Source:
private static int verifyLane(final IlluminaFileUtil fileUtil, final List<Integer> expectedTiles, final int[] cycles, final Set<IlluminaDataType> dataTypes, final boolean fakeFiles) { if (expectedTiles.isEmpty()) { throw new PicardException( "0 input tiles were specified! Check to make sure this lane is in the InterOp file!"); } if (cycles.length == 0) { throw new PicardException("0 output cycles were specified!"); } int numFailures = 0; final Map<IlluminaFileUtil.SupportedIlluminaFormat, Set<IlluminaDataType>> formatToDataTypes = IlluminaDataProviderFactory.determineFormats(dataTypes, fileUtil); final Set<IlluminaDataType> unmatchedDataTypes = IlluminaDataProviderFactory.findUnmatchedTypes(dataTypes, formatToDataTypes); if (!unmatchedDataTypes.isEmpty()) { if (fakeFiles) { for (final IlluminaDataType dataType : unmatchedDataTypes) { final IlluminaFileUtil.SupportedIlluminaFormat format = IlluminaDataProviderFactory.findPreferredFormat(dataType, fileUtil); fileUtil.getUtil(format).fakeFiles(expectedTiles, cycles, format); } } log.info("Could not find a format with available files for the following data types: " + StringUtil .join(", ", new ArrayList<>(unmatchedDataTypes))); numFailures += unmatchedDataTypes.size(); } for (final IlluminaFileUtil.SupportedIlluminaFormat format : formatToDataTypes.keySet()) { final ParameterizedFileUtil util = fileUtil.getUtil(format); if(util instanceof PerTileOrPerRunFileUtil){ util.setTiles(expectedTiles); } final List<String> failures = util.verify(expectedTiles, cycles); if (!failures.isEmpty() && fakeFiles) { util.fakeFiles(expectedTiles, cycles, format); } numFailures += failures.size(); for (final String failure : failures) { log.info(failure); } } return numFailures; }

Target:
private static int verifyLane(final IlluminaFileUtil fileUtil, final List<Integer> expectedTiles, final int[] cycles, final Set<IlluminaDataType> dataTypes, final boolean fakeFiles) { if (expectedTiles.isEmpty()) { throw new PicardException( "0 input tiles were specified! Check to make sure this lane is in the InterOp file!"); } if (cycles.length == 0) { throw new PicardException("0 output cycles were specified!"); } int numFailures = 0; final Map<IlluminaFileUtil.SupportedIlluminaFormat, Set<IlluminaDataType>> formatToDataTypes = IlluminaDataProviderFactory.determineFormats(dataTypes, fileUtil); final Set<IlluminaDataType> unmatchedDataTypes = IlluminaDataProviderFactory.findUnmatchedTypes(dataTypes, formatToDataTypes); if (!unmatchedDataTypes.isEmpty()) { if (fakeFiles) { for (final IlluminaDataType dataType : unmatchedDataTypes) { final IlluminaFileUtil.SupportedIlluminaFormat format = IlluminaDataProviderFactory.findPreferredFormat(dataType, fileUtil); fileUtil.getUtil(format).fakeFiles(expectedTiles, cycles, format); } } log.info("Could not find a format with available files for the following data types: " + StringUtil .join(", ", new ArrayList<>(unmatchedDataTypes))); numFailures += unmatchedDataTypes.size(); } for (final IlluminaFileUtil.SupportedIlluminaFormat format : formatToDataTypes.keySet()) { final ParameterizedFileUtil util = fileUtil.getUtil(format); util.setTilesForPerRunFile(expectedTiles); final List<String> failures = util.verify(expectedTiles, cycles); if (!failures.isEmpty() && fakeFiles) { util.fakeFiles(expectedTiles, cycles, format); } numFailures += failures.size(); for (final String failure : failures) { log.info(failure); } } return numFailures; }