GATKSAMRecord read = ReadUtils.createRandomRead(1000);
GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, RAC.LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS);
ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
covariate.recordValues(read, readCovariates);
verifyCovariateArray(readCovariates.getMismatchesKeySet(), RAC.MISMATCHES_CONTEXT_SIZE, clippedRead, covariate);
<BUG>verifyCovariateArray(readCovariates.getInsertionsKeySet(), RAC.INSERTIONS_CONTEXT_SIZE, clippedRead, covariate);

verifyCovariateArray(readCovariates.getDeletionsKeySet(),  RAC.DELETIONS_CONTEXT_SIZE,  clippedRead, covariate);
</BUG>
}

GATKSAMRecord read = ReadUtils.createRandomRead(1000);
GATKSAMRecord clippedRead = ReadClipper.clipLowQualEnds(read, RAC.LOW_QUAL_TAIL, ClippingRepresentation.WRITE_NS);
ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
covariate.recordValues(read, readCovariates);
verifyCovariateArray(readCovariates.getMismatchesKeySet(), RAC.MISMATCHES_CONTEXT_SIZE, clippedRead, covariate);
verifyCovariateArray(readCovariates.getInsertionsKeySet(), RAC.INDELS_CONTEXT_SIZE, clippedRead, covariate);
verifyCovariateArray(readCovariates.getDeletionsKeySet(),  RAC.INDELS_CONTEXT_SIZE,  clippedRead, covariate);
}
