a963dba7ecba5dd76802"));
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Arrays.asList("e7ad858e9d6617534761918561f3ed4c"));
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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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@ -317,7 +317,7 @@ public class UnifiedGenotyperIntegrationTest 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("d6b2657cd5a4a949968cdab50efce515"));
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Arrays.asList("39c7a813fd6ee82d3604f2a868b35b2a"));
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executeTest(String.format("test indel calling, multiple technologies"), spec);
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}
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@ -327,7 +327,7 @@ public class UnifiedGenotyperIntegrationTest 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("9cff66a321284c362f393bc4db21f756"));
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Arrays.asList("9430fe36789a791fcff6162f768ae563"));
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executeTest("test MultiSample Pilot2 indels with alleles passed in", spec);
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}
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@ -337,7 +337,7 @@ public class UnifiedGenotyperIntegrationTest 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("90c8cfcf65152534c16ed81104fc3bcd"));
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Arrays.asList("8d8dbf483526b0b309f5728619a74a86"));
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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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@ -345,13 +345,13 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
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public void testMultiSampleIndels1() {
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WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec(
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baseCommandIndels + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
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Arrays.asList("457b8f899cf1665de61e75084dbb79d0"));
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Arrays.asList("5667a699a3a13474f2d1cd2d6b01cd5b"));
|
||||
List<File> result = executeTest("test MultiSample Pilot1 CEU indels", spec1).getFirst();
|
||||
|
||||
WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation +
|
||||
"low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10450700-10551000", 1,
|
||||
Arrays.asList("a13fe7aa3b9e8e091b3cf3442a056ec1"));
|
||||
Arrays.asList("b6c1d5cd28ff584c5f5037afef4e883a"));
|
||||
executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2);
|
||||
}
|
||||
|
||||
|
|
@ -361,7 +361,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
baseCommandIndelsb37 + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + privateTestDir + vcf + " -I " + validationDataLocation +
|
||||
"NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam -o %s -L " + validationDataLocation + vcf, 1,
|
||||
Arrays.asList("d075ad318739c8c56bdce857da1e48b9"));
|
||||
Arrays.asList("d76eacc4021b78ccc0a9026162e814a7"));
|
||||
executeTest("test GENOTYPE_GIVEN_ALLELES with no evidence in reads", spec);
|
||||
}
|
||||
|
||||
|
|
@ -373,7 +373,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
" -o %s" +
|
||||
" -L 20:10,000,000-10,100,000",
|
||||
1,
|
||||
Arrays.asList("91c632ab17a1dd89ed19ebb20324f905"));
|
||||
Arrays.asList("1e0d2c15546c3b0959b00ffb75488b56"));
|
||||
|
||||
executeTest(String.format("test UG with base indel quality scores"), spec);
|
||||
}
|
||||
|
|
@ -407,7 +407,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMinIndelFraction0() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
assessMinIndelFraction + " -minIndelFrac 0.0", 1,
|
||||
Arrays.asList("1d80e135d611fe19e1fb1882aa588a73"));
|
||||
Arrays.asList("db3026c49a3de7a5cb9a3d77635d0706"));
|
||||
executeTest("test minIndelFraction 0.0", spec);
|
||||
}
|
||||
|
||||
|
|
@ -415,7 +415,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMinIndelFraction25() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
assessMinIndelFraction + " -minIndelFrac 0.25", 1,
|
||||
Arrays.asList("752139616752902fca13c312d8fe5e22"));
|
||||
Arrays.asList("7ab8e5ee15ab98d6756b0eea0f4d3798"));
|
||||
executeTest("test minIndelFraction 0.25", spec);
|
||||
}
|
||||
|
||||
|
|
@ -423,7 +423,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testMinIndelFraction100() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
assessMinIndelFraction + " -minIndelFrac 1", 1,
|
||||
Arrays.asList("d66b9decf26e1704abda1a919ac149cd"));
|
||||
Arrays.asList("3f07efb768e08650a7ce333edd4f9a52"));
|
||||
executeTest("test minIndelFraction 1.0", spec);
|
||||
}
|
||||
|
||||
|
|
@ -437,7 +437,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testNsInCigar() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T UnifiedGenotyper -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "testWithNs.bam -o %s -L 8:141813600-141813700 -out_mode EMIT_ALL_SITES", 1,
|
||||
Arrays.asList("b62ba9777efc05af4c36e2d4ce3ee67c"));
|
||||
Arrays.asList("4d36969d4f8f1094f1fb6e7e085c19f6"));
|
||||
executeTest("test calling on reads with Ns in CIGAR", spec);
|
||||
}
|
||||
|
||||
|
|
@ -451,18 +451,18 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
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("f72ecd00b2913f63788faa7dabb1d102"));
|
||||
Arrays.asList("092e42a712afb660ec79ff11c55933e2"));
|
||||
executeTest("test calling on a ReducedRead BAM", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testReducedBamSNPs() {
|
||||
testReducedCalling("SNP", "f059743858004ceee325f2a7761a2362");
|
||||
testReducedCalling("SNP", "c0de74ab8f4f14eb3a2c5d55c200ac5f");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testReducedBamINDELs() {
|
||||
testReducedCalling("INDEL", "04845ba1ec7d8d8b0eab2ca6bdb9c1a6");
|
||||
testReducedCalling("INDEL", "1c9aaf65ffaa12bb766855265a1c3f8e");
|
||||
}
|
||||
|
||||
|
||||
|
|
@ -483,7 +483,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
|
|||
public void testContaminationDownsampling() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 --contamination_fraction_to_filter 0.20", 1,
|
||||
Arrays.asList("b500ad5959bce69f888a2fac024647e5"));
|
||||
Arrays.asList("1f9071466fc40f4c6a0f58ac8e9135fb"));
|
||||
executeTest("test contamination_percentage_to_filter 0.20", spec);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -21,19 +21,19 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerMultiSample() {
|
||||
HCTest(CEUTRIO_BAM, "", "7122d4f0ef94c5274aa3047cfebe08ed");
|
||||
HCTest(CEUTRIO_BAM, "", "47fdbe5f01d3ce5e53056eea8c488e45");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSample() {
|
||||
HCTest(NA12878_BAM, "", "6cd6e6787521c07a7bae98766fd628ab");
|
||||
HCTest(NA12878_BAM, "", "a2c63f6e6e51a01019bdbd23125bdb15");
|
||||
}
|
||||
|
||||
// TODO -- add more tests for GGA mode, especially with input alleles that are complex variants and/or not trimmed
|
||||
@Test
|
||||
public void testHaplotypeCallerMultiSampleGGA() {
|
||||
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
|
||||
"44df2a9da4fbd2162ae44c3f2a6ef01f");
|
||||
"54b7cc3da3d8349ff4302f99883ab188");
|
||||
}
|
||||
|
||||
private void HCTestComplexVariants(String bam, String args, String md5) {
|
||||
|
|
@ -44,7 +44,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerMultiSampleComplex() {
|
||||
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "4a413eeb7a75cab0ab5370b4c08dcf8e");
|
||||
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6c0c441b71848c2eea38ab5e2afe1120");
|
||||
}
|
||||
|
||||
private void HCTestSymbolicVariants(String bam, String args, String md5) {
|
||||
|
|
@ -55,7 +55,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSampleSymbolic() {
|
||||
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "77cf5b5273828dd1605bb23a5aeafcaa");
|
||||
HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "0761ff5cbf279be467833fa6708bf360");
|
||||
}
|
||||
|
||||
private void HCTestIndelQualityScores(String bam, String args, String md5) {
|
||||
|
|
@ -66,20 +66,20 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "87ca97f90e74caee35c35616c065821c");
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "29f1125df5ab27cc937a144ae08ac735");
|
||||
}
|
||||
|
||||
@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 WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("3df42d0550b51eb9b55aac61e8b3c452"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ece627de486aee69d02872891c6cb0ff"));
|
||||
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 WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("4dbc72b72e3e2d9d812d5a398490e213"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("add0f4f51969b7caeea99005a7ba1aa4"));
|
||||
executeTest("HCTestStructuralIndels: ", spec);
|
||||
}
|
||||
|
||||
|
|
@ -93,7 +93,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
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,
|
||||
Arrays.asList("f8c2745bf71f2659a57494fcaa2c103b"));
|
||||
Arrays.asList("8a400b0c46f41447fcc35a907e34f384"));
|
||||
executeTest("HC calling on a ReducedRead BAM", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
package org.broadinstitute.sting.gatk.walkers.annotator;
|
||||
|
||||
import com.sun.org.apache.bcel.internal.generic.AALOAD;
|
||||
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
|
||||
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
|
||||
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
|
||||
|
|
@ -68,50 +69,17 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati
|
|||
if ( depth == 0 )
|
||||
return null;
|
||||
|
||||
double QD = -10.0 * vc.getLog10PError() / (double)depth;
|
||||
double altAlleleLength = AverageAltAlleleLength.getMeanAltAlleleLength(vc);
|
||||
double QD = -10.0 * vc.getLog10PError() / ((double)depth * altAlleleLength);
|
||||
Map<String, Object> map = new HashMap<String, Object>();
|
||||
|
||||
if ( ! vc.isSNP() && ! vc.isSymbolic() ) {
|
||||
// adjust for the event length
|
||||
int averageLengthNum = 0;
|
||||
int averageLengthDenom = 0;
|
||||
int refLength = vc.getReference().length();
|
||||
for ( Allele a : vc.getAlternateAlleles() ) {
|
||||
int numAllele = vc.getCalledChrCount(a);
|
||||
int alleleSize;
|
||||
if ( a.length() == refLength ) {
|
||||
// SNP or MNP
|
||||
byte[] a_bases = a.getBases();
|
||||
byte[] ref_bases = vc.getReference().getBases();
|
||||
int n_mismatch = 0;
|
||||
for ( int idx = 0; idx < a_bases.length; idx++ ) {
|
||||
if ( a_bases[idx] != ref_bases[idx] )
|
||||
n_mismatch++;
|
||||
}
|
||||
alleleSize = n_mismatch;
|
||||
}
|
||||
else if ( a.isSymbolic() ) {
|
||||
alleleSize = 1;
|
||||
} else {
|
||||
alleleSize = Math.abs(refLength-a.length());
|
||||
}
|
||||
averageLengthNum += alleleSize*numAllele;
|
||||
averageLengthDenom += numAllele;
|
||||
}
|
||||
double averageLength = ( (double) averageLengthNum )/averageLengthDenom;
|
||||
QD /= averageLength;
|
||||
map.put(getKeyNames().get(1),String.format("%.2f",averageLength));
|
||||
}
|
||||
|
||||
map.put(getKeyNames().get(0), String.format("%.2f", QD));
|
||||
return map;
|
||||
}
|
||||
|
||||
public List<String> getKeyNames() { return Arrays.asList("QD","AAL"); }
|
||||
public List<String> getKeyNames() { return Arrays.asList("QD"); }
|
||||
|
||||
public List<VCFInfoHeaderLine> getDescriptions() {
|
||||
return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth"),
|
||||
new VCFInfoHeaderLine(getKeyNames().get(1), 1, VCFHeaderLineType.Float, "Average Allele Length"));
|
||||
return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth"));
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testHasAnnotsAsking1() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("a127623a26bac4c17c9df491e170ed88"));
|
||||
Arrays.asList("fbfbd4d13b7ba3d76e8e186902e81378"));
|
||||
executeTest("test file has annotations, asking for annotations, #1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -40,7 +40,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testHasAnnotsAsking2() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
|
||||
Arrays.asList("13e24e6b9dfa241df5baa2c3f53415b9"));
|
||||
Arrays.asList("19aef8914efc497192f89a9038310ca5"));
|
||||
executeTest("test file has annotations, asking for annotations, #2", spec);
|
||||
}
|
||||
|
||||
|
|
@ -66,7 +66,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testNoAnnotsAsking1() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("07cb4d427235878aeec0066d7d298e54"));
|
||||
Arrays.asList("4f0b8033da18e6cf6e9b8d5d36c21ba2"));
|
||||
executeTest("test file doesn't have annotations, asking for annotations, #1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -74,7 +74,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testNoAnnotsAsking2() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1,
|
||||
Arrays.asList("e579097677d5e56a5776151251947961"));
|
||||
Arrays.asList("64ca176d587dfa2b3b9dec9f7999305c"));
|
||||
executeTest("test file doesn't have annotations, asking for annotations, #2", spec);
|
||||
}
|
||||
|
||||
|
|
@ -82,7 +82,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testExcludeAnnotations() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard -XA FisherStrand -XA ReadPosRankSumTest --variant " + privateTestDir + "vcfexample2empty.vcf -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1,
|
||||
Arrays.asList("348314945436ace71ce6b1a52559d9ee"));
|
||||
Arrays.asList("f33f417fad98c05d9cd08ffa22943b0f"));
|
||||
executeTest("test exclude annotations", spec);
|
||||
}
|
||||
|
||||
|
|
@ -90,7 +90,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testOverwritingHeader() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample4.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,001,292", 1,
|
||||
Arrays.asList("ae7930e37a66c0aa4cfe0232736864fe"));
|
||||
Arrays.asList("0c810f6c4abef9d9dc5513ca872d3d22"));
|
||||
executeTest("test overwriting header", spec);
|
||||
}
|
||||
|
||||
|
|
@ -98,7 +98,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testNoReads() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
Arrays.asList("a0ba056c2625033e5e859fd6bcec1256"));
|
||||
Arrays.asList("1c423b7730b9805e7b885ece924286e0"));
|
||||
executeTest("not passing it any reads", spec);
|
||||
}
|
||||
|
||||
|
|
@ -106,7 +106,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testDBTagWithDbsnp() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
Arrays.asList("0be7da17340111a94e8581ee3808c88a"));
|
||||
Arrays.asList("54d7d5bb9404652857adf5e50d995f30"));
|
||||
executeTest("getting DB tag with dbSNP", spec);
|
||||
}
|
||||
|
||||
|
|
@ -114,7 +114,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testMultipleIdsWithDbsnp() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --alwaysAppendDbsnpId --dbsnp " + b36dbSNP129 + " -G Standard --variant " + privateTestDir + "vcfexample3withIDs.vcf -L " + privateTestDir + "vcfexample3withIDs.vcf", 1,
|
||||
Arrays.asList("e40e625302a496ede42eed61c2ce524b"));
|
||||
Arrays.asList("5fe63e511061ed4f91d938e72e7e3c39"));
|
||||
executeTest("adding multiple IDs with dbSNP", spec);
|
||||
}
|
||||
|
||||
|
|
@ -122,7 +122,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testDBTagWithHapMap() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --comp:H3 " + privateTestDir + "fakeHM3.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
Arrays.asList("cb50876477d3e035b6eda5d720d7ba8d"));
|
||||
Arrays.asList("cc7184263975595a6e2473d153227146"));
|
||||
executeTest("getting DB tag with HM3", spec);
|
||||
}
|
||||
|
||||
|
|
@ -130,7 +130,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testNoQuals() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --variant " + privateTestDir + "noQual.vcf -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L " + privateTestDir + "noQual.vcf -A QualByDepth", 1,
|
||||
Arrays.asList("458412261d61797d39f802c1e03d63f6"));
|
||||
Arrays.asList("aea983adc01cd059193538cc30adc17d"));
|
||||
executeTest("test file doesn't have QUALs", spec);
|
||||
}
|
||||
|
||||
|
|
@ -138,7 +138,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testUsingExpression() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.AF -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
Arrays.asList("39defa8108dca9fa3e54b22a7da43f77"));
|
||||
Arrays.asList("2b0e8cdfd691779befc5ac123d1a1887"));
|
||||
executeTest("using expression", spec);
|
||||
}
|
||||
|
||||
|
|
@ -146,7 +146,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest {
|
|||
public void testUsingExpressionWithID() {
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
baseTestString() + " --resource:foo " + privateTestDir + "targetAnnotations.vcf -G Standard --variant " + privateTestDir + "vcfexample3empty.vcf -E foo.ID -L " + privateTestDir + "vcfexample3empty.vcf", 1,
|
||||
Arrays.asList("a917edd58a0c235e9395bfc2d2020a8c"));
|
||||
Arrays.asList("3de1d1998203518098ffae233f3e2352"));
|
||||
executeTest("using expression with ID", spec);
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue