From ec9920b04f7a95918ed3b76a4e971143ed8084b0 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 27 Jan 2012 08:51:39 -0500 Subject: [PATCH] Updating the SAM TAG for Original Alignment Start to "OP" per Mark's recommendation to reuse the Indel Realigner tag that made it to the SAM spec. The Alignment end tag is still "OE" as there is no official tag to reuse. --- .../src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java index f17772f40..03b794ae3 100755 --- a/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java +++ b/public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java @@ -45,7 +45,7 @@ import java.util.Map; public class GATKSAMRecord extends BAMRecord { // ReduceReads specific attribute tags public static final String REDUCED_READ_CONSENSUS_TAG = "RR"; // marks a synthetic read produced by the ReduceReads tool - public static final String REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT = "OS"; // reads that are clipped may use this attribute to keep track of their original alignment start + public static final String REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT = "OP"; // reads that are clipped may use this attribute to keep track of their original alignment start public static final String REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT = "OE"; // reads that are clipped may use this attribute to keep track of their original alignment end // the SAMRecord data we're caching