From c54fc94505e6d1b913081b8854d5063d5ed11593 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Tue, 20 Nov 2012 23:19:59 -0500 Subject: [PATCH] Protect against features that start off the end of the read (otherwise, Arrays.fill fails) --- .../gatk/walkers/bqsr/BaseRecalibrator.java | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java index 9506510a9..b415bb1f5 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java @@ -268,16 +268,25 @@ public class BaseRecalibrator extends ReadWalker implements NanoSche } protected boolean[] calculateKnownSites( final GATKSAMRecord read, final List features ) { - final int BUFFER_SIZE = 0; final int readLength = read.getReadBases().length; final boolean[] knownSites = new boolean[readLength]; Arrays.fill(knownSites, false); for( final Feature f : features ) { int featureStartOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getStart(), ReadUtils.ClippingTail.LEFT_TAIL, true); // BUGBUG: should I use LEFT_TAIL here? - if( featureStartOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) { featureStartOnRead = 0; } + if( featureStartOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) { + featureStartOnRead = 0; + } + int featureEndOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getEnd(), ReadUtils.ClippingTail.LEFT_TAIL, true); - if( featureEndOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) { featureEndOnRead = readLength; } - Arrays.fill(knownSites, Math.max(0, featureStartOnRead - BUFFER_SIZE), Math.min(readLength, featureEndOnRead + 1 + BUFFER_SIZE), true); + if( featureEndOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) { + featureEndOnRead = readLength; + } + + if( featureStartOnRead > readLength ) { + featureStartOnRead = featureEndOnRead = readLength; + } + + Arrays.fill(knownSites, Math.max(0, featureStartOnRead), Math.min(readLength, featureEndOnRead + 1), true); } return knownSites; }