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gatk-3.8
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Fixed most indexing bugs 

* added bases and quals to consensus
* fixed consensus read cigar generation.
This commit is contained in:
Mauricio Carneiro 2011-08-27 23:25:26 -04:00
parent 32e74affe1
commit 66a8b36cf5
1 changed files with 4 additions and 0 deletions
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4
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -4,6 +4,7 @@ import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement; import net.sf.samtools.CigarElement;
import net.sf.samtools.SAMRecord; import net.sf.samtools.SAMRecord;
import org.broad.tribble.util.PositionalStream; import org.broad.tribble.util.PositionalStream;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.ReadUtils; import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.jets3t.service.multi.ThreadedStorageService; import org.jets3t.service.multi.ThreadedStorageService;
@ -54,6 +55,9 @@ public class ReadClipper {
int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart); int start = (refStart < 0) ? 0 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStart);
int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop); int stop = (refStop < 0) ? read.getReadLength() - 1 : ReadUtils.getReadCoordinateForReferenceCoordinate(read, refStop);
if (start < 0 || stop > read.getReadLength() - 1)
throw new ReviewedStingException("Trying to clip before the start or after the end of a read");
//System.out.println("Clipping start/stop: " + start + "/" + stop); //System.out.println("Clipping start/stop: " + start + "/" + stop);
this.addOp(new ClippingOp(start, stop)); this.addOp(new ClippingOp(start, stop));
return clipRead(ClippingRepresentation.HARDCLIP_BASES); return clipRead(ClippingRepresentation.HARDCLIP_BASES);