From 7852871f7d144a5f622777cebdc4b0c3cc22b3b2 Mon Sep 17 00:00:00 2001 From: Dror Kessler Date: Sun, 25 Jun 2023 23:14:47 +0300 Subject: [PATCH] hmer ondel must have mon length --- .../tools/walkers/annotator/flow/FlowAnnotatorBase.java | 2 +- .../tools/walkers/annotator/flow/FlowAnnotatorUnitTest.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) 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..e575547daf4 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 @@ -295,7 +295,7 @@ protected void isHmerIndel(final VariantContext vc, final LocalContext localCont if ( diffIndex < 0 ) { continue; } - if ( Math.max(refKey[diffIndex], altKey[diffIndex]) == 0 ) { + if ( Math.min(refKey[diffIndex], altKey[diffIndex]) == 0 ) { continue; } 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..be0e16cbc64 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 @@ -57,7 +57,7 @@ public Object[][] getTestData() { { // not hmer indel "TATCT CA TTGACCAA", "C", - "del", "1", "1", "A", "ATCTC", "TTGAC", "0.3", "NA", "non-h-indel" + "del", "1", "0", "", "ATCTC", "TTGAC", "0.3", "NA", "non-h-indel" }, { // del hmer indel