zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Reduced reads are now aware of their original alignments 

* Added annotations for reads that had been soft clipped prior to being reduced so that we can later recuperate their original alignments (start and end).
   * Tags keep the alignment shifts, not real alignment, for better compression
   * Tags are defined in the GATKSAMRecord
   * GATKSAMRecord has new functionality to retrieve original alignment start of all reads (trimmed or not) -- getOriginalAlignmentStart() and getOriginalAligmentEnd()
   * Updated ReduceReads MD5s accordingly
This commit is contained in:
Mauricio Carneiro 2012-01-26 16:07:29 -05:00
parent 07f72516ae
commit 0d4027104f
1 changed files with 51 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

52
public/java/src/org/broadinstitute/sting/utils/sam/GATKSAMRecord.java
View File

@ -43,7 +43,10 @@ import java.util.Map;
*
*/
public class GATKSAMRecord extends BAMRecord {
public static final String REDUCED_READ_CONSENSUS_TAG = "RR";
// 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_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
private String mReadString = null;
@ -321,6 +324,36 @@ public class GATKSAMRecord extends BAMRecord {
return (lastOperator == CigarOperator.HARD_CLIP) ? stop-1 : stop+shift-1 ;
}
/**
* Determines the original alignment start of a previously clipped read.
*
* This is useful for reads that have been trimmed to a variant region and lost the information of it's original alignment end
*
* @return the alignment start of a read before it was clipped
*/
public int getOriginalAlignmentStart() {
int originalAlignmentStart = getUnclippedStart();
Integer alignmentShift = (Integer) getAttribute(REDUCED_READ_ORIGINAL_ALIGNMENT_START_SHIFT);
if (alignmentShift != null)
originalAlignmentStart += alignmentShift;
return originalAlignmentStart;
}
/**
* Determines the original alignment end of a previously clipped read.
*
* This is useful for reads that have been trimmed to a variant region and lost the information of it's original alignment end
*
* @return the alignment end of a read before it was clipped
*/
public int getOriginalAlignmentEnd() {
int originalAlignmentEnd = getUnclippedEnd();
Integer alignmentShift = (Integer) getAttribute(REDUCED_READ_ORIGINAL_ALIGNMENT_END_SHIFT);
if (alignmentShift != null)
originalAlignmentEnd -= alignmentShift;
return originalAlignmentEnd;
}
/**
* Creates an empty GATKSAMRecord with the read's header, read group and mate
* information, but empty (not-null) fields:
@ -363,4 +396,21 @@ public class GATKSAMRecord extends BAMRecord {
return emptyRead;
}
/**
* Shallow copy of everything, except for the attribute list and the temporary attributes.
* A new list of the attributes is created for both, but the attributes themselves are copied by reference.
* This should be safe because callers should never modify a mutable value returned by any of the get() methods anyway.
*
* @return a shallow copy of the GATKSAMRecord
* @throws CloneNotSupportedException
*/
@Override
public Object clone() throws CloneNotSupportedException {
final GATKSAMRecord clone = (GATKSAMRecord) super.clone();
if (temporaryAttributes != null) {
for (Object attribute : temporaryAttributes.keySet())
clone.setTemporaryAttribute(attribute, temporaryAttributes.get(attribute));
}
return clone;
}
}