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Now uses the NO_HEADER option to avoid breaking MD5s due to changes in GATKArgumentCollection 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5518 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-03-26 12:00:37 +00:00
parent 27c8fb1e4d
commit 7272fcf539
1 changed files with 3 additions and 2 deletions
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5
java/test/org/broadinstitute/sting/playground/gatk/walkers/variantrecalibration/VariantRecalibrationWalkersV2IntegrationTest.java
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@ -27,12 +27,12 @@ public class VariantRecalibrationWalkersV2IntegrationTest extends WalkerTest {
VRTest yriTrio = new VRTest("yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf",
"aa211561e6e9b1e323dec4eeaa318088", // tranches
"226adf939e90ad20599108e77ad25dae", // recal file
"943cb30cad3bc23e4d945b523e1a67cd"); // cut VCF
"06c2335e860e19f23bcacff8d4ab906d"); // cut VCF
VRTest lowPass = new VRTest("lowpass.N3.chr1.raw.vcf",
"f4f2057a8c010206f0f56deff0602452", // tranches
"dd36d252a6dc6e3207addddae731dd88", // recal file
"c142f2a3524dcd7a1a16233670aa5772"); // cut VCF
"af4fe8bd0c2eca92d1990b1a49fae810"); // cut VCF
@DataProvider(name = "VRTest")
public Object[][] createData1() {
@ -64,6 +64,7 @@ public class VariantRecalibrationWalkersV2IntegrationTest extends WalkerTest {
"-R " + b36KGReference +
" -T ApplyRecalibration" +
" -L 1:60,000,000-115,000,000" +
" -NO_HEADER" +
" -B:input,VCF " + params.inVCF +
" -o %s" +
" -tranchesFile " + getFileForMD5(params.tranchesMD5) +