├── .gitignore ├── LICENSE ├── NOTICES ├── README ├── README.md ├── RELEASE_NOTES ├── licenses ├── Apache2.0.txt ├── CDDL1.0.txt ├── CDDL1.1.txt ├── EPL1.0.txt ├── JSON.txt ├── LGPL2.1.txt └── MIT.txt ├── pipelines └── mga.xml ├── pom.xml ├── resources ├── adapters.fa ├── reference_genome_mappings.txt └── results.xsl ├── src └── main │ ├── assembly │ └── assembly.xml │ ├── config │ └── log4j.xml │ ├── java │ └── org │ │ └── cruk │ │ ├── mga │ │ ├── Alignment.java │ │ ├── AlignmentReader.java │ │ ├── AlignmentSummary.java │ │ ├── CreateReport.java │ │ ├── MGAConfig.java │ │ ├── MultiGenomeAlignmentSummary.java │ │ ├── ReferenceGenomeSpeciesMapping.java │ │ ├── basespace │ │ │ └── BaseSpaceWrapper.java │ │ ├── export │ │ │ ├── AllMGASummaries.java │ │ │ ├── LimitedPrecisionFloatAdapter.java │ │ │ ├── MGAAlignmentSummary.java │ │ │ ├── MGASummary.java │ │ │ ├── Properties.java │ │ │ ├── Property.java │ │ │ ├── ReferenceGenome.java │ │ │ ├── Sample.java │ │ │ └── package-info.java │ │ ├── report │ │ │ ├── AlignmentSummaryComparator.java │ │ │ ├── MGAReportWriter.java │ │ │ ├── SummaryPlotter.java │ │ │ └── XMLReportWriter.java │ │ └── workflow │ │ │ ├── AlignmentWrapperTask.java │ │ │ ├── CreateDatasetListing.java │ │ │ ├── CreateMetadataFromSampleSheet.java │ │ │ └── MetaDataValidator.java │ │ ├── seq │ │ ├── CountFastq.java │ │ ├── Fastq.java │ │ ├── FastqFormatException.java │ │ ├── FastqReader.java │ │ ├── FastqToFasta.java │ │ ├── MergeAndSplitFastq.java │ │ ├── SampleFastq.java │ │ ├── SamplingSummary.java │ │ └── TrimFastq.java │ │ └── util │ │ ├── CommandLineUtility.java │ │ ├── LineCounter.java │ │ └── OrderedProperties.java │ └── resources │ └── org │ └── cruk │ └── mga │ └── export │ └── jaxb.index └── tasks ├── alignmentWrapper.xml ├── bowtie.xml ├── countFastq.xml ├── createDatasetListing.xml ├── createReport.xml ├── exonerate.xml ├── fastqToFasta.xml ├── mergeSplitFastq.xml ├── sampleFastq.xml └── trimFastq.xml /.gitignore: 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