Examples with ReadClipper org.broadinstitute.hellbender.utils.clipping.ReadClipper used on opensource projects

Example 1 with ReadClipper

use of org.broadinstitute.hellbender.utils.clipping.ReadClipper in project gatk by broadinstitute.

the class BaseRecalibrationEngine method makeReadTransform.

private ReadTransformer makeReadTransform() {
    ReadTransformer f0 = BaseRecalibrationEngine::consolidateCigar;
    ReadTransformer f = f0.andThen(this::setDefaultBaseQualities).andThen(this::resetOriginalBaseQualities).andThen(ReadClipper::hardClipAdaptorSequence).andThen(ReadClipper::hardClipSoftClippedBases);
    return f;
}