AmpliconSuite-pipeline.py
GroupedAnalysisAmpSuite.py
LICENSE
LICENSE-AA
MANIFEST.in
README.md
setup.py
UNKNOWN.egg-info/PKG-INFO
UNKNOWN.egg-info/SOURCES.txt
UNKNOWN.egg-info/dependency_links.txt
UNKNOWN.egg-info/top_level.txt
ampclasslib/__init__.py
ampclasslib/_version.py
ampclasslib/ac_annotation.py
ampclasslib/ac_io.py
ampclasslib/ac_util.py
ampclasslib/amplicon_similarity.py
ampclasslib/check_SV_support.py
ampclasslib/config_params.py
ampclasslib/convert_cycles_file.py
ampclasslib/default_config.json
ampclasslib/ecDNA_context.py
ampclasslib/make_input.sh
ampclasslib/profile_connections.py
ampclasslib/radar_plotting.py
ampclasslib/read_support_utils.py
ampclasslib/resources/combined_oncogene_list.txt
ampclasslib/resources/gencode_GRCh38_long_noncoding_RNAs.gff3.gz
ampclasslib/resources/gencode_hg19_long_noncoding_RNAs.gff3.gz
ampclasslib/resources/gencode_mm10_long_noncoding_RNAs.gff3.gz
ampclasslib/resources/patch_regions.tsv
ampclasslib/resources/sorted_background_scores.txt
ampliconarchitectlib/AmpliconArchitect.py
ampliconarchitectlib/__init__.py
ampliconarchitectlib/abstract_graph.py
ampliconarchitectlib/amplified_intervals.py
ampliconarchitectlib/bam_to_breakpoint.py
ampliconarchitectlib/breakpoint_graph.py
ampliconarchitectlib/downsample.py
ampliconarchitectlib/external_data_handler.py
ampliconarchitectlib/global_names.py
ampliconarchitectlib/mosek_solver.py
ampliconarchitectlib/mycolors.py
ampliconarchitectlib/ref_util.py
paalib/__init__.py
paalib/_version.py
paalib/argument_parser.py
paalib/check_reference.py
paalib/cnv_plots.py
paalib/cnv_prefilter.py
paalib/config_validator.py
paalib/reduce_fasta.py
paalib/repo_downloader.py
paalib/run_uploader.py
paalib/sample_metadata_skeleton.json