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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
This commit is contained in:
ebanks 2011-03-18 19:55:22 +00:00
parent 22ff2573d5
commit 9568c84af9
1 changed files with 3 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -448,7 +448,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
}
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<Integer, Integer> {
// 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<Integer, Integer> {
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;
}