README.md
setup.py
pvacseq/__init__.py
pvacseq/pvacseq.py
pvacseq.egg-info/PKG-INFO
pvacseq.egg-info/SOURCES.txt
pvacseq.egg-info/dependency_links.txt
pvacseq.egg-info/entry_points.txt
pvacseq.egg-info/requires.txt
pvacseq.egg-info/top_level.txt
pvacseq/VEP_plugins/Wildtype.pm
pvacseq/example_data/additional_input_file_list.yaml
pvacseq/example_data/genes.fpkm_tracking
pvacseq/example_data/indels.bam_readcount
pvacseq/example_data/input.vcf
pvacseq/example_data/isoforms.fpkm_tracking
pvacseq/example_data/snvs.bam_readcount
pvacseq/example_data/MHC_Class_I/Test.chop.tsv
pvacseq/example_data/MHC_Class_I/Test.combined.parsed.tsv
pvacseq/example_data/MHC_Class_I/Test.filtered.binding.tsv
pvacseq/example_data/MHC_Class_I/Test.filtered.coverage.tsv
pvacseq/example_data/MHC_Class_I/Test.final.tsv
pvacseq/example_data/MHC_Class_I/Test.stab.tsv
pvacseq/example_data/MHC_Class_I/Test.tsv
pvacseq/example_data/MHC_Class_I/Test.tsv_1-24
pvacseq/example_data/MHC_Class_I/log/inputs.yml
pvacseq/example_data/MHC_Class_I/tmp/Test.HLA-E*01:01.10.parsed.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test.HLA-E*01:01.9.parsed.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test.HLA-G*01:09.10.parsed.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test.HLA-G*01:09.9.parsed.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test.ann.HLA-E*01:01.10.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test.ann.HLA-E*01:01.9.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test.pickpocket.HLA-E*01:01.10.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test.pickpocket.HLA-E*01:01.9.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test.pickpocket.HLA-G*01:09.10.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test.pickpocket.HLA-G*01:09.9.tsv_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test_21.fa.split_1-48
pvacseq/example_data/MHC_Class_I/tmp/Test_21.fa.split_1-48.key
pvacseq/example_data/MHC_Class_II/Test.chop.tsv
pvacseq/example_data/MHC_Class_II/Test.combined.parsed.tsv
pvacseq/example_data/MHC_Class_II/Test.filtered.binding.tsv
pvacseq/example_data/MHC_Class_II/Test.filtered.coverage.tsv
pvacseq/example_data/MHC_Class_II/Test.final.tsv
pvacseq/example_data/MHC_Class_II/Test.tsv
pvacseq/example_data/MHC_Class_II/Test.tsv_1-24
pvacseq/example_data/MHC_Class_II/log/inputs.yml
pvacseq/example_data/MHC_Class_II/tmp/Test.H2-IAb.parsed.tsv_1-48
pvacseq/example_data/MHC_Class_II/tmp/Test.nn_align.H2-IAb.tsv_1-48
pvacseq/example_data/MHC_Class_II/tmp/Test_31.fa.split_1-48
pvacseq/example_data/MHC_Class_II/tmp/Test_31.fa.split_1-48.key
pvacseq/iedb_alleles/class_i/ann.tsv
pvacseq/iedb_alleles/class_i/netmhccons.tsv
pvacseq/iedb_alleles/class_i/netmhcpan.tsv
pvacseq/iedb_alleles/class_i/pickpocket.tsv
pvacseq/iedb_alleles/class_i/smm.tsv
pvacseq/iedb_alleles/class_i/smmpmbec.tsv
pvacseq/iedb_alleles/class_ii/NetMHCIIpan.tsv
pvacseq/iedb_alleles/class_ii/nn_align.tsv
pvacseq/iedb_alleles/class_ii/smm_align.tsv
pvacseq/lib/__init__.py
pvacseq/lib/binding_filter.py
pvacseq/lib/call_iedb.py
pvacseq/lib/combine_parsed_outputs.py
pvacseq/lib/config_files.py
pvacseq/lib/convert_vcf.py
pvacseq/lib/coverage_filter.py
pvacseq/lib/download_example_data.py
pvacseq/lib/generate_fasta.py
pvacseq/lib/generate_protein_fasta.py
pvacseq/lib/install_vep_plugin.py
pvacseq/lib/main.py
pvacseq/lib/net_chop.py
pvacseq/lib/netmhc_stab.py
pvacseq/lib/parse_output.py
pvacseq/lib/pipeline.py
pvacseq/lib/prediction_class.py
pvacseq/lib/valid_alleles.py
pvacseq/server/__init__.py
pvacseq/server/app.py