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Outputting both consensus base qualities and counts 

The base qualities of a consensus reads are now the average quality of the bases forming the consensus base (most common base) and the consensus quality tag now carry an array with the counts of each base in the consensus. This should increase file size but improve calling sensitivity/specificity.
This commit is contained in:
Mauricio Carneiro 2011-09-29 12:54:18 -04:00
parent d62f2f33bc
commit a5e75cd14c
1 changed files with 1 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -52,6 +52,7 @@ public class ReadUtils {
// ----------------------------------------------------------------------------------------------------
public static final String REDUCED_READ_QUALITY_TAG = "RQ";
public static final String REDUCED_READ_CONSENSUS_COUNTS_TAG = "CC";
public final static Integer getReducedReadQualityTagValue(final SAMRecord read) {
return read.getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);