LICENSE.txt
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/CommandMakeKnownOccurrences.py
vtam/CommandMerge.py
vtam/CommandPoolRunMarkers.py
vtam/CommandRandomize.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/snake.tuto.data_makeknownoccurrences.yml
vtam/data/snakefile.yml
vtam/data/snakefile_makeknownoccurrences.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/mock_composition_mfzr.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/sample_types.tsv
vtam/data/example/snakeconfig.yml
vtam/data/example/snakeconfig_mfzr.yml
vtam/data/example/snakeconfig_mfzr_makeknownoccurrences.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/DataframeVariant.py
vtam/utils/DataframeVariantReadCountLike.py
vtam/utils/FileCompression.py
vtam/utils/FileCutoffSpecific.py
vtam/utils/FileKnownOccurrences.py
vtam/utils/FileParams.py
vtam/utils/FileRunMarker.py
vtam/utils/FileSampleInformation.py
vtam/utils/FilesInputCutadapt.py
vtam/utils/LineCounter.py
vtam/utils/Logger.py
vtam/utils/ModelVariantReadCountLike.py
vtam/utils/NameIdConverter.py
vtam/utils/PathManager.py
vtam/utils/RunnerAsvTable.py
vtam/utils/RunnerBlast.py
vtam/utils/RunnerFilterChimera.py
vtam/utils/RunnerFilterCodonStop.py
vtam/utils/RunnerFilterIndel.py
vtam/utils/RunnerFilterLFN.py
vtam/utils/RunnerFilterLFNreplicateRemain.py
vtam/utils/RunnerFilterMinReplicateNumber.py
vtam/utils/RunnerFilterPCRerror.py
vtam/utils/RunnerFilterRenkonen.py
vtam/utils/RunnerLTGselection.py
vtam/utils/RunnerOptimizeLFNreadCountAndVariant.py
vtam/utils/RunnerOptimizeLFNreadCountAndVariantRunMarker.py
vtam/utils/RunnerOptimizeLFNsampleReplicate.py
vtam/utils/RunnerOptimizePCRerror.py
vtam/utils/RunnerTaxAssign.py
vtam/utils/RunnerVSearch.py
vtam/utils/RunnerWopmars.py
vtam/utils/SequenceClusterer.py
vtam/utils/Singleton.py
vtam/utils/TaxLineage.py
vtam/utils/Taxonomy.py
vtam/utils/VTAMexception.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