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ReadClipper won't modify the original read 

Reverting back to the original implementation, but now including write N's and write Q0's due to walkers that look at the same read multiple times in different reference windows
This commit is contained in:
Mauricio Carneiro 2012-08-28 13:33:28 -04:00
parent 19cc0b373e
commit 69b56e11c8
1 changed files with 42 additions and 16 deletions
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58
public/java/src/org/broadinstitute/sting/utils/clipping/ClippingOp.java
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@ -37,34 +37,60 @@ public class ClippingOp {
* Clips the bases in read according to this operation's start and stop. Uses the clipping
* representation used is the one provided by algorithm argument.
*
* @param algorithm
* @param read
* @param algorithm clipping algorithm to use
* @param originalRead the read to be clipped
*/
public GATKSAMRecord apply(ClippingRepresentation algorithm, GATKSAMRecord read) {
public GATKSAMRecord apply(ClippingRepresentation algorithm, GATKSAMRecord originalRead) {
GATKSAMRecord read;
try {
read = (GATKSAMRecord) originalRead.clone();
} catch (CloneNotSupportedException e) {
throw new ReviewedStingException("Where did the clone go?");
}
byte[] quals = read.getBaseQualities();
byte[] bases = read.getReadBases();
byte[] newBases = new byte[bases.length];
byte[] newQuals = new byte[quals.length];
switch (algorithm) {
// important note:
// it's not safe to call read.getReadBases()[i] = 'N' or read.getBaseQualities()[i] = 0
// because you're not guaranteed to get a pointer to the actual array of bytes in the GATKSAMRecord
case WRITE_NS:
for (int i = start; i <= stop; i++)
bases[i] = 'N';
read.setReadBases(bases);
for (int i = 0; i < bases.length; i++) {
if (i >= start && i <= stop) {
newBases[i] = 'N';
}
else {
newBases[i] = bases[i];
}
}
read.setReadBases(newBases);
break;
case WRITE_Q0S:
for (int i = start; i <= stop; i++)
quals[i] = 0;
read.setBaseQualities(quals);
for (int i = 0; i < quals.length; i++) {
if (i >= start && i <= stop) {
newQuals[i] = 0;
}
else {
newQuals[i] = quals[i];
}
}
read.setBaseQualities(newQuals);
break;
case WRITE_NS_Q0S:
for (int i = start; i <= stop; i++) {
bases[i] = 'N';
quals[i] = 0;
for (int i = 0; i < bases.length; i++) {
if (i >= start && i <= stop) {
newQuals[i] = 0;
newBases[i] = 'N';
}
else {
newQuals[i] = quals[i];
newBases[i] = bases[i];
}
}
read.setReadBases(bases);
read.setBaseQualities(quals);
read.setBaseQualities(newBases);
read.setReadBases(newBases);
break;
case HARDCLIP_BASES:
read = hardClip(read, start, stop);
@ -437,8 +463,8 @@ public class ClippingOp {
* Checks if a hard clipped cigar left a read starting or ending with insertions/deletions
* and cleans it up accordingly.
*
* @param cigar
* @return
* @param cigar the original cigar
* @return an object with the shifts (see CigarShift class)
*/
private CigarShift cleanHardClippedCigar(Cigar cigar) {
Cigar cleanCigar = new Cigar();