zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Update md5s for VQSR, as VQSLOD is now a double and gets the standard double precision treatment in VCF

This commit is contained in:
Mark DePristo 2012-08-30 19:41:36 -04:00
parent 2f749b5e52
commit 39400c56a9
1 changed files with 7 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

14
public/java/test/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersIntegrationTest.java
View File

@ -1,10 +1,10 @@
package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.Test;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.*;
import java.util.Arrays;
public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
private static class VRTest {
@ -28,7 +28,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest lowPass = new VRTest(validationDataLocation + "phase1.projectConsensus.chr20.raw.snps.vcf",
"f360ce3eb2b0b887301be917a9843e2b", // tranches
"287fea5ea066bf3fdd71f5ce9b58eab3", // recal file
"356b9570817b9389da71fbe991d8b2f5"); // cut VCF
"afa297c743437551cc2bd36ddd6d6d75"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {
@ -77,7 +77,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
VRTest bcfTest = new VRTest(privateTestDir + "vqsr.bcf_test.snps.unfiltered.bcf",
"a8ce3cd3dccafdf7d580bcce7d660a9a", // tranches
"74c10fc15f9739a938b7138909fbde04", // recal file
"62fda105e14b619a1c263855cf56af1d"); // cut VCF
"c30d163871a37f2bbf8ee7f761e870b4"); // cut VCF
@DataProvider(name = "VRBCFTest")
public Object[][] createVRBCFTest() {
@ -129,13 +129,13 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
validationDataLocation + "combined.phase1.chr20.raw.indels.unfiltered.sites.vcf", // all FILTERs as .
"b7589cd098dc153ec64c02dcff2838e4", // tranches
"a04a9001f62eff43d363f4d63769f3ee", // recal file
"64f576881e21323dd4078262604717a2"); // cut VCF
"b2c6827be592c24a4692b1753edc7d23"); // cut VCF
VRTest indelFiltered = new VRTest(
validationDataLocation + "combined.phase1.chr20.raw.indels.filtered.sites.vcf", // all FILTERs as PASS
"b7589cd098dc153ec64c02dcff2838e4", // tranches
"a04a9001f62eff43d363f4d63769f3ee", // recal file
"af22c55d91394c56a222fd40d6d54781"); // cut VCF
"5d483fe1ba2ef36ee9e6c14cbd654706"); // cut VCF
@DataProvider(name = "VRIndelTest")
public Object[][] createTestVariantRecalibratorIndel() {
@ -193,7 +193,7 @@ public class VariantRecalibrationWalkersIntegrationTest extends WalkerTest {
" -o %s" +
" -tranchesFile " + privateTestDir + "VQSR.mixedTest.tranches" +
" -recalFile " + privateTestDir + "VQSR.mixedTest.recal",
Arrays.asList("ec519e1f01459813dab57aefffc019e2"));
Arrays.asList("018b3a5cc7cf0cb5468c6a0c80ccaa8b"));
executeTest("testApplyRecalibrationSnpAndIndelTogether", spec);
}
}