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Static versions of the hard clipping utilities 

For simplified access to the hard clipping utilities. No need to create a ReadClipper object if you are not doing multiple complicated clipping operations, just use the static methods.

 examples:
   ReadClipper.hardClipLowQualEnds(2);
   ReadClipper.hardClipAdaptorSequence();
This commit is contained in:
Mauricio Carneiro 2011-12-20 14:30:06 -05:00
parent f73ad1c2e2
commit 1c4774c475
1 changed files with 83 additions and 31 deletions
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114
public/java/src/org/broadinstitute/sting/utils/clipping/ReadClipper.java
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@ -50,6 +50,44 @@ public class ReadClipper {
return read;
}
/**
* Return a new read corresponding to this.read that's been clipped according to ops, if any are present.
*
* @param algorithm
* @return
*/
public GATKSAMRecord clipRead(ClippingRepresentation algorithm) {
if (ops == null)
return getRead();
else {
try {
GATKSAMRecord clippedRead = (GATKSAMRecord) read.clone();
for (ClippingOp op : getOps()) {
//check if the clipped read can still be clipped in the range requested
if (op.start < clippedRead.getReadLength()) {
ClippingOp fixedOperation = op;
if (op.stop >= clippedRead.getReadLength())
fixedOperation = new ClippingOp(op.start, clippedRead.getReadLength() - 1);
clippedRead = fixedOperation.apply(algorithm, clippedRead);
}
}
wasClipped = true;
ops.clear();
if ( clippedRead.isEmpty() )
return new GATKSAMRecord( clippedRead.getHeader() );
return clippedRead;
} catch (CloneNotSupportedException e) {
throw new RuntimeException(e); // this should never happen
}
}
}
// QUICK USE UTILITY FUNCTION
public GATKSAMRecord hardClipByReferenceCoordinatesLeftTail(int refStop) {
return hardClipByReferenceCoordinates(-1, refStop);
}
@ -163,39 +201,13 @@ public class ReadClipper {
return clipRead(ClippingRepresentation.HARDCLIP_BASES);
}
public GATKSAMRecord hardClipAdaptorSequence () {
final Integer adaptorBoundary = ReadUtils.getAdaptorBoundary(read);
if (adaptorBoundary == null || !ReadUtils.isInsideRead(read, adaptorBoundary))
return read;
/**
* Return a new read corresponding to this.read that's been clipped according to ops, if any are present.
*
* @param algorithm
* @return
*/
public GATKSAMRecord clipRead(ClippingRepresentation algorithm) {
if (ops == null)
return getRead();
else {
try {
GATKSAMRecord clippedRead = (GATKSAMRecord) read.clone();
for (ClippingOp op : getOps()) {
//check if the clipped read can still be clipped in the range requested
if (op.start < clippedRead.getReadLength()) {
ClippingOp fixedOperation = op;
if (op.stop >= clippedRead.getReadLength())
fixedOperation = new ClippingOp(op.start, clippedRead.getReadLength() - 1);
clippedRead = fixedOperation.apply(algorithm, clippedRead);
}
}
wasClipped = true;
ops.clear();
if ( clippedRead.isEmpty() )
return new GATKSAMRecord( clippedRead.getHeader() );
return clippedRead;
} catch (CloneNotSupportedException e) {
throw new RuntimeException(e); // this should never happen
}
}
return read.getReadNegativeStrandFlag() ? hardClipByReferenceCoordinatesLeftTail(adaptorBoundary) : hardClipByReferenceCoordinatesRightTail(adaptorBoundary);
}
public GATKSAMRecord hardClipLeadingInsertions() {
@ -218,4 +230,44 @@ public class ReadClipper {
this.addOp(new ClippingOp(0, 0)); // UNSOFTCLIP_BASES doesn't need coordinates
return this.clipRead(ClippingRepresentation.REVERT_SOFTCLIPPED_BASES);
}
// STATIC VERSIONS OF THE QUICK CLIPPING FUNCTIONS
public static GATKSAMRecord hardClipByReferenceCoordinatesLeftTail(GATKSAMRecord read, int refStop) {
return (new ReadClipper(read)).hardClipByReferenceCoordinates(-1, refStop);
}
public static GATKSAMRecord hardClipByReferenceCoordinatesRightTail(GATKSAMRecord read, int refStart) {
return (new ReadClipper(read)).hardClipByReferenceCoordinates(refStart, -1);
}
public static GATKSAMRecord hardClipByReadCoordinates(GATKSAMRecord read, int start, int stop) {
return (new ReadClipper(read)).hardClipByReadCoordinates(start, stop);
}
public static GATKSAMRecord hardClipBothEndsByReferenceCoordinates(GATKSAMRecord read, int left, int right) {
return (new ReadClipper(read)).hardClipBothEndsByReferenceCoordinates(left, right);
}
public static GATKSAMRecord hardClipLowQualEnds(GATKSAMRecord read, byte lowQual) {
return (new ReadClipper(read)).hardClipLowQualEnds(lowQual);
}
public static GATKSAMRecord hardClipSoftClippedBases (GATKSAMRecord read) {
return (new ReadClipper(read)).hardClipSoftClippedBases();
}
public static GATKSAMRecord hardClipAdaptorSequence (GATKSAMRecord read) {
return (new ReadClipper(read)).hardClipAdaptorSequence();
}
public static GATKSAMRecord hardClipLeadingInsertions(GATKSAMRecord read) {
return (new ReadClipper(read)).hardClipLeadingInsertions();
}
public static GATKSAMRecord revertSoftClippedBases(GATKSAMRecord read) {
return (new ReadClipper(read)).revertSoftClippedBases();
}
}