From 6230315ff2ae7e7a000d064d98b403d7ef6383ec Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Wed, 27 Jul 2011 22:51:21 -0400 Subject: [PATCH] Along with my half-written commit message from earlier, I also forgot to commit the integration test updates. This is what happens when you try to do things 30 seconds before you leave for the day. To finish up from before: complex events weren't being padded with the reference base as per the VCF spec. They are now. --- .../VariantContextIntegrationTest.java | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java index a344817a0..ced2bf00b 100755 --- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextIntegrationTest.java @@ -19,14 +19,14 @@ public class VariantContextIntegrationTest extends WalkerTest { static HashMap expectations = new HashMap(); static { - expectations.put("-L 1:1-10000 --printPerLocus", "e4ee2eaa3114888e918a1c82df7a027a"); - expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "5b5635e4877d82e8a27d70dac24bda2f"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "ceced3f270b4fe407ee83bc9028becde"); - expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "9a9b9e283553c28bf58de1cafa38fe92"); + expectations.put("-L 1:1-10000 --printPerLocus", "e9d96677a57bc3a10fb6d9ba942c19f0"); + expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "8a1174d2b18b98e624abbe93e6af8fdd"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "3933f1fae5453c54c3f791a23de07599"); + expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "c9cf2f01bf045a58dcc7649fd6ea2396"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "2097e32988d603d3b353b50218c86d3b"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "033bd952fca048fe1a4f6422b57ab2ed"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5e40980c02797f90821317874426a87a"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "e5a00766f8c1ff9cf92310bafdec3126"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "a103d856e8bc558c949c6e3f184e8913"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "5f2265ac6c6d80d64dc6e69a05c1250b"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "06a3ae4c0afa23b429a9491ab7707f3c"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc"); } @@ -58,7 +58,7 @@ public class VariantContextIntegrationTest extends WalkerTest { // this really just tests that we are seeing the same number of objects over all of chr1 WalkerTestSpec spec = new WalkerTestSpec( root + " -L 1" + " -o %s", 1, // just one output file - Arrays.asList("529f936aa6c303658b23caf4e527782f")); + Arrays.asList("2532234d2c934a5e14849655dd7b5f4f")); executeTest("testLargeScaleConversion", spec); } }