From a5e75cd14cf7a8b6d3c4c8271302468fc5f256b4 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Thu, 29 Sep 2011 12:54:18 -0400 Subject: [PATCH] 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. --- .../java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java | 1 + 1 file changed, 1 insertion(+) 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 e0a3a5a53..fcb3089cd 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java @@ -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);