v0.35.0

0.35.0 (2025-06-16)

Bug Fixes

• Fix ambiguous castings in VersionTest test class. (64f4e8a)
• Fix code line removed by mistake in FileGenomeMapperIndexer. (ae025b1)
• Fix dependency issue with jhdf5. (bf01f86)
• Fix META-INF/services file names and class names. (9ede964)
• For compatibility with previous serialization of expected results, the EnhancedBloomFilter move to its original package. (bb6b2f2)
• In AbstractFileGenomeIndexStorage, sequence count and genome length were not read when load the genomes_index_storage.txt file. (265e7a3)
• In BinariesInstaller, application version was not set in constructor. (0382a3a)
• In BundledMapperExecutor constructor, logger was not used. (e250a89)
• In ErrorMetricsReader.getExpectedRecordSize(), result for version 6 was not implemented. (3d450cd)
• In FallBackDockerImageInstance.start(), fix filtering of null file used values. (a163599)
• In FileDataPath.symlinkOrCopy(), link was not created. (4ac5ad9)
• In FileGenomeMapperIndexer constructor, handle the case were no genome index storage is set. (cab92cf)
• In FileLogger and StandardErrorLogger, remove aozan string from logger configuration keys. (a721404)
• In kenetre-illumina, add missing commons-csv dependency for parsing PrimaryAnalysisMetrics.csv files. (c0dc413)
• In Mapper constructor, application version was not correctly set. (e250a89)
• In MapperBuilder.build(), now return null if mapper is unknown instead of a new instance of Mapper that will produce an exception in the constructor. (f2cde7e)
• In MapperIndex.unzipArchiveIndexFile(), a log message showed a reference. (e250a89)
• In MapperInstanceBuilder, withMapperVersion() and withMapperFlavor() methods now allow null parameters to keep compatibility with Eoulsan code. (d7a89ce)
• In Nanopore SampleSheet class, non canonical field were not protected if value had comma. (3013918)
• In pom.xml for kenetre-extra, service directory in META-INF of the jar file was not generated. (eee74b6)
• In PropertySection.containsKey(), fix infinite recursion. (ca2d79f)
• In PseudoMapReduce.sort(), now handle the case where there is no file to sort. (4ccebc6)
• In SampleSheetCSVReader, now remove BOM character at the beginning of the file if exists. (c2953a6)
• In SampleSheetParser, the "sample_ref" field is not barcode field. (81fb214)
• In SampleSheetV2Parser.parseLine(), do not add empty fields in samples. (4677ecd)
• In SAMUtils.parseIntervals() now handle '=' and 'X' Cigar operations. (18d1c8f)
• In ServiceNameLoader, now use the same class loader to load the class and to read the service file in META-INF. (48552d2)
• In ServiceNameLoader, now use this.getClass().getClassLoader() instead of Thread.currentThread().getContextClassLoader() as ClassLoader. (48552d2)
• In ServiceNameLoader, the reload() method is now synchronized. (48552d2)
• In SortedBEDWriter, charset was missed when creating a Writer for temporary file. (213d8b6)
• Rename unit test SampleSheetCSVReader to SampleSheetCVSReaderWriterTest to be handled by Maven. (8dd4eac)
• Some fixes for using Kenetre in Eoulsan. (ec33b65)