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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.
This commit is contained in:
Mauricio Carneiro 2012-01-27 08:51:39 -05:00
parent 2a565ebf90
commit ec9920b04f
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
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@ -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