MANIFEST.in
Makefile
README.rst
environment-dev.yml
environment.yml
requirements.txt
setup.cfg
setup.py
vtam/CommandBlastCOI.py
vtam/CommandExample.py
vtam/CommandFilterOptimize.py
vtam/CommandMerge.py
vtam/CommandPoolRunMarkers.py
vtam/CommandSortReads.py
vtam/CommandTaxAssign.py
vtam/CommandTaxonomy.py
vtam/__init__.py
vtam.egg-info/PKG-INFO
vtam.egg-info/SOURCES.txt
vtam.egg-info/dependency_links.txt
vtam.egg-info/entry_points.txt
vtam.egg-info/requires.txt
vtam.egg-info/top_level.txt
vtam/data/block_wopfile_filter_optimize.yml
vtam/data/macros.yml
vtam/data/snake.tuto.data.yml
vtam/data/snakefile.yml
vtam/data/wopfile_filter.yml
vtam/data/wopfile_optimize.yml
vtam/data/example/fastqinfo.tsv
vtam/data/example/fastqinfo_mfzr.tsv
vtam/data/example/fastqinfo_zfzr.tsv
vtam/data/example/known_occurrences.tsv
vtam/data/example/known_occurrences_mfzr.tsv
vtam/data/example/known_occurrences_zfzr.tsv
vtam/data/example/params.yml
vtam/data/example/params_mfzr.yml
vtam/data/example/params_optimize_mfzr.yml
vtam/data/example/params_zfzr.yml
vtam/data/example/pool_run_marker.tsv
vtam/data/example/snakeconfig.yml
vtam/data/example/snakeconfig_mfzr.yml
vtam/data/example/snakeconfig_zfzr.yml
vtam/data/example/sortedinfo_mfzr.tsv
vtam/data/example/sortedinfo_zfzr.tsv
vtam/models/FilterChimera.py
vtam/models/FilterChimeraBorderline.py
vtam/models/FilterCodonStop.py
vtam/models/FilterIndel.py
vtam/models/FilterLFN.py
vtam/models/FilterMinReplicateNumber.py
vtam/models/FilterMinReplicateNumber2.py
vtam/models/FilterMinReplicateNumber3.py
vtam/models/FilterPCRerror.py
vtam/models/FilterRenkonen.py
vtam/models/Marker.py
vtam/models/ReadCount.py
vtam/models/ReadCountAverageOverReplicates.py
vtam/models/Run.py
vtam/models/Sample.py
vtam/models/SampleInformation.py
vtam/models/SortedReadFile.py
vtam/models/TaxAssign.py
vtam/models/Variant.py
vtam/models/VariantReadCount.py
vtam/models/__init__.py
vtam/utils/ArgParser.py
vtam/utils/AsvTableRunner.py
vtam/utils/CutoffSpecificFile.py
vtam/utils/FilterChimeraRunner.py
vtam/utils/FilterCodonStopRunner.py
vtam/utils/FilterIndelRunner.py
vtam/utils/FilterLFNRunner.py
vtam/utils/FilterLFNreplicateRemainRunner.py
vtam/utils/FilterMinReplicateNumberRunner.py
vtam/utils/FilterPCRerrorRunner.py
vtam/utils/FilterRenkonenRunner.py
vtam/utils/KnownOccurrences.py
vtam/utils/Logger.py
vtam/utils/MyProgressBar.py
vtam/utils/NameIdConverter.py
vtam/utils/OptimizeLFNreadCountAndVariantRunMarkerRunner.py
vtam/utils/OptimizeLFNreadCountAndVariantRunner.py
vtam/utils/OptimizeLFNsampleReplicateRunner.py
vtam/utils/OptimizePCRerrorRunner.py
vtam/utils/ParamsFile.py
vtam/utils/PathManager.py
vtam/utils/RunMarkerFile.py
vtam/utils/SampleInformationFile.py
vtam/utils/SequenceClusterer.py
vtam/utils/Singleton.py
vtam/utils/SummaryFile.py
vtam/utils/TaxAssignRunner.py
vtam/utils/TaxLineage.py
vtam/utils/VSearch.py
vtam/utils/VTAMexception.py
vtam/utils/VariantDF.py
vtam/utils/VariantReadCountLikeDF.py
vtam/utils/VariantReadCountLikeTable.py
vtam/utils/WopmarsRunner.py
vtam/utils/__init__.py
vtam/utils/constants.py
vtam/wrapper/FilterChimera.py
vtam/wrapper/FilterCodonStop.py
vtam/wrapper/FilterIndel.py
vtam/wrapper/FilterLFN.py
vtam/wrapper/FilterMinReplicateNumber.py
vtam/wrapper/FilterPCRerror.py
vtam/wrapper/FilterRenkonen.py
vtam/wrapper/MakeAsvTable.py
vtam/wrapper/OptimizeLFNreadCountAndLFNvariant.py
vtam/wrapper/OptimizeLFNsampleReplicate.py
vtam/wrapper/OptimizePCRerror.py
vtam/wrapper/ReadCountAverageOverReplicates.py
vtam/wrapper/SampleInformation.py
vtam/wrapper/VariantReadCount.py
vtam/wrapper/__init__.py