@Test(dataProvider = "ArtificialSingleSampleReadStreamInvalidArgumentsTestDataProvider", expectedExceptions = ReviewedGATKException.class) public void testInvalidArguments( String testName, SAMFileHeader header, String readGroupID, int numContigs, int numStacksPerContig, int minReadsPerStack, int maxReadsPerStack, int minDistanceBetweenStacks, int maxDistanceBetweenStacks, int minReadLength, int maxReadLength, int numUnmappedReads ) { logger.warn("Running test: " + testName); ArtificialSingleSampleReadStream stream = new ArtificialSingleSampleReadStream(header, readGroupID, numContigs, numStacksPerContig, minReadsPerStack, maxReadsPerStack, minDistanceBetweenStacks, maxDistanceBetweenStacks, minReadLength, maxReadLength, numUnmappedReads); } }
new DownsamplingReadsIteratorTest(new ArtificialSingleSampleReadStream(header, readGroupID, numContigs,
private void createReadStreams() { perSampleArtificialReadStreams = new HashMap<String, ArtificialSingleSampleReadStream>(numSamples); perSampleStreamAnalyzers = new HashMap<String, ArtificialSingleSampleReadStreamAnalyzer>(numSamples); for (SAMReadGroupRecord readGroup : header.getReadGroups() ) { String readGroupID = readGroup.getReadGroupId(); String sampleName = readGroup.getSample(); int thisSampleNumContigs = MathUtils.randomIntegerInRange(minContigs, maxContigs); int thisSampleStacksPerContig = MathUtils.randomIntegerInRange(streamStacksPerContig.minStacksPerContig, streamStacksPerContig.maxStacksPerContig); int thisSampleNumUnmappedReads = Utils.getRandomGenerator().nextDouble() < unmappedReadsFraction ? unmappedReadsCount : 0; ArtificialSingleSampleReadStream thisSampleStream = new ArtificialSingleSampleReadStream(header, readGroupID, thisSampleNumContigs, thisSampleStacksPerContig, streamStackDepth.minReadsPerStack, streamStackDepth.maxReadsPerStack, streamDensity.minDistanceBetweenStacks, streamDensity.maxDistanceBetweenStacks, MIN_READ_LENGTH, MAX_READ_LENGTH, thisSampleNumUnmappedReads); perSampleArtificialReadStreams.put(sampleName, thisSampleStream); perSampleStreamAnalyzers.put(sampleName, new PositionallyDownsampledArtificialSingleSampleReadStreamAnalyzer(thisSampleStream, targetCoverage)); } mergedReadStream = new ArtificialMultiSampleReadStream(perSampleArtificialReadStreams.values()); }
((numContigs > 0 && stacksPerContig > 0) || (numContigs == 0 && stacksPerContig == 0)) ) { new ArtificialSingleSampleReadStreamTest(new ArtificialSingleSampleReadStream(header, readGroupID, numContigs,
private void createTestBAM() { header = ArtificialSAMUtils.createArtificialSamHeader(numContigs, 1, 100000); SAMReadGroupRecord readGroup = new SAMReadGroupRecord("foo"); readGroup.setSample("testSample"); header.addReadGroup(readGroup); ArtificialSingleSampleReadStream artificialReads = new ArtificialSingleSampleReadStream(header, "foo", numContigs, numStacksPerContig, stackSize, stackSize, 1, 100, 50, 150, numUnmappedReads); final File testBAMFile = createTempFile("SAMDataSourceFillShardBoundaryTest", ".bam"); SAMFileWriter bamWriter = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(header, true, testBAMFile); for ( SAMRecord read : artificialReads ) { bamWriter.addAlignment(read); } bamWriter.close(); testBAM = new SAMReaderID(testBAMFile, new Tags()); new File(testBAM.getSamFilePath().replace(".bam", ".bai")).deleteOnExit(); new File(testBAM.getSamFilePath() + ".bai").deleteOnExit(); } }