From 9568c84af9a259e6c256cd6be74032b5ed96f803 Mon Sep 17 00:00:00 2001 From: ebanks Date: Fri, 18 Mar 2011 19:55:22 +0000 Subject: [PATCH] Don't output these messages in INFO mode because they are scaring people unnecessarily git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5475 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelRealigner.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java index e56c05c41..3142e9438 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java @@ -448,7 +448,7 @@ public class IndelRealigner extends ReadWalker { } if ( readsToClean.size() + readsNotToClean.size() >= MAX_READS ) { - logger.info("We are aborting the realignment in interval " + currentInterval + " because there are too many reads (see --maxReadsForRealignment for details)"); + logger.info("Not attempting realignment in interval " + currentInterval + " because there are too many reads."); abortCleanForCurrentInterval(); } } @@ -1409,7 +1409,7 @@ public class IndelRealigner extends ReadWalker { // no indel? String str = cigar.toString(); if ( !str.contains("D") && !str.contains("I") ) { - logger.info("Modifying a read with no associated indel; although this is possible, it is highly unlikely. Perhaps this region should be double-checked: " + read.getReadName() + " near " + read.getReferenceName() + ":" + read.getAlignmentStart()); + logger.debug("Modifying a read with no associated indel; although this is possible, it is highly unlikely. Perhaps this region should be double-checked: " + read.getReadName() + " near " + read.getReferenceName() + ":" + read.getAlignmentStart()); // newCigar = null; // return; } @@ -1444,7 +1444,7 @@ public class IndelRealigner extends ReadWalker { if ( newStart == -1 ) newStart = read.getAlignmentStart(); else if ( Math.abs(newStart - read.getAlignmentStart()) > MAX_POS_MOVE_ALLOWED ) { - logger.warn(String.format("Attempting to realign read %s at %d more than %d bases to %d.", read.getReadName(), read.getAlignmentStart(), MAX_POS_MOVE_ALLOWED, newStart)); + logger.debug(String.format("Attempting to realign read %s at %d more than %d bases to %d.", read.getReadName(), read.getAlignmentStart(), MAX_POS_MOVE_ALLOWED, newStart)); return false; }