if ( (originalStream.getNumContigs() == 0 || originalStream.getNumStacksPerContig() == 0) && originalStream.getNumUnmappedReads() == 0 ) { if ( totalReads != 0 ) { throw new ReviewedGATKException("got reads from the stream, but the stream was configured to have 0 reads"); if ( numContigs != originalStream.getNumContigs() ) { throw new ReviewedGATKException("number of contigs not correct"); if ( stacksPerContig.size() != originalStream.getNumContigs() ) { throw new ReviewedGATKException(String.format("bug in analyzer code: calculated sizes for %d contigs even though there were only %d contigs", stacksPerContig.size(), originalStream.getNumContigs())); if ( (originalStream.getNumContigs() == 0 || originalStream.getNumStacksPerContig() == 0) && numUnmappedReads != totalReads ) { throw new ReviewedGATKException("stream should have consisted only of unmapped reads, but saw some mapped reads");
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 ( (originalStream.getNumContigs() == 0 || originalStream.getNumStacksPerContig() == 0) && originalStream.getNumUnmappedReads() == 0 ) { if ( totalReads != 0 ) { throw new ReviewedGATKException("got reads from the stream, but the stream was configured to have 0 reads"); if ( numContigs != originalStream.getNumContigs() ) { throw new ReviewedGATKException("number of contigs not correct"); if ( stacksPerContig.size() != originalStream.getNumContigs() ) { throw new ReviewedGATKException(String.format("bug in analyzer code: calculated sizes for %d contigs even though there were only %d contigs", stacksPerContig.size(), originalStream.getNumContigs())); if ( (originalStream.getNumContigs() == 0 || originalStream.getNumStacksPerContig() == 0) && numUnmappedReads != totalReads ) { throw new ReviewedGATKException("stream should have consisted only of unmapped reads, but saw some mapped reads");