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Merged bug fix from Stable into Unstable

This commit is contained in:
Eric Banks 2012-11-28 13:26:52 -05:00
parent c676853731 6030605242
commit 3463774f2a
2 changed files with 10 additions and 5 deletions
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2
public/java/src/org/broadinstitute/sting/utils/QualityUtils.java
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@ -9,7 +9,7 @@ import net.sf.samtools.SAMUtils;
* @author Kiran Garimella * @author Kiran Garimella
*/ */
public class QualityUtils { public class QualityUtils {
public final static byte MAX_RECALIBRATED_Q_SCORE = 93; public final static byte MAX_RECALIBRATED_Q_SCORE = SAMUtils.MAX_PHRED_SCORE;
public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE; public final static byte MAX_QUAL_SCORE = SAMUtils.MAX_PHRED_SCORE;
public final static double ERROR_RATE_OF_MAX_QUAL_SCORE = qualToErrorProbRaw(MAX_QUAL_SCORE); public final static double ERROR_RATE_OF_MAX_QUAL_SCORE = qualToErrorProbRaw(MAX_QUAL_SCORE);

13
public/java/src/org/broadinstitute/sting/utils/baq/BAQ.java
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@ -406,10 +406,15 @@ public class BAQ {
// so BQi = Qi - BAQi + 64 // so BQi = Qi - BAQi + 64
byte[] bqTag = new byte[baq.length]; byte[] bqTag = new byte[baq.length];
for ( int i = 0; i < bqTag.length; i++) { for ( int i = 0; i < bqTag.length; i++) {
int bq = (int)read.getBaseQualities()[i] + 64; final int bq = (int)read.getBaseQualities()[i] + 64;
int baq_i = (int)baq[i]; final int baq_i = (int)baq[i];
int tag = bq - baq_i; final int tag = bq - baq_i;
if ( tag < 0 ) throw new ReviewedStingException("BAQ tag calculation error. BAQ value above base quality at " + read); // problem with the calculation of the correction factor; this is our problem
if ( tag < 0 )
throw new ReviewedStingException("BAQ tag calculation error. BAQ value above base quality at " + read);
// the original quality is too high, almost certainly due to using the wrong encoding in the BAM file
if ( tag > Byte.MAX_VALUE )
throw new UserException.MalformedBAM(read, "we encountered an extremely high quality score (" + (bq - 64) + ") with BAQ correction factor of " + baq_i + "; the BAM file appears to be using the wrong encoding for quality scores");
bqTag[i] = (byte)tag; bqTag[i] = (byte)tag;
} }
return new String(bqTag); return new String(bqTag);