public ArtificialSingleSampleReadStreamTest( ArtificialSingleSampleReadStream stream ) { super(ArtificialSingleSampleReadStreamTest.class); this.stream = stream; setName(String.format("%s: numContigs=%d stacksPerContig=%d readsPerStack=%d-%d distanceBetweenStacks=%d-%d readLength=%d-%d unmappedReads=%d", getClass().getSimpleName(), stream.getNumContigs(), stream.getNumStacksPerContig(), stream.getMinReadsPerStack(), stream.getMaxReadsPerStack(), stream.getMinDistanceBetweenStacks(), stream.getMaxDistanceBetweenStacks(), stream.getMinReadLength(), stream.getMaxReadLength(), stream.getNumUnmappedReads())); }
public DownsamplingReadsIteratorTest( ArtificialSingleSampleReadStream stream, int targetCoverage ) { super(DownsamplingReadsIteratorTest.class); this.stream = stream; this.targetCoverage = targetCoverage; setName(String.format("%s: targetCoverage=%d numContigs=%d stacksPerContig=%d readsPerStack=%d-%d distanceBetweenStacks=%d-%d readLength=%d-%d unmappedReads=%d", getClass().getSimpleName(), targetCoverage, stream.getNumContigs(), stream.getNumStacksPerContig(), stream.getMinReadsPerStack(), stream.getMaxReadsPerStack(), stream.getMinDistanceBetweenStacks(), stream.getMaxDistanceBetweenStacks(), stream.getMinReadLength(), stream.getMaxReadLength(), stream.getNumUnmappedReads())); }
throw new ReviewedGATKException("stacks were separated by less than the minimum distance"); if ( maxDistanceBetweenStacks > originalStream.getMaxDistanceBetweenStacks() ) { throw new ReviewedGATKException("stacks were separated by more than the maximum distance");
throw new ReviewedGATKException("stacks were separated by less than the minimum distance"); if ( maxDistanceBetweenStacks > originalStream.getMaxDistanceBetweenStacks() ) { throw new ReviewedGATKException("stacks were separated by more than the maximum distance");