├── Docker ├── Dockerfile ├── build_docker.sh ├── make_simg.sh ├── push_docker.sh ├── run_docker.sh ├── run_eval.sh └── run_singularity.sh ├── PerlLib ├── DelimParser.pm ├── Fasta_reader.pm ├── Overlap_piler.pm ├── Pipeliner.pm └── Process_cmd.pm ├── README.md ├── alt_methods ├── STAR-Fusion │ └── uger │ │ ├── starF_v1.5_hg19.cmd │ │ └── starF_v1.5_hg19.conf ├── TrinityFusion │ ├── uger │ │ ├── TrinityFusion-C │ │ │ ├── TrinityFusion-C.hg19.cmd │ │ │ └── TrinityFusion-C.hg19.conf │ │ ├── TrinityFusion-D │ │ │ ├── TrinityFusion-D.hg19.cmd │ │ │ └── TrinityFusion-D.hg19.conf │ │ └── TrinityFusion-UC │ │ │ ├── TrinityFusion-UC.hg19.cmd │ │ │ └── TrinityFusion-UC.hg19.conf │ └── wdl │ │ ├── TrinityFusion.wdl │ │ ├── inputs.json │ │ ├── make_wdl_input_template.sh │ │ └── run.sh ├── arriba │ ├── README.md │ ├── arriba_wrapper.pl │ └── uger │ │ ├── arriba.uger.cmd │ │ └── arriba.uger.conf ├── prada │ ├── Dockerfile │ ├── VERSION.txt │ └── build_docker.sh ├── star-seqr │ ├── docker │ │ ├── make_simg.sh │ │ └── run_test.sh │ └── uger │ │ ├── star-seqr.uger.cmd │ │ └── star-seqr.uger.conf └── starchip │ ├── Docker │ ├── Dockerfile │ ├── Pipeliner.pm │ ├── VERSION.txt │ ├── build_docker.sh │ ├── make_simg.sh │ ├── push_docker.sh │ └── starchip_wrapper.pl │ ├── README.md │ ├── cleanMe.sh │ ├── run_test.sh │ ├── test_data │ ├── reads_1.fq.gz │ └── reads_2.fq.gz │ ├── test_outdir │ ├── Aligned.out.bam │ ├── Chimeric.out.junction │ ├── Chimeric.out.sam │ ├── Log.final.out │ ├── Log.out │ ├── Log.progress.out │ ├── ReadsPerGene.out.tab │ ├── SJ.out.tab │ ├── Unmapped.out.mate1 │ ├── Unmapped.out.mate2 │ ├── __starchip_chkpts │ │ ├── pipeliner.2350.cmds │ │ ├── pipeliner.2900.cmds │ │ ├── star_align.ok │ │ └── starchip.ok │ ├── starchip.summary │ └── starchip.summary.annotated │ └── uger │ ├── starchip.uger.cmd │ └── starchip.uger.conf ├── benchmarking ├── FusionProgParsers │ ├── ARRIBA_hc_parser.pm │ ├── ARRIBA_parser.pm │ ├── ChimPipe_parser.pm │ ├── ChimeraScan_parser.pm │ ├── DEFUSE_parser.pm │ ├── EricScript_parser.pm │ ├── FusionCatcher_KP_parser.pm │ ├── FusionCatcher_parser.pm │ ├── FusionHunter_parser.pm │ ├── FusionInspector_parser.pm │ ├── InFusion_parser.pm │ ├── JAFFA_parser.pm │ ├── MapSplice_parser.pm │ ├── NFuse_parser.pm │ ├── PIZZLY_parser.pm │ ├── PRADA_parser.pm │ ├── SOAPfuse_parser.pm │ ├── STARCHIP_parser.pm │ ├── STARFusion_parser.pm │ ├── STARSEQR_parser.pm │ ├── TopHatFusion_parser.pm │ └── TrinityFusion_parser.pm ├── Venn_analysis_strategy.pl ├── aggregate_peak_F1_stats.R ├── all_TP_FP_FN_to_ROC.pl ├── all_TP_FP_FN_to_ROC.vary_minF_minS.pl ├── all_TP_FP_FN_to_ROC.vary_minF_minS.plot.Rscript ├── calc_PR.py ├── collect_preds.pl ├── collected_preds_to_fusion_prog_support_listing.pl ├── compare_A_vs_B_scored_preds.pl ├── define_truth_n_unsure_set.pl ├── examine_FPs.pl ├── filter_collected_preds.pl ├── fusion_preds_sensitivity_vs_expr.avg_replicates.pl ├── fusion_preds_sensitivity_vs_expr.pl ├── fusion_preds_to_TP_FP_FN.pl ├── fusion_preds_to_matrix.pl ├── fusion_progs_agree_to_matrix.pl ├── fusion_sample_TPs_to_matrix.pl ├── map_gene_symbols_to_gencode.pl ├── notes ├── plotters │ ├── AUC_barplot.Rscript │ ├── AUC_boxplot.from_separate_auc_files.Rscript │ ├── AUC_boxplot.from_single_summary_AUC_file.Rscript │ ├── plotPRcurves.R │ ├── plot_AUC_50_vs_101_boxplots.Rscript │ ├── plot_F1_vs_min_frags.R │ ├── plot_ROC.Rscript │ ├── plot_TP_FP_vs_minSum_per_prog.R │ ├── plot_all_auc_barplots.Rscript │ ├── plot_before_vs_after_filt_TP_FP_compare.Rscript │ ├── plot_median_accuracy_ranking_vs_median_runtime.R │ ├── plot_peak_F1_scatter.R │ └── plot_upsetR.R └── run_prediction_accuracy_assessment_pipeline.pl ├── cancer_cell_lines ├── Edgren_subset │ ├── analyze_Edgren_subset.pl │ ├── cleanMe.sh │ ├── edgren.truthset │ ├── edgren.truthset.raw │ ├── eval_edgren_min_agree.consolidated.pl │ ├── eval_edgren_min_agree.pl │ ├── examine_validated_enrichment.R │ └── runMe.sh ├── SuppTable-cancer_cell_lines.csv ├── analyze_cancer_data.pl ├── cleanMe.sh ├── progs_select.txt └── runMe.sh ├── cleanMe.sh ├── progs_restrict.txt ├── resources ├── genes.aliases ├── genes.coords.gz ├── notes ├── notes.paralog_clustering.2020.txt ├── paralog_clusters.2020.I3.dat ├── paralog_clusters.2020.I5.dat ├── paralog_clusters.dat └── paralog_clusters.dat.2019 ├── runMe.sh ├── runtime_analysis ├── STAR_F_multicore │ └── runtimes.txt ├── all_progs_cancer │ ├── __origfmt │ │ └── runtimes.orignames.dat │ └── runtimes.txt ├── cleanMe.sh └── runMe.sh ├── simulated_data ├── SuppTable-sim_reads.csv ├── analyze_simulated_data.pl ├── cleanMe.sh ├── runMe.sh ├── sim_101 │ ├── cleanMe.sh │ ├── runMe.sh │ ├── sim_101.fusion_TPM_values.dat │ └── sim_101.truth_set.dat └── sim_50 │ ├── cleanMe.sh │ ├── runMe.sh │ ├── sim_50.fusion_TPM_values.dat │ └── sim_50.truth_set.dat └── util ├── Terra ├── organize_FI_results_for_benchmarking.py └── organize_StarF_results_for_benchmarking.py ├── __get_figs_for_paper.pl ├── 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