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Cleaning up reduced read code accessors

This commit is contained in:
Mark DePristo 2011-10-19 15:46:44 -04:00
parent 7928b287fc
commit 1b38aa1a7e
1 changed files with 1 additions and 15 deletions
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16
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -55,6 +55,7 @@ public class ReadUtils {
public static final String REDUCED_READ_CONSENSUS_COUNTS_TAG = "CC"; public static final String REDUCED_READ_CONSENSUS_COUNTS_TAG = "CC";
public final static byte[] getReducedReadQualityTagValue(final SAMRecord read) { 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); return read.getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
} }
@ -70,21 +71,6 @@ public class ReadUtils {
return getReducedReadQualityTagValue(read)[i]; 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 // General utilities