├── .gitmodules ├── Changelog.txt ├── Docker ├── Dockerfile ├── VERSION.txt ├── build_docker.sh ├── make_simg.sh ├── notes ├── push_docker.sh └── sam_readname_cleaner.py ├── LICENSE ├── Makefile ├── PyLib └── Pipeliner.py ├── README.md ├── WDL ├── LRsplice_VIF.config.json ├── LRsplice_VIF.wdl ├── TCGA-RNA_bhaas.config.json ├── Terra │ ├── ctat_VIF.Terra.hg19.wdl │ ├── ctat_VIF.Terra.hg38.wdl │ └── ctat_VIF.Terra.wdl ├── __deprecated │ ├── VirusInsertionFinder.5.wdl │ ├── VirusInsertionFinder.9.wdl │ ├── VirusInsertionFinder.config.json │ ├── ctat_virus_integration_finder.wdl │ └── vif.terra.workspace.inputs.json ├── cromwell.conf ├── ctat-testing-2018.config.json ├── ctat_VIF.wdl └── testing │ ├── CTAT_VIF.wdl.bam_input.json │ ├── CTAT_VIF.wdl.fastq_tar_gz_input.json │ └── CTAT_VIF.wdl.fq_inputs.json ├── ctat-vif ├── download_cromwell.sh ├── prep_genome_lib ├── PyLib │ └── Pipeliner.py ├── ctat-vif-lib-integration.py └── misc │ ├── README.md │ └── select_cluster_rep_HPV_pref.py ├── testing ├── HPV16.fa ├── HPV16.fa.fai ├── Makefile ├── __testdata │ ├── human_virus_chimJ.tsv.gz │ ├── test.GRCH38.insertion_candidates.tsv │ ├── test.hgOnly.Unmapped.out.mate1.gz │ ├── test.hgOnly.Unmapped.out.mate2.gz │ ├── test.hgPlusVirus.Aligned.sortedByCoord.out.bam │ └── test.hgPlusVirus.Aligned.sortedByCoord.out.bam.bai ├── reads_1.fastq.gz ├── reads_2.fastq.gz ├── red_herrings_1.fastq.gz ├── red_herrings_2.fastq.gz ├── test.novirus.reads_1.fastq.gz └── test.novirus.reads_2.fastq.gz └── util ├── LRsplice_util ├── partition_alignments_virus_vs_host.py └── prep_viral_genome_insertion_w_flank.py ├── STAR_chimeric_patch_runner.py ├── STAR_nonchimeric_patchless_runner.py ├── Trimmomatic ├── LICENSE ├── adapters │ ├── NexteraPE-PE.fa │ ├── TruSeq2-PE.fa │ ├── TruSeq2-SE.fa │ ├── TruSeq3-PE-2.fa │ ├── TruSeq3-PE.fa │ └── TruSeq3-SE.fa ├── trimmomatic-0.36.jar └── trimmomatic.jar ├── add_to_html.py ├── bam_mark_duplicates.py ├── chimJ_to_virus_insertion_candidate_sites.py ├── chimeric_contig_evidence_analyzer.py ├── create_igvjs_virus_bed.py ├── create_igvjs_virus_fa.py ├── create_insertion_site_inspector_js.py ├── ctat-VIF.longrange_virus_splice.py ├── distill_to_primary_target_list_via_brkpt_homologies.py ├── examine_flanking_uniq_kmer_composition.py ├── extract_chimeric_genomic_targets.py ├── extract_genomic_targets_for_draft_eval.py ├── extract_insertion_evidence_reads.py ├── extract_prelim_chimeric_genome_read_alignments.py ├── fastq_polyA_stripper.py ├── find_closest.py ├── greedily_assign_multimapping_reads_among_insertions.py ├── incorporate_breakpoint_entropy_info.py ├── incorporate_breakpoint_entropy_n_splice_info.py ├── incorporate_read_alignment_stats.py ├── make_VIF_genome_abundance_plot.Rscript ├── make_VIF_genome_abundance_plot.prelim.Rscript ├── make_VIF_igvjs_html.py ├── misc ├── extract_human_viruses.py ├── filter_by_fraction_masked.py ├── mask_nonunique_kmers_except_first_occurrence.py ├── mask_nucmer_hits.pl └── unpack_drs.py ├── 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