From a90c01f1b3f613504b2b74cb54e0e9ea2f0eec60 Mon Sep 17 00:00:00 2001 From: Dror Kessler Date: Mon, 13 Nov 2023 13:53:28 +0000 Subject: [PATCH] Ultima.flow annotations.fix (#8442) * hmer ondel must have mon length * Revert "hmer ondel must have mon length" This reverts commit 7852871f7d144a5f622777cebdc4b0c3cc22b3b2. * remove superfluous variant type condition * fix error message to actually reflect missing argument * fixed unittest to include variant type * Remove conflict --- .../tools/walkers/annotator/flow/FlowAnnotatorBase.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 0c4a07f015a..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;