From 81d4eaea29beb68710e0a2862c1572fc34a23dac Mon Sep 17 00:00:00 2001 From: Geraldine Van der Auwera Date: Fri, 27 May 2016 11:49:48 -0400 Subject: [PATCH] Fixed warnings in LAATV and ValidateVariants --- .../tools/walkers/variantutils/LeftAlignAndTrimVariants.java | 2 +- .../gatk/tools/walkers/variantutils/ValidateVariants.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java index 834c19753..c169a2844 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java @@ -249,7 +249,7 @@ public class LeftAlignAndTrimVariants extends RodWalker { // ignore if the reference length is greater than the reference window stop before and after expansion if ( refLength > MAX_INDEL_LENGTH && refLength > referenceWindowStop ) { - logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d", + logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --reference_window_stop >= %d", REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getChr(), vc.getStart(), refLength)); return 0; } diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java index 653bdaf50..6c9912f06 100644 --- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java +++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java @@ -283,7 +283,7 @@ public class ValidateVariants extends RodWalker { // reference length is greater than the reference window stop before and after expansion if ( refLength > 100 && refLength > referenceWindowStop ) { - logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d", + logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --reference_window_stop >= %d", REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getContig(), vc.getStart(), refLength)); return; }