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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

This commit is contained in:
Ryan Poplin 2012-08-29 11:39:30 -04:00
parent b132a33dac 69b56e11c8
commit 4ea38bbfe8
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 * 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. * representation used is the one provided by algorithm argument.
* *
* @param algorithm * @param algorithm clipping algorithm to use
* @param read * @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[] quals = read.getBaseQualities();
byte[] bases = read.getReadBases(); byte[] bases = read.getReadBases();
byte[] newBases = new byte[bases.length];
byte[] newQuals = new byte[quals.length];
switch (algorithm) { switch (algorithm) {
// important note: // important note:
// it's not safe to call read.getReadBases()[i] = 'N' or read.getBaseQualities()[i] = 0 // 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 // because you're not guaranteed to get a pointer to the actual array of bytes in the GATKSAMRecord
case WRITE_NS: case WRITE_NS:
for (int i = start; i <= stop; i++) for (int i = 0; i < bases.length; i++) {
bases[i] = 'N'; if (i >= start && i <= stop) {
read.setReadBases(bases); newBases[i] = 'N';
}
else {
newBases[i] = bases[i];
}
}
read.setReadBases(newBases);
break; break;
case WRITE_Q0S: case WRITE_Q0S:
for (int i = start; i <= stop; i++) for (int i = 0; i < quals.length; i++) {
quals[i] = 0; if (i >= start && i <= stop) {
read.setBaseQualities(quals); newQuals[i] = 0;
}
else {
newQuals[i] = quals[i];
}
}
read.setBaseQualities(newQuals);
break; break;
case WRITE_NS_Q0S: case WRITE_NS_Q0S:
for (int i = start; i <= stop; i++) { for (int i = 0; i < bases.length; i++) {
bases[i] = 'N'; if (i >= start && i <= stop) {
quals[i] = 0; newQuals[i] = 0;
newBases[i] = 'N';
}
else {
newQuals[i] = quals[i];
newBases[i] = bases[i];
}
} }
read.setReadBases(bases); read.setBaseQualities(newBases);
read.setBaseQualities(quals); read.setReadBases(newBases);
break; break;
case HARDCLIP_BASES: case HARDCLIP_BASES:
read = hardClip(read, start, stop); 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 * Checks if a hard clipped cigar left a read starting or ending with insertions/deletions
* and cleans it up accordingly. * and cleans it up accordingly.
* *
* @param cigar * @param cigar the original cigar
* @return * @return an object with the shifts (see CigarShift class)
*/ */
private CigarShift cleanHardClippedCigar(Cigar cigar) { private CigarShift cleanHardClippedCigar(Cigar cigar) {
Cigar cleanCigar = new Cigar(); Cigar cleanCigar = new Cigar();