.gitignore
LICENSE
MANIFEST.in
PatchWorkPlot.py
README.md
generate_alignment_files.py
generate_igdetective_config.py
pyproject.toml
PatchWorkPlot.egg-info/PKG-INFO
PatchWorkPlot.egg-info/SOURCES.txt
PatchWorkPlot.egg-info/dependency_links.txt
PatchWorkPlot.egg-info/entry_points.txt
PatchWorkPlot.egg-info/requires.txt
PatchWorkPlot.egg-info/top_level.txt
examples/lower_annot.png
examples/lower_no_annot.png
examples/upper_annot.png
examples/upper_no_annot.png
py/.gitignore
py/config_utils.py
py/data_utils.py
py/paf_utils.py
py/tool_builder.py
py/utils.py
py/visualization_utils.py
test_dataset/config_example.csv
test_dataset/01_mPumCon1.1_hap1_igdetective/combined_genes_IGH.txt
test_dataset/01_mPumCon1.1_hap1_igdetective/combined_genes_IGK.txt
test_dataset/01_mPumCon1.1_hap1_igdetective/combined_genes_IGL.txt
test_dataset/01_mPumCon1.1_hap1_igdetective/combined_genes_TRA.txt
test_dataset/01_mPumCon1.1_hap1_igdetective/combined_genes_TRB.txt
test_dataset/01_mPumCon1.1_hap1_igdetective/combined_genes_TRG.txt
test_dataset/01_mPumCon1.1_hap1_igdetective/refined_ig_loci/summary.csv
test_dataset/01_mPumCon1.1_hap1_igdetective/refined_ig_loci/igloci_fasta/IGH_CM060209.1_61Vs.fasta
test_dataset/01_mPumCon1.1_hap1_igdetective/refined_ig_loci/igloci_fasta/IGK_CM060206.1_12Vs.fasta
test_dataset/01_mPumCon1.1_hap1_igdetective/refined_ig_loci/igloci_fasta/IGL_CM060215.1_116Vs.fasta
test_dataset/01_mPumCon1.1_hap1_igdetective/refined_ig_loci/igloci_fasta/TRA_CM060209.1_29Vs.fasta
test_dataset/01_mPumCon1.1_hap1_igdetective/refined_ig_loci/igloci_fasta/TRB_CM060205.1_7Vs.fasta
test_dataset/02_mPumCon1.1_hap2_igdetective/combined_genes_IGH.txt
test_dataset/02_mPumCon1.1_hap2_igdetective/combined_genes_IGK.txt
test_dataset/02_mPumCon1.1_hap2_igdetective/combined_genes_IGL.txt
test_dataset/02_mPumCon1.1_hap2_igdetective/combined_genes_TRA.txt
test_dataset/02_mPumCon1.1_hap2_igdetective/combined_genes_TRB.txt
test_dataset/02_mPumCon1.1_hap2_igdetective/combined_genes_TRG.txt
test_dataset/02_mPumCon1.1_hap2_igdetective/refined_ig_loci/summary.csv
test_dataset/02_mPumCon1.1_hap2_igdetective/refined_ig_loci/igloci_fasta/IGH_CM060229.1_44Vs.fasta
test_dataset/02_mPumCon1.1_hap2_igdetective/refined_ig_loci/igloci_fasta/IGK_CM060226.1_13Vs.fasta
test_dataset/02_mPumCon1.1_hap2_igdetective/refined_ig_loci/igloci_fasta/IGL_CM060235.1_103Vs.fasta
test_dataset/02_mPumCon1.1_hap2_igdetective/refined_ig_loci/igloci_fasta/TRA_CM060229.1_29Vs.fasta
test_dataset/02_mPumCon1.1_hap2_igdetective/refined_ig_loci/igloci_fasta/TRB_CM060225.1_7Vs.fasta
test_dataset/03_mNeoNeb1_igdetective/combined_genes_IGH.txt
test_dataset/03_mNeoNeb1_igdetective/combined_genes_IGK.txt
test_dataset/03_mNeoNeb1_igdetective/combined_genes_IGL.txt
test_dataset/03_mNeoNeb1_igdetective/combined_genes_TRA.txt
test_dataset/03_mNeoNeb1_igdetective/combined_genes_TRB.txt
test_dataset/03_mNeoNeb1_igdetective/combined_genes_TRG.txt
test_dataset/03_mNeoNeb1_igdetective/refined_ig_loci/summary.csv
test_dataset/03_mNeoNeb1_igdetective/refined_ig_loci/igloci_fasta/IGH_SUPER_7_87Vs.fasta
test_dataset/03_mNeoNeb1_igdetective/refined_ig_loci/igloci_fasta/IGK_SUPER_9_11Vs.fasta
test_dataset/03_mNeoNeb1_igdetective/refined_ig_loci/igloci_fasta/IGL_SUPER_11_104Vs.fasta
test_dataset/03_mNeoNeb1_igdetective/refined_ig_loci/igloci_fasta/TRA_SUPER_7_28Vs.fasta
test_dataset/03_mNeoNeb1_igdetective/refined_ig_loci/igloci_fasta/TRB_SUPER_4_6Vs.fasta
test_dataset/04_mLynRuf1_igdetective/combined_genes_IGH.txt
test_dataset/04_mLynRuf1_igdetective/combined_genes_IGK.txt
test_dataset/04_mLynRuf1_igdetective/combined_genes_IGL.txt
test_dataset/04_mLynRuf1_igdetective/combined_genes_TRA.txt
test_dataset/04_mLynRuf1_igdetective/combined_genes_TRB.txt
test_dataset/04_mLynRuf1_igdetective/combined_genes_TRG.txt
test_dataset/04_mLynRuf1_igdetective/refined_ig_loci/summary.csv
test_dataset/04_mLynRuf1_igdetective/refined_ig_loci/igloci_fasta/IGH_NW_025814831.1_45Vs.fasta
test_dataset/04_mLynRuf1_igdetective/refined_ig_loci/igloci_fasta/IGK_NW_025814896.1_13Vs.fasta
test_dataset/04_mLynRuf1_igdetective/refined_ig_loci/igloci_fasta/IGL_NW_025814839.1_108Vs.fasta
test_dataset/04_mLynRuf1_igdetective/refined_ig_loci/igloci_fasta/TRA_NW_025814827.1_30Vs.fasta
test_dataset/04_mLynRuf1_igdetective/refined_ig_loci/igloci_fasta/TRB_NW_025814856.1_6Vs.fasta
test_dataset/05_mFelCat1_igdetective/combined_genes_IGH.txt
test_dataset/05_mFelCat1_igdetective/combined_genes_IGK.txt
test_dataset/05_mFelCat1_igdetective/combined_genes_IGL.txt
test_dataset/05_mFelCat1_igdetective/combined_genes_TRA.txt
test_dataset/05_mFelCat1_igdetective/combined_genes_TRB.txt
test_dataset/05_mFelCat1_igdetective/combined_genes_TRG.txt
test_dataset/05_mFelCat1_igdetective/refined_ig_loci/summary.csv
test_dataset/05_mFelCat1_igdetective/refined_ig_loci/igloci_fasta/IGH_AP023157.1_71Vs.fasta
test_dataset/05_mFelCat1_igdetective/refined_ig_loci/igloci_fasta/IGK_AP023154.1_10Vs.fasta
test_dataset/05_mFelCat1_igdetective/refined_ig_loci/igloci_fasta/IGL_AP023163.1_127Vs.fasta
test_dataset/05_mFelCat1_igdetective/refined_ig_loci/igloci_fasta/IGL_AP023163.1_167Vs.fasta
test_dataset/05_mFelCat1_igdetective/refined_ig_loci/igloci_fasta/IGL_AP023163.1_7Vs.fasta
test_dataset/05_mFelCat1_igdetective/refined_ig_loci/igloci_fasta/TRA_AP023157.1_28Vs.fasta
test_dataset/05_mFelCat1_igdetective/refined_ig_loci/igloci_fasta/TRB_AP023153.1_7Vs.fasta
test_dataset/beds/01_mPumCon1.1_hap1.bed
test_dataset/beds/02_mPumCon1.1_hap2.bed
test_dataset/beds/03_mNeoNeb1.bed
test_dataset/beds/04_mLynRuf1.bed
test_dataset/beds/05_mFelCat1.bed