diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java index 674006661..7e7926f3a 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFs.java @@ -148,6 +148,16 @@ public class CombineGVCFs extends RodWalker 0 && (loc.getStart()+1) % multipleAtWhichToBreakBands == 0); // add +1 to the loc because we want to break BEFORE this base + } + /** * Is it okay to skip the given position? * diff --git a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java index d0a979294..3f202dab4 100644 --- a/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java +++ b/protected/gatk-tools-protected/src/test/java/org/broadinstitute/gatk/tools/walkers/variantutils/CombineGVCFsIntegrationTest.java @@ -203,6 +203,14 @@ public class CombineGVCFsIntegrationTest extends WalkerTest { executeTest("testBasepairResolutionOutput", spec); } + @Test + public void testBreakBlocks() throws Exception { + final String cmd = baseTestString(" -L 1:69485-69791 --breakBandsAtMultiplesOf 5"); + final WalkerTestSpec spec = new WalkerTestSpec(cmd, 1, Arrays.asList("3a8e53b8b590eaa2675149ceccb80a7a")); + spec.disableShadowBCF(); + executeTest("testBreakBlocks", spec); + } + @Test public void testWrongReferenceBaseBugFix() throws Exception { final String cmd = "-T CombineGVCFs -R " + b37KGReference + " -V " + (privateTestDir + "combine-gvcf-wrong-ref-input1.vcf"