diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java index 30531f9b153..acf1c74bf9c 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorBase.java @@ -4,6 +4,7 @@ import htsjdk.variant.variantcontext.VariantContext; import org.apache.logging.log4j.LogManager; import org.apache.logging.log4j.Logger; +import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.engine.ReferenceContext; import org.broadinstitute.hellbender.exceptions.GATKException; import org.broadinstitute.hellbender.tools.walkers.annotator.InfoFieldAnnotation; @@ -149,7 +150,7 @@ private String establishReadGroupFlowOrder(final LocalContext localContext, fina // if here, no flow order was found. may we use a default? if ( isActualFlowOrderRequired() ) { localContext.generateAnnotation = false; - flowMissingOneShotLogger.warn("this.getClass().getSimpleName() + \" annotation will not be calculated, no '\" + StandardArgumentDefinitions.FLOW_ORDER_FOR_ANNOTATIONS + \"' argument provided\""); + flowMissingOneShotLogger.warn(this.getClass().getSimpleName() + " annotation will not be calculated, no '" + StandardArgumentDefinitions.FLOW_ORDER_FOR_ANNOTATIONS + "' argument provided"); } return FlowBasedRead.DEFAULT_FLOW_ORDER; @@ -204,10 +205,6 @@ protected void variantType(final VariantContext vc, final LocalContext localCont if ((localContext.hmerIndelLength.get(i)==null) || (localContext.hmerIndelLength.get(i)==0)){ isHmer=false; } - if ((localContext.hmerIndelLength.get(i)==1) && (localContext.indel.equals(C_DELETE))){ // new definition 1->0 has hmer indel 1 - isHmer=false; - } - } if (isHmer){ diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java index 6a71d8c82aa..5e399ea662c 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java @@ -27,7 +27,8 @@ public class FlowAnnotatorUnitTest extends GATKBaseTest { new HmerIndelNuc(), new HmerMotifs(), new GcContent(), - new CycleSkipStatus() + new CycleSkipStatus(), + new VariantType() }; @DataProvider(name = "testData") @@ -57,7 +58,7 @@ public Object[][] getTestData() { { // not hmer indel "TATCT CA TTGACCAA", "C", - "del", "1", "1", "A", "ATCTC", "TTGAC", "0.3", "NA", "non-h-indel" + "del", "1", "1", "A", "ATCTC", "TTGAC", "0.3", "NA", "h-indel" }, { // del hmer indel @@ -99,7 +100,7 @@ public void testBasic(final String refBases, final String altAllele, // check that all expected attributes are there String[] testResults = {indelClass, indelLength, hmerIndelLength, hmerIndelNuc, leftMotif, rightMotif, gcContent, cycleskipStatus, variantType}; - for ( int n = 0 ; n < 8 ; n++ ) { + for ( int n = 0 ; n < 9 ; n++ ) { String key = expectedAttrs.get(n); String elem = testResults[n]; String keyMsg = "on " + key + " " + msg;