From fdded73861a5016222a7d88b079edc605aac487d Mon Sep 17 00:00:00 2001 From: weisburd Date: Wed, 9 Jun 2010 17:52:48 +0000 Subject: [PATCH] Improved error reporting git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3520 348d0f76-0448-11de-a6fe-93d51630548a --- .../playground/gatk/walkers/annotator/TranscriptToInfo.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java index 2033da591..37d5048cc 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java @@ -398,7 +398,7 @@ public class TranscriptToInfo extends RodWalker, TreeMap if(isProteinCodingTranscript && parsedTranscriptRod.cdsSequence.length() % 3 != 0) { if (!isMitochondrialTranscript) { - logger.warn("WARNING: Transcript " + parsedTranscriptRod +" at position ["+ parsedTranscriptRod.txChrom + ":" +parsedTranscriptRod.txStart + "-" + parsedTranscriptRod.txEnd + "] has " + parsedTranscriptRod.cdsSequence.length() + " nucleotides in its CDS region, which is not divisible by 3. Skipping..."); + logger.error("ERROR: Transcript " + parsedTranscriptRod +" at position ["+ parsedTranscriptRod.txChrom + ":" +parsedTranscriptRod.txStart + "-" + parsedTranscriptRod.txEnd + "] has " + parsedTranscriptRod.cdsSequence.length() + " nucleotides in its CDS region, which is not divisible by 3. Skipping..."); //discard transcripts where CDS length is not a multiple of 3 skippedTranscriptCounter++; return; @@ -426,7 +426,7 @@ public class TranscriptToInfo extends RodWalker, TreeMap } while( parsedTranscriptRod.cdsSequence.length() % 3 != 0); } else { - logger.warn("WARNING: Mitochnodrial transcript " + parsedTranscriptRod +" at position ["+ parsedTranscriptRod.txChrom + ":" +parsedTranscriptRod.txStart + "-" + parsedTranscriptRod.txEnd + "] has " + parsedTranscriptRod.cdsSequence.length() + " nucleotides in its CDS region, which is not divisible by 3. The CDS does not cover the entire transcript, so its not possible to use A's from the polyA tail. Skipping..."); + logger.error("ERROR: Mitochnodrial transcript " + parsedTranscriptRod +" at position ["+ parsedTranscriptRod.txChrom + ":" +parsedTranscriptRod.txStart + "-" + parsedTranscriptRod.txEnd + "] has " + parsedTranscriptRod.cdsSequence.length() + " nucleotides in its CDS region, which is not divisible by 3. The CDS does not cover the entire transcript, so its not possible to use A's from the polyA tail. Skipping..."); skippedTranscriptCounter++; return; }