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())); }
if ( minReadsPerStack < originalStream.getMinReadsPerStack() ) { throw new ReviewedGATKException("stack had fewer than the minimum number of reads");
int stackMinimumAfterDownsampling = Math.min(targetCoverage, originalStream.getMinReadsPerStack()); int stackMaximumAfterDownsampling = targetCoverage;