LICENSE
MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
docs/Makefile
docs/conf.py
docs/index.rst
docs/installation.rst
docs/make.bat
docs/readme.rst
docs/usage.rst
immunopepper/__init__.py
immunopepper/constant.py
immunopepper/immuno_filter.py
immunopepper/immuno_model.py
immunopepper/immuno_mutation.py
immunopepper/immuno_nametuple.py
immunopepper/immuno_preprocess.py
immunopepper/immunopepper_build.py
immunopepper/immunopepper_diff.py
immunopepper/immunopepper_filter.py
immunopepper/immunopepper_makebg.py
immunopepper/io_utils.py
immunopepper/main_immuno.py
immunopepper/utils.py
immunopepper.egg-info/PKG-INFO
immunopepper.egg-info/SOURCES.txt
immunopepper.egg-info/dependency_links.txt
immunopepper.egg-info/entry_points.txt
immunopepper.egg-info/not-zip-safe
immunopepper.egg-info/requires.txt
immunopepper.egg-info/top_level.txt
tests/__init__.py
tests/test_end_to_end.py
tests/test_immunopepper.py
tests/mouse_usecase/immunopepper_usecase.count.hdf5
tests/mouse_usecase/immunopepper_usecase.gtf
tests/mouse_usecase/immunopepper_usecase.maf
tests/mouse_usecase/immunopepper_usecase.pickle
tests/mouse_usecase/immunopepper_usecase.vcf
tests/mouse_usecase/mouse_usecase.sh
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/background_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/expression_counts.libsize.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/maf.pickle
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/gene_expression_detail.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/germline_back_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/germline_back_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/germline_junction_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/germline_metadata.tsv.gz
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/germline_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/ref_back_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/ref_back_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/ref_junction_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/ref_metadata.tsv.gz
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/ref_mode_background_kmer.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/ref_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_and_germline_back_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_and_germline_back_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_and_germline_junction_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_and_germline_metadata.tsv.gz
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_and_germline_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_back_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_back_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_junction_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_metadata.tsv.gz
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ENCSR000BZG/somatic_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/gene_expression_detail.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/germline_back_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/germline_back_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/germline_junction_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/germline_junction_kmer_remove_bg.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/germline_junction_kmer_remove_bg_filter.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/germline_metadata.tsv.gz
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/germline_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/ref_back_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/ref_back_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/ref_junction_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/ref_junction_kmer_remove_bg.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/ref_junction_kmer_remove_bg_filter.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/ref_metadata.tsv.gz
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/ref_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_and_germline_back_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_and_germline_back_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_and_germline_junction_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_and_germline_junction_kmer_remove_bg.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_and_germline_junction_kmer_remove_bg_filter.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_and_germline_metadata.tsv.gz
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_and_germline_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_back_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_back_peptides.fa
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_junction_kmer.txt
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_junction_kmer_remove_bg.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_junction_kmer_remove_bg_filter.tsv
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_metadata.tsv.gz
tests/mouse_usecase/immunopepper_usecase_out_groundtruth/ERR2130621/somatic_peptides.fa
tests/test1/build/neg/expression_counts.libsize.tsv
tests/test1/build/neg/maf.pickle
tests/test1/build/neg/test1neg/gene_expression_detail.tsv
tests/test1/build/neg/test1neg/germline_back_kmer.txt
tests/test1/build/neg/test1neg/germline_back_peptides.fa
tests/test1/build/neg/test1neg/germline_junction_kmer.txt
tests/test1/build/neg/test1neg/germline_metadata.tsv.gz
tests/test1/build/neg/test1neg/germline_peptides.fa
tests/test1/build/neg/test1neg/ref_back_kmer.txt
tests/test1/build/neg/test1neg/ref_back_peptides.fa
tests/test1/build/neg/test1neg/ref_junction_kmer.txt
tests/test1/build/neg/test1neg/ref_metadata.tsv.gz
tests/test1/build/neg/test1neg/ref_peptides.fa
tests/test1/build/neg/test1neg/somatic_and_germline_back_kmer.txt
tests/test1/build/neg/test1neg/somatic_and_germline_back_peptides.fa
tests/test1/build/neg/test1neg/somatic_and_germline_junction_kmer.txt
tests/test1/build/neg/test1neg/somatic_and_germline_metadata.tsv.gz
tests/test1/build/neg/test1neg/somatic_and_germline_peptides.fa
tests/test1/build/neg/test1neg/somatic_back_kmer.txt
tests/test1/build/neg/test1neg/somatic_back_peptides.fa
tests/test1/build/neg/test1neg/somatic_junction_kmer.txt
tests/test1/build/neg/test1neg/somatic_metadata.tsv.gz
tests/test1/build/neg/test1neg/somatic_peptides.fa
tests/test1/build/pos/expression_counts.libsize.tsv
tests/test1/build/pos/maf.pickle
tests/test1/build/pos/test1pos/error.log
tests/test1/build/pos/test1pos/gene_expression_detail.tsv
tests/test1/build/pos/test1pos/germline_back_kmer.txt
tests/test1/build/pos/test1pos/germline_back_peptides.fa
tests/test1/build/pos/test1pos/germline_junction_kmer.txt
tests/test1/build/pos/test1pos/germline_metadata.tsv.gz
tests/test1/build/pos/test1pos/germline_peptides.fa
tests/test1/build/pos/test1pos/ref_back_kmer.txt
tests/test1/build/pos/test1pos/ref_back_peptides.fa
tests/test1/build/pos/test1pos/ref_junction_kmer.txt
tests/test1/build/pos/test1pos/ref_metadata.tsv.gz
tests/test1/build/pos/test1pos/ref_peptides.fa
tests/test1/build/pos/test1pos/somatic_and_germline_back_kmer.txt
tests/test1/build/pos/test1pos/somatic_and_germline_back_peptides.fa
tests/test1/build/pos/test1pos/somatic_and_germline_junction_kmer.txt
tests/test1/build/pos/test1pos/somatic_and_germline_metadata.tsv.gz
tests/test1/build/pos/test1pos/somatic_and_germline_peptides.fa
tests/test1/build/pos/test1pos/somatic_back_kmer.txt
tests/test1/build/pos/test1pos/somatic_back_peptides.fa
tests/test1/build/pos/test1pos/somatic_junction_kmer.txt
tests/test1/build/pos/test1pos/somatic_metadata.tsv.gz
tests/test1/build/pos/test1pos/somatic_peptides.fa
tests/test1/data/small.gencode.v19.gff
tests/test1/data/small.gencode.v19.gtf
tests/test1/data/small.gencode.v29.gff3
tests/test1/data/small.gencode.v29.gtf
tests/test1/data/test1_1.fq
tests/test1/data/test1neg.fa
tests/test1/data/test1neg.gtf
tests/test1/data/test1neg.maf
tests/test1/data/test1neg.vcf
tests/test1/data/test1pos.fa
tests/test1/data/test1pos.gtf
tests/test1/data/test1pos.maf
tests/test1/data/test1pos.vcf
tests/test1/data/test1vcf.h5
tests/test1/data/align/test1neg.bam
tests/test1/data/align/test1neg.bam.bai
tests/test1/data/align/test1pos.bam
tests/test1/data/align/test1pos.bam.bai
tests/test1/data/neggraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5
tests/test1/data/neggraph/spladder/genes_graph_conf3.merge_graphs.pickle
tests/test1/data/neggraph/spladder/genes_graph_conf3.test1neg.pickle
tests/test1/data/posgraph/spladder/genes_graph_conf3.merge_graphs.count.hdf5
tests/test1/data/posgraph/spladder/genes_graph_conf3.merge_graphs.pickle
tests/test1/data/posgraph/spladder/genes_graph_conf3.test1pos.pickle
tests/test1/diff/neg/neg_germline_junction_kmer_with_bg.txt
tests/test1/diff/neg/neg_ref_junction_kmer_with_bg.txt
tests/test1/diff/neg/neg_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/diff/neg/neg_somatic_junction_kmer_with_bg.txt
tests/test1/diff/pos/pos_germline_junction_kmer_with_bg.txt
tests/test1/diff/pos/pos_ref_junction_kmer_with_bg.txt
tests/test1/diff/pos/pos_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/diff/pos/pos_somatic_junction_kmer_with_bg.txt
tests/test1/filter/neg/cj_neg_germline_junction_kmer_with_bg.txt
tests/test1/filter/neg/cj_neg_ref_junction_kmer_with_bg.txt
tests/test1/filter/neg/cj_neg_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/filter/neg/cj_neg_somatic_junction_kmer_with_bg.txt
tests/test1/filter/neg/junc_expr_0_neg_germline_junction_kmer_with_bg.txt
tests/test1/filter/neg/junc_expr_0_neg_ref_junction_kmer_with_bg.txt
tests/test1/filter/neg/junc_expr_0_neg_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/filter/neg/junc_expr_0_neg_somatic_junction_kmer_with_bg.txt
tests/test1/filter/neg/junc_expr_500_seg_expr_1300_cj_neg_germline_junction_kmer_with_bg.txt
tests/test1/filter/neg/junc_expr_500_seg_expr_1300_cj_neg_ref_junction_kmer_with_bg.txt
tests/test1/filter/neg/junc_expr_500_seg_expr_1300_cj_neg_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/filter/neg/junc_expr_500_seg_expr_1300_cj_neg_somatic_junction_kmer_with_bg.txt
tests/test1/filter/neg/seg_expr_1300_neg_germline_junction_kmer_with_bg.txt
tests/test1/filter/neg/seg_expr_1300_neg_ref_junction_kmer_with_bg.txt
tests/test1/filter/neg/seg_expr_1300_neg_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/filter/neg/seg_expr_1300_neg_somatic_junction_kmer_with_bg.txt
tests/test1/filter/pos/cj_pos_germline_junction_kmer_with_bg.txt
tests/test1/filter/pos/cj_pos_ref_junction_kmer_with_bg.txt
tests/test1/filter/pos/cj_pos_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/filter/pos/cj_pos_somatic_junction_kmer_with_bg.txt
tests/test1/filter/pos/junc_expr_0_pos_germline_junction_kmer_with_bg.txt
tests/test1/filter/pos/junc_expr_0_pos_ref_junction_kmer_with_bg.txt
tests/test1/filter/pos/junc_expr_0_pos_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/filter/pos/junc_expr_0_pos_somatic_junction_kmer_with_bg.txt
tests/test1/filter/pos/junc_expr_500_seg_expr_1300_cj_pos_germline_junction_kmer_with_bg.txt
tests/test1/filter/pos/junc_expr_500_seg_expr_1300_cj_pos_ref_junction_kmer_with_bg.txt
tests/test1/filter/pos/junc_expr_500_seg_expr_1300_cj_pos_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/filter/pos/junc_expr_500_seg_expr_1300_cj_pos_somatic_junction_kmer_with_bg.txt
tests/test1/filter/pos/seg_expr_1300_pos_germline_junction_kmer_with_bg.txt
tests/test1/filter/pos/seg_expr_1300_pos_ref_junction_kmer_with_bg.txt
tests/test1/filter/pos/seg_expr_1300_pos_somatic_and_germline_junction_kmer_with_bg.txt
tests/test1/filter/pos/seg_expr_1300_pos_somatic_junction_kmer_with_bg.txt
tests/test1/make_bg/neg/neg_integrated_background_kmer.txt
tests/test1/make_bg/pos/pos_integrated_background_kmer.txt