├── LICENSE ├── README.md ├── bin.tar.gz ├── docs ├── Makefile └── source │ ├── conf.py │ ├── contents │ ├── hadoop.rst │ ├── hadoop~ │ ├── installation.rst │ ├── introduction.rst │ ├── options.rst │ ├── preprocessing.rst │ ├── references.rst │ ├── run.rst │ ├── samples.rst │ └── upload.rst │ └── index.rst ├── halvade ├── build.xml ├── gpl.txt ├── lib │ ├── bzip2.jar │ ├── commons-cli-1.2.jar │ ├── hadoop-bam-7.0.0.jar │ ├── hadoop-common-2.4.0.jar │ ├── hadoop-mapreduce-client-core-2.4.0.jar │ └── htsjdk-1.137.jar ├── nbproject │ ├── build-impl.xml │ ├── genfiles.properties │ ├── private │ │ ├── config.properties │ │ ├── private.properties │ │ └── private.xml │ ├── project.properties │ └── project.xml └── src │ └── be │ └── ugent │ └── intec │ └── halvade │ ├── Halvade.java │ ├── HalvadeOptions.java │ ├── HalvadeResourceManager.java │ ├── MapReduceRunner.java │ ├── hadoop │ ├── datatypes │ │ ├── ChromosomeRegion.java │ │ └── GenomeSJ.java │ ├── mapreduce │ │ ├── AlignedBamMapper.java │ │ ├── BWAAlnMapper.java │ │ ├── BWAMemMapper.java │ │ ├── BamMergeReducer.java │ │ ├── Bowtie2Mapper.java │ │ ├── CountReadsReducer.java │ │ ├── Cushaw2Mapper.java │ │ ├── DnaGATKReducer.java │ │ ├── GATKReducer.java │ │ ├── HTSeqCombineMapper.java │ │ ├── HTSeqCombineReducer.java │ │ ├── HalvadeCounters.java │ │ ├── HalvadeMapper.java │ │ ├── HalvadeReducer.java │ │ ├── HalvadeTextInputFormat.java │ │ ├── RebuildStarGenomeReducer.java │ │ ├── RnaGATKReducer.java │ │ ├── StarAlignPassXMapper.java │ │ ├── VCFCombineMapper.java │ │ └── VCFCombineReducer.java │ └── partitioners │ │ ├── ChrRgGroupingComparator.java │ │ ├── ChrRgPartitioner.java │ │ ├── ChrRgSortComparator.java │ │ ├── GenomeSJGroupingComparator.java │ │ ├── GenomeSJSortComparator.java │ │ └── SimpleChrRegionComparator.java │ ├── tools │ ├── AlignerInstance.java │ ├── BWAAlnInstance.java │ ├── BWAMemInstance.java │ ├── Bowtie2Instance.java │ ├── Cushaw2Instance.java │ ├── DummyAlignerInstance.java │ ├── GATKTools.java │ ├── PreprocessingTools.java │ ├── ProcessException.java │ ├── QualityEncoding.java │ ├── QualityException.java │ └── STARInstance.java │ └── utils │ ├── ChromosomeRange.java │ ├── ChromosomeSplitter.java │ ├── CommandGenerator.java │ ├── HalvadeConf.java │ ├── HalvadeFileLock.java │ ├── HalvadeFileUtils.java │ ├── Logger.java │ ├── ProcessBuilderWrapper.java │ ├── SAMRecordIterator.java │ ├── SAMStreamHandler.java │ ├── StreamGobbler.java │ └── Timer.java ├── halvade_upload_tool ├── build.xml ├── gpl.txt ├── lib │ ├── aspectjrt.jar │ ├── aspectjweaver.jar │ ├── aws-java-sdk-1.7.12.jar │ ├── bzip2.jar │ ├── commons-cli-1.2.jar │ ├── commons-codec-1.3.jar │ ├── commons-logging-1.1.1.jar │ ├── freemarker-2.3.18.jar │ ├── hadoop-common-2.4.0.jar │ ├── hadoop-mapreduce-client-core-2.4.0.jar │ ├── httpclient-4.2.3.jar │ ├── httpcore-4.2.jar │ ├── jackson-annotations-2.1.1.jar │ ├── jackson-core-2.1.1.jar │ ├── jackson-databind-2.1.1.jar │ ├── joda-time-2.2.jar │ ├── mail-1.4.3.jar │ ├── spring-beans-3.0.7.jar │ ├── spring-context-3.0.7.jar │ ├── spring-core-3.0.7.jar │ ├── stax-1.2.0.jar │ └── stax-api-1.0.1.jar ├── nbproject │ ├── build-impl.xml │ ├── genfiles.properties │ ├── private │ │ ├── config.properties │ │ ├── private.properties │ │ └── private.xml │ ├── project.properties │ └── project.xml └── src │ ├── be │ └── ugent │ │ └── intec │ │ └── halvade │ │ └── uploader │ │ ├── AWSInterleaveFiles.java │ │ ├── AWSUploader.java │ │ ├── BaseInterleaveFiles.java │ │ ├── HDFSInterleaveFiles.java │ │ ├── HalvadeUploader.java │ │ ├── Logger.java │ │ ├── Timer.java │ │ └── input │ │ ├── BaseFileReader.java │ │ ├── FileReaderFactory.java │ │ ├── PairedFastQReader.java │ │ ├── ReadBlock.java │ │ └── SingleFastQReader.java │ └── org │ └── apache │ └── tools │ └── bzip2 │ ├── BZip2Constants.java │ ├── CBZip2InputStream.java │ ├── CBZip2InputStream.java~ │ ├── CBZip2OutputStream.java │ └── CRC.java └── scripts ├── example.config ├── halvade_bootstrap.sh └── runHalvade.py 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