Use ReadClipper in BaseQualityClipReadTransformer #3388
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Codecov Report
@@ Coverage Diff @@
## master #3388 +/- ##
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+ Coverage 80.467% 80.549% +0.081%
- Complexity 17507 17639 +132
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Files 1173 1175 +2
Lines 63376 63749 +373
Branches 9878 9963 +85
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+ Hits 50997 51349 +352
- Misses 8431 8443 +12
- Partials 3948 3957 +9
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SHuang-Broad
approved these changes
Aug 2, 2017
| public GATKRead apply(GATKRead read) { | ||
| GATKRead readClippedRightEnd = clipReadRightEnd(read); | ||
| public GATKRead apply(final GATKRead read) { | ||
| final GATKRead readClippedRightEnd = clipReadRightEnd(read); | ||
| return clipReadLeftEnd(readClippedRightEnd); | ||
| } | ||
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I know this exists before this PR, but while you are at it, could you add a documentation to getRightClipPoint(byte[]) and getLeftClipPoint(byte[]) explicitly saying that a negative return value means no clipping necessary?
| public GATKRead apply(GATKRead read) { | ||
| GATKRead readClippedRightEnd = clipReadRightEnd(read); | ||
| public GATKRead apply(final GATKRead read) { | ||
| final GATKRead readClippedRightEnd = clipReadRightEnd(read); | ||
| return clipReadLeftEnd(readClippedRightEnd); | ||
| } | ||
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And, while looking at these two functions, they are very similar.
Considering that even though it is public but seemingly only this class itself is using it, I suggest the following change, but it is totally up to you:
@override
public GATKRead apply(final GATKRead read) {
return clipRead(clipRead(read, false), true);
}
private int getClipPoint( final byte[] quals, final boolean fromLeft ) {
final int readLength = quals.length;
final int start, end, step;
if (fromLeft) {
start = 0; end = readLength; step = 1;
} else {
start = readLength - 1; end = -1; step = -1;
}
int clipSum = 0, lastMax = -1, clipPoint = -1; // -1 means no clip
for (int i = start; i != end; i+= step) {
clipSum += (qTrimmingThreshold - quals[i]);
if (clipSum >= 0 && (clipSum >= lastMax)) {
lastMax = clipSum;
clipPoint = i;
}
}
return clipPoint;
}
private GATKRead clipRead(final GATKRead read, final boolean fromLeft) {
final byte[] quals = read.getBaseQualities();
final int clipPoint = getClipPoint(quals, fromLeft);
if (clipPoint != -1) {
final ReadClipper readClipper = new ReadClipper(read);
readClipper.addOp(fromLeft ? new ClippingOp(0, clipPoint) : new ClippingOp(clipPoint, read.getLength()));
return readClipper.clipRead(ClippingRepresentation.HARDCLIP_BASES);
} else {
return read;
}
}
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That was my original approach, but I think it's easier to have two simple functions instead of one complicated function in this case.
SHuang-Broad
reviewed
Aug 2, 2017
| import org.broadinstitute.hellbender.utils.read.GATKRead; | ||
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| import java.util.Arrays; | ||
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| /** | ||
| * Clips reads on both ends using base quality scores | ||
| */ | ||
| public class BaseQualityClipReadTransformer implements ReadTransformer { |
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I forgot to mention that you probably intended this class to be final too, and its serialVersionUID to be private.
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The earlier version of BaseQualityClipReadTransformer clipped bases by just removing them from the bases and base qualities arrays, but did not adjust the cigar, coordinate, etc. (thanks to @SHuang-Broad for catching this in #3354).
This commit fixes this behavior by invoking the ReadClipper class and adds cigar checking to the unit test. It also makes some minor style changes to the transformer and test code.