diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java index f91d77244..9fa8fc544 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -55,6 +55,7 @@ public class ReadUtils { public static final String REDUCED_READ_CONSENSUS_COUNTS_TAG = "CC"; public final static byte[] getReducedReadQualityTagValue(final SAMRecord read) { + // TODO -- warning of performance problem. Should be cached in GATKSamRecord return read.getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG); } @@ -70,21 +71,6 @@ public class ReadUtils { return getReducedReadQualityTagValue(read)[i]; } - public final static SAMRecord reducedReadWithReducedQuals(final SAMRecord read) { - if ( ! isReducedRead(read) ) throw new IllegalArgumentException("read must be a reduced read"); - return read; -// try { -// SAMRecord newRead = (SAMRecord)read.clone(); -// byte reducedQual = (byte)(int)getReducedReadQualityTagValue(read); -// byte[] newQuals = new byte[read.getBaseQualities().length]; -// Arrays.fill(newQuals, reducedQual); -// newRead.setBaseQualities(newQuals); -// return newRead; -// } catch ( CloneNotSupportedException e ) { -// throw new ReviewedStingException("SAMRecord no longer supports clone", e); -// } - } - // ---------------------------------------------------------------------------------------------------- // // General utilities