README.md
setup.py
vidrl_hiv.egg-info/PKG-INFO
vidrl_hiv.egg-info/SOURCES.txt
vidrl_hiv.egg-info/dependency_links.txt
vidrl_hiv.egg-info/entry_points.txt
vidrl_hiv.egg-info/requires.txt
vidrl_hiv.egg-info/top_level.txt
vidrlhiv/__init__.py
vidrlhiv/files_to_input.py
vidrlhiv/hiv.py
vidrlhiv/dirty_pipeline_ammar/conda.yaml
vidrlhiv/dirty_pipeline_ammar/snakefile
vidrlhiv/dirty_pipeline_ammar/resources/depth.totals.csv
vidrlhiv/dirty_pipeline_ammar/resources/drm.bed
vidrlhiv/dirty_pipeline_ammar/resources/drm1.tsv
vidrlhiv/dirty_pipeline_ammar/resources/genes.bed
vidrlhiv/dirty_pipeline_ammar/resources/references/01_AE.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/02_AG.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/03_A6B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/04_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/05_DF.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/06_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/07_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/08_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/09_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/100_01C.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/101_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/102_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/103_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/104_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/105_0108.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/106_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/107_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/108_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/109_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/10_CD.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/110_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/111_01C.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/112_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/113_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/114_0155.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/115_01C.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/116_0108.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/117_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/118_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/119_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/11_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/120_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/121_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/122_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/123_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/124_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/125_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/126_0755.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/128_07B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/12_BF.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/130_A1B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/131_A1B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/132_94B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/133_A6B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/134_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/137_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/138_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/13_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/140_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/141_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/143_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/146_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/14_BG.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/151_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/152_DG.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/153_55B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/154_0755.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/155_0755.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/156_0755.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/157_A6C.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/159_01103.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/15_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/16_A2D.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/17_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/18_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/19_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/20_BG.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/21_A2D.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/22_01A1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/23_BG.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/24_BG.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/25_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/26_A5U.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/27_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/28_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/29_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/31_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/32_06A6.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/33_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/34_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/35_A1D.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/36_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/37_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/38_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/39_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/40_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/41_CD.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/42_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/43_02G.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/44_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/45_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/46_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/47_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/48_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/49_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/50_A1D.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/51_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/52_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/53_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/54_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/55_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/56_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/57_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/58_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/59_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/60_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/61_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/62_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/63_02A6.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/64_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/65_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/66_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/67_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/68_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/69_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/70_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/71_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/72_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/73_BG.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/74_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/75_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/76_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/77_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/78_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/79_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/80_0107.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/81_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/82_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/83_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/84_A1D.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/85_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/86_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/87_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/88_BC.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/89_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/90_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/91_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/92_C2U.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/93_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/94_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/95_02B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/96_cpx.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/97_01B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/98_06B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/99_BF1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/A1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/A2.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/A3.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/A4.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/A6.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/A7.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/A8.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/B.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/C.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/CPZ.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/D.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/F1.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/F2.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/G.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/GOR.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/H.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/J.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/K.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/L.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/N.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/O.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/P.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/all.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/hxb2.fasta
vidrlhiv/dirty_pipeline_ammar/resources/references/hxb2.gff3
vidrlhiv/dirty_pipeline_ammar/resources/superceded/drm.tsv
vidrlhiv/dirty_pipeline_ammar/rules/common.smk
vidrlhiv/dirty_pipeline_ammar/scripts/create_bed_drm.R
vidrlhiv/dirty_pipeline_ammar/scripts/plot.R
vidrlhiv/dirty_pipeline_ammar/scripts/plot_mosdepth_drm.R
vidrlhiv/dirty_pipeline_ammar/scripts/plot_mosdepth_genes.R
vidrlhiv/dirty_pipeline_ammar/wrappers/mosdepth.smk
vidrlhiv/resources/Snakefile
vidrlhiv/resources/config.yaml
vidrlhiv/resources/envs/fastp.yaml
vidrlhiv/resources/envs/kraken2.yaml
vidrlhiv/resources/envs/none.yaml
vidrlhiv/resources/envs/rasusa.yaml
vidrlhiv/resources/envs/scrubby.yaml