diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index 91a870dcc..de9c592f7 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -271,4 +271,4 @@ public class VariantContextAdaptors { keys.add(VCFGenotypeRecord.GENOTYPE_QUALITY_KEY); return Utils.sorted(new ArrayList(keys)); } -} \ No newline at end of file +} diff --git a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java index 545f68974..d491fda8f 100755 --- a/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextIntegrationTest.java @@ -19,20 +19,19 @@ public class VariantContextIntegrationTest extends WalkerTest { static HashMap expectations = new HashMap(); static { - expectations.put("-L 1:1-10000 --printPerLocus", "eb5802e7e615fa79b788a9447b7e824c"); - expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "f4580866bcff10e0e742f422c45695d3"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "85c949c985d8aa340030362ea1fc13d2"); - expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "a45430cfed2f574fb69e79d74ed41017"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "105547f432744e0776bd58e753cfa859"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "d758adbab9011e42c77d502fe4d62c27"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "933ec8327192c5ed58a1952c73fb4f73"); - expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "7d5d0283d92220ee78db7465d675b37f"); + expectations.put("-L 1:1-10000 --printPerLocus", "63fd69e4ab430b79fb213dd27b58ae1c"); + expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly", "276ed96efaaffc2fc1c3b3deb4e04d1d"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsStartinAtCurrentPosition", "a37f7bc34c1824688d3e475945c19d5a"); + expectations.put("-L 1:1-10000 --printPerLocus --takeFirstOnly --onlyContextsStartinAtCurrentPosition", "1715a6e0daf873f2e2cd10cb56085174"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType SNP", "bf33ab1ed65da7f56c02ca7956d9c31e"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL", "629ffd6b3b9ea1bce29cb715576f5c8a"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType INDEL --onlyContextsStartinAtCurrentPosition", "d4b812b2fec231f8f5b61d6f26cf86a5"); + expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType MIXED", "546e8e546f2cdfba31f91ed083137c42"); expectations.put("-L 1:1-10000 --printPerLocus --onlyContextsOfType NO_VARIATION", "39335acdb34c8a2af433dc50d619bcbc"); } @Test public void testConversionSelection() { - for ( Map.Entry entry : expectations.entrySet() ) { String extraArgs = entry.getKey(); String md5 = entry.getValue(); @@ -62,4 +61,4 @@ public class VariantContextIntegrationTest extends WalkerTest { Arrays.asList("3fcdd982df080e6abc0afaba6abdf386")); executeTest("testLargeScaleConversion", spec); } -} \ No newline at end of file +}