├── .circleci └── config.yml ├── .editorconfig ├── .github └── ISSUE_TEMPLATE.md ├── .gitignore ├── .prospector ├── fast.yaml └── minimal.yaml ├── AUTHORS ├── COPYRIGHT ├── MANIFEST.in ├── Makefile ├── README.md ├── docs ├── Makefile └── source │ ├── conf.py │ ├── file_formats.rst │ ├── general.rst │ ├── img │ ├── splice_events.pdf │ └── splice_events.png │ ├── index.rst │ ├── installation.rst │ ├── spladder_cohort.rst │ └── spladder_modes.rst ├── requirements.txt ├── requirements_dev.txt ├── scripts ├── create_bam_file.py ├── create_event_testcases.py ├── generate_test_data.sh ├── generate_test_data_events.sh ├── generate_test_data_events_cram.sh ├── generate_test_results.sh ├── generate_test_results_events.sh ├── generate_test_results_events_cram.sh ├── generate_test_results_noevents.sh ├── generate_test_results_viz.sh ├── simulate_abundances.py ├── testcase_events_abundances.tsv ├── testcase_events_blocks.tsv ├── testcase_noevents_abundances.tsv └── testcase_noevents_blocks.tsv ├── setup.cfg ├── setup.py ├── spladder ├── __init__.py ├── alt_splice │ ├── __init__.py │ ├── analyze.py │ ├── collect.py │ ├── detect.py │ ├── events.py │ ├── quantify.py │ ├── verify.py │ └── write.py ├── classes │ ├── __init__.py │ ├── counts.py │ ├── datatrack.py │ ├── event.py │ ├── gene.py │ ├── region.py │ ├── segmentgraph.py │ └── splicegraph.py ├── core │ ├── __init__.py │ ├── gen_graphs.py │ └── spladdercore.py ├── count.py ├── editgraph.py ├── hdf5.py ├── helpers.py ├── helpers_viz.py ├── init.py ├── merge.py ├── reads.py ├── settings.py ├── spladder.py ├── spladder_build.py ├── spladder_prep.py ├── spladder_test.py ├── spladder_viz.py ├── testing │ ├── __init__.py │ └── likelihood.py ├── utils.py └── viz │ ├── __init__.py │ ├── axes.py │ ├── coverage.py │ ├── diagnose.py │ ├── genelets.py │ ├── graph.py │ └── highlight.py ├── tests ├── __init__.py ├── templates │ └── annotation_pos.gtf ├── test_end_to_end.py ├── testcase_basic │ ├── data │ │ ├── align │ │ │ ├── neg_1.bam │ │ │ ├── neg_1.bam.bai │ │ │ ├── neg_1.conf_3.filt.hdf5 │ │ │ ├── neg_1.hdf5 │ │ │ ├── neg_1 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ │ ├── neg_2.bam │ │ │ ├── neg_2.bam.bai │ │ │ ├── neg_2 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ │ ├── neg_3.bam │ │ │ ├── neg_3.bam.bai │ │ │ ├── neg_3 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ │ ├── neg_4.bam │ │ │ ├── neg_4.bam.bai │ │ │ ├── neg_4 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ │ ├── neg_5.bam │ │ │ ├── neg_5.bam.bai │ │ │ ├── neg_5 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ │ ├── pos_1.bam │ │ │ ├── pos_1.bam.bai │ │ │ ├── pos_1.conf_3.filt.hdf5 │ │ │ ├── pos_1.hdf5 │ │ │ ├── pos_1 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ │ ├── pos_2.bam │ │ │ ├── pos_2.bam.bai │ │ │ ├── pos_2 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ │ ├── pos_3.bam │ │ │ ├── pos_3.bam.bai │ │ │ ├── pos_3 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ │ ├── pos_4.bam │ │ │ ├── pos_4.bam.bai │ │ │ ├── pos_4 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ │ ├── pos_5.bam │ │ │ ├── pos_5.bam.bai │ │ │ └── pos_5 │ │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── annotation_neg.gtf │ │ ├── annotation_neg.gtf.pickle │ │ ├── annotation_pos.gtf │ │ ├── annotation_pos.gtf.pickle │ │ ├── expr_ts.txt │ │ ├── genome_neg.fa │ │ ├── genome_pos.fa │ │ ├── testcase_basic_1.fq │ │ ├── testcase_basic_2.fq │ │ ├── testcase_basic_3.fq │ │ ├── testcase_basic_4.fq │ │ └── testcase_basic_5.fq │ ├── results_merged_neg │ │ ├── merge_graphs_alt_3prime_C3.confirmed.pickle │ │ ├── merge_graphs_alt_3prime_C3.counts.hdf5 │ │ ├── merge_graphs_alt_3prime_C3.pickle │ │ ├── merge_graphs_alt_5prime_C3.bed │ │ ├── merge_graphs_alt_5prime_C3.confirmed.bed │ │ ├── merge_graphs_alt_5prime_C3.confirmed.gff3 │ │ ├── merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.confirmed.pickle │ │ ├── merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.confirmed.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.counts.hdf5 │ │ ├── merge_graphs_alt_5prime_C3.gff3 │ │ ├── merge_graphs_alt_5prime_C3.pickle │ │ ├── merge_graphs_alt_5prime_C3.struc.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.txt.gz │ │ ├── merge_graphs_exon_skip_C3.confirmed.pickle │ │ ├── merge_graphs_exon_skip_C3.counts.hdf5 │ │ ├── merge_graphs_exon_skip_C3.pickle │ │ ├── merge_graphs_intron_retention_C3.bed │ │ ├── merge_graphs_intron_retention_C3.confirmed.bed │ │ ├── merge_graphs_intron_retention_C3.confirmed.gff3 │ │ ├── merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz │ │ ├── merge_graphs_intron_retention_C3.confirmed.pickle │ │ ├── merge_graphs_intron_retention_C3.confirmed.struc.txt.gz │ │ ├── merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz │ │ ├── merge_graphs_intron_retention_C3.confirmed.txt.gz │ │ ├── merge_graphs_intron_retention_C3.counts.hdf5 │ │ ├── merge_graphs_intron_retention_C3.gff3 │ │ ├── merge_graphs_intron_retention_C3.pickle │ │ ├── merge_graphs_intron_retention_C3.struc.txt.gz │ │ ├── merge_graphs_intron_retention_C3.txt.gz │ │ ├── merge_graphs_mult_exon_skip_C3.confirmed.pickle │ │ ├── merge_graphs_mult_exon_skip_C3.counts.hdf5 │ │ ├── merge_graphs_mult_exon_skip_C3.pickle │ │ ├── merge_graphs_mutex_exons_C3.confirmed.pickle │ │ ├── merge_graphs_mutex_exons_C3.counts.hdf5 │ │ ├── merge_graphs_mutex_exons_C3.pickle │ │ └── spladder │ │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5 │ │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_edge_idx │ │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_edges │ │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_segs │ │ │ ├── genes_graph_conf3.merge_graphs.gene_exp.hdf5 │ │ │ ├── genes_graph_conf3.merge_graphs.pickle │ │ │ ├── genes_graph_conf3.neg_1.pickle │ │ │ ├── genes_graph_conf3.neg_2.pickle │ │ │ ├── genes_graph_conf3.neg_3.pickle │ │ │ ├── genes_graph_conf3.neg_4.pickle │ │ │ └── genes_graph_conf3.neg_5.pickle │ ├── results_merged_pos │ │ ├── merge_graphs_alt_3prime_C3.confirmed.pickle │ │ ├── merge_graphs_alt_3prime_C3.counts.hdf5 │ │ ├── merge_graphs_alt_3prime_C3.pickle │ │ ├── merge_graphs_alt_5prime_C3.bed │ │ ├── merge_graphs_alt_5prime_C3.confirmed.bed │ │ ├── merge_graphs_alt_5prime_C3.confirmed.gff3 │ │ ├── merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.confirmed.pickle │ │ ├── merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.confirmed.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.counts.hdf5 │ │ ├── merge_graphs_alt_5prime_C3.gff3 │ │ ├── merge_graphs_alt_5prime_C3.pickle │ │ ├── merge_graphs_alt_5prime_C3.struc.txt.gz │ │ ├── merge_graphs_alt_5prime_C3.txt.gz │ │ ├── merge_graphs_exon_skip_C3.confirmed.pickle │ │ ├── merge_graphs_exon_skip_C3.counts.hdf5 │ │ ├── merge_graphs_exon_skip_C3.pickle │ │ ├── merge_graphs_intron_retention_C3.bed │ │ ├── merge_graphs_intron_retention_C3.confirmed.bed │ │ ├── merge_graphs_intron_retention_C3.confirmed.gff3 │ │ ├── merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz │ │ ├── merge_graphs_intron_retention_C3.confirmed.pickle │ │ ├── merge_graphs_intron_retention_C3.confirmed.struc.txt.gz │ │ ├── merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz │ │ ├── merge_graphs_intron_retention_C3.confirmed.txt.gz │ │ ├── merge_graphs_intron_retention_C3.counts.hdf5 │ │ ├── merge_graphs_intron_retention_C3.gff3 │ │ ├── merge_graphs_intron_retention_C3.pickle │ │ ├── merge_graphs_intron_retention_C3.struc.txt.gz │ │ ├── merge_graphs_intron_retention_C3.txt.gz │ │ ├── merge_graphs_mult_exon_skip_C3.confirmed.pickle │ │ ├── merge_graphs_mult_exon_skip_C3.counts.hdf5 │ │ ├── merge_graphs_mult_exon_skip_C3.pickle │ │ ├── merge_graphs_mutex_exons_C3.confirmed.pickle │ │ ├── merge_graphs_mutex_exons_C3.counts.hdf5 │ │ ├── merge_graphs_mutex_exons_C3.pickle │ │ └── spladder │ │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5 │ │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_edge_idx │ │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_edges │ │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_segs │ │ │ ├── genes_graph_conf3.merge_graphs.gene_exp.hdf5 │ │ │ ├── genes_graph_conf3.merge_graphs.pickle │ │ │ ├── genes_graph_conf3.pos_1.pickle │ │ │ ├── genes_graph_conf3.pos_2.pickle │ │ │ ├── genes_graph_conf3.pos_3.pickle │ │ │ ├── genes_graph_conf3.pos_4.pickle │ │ │ └── genes_graph_conf3.pos_5.pickle │ ├── results_single_neg │ │ ├── neg_1_alt_3prime_C3.confirmed.pickle │ │ ├── neg_1_alt_3prime_C3.counts.hdf5 │ │ ├── neg_1_alt_3prime_C3.pickle │ │ ├── neg_1_alt_5prime_C3.confirmed.gff3 │ │ ├── neg_1_alt_5prime_C3.confirmed.icgc.txt.gz │ │ ├── neg_1_alt_5prime_C3.confirmed.pickle │ │ ├── neg_1_alt_5prime_C3.confirmed.txt.gz │ │ ├── neg_1_alt_5prime_C3.counts.hdf5 │ │ ├── neg_1_alt_5prime_C3.pickle │ │ ├── neg_1_exon_skip_C3.confirmed.pickle │ │ ├── neg_1_exon_skip_C3.counts.hdf5 │ │ ├── neg_1_exon_skip_C3.pickle │ │ ├── neg_1_intron_retention_C3.confirmed.gff3 │ │ ├── neg_1_intron_retention_C3.confirmed.icgc.txt.gz │ │ ├── neg_1_intron_retention_C3.confirmed.pickle │ │ ├── neg_1_intron_retention_C3.confirmed.txt.gz │ │ ├── neg_1_intron_retention_C3.counts.hdf5 │ │ ├── neg_1_intron_retention_C3.pickle │ │ ├── neg_1_mult_exon_skip_C3.confirmed.pickle │ │ ├── neg_1_mult_exon_skip_C3.counts.hdf5 │ │ ├── neg_1_mult_exon_skip_C3.pickle │ │ ├── neg_1_mutex_exons_C3.confirmed.pickle │ │ ├── neg_1_mutex_exons_C3.counts.hdf5 │ │ ├── neg_1_mutex_exons_C3.pickle │ │ └── spladder │ │ │ ├── genes_graph_conf3.neg_1.count.hdf5 │ │ │ ├── genes_graph_conf3.neg_1.count.hdf5.quick_edge_idx │ │ │ ├── genes_graph_conf3.neg_1.count.hdf5.quick_ids_edges │ │ │ ├── genes_graph_conf3.neg_1.count.hdf5.quick_ids_segs │ │ │ ├── genes_graph_conf3.neg_1.gene_exp.hdf5 │ │ │ └── genes_graph_conf3.neg_1.pickle │ └── results_single_pos │ │ ├── pos_1_alt_3prime_C3.confirmed.pickle │ │ ├── pos_1_alt_3prime_C3.counts.hdf5 │ │ ├── pos_1_alt_3prime_C3.pickle │ │ ├── pos_1_alt_5prime_C3.confirmed.gff3 │ │ ├── pos_1_alt_5prime_C3.confirmed.icgc.txt.gz │ │ ├── pos_1_alt_5prime_C3.confirmed.pickle │ │ ├── pos_1_alt_5prime_C3.confirmed.txt.gz │ │ ├── pos_1_alt_5prime_C3.counts.hdf5 │ │ ├── pos_1_alt_5prime_C3.pickle │ │ ├── pos_1_exon_skip_C3.confirmed.pickle │ │ ├── pos_1_exon_skip_C3.counts.hdf5 │ │ ├── pos_1_exon_skip_C3.pickle │ │ ├── pos_1_intron_retention_C3.confirmed.gff3 │ │ ├── pos_1_intron_retention_C3.confirmed.icgc.txt.gz │ │ ├── pos_1_intron_retention_C3.confirmed.pickle │ │ ├── pos_1_intron_retention_C3.confirmed.txt.gz │ │ ├── pos_1_intron_retention_C3.counts.hdf5 │ │ ├── pos_1_intron_retention_C3.pickle │ │ ├── pos_1_mult_exon_skip_C3.confirmed.pickle │ │ ├── pos_1_mult_exon_skip_C3.counts.hdf5 │ │ ├── pos_1_mult_exon_skip_C3.pickle │ │ ├── pos_1_mutex_exons_C3.confirmed.pickle │ │ ├── pos_1_mutex_exons_C3.counts.hdf5 │ │ ├── pos_1_mutex_exons_C3.pickle │ │ └── spladder │ │ ├── genes_graph_conf3.pos_1.count.hdf5 │ │ ├── genes_graph_conf3.pos_1.count.hdf5.quick_edge_idx │ │ ├── genes_graph_conf3.pos_1.count.hdf5.quick_ids_edges │ │ ├── genes_graph_conf3.pos_1.count.hdf5.quick_ids_segs │ │ ├── genes_graph_conf3.pos_1.gene_exp.hdf5 │ │ └── genes_graph_conf3.pos_1.pickle └── testcase_events │ ├── .gitignore │ ├── data │ ├── align │ │ ├── testcase_events_1_sample1.bam │ │ ├── testcase_events_1_sample1.bam.bai │ │ ├── testcase_events_1_sample1.cram │ │ ├── testcase_events_1_sample1.cram.crai │ │ ├── testcase_events_1_sample1 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample10.bam │ │ ├── testcase_events_1_sample10.bam.bai │ │ ├── testcase_events_1_sample10.cram │ │ ├── testcase_events_1_sample10.cram.crai │ │ ├── testcase_events_1_sample10 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample11.bam │ │ ├── testcase_events_1_sample11.bam.bai │ │ ├── testcase_events_1_sample11.cram │ │ ├── testcase_events_1_sample11.cram.crai │ │ ├── testcase_events_1_sample11 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample12.bam │ │ ├── testcase_events_1_sample12.bam.bai │ │ ├── testcase_events_1_sample12.cram │ │ ├── testcase_events_1_sample12.cram.crai │ │ ├── testcase_events_1_sample12 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample13.bam │ │ ├── testcase_events_1_sample13.bam.bai │ │ ├── testcase_events_1_sample13.cram │ │ ├── testcase_events_1_sample13.cram.crai │ │ ├── testcase_events_1_sample13 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample14.bam │ │ ├── testcase_events_1_sample14.bam.bai │ │ ├── testcase_events_1_sample14.cram │ │ ├── testcase_events_1_sample14.cram.crai │ │ ├── testcase_events_1_sample14 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample15.bam │ │ ├── testcase_events_1_sample15.bam.bai │ │ ├── testcase_events_1_sample15.cram │ │ ├── testcase_events_1_sample15.cram.crai │ │ ├── testcase_events_1_sample15 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample16.bam │ │ ├── testcase_events_1_sample16.bam.bai │ │ ├── testcase_events_1_sample16.cram │ │ ├── testcase_events_1_sample16.cram.crai │ │ ├── testcase_events_1_sample16 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample17.bam │ │ ├── testcase_events_1_sample17.bam.bai │ │ ├── testcase_events_1_sample17.cram │ │ ├── testcase_events_1_sample17.cram.crai │ │ ├── testcase_events_1_sample17 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample18.bam │ │ ├── testcase_events_1_sample18.bam.bai │ │ ├── testcase_events_1_sample18.cram │ │ ├── testcase_events_1_sample18.cram.crai │ │ ├── testcase_events_1_sample18 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample19.bam │ │ ├── testcase_events_1_sample19.bam.bai │ │ ├── testcase_events_1_sample19.cram │ │ ├── testcase_events_1_sample19.cram.crai │ │ ├── testcase_events_1_sample19 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample2.bam │ │ ├── testcase_events_1_sample2.bam.bai │ │ ├── testcase_events_1_sample2.cram │ │ ├── testcase_events_1_sample2.cram.crai │ │ ├── testcase_events_1_sample2 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample20.bam │ │ ├── testcase_events_1_sample20.bam.bai │ │ ├── testcase_events_1_sample20.cram │ │ ├── testcase_events_1_sample20.cram.crai │ │ ├── testcase_events_1_sample20 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample3.bam │ │ ├── testcase_events_1_sample3.bam.bai │ │ ├── testcase_events_1_sample3.cram │ │ ├── testcase_events_1_sample3.cram.crai │ │ ├── testcase_events_1_sample3 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample4.bam │ │ ├── testcase_events_1_sample4.bam.bai │ │ ├── testcase_events_1_sample4.cram │ │ ├── testcase_events_1_sample4.cram.crai │ │ ├── testcase_events_1_sample4 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample5.bam │ │ ├── testcase_events_1_sample5.bam.bai │ │ ├── testcase_events_1_sample5.cram │ │ ├── testcase_events_1_sample5.cram.crai │ │ ├── testcase_events_1_sample5 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample6.bam │ │ ├── testcase_events_1_sample6.bam.bai │ │ ├── testcase_events_1_sample6.cram │ │ ├── testcase_events_1_sample6.cram.crai │ │ ├── testcase_events_1_sample6 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample7.bam │ │ ├── testcase_events_1_sample7.bam.bai │ │ ├── testcase_events_1_sample7.cram │ │ ├── testcase_events_1_sample7.cram.crai │ │ ├── testcase_events_1_sample7 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample8.bam │ │ ├── testcase_events_1_sample8.bam.bai │ │ ├── testcase_events_1_sample8.cram │ │ ├── testcase_events_1_sample8.cram.crai │ │ ├── testcase_events_1_sample8 │ │ │ └── Aligned.sortedByCoord.out.bam │ │ ├── testcase_events_1_sample9.bam │ │ ├── testcase_events_1_sample9.bam.bai │ │ ├── testcase_events_1_sample9.cram │ │ ├── testcase_events_1_sample9.cram.crai │ │ └── testcase_events_1_sample9 │ │ │ └── Aligned.sortedByCoord.out.bam │ ├── genome.fa │ ├── genome.fa.fai │ ├── testcase_events.gtf │ ├── testcase_events_1_sample1.fq │ ├── testcase_events_1_sample10.fq │ ├── testcase_events_1_sample11.fq │ ├── testcase_events_1_sample12.fq │ ├── testcase_events_1_sample13.fq │ ├── testcase_events_1_sample14.fq │ ├── testcase_events_1_sample15.fq │ ├── testcase_events_1_sample16.fq │ ├── testcase_events_1_sample17.fq │ ├── testcase_events_1_sample18.fq │ ├── testcase_events_1_sample19.fq │ ├── testcase_events_1_sample2.fq │ ├── testcase_events_1_sample20.fq │ ├── testcase_events_1_sample3.fq │ ├── testcase_events_1_sample4.fq │ ├── testcase_events_1_sample5.fq │ ├── testcase_events_1_sample6.fq │ ├── testcase_events_1_sample7.fq │ ├── testcase_events_1_sample8.fq │ ├── testcase_events_1_sample9.fq │ └── testcase_events_spladder.gtf │ ├── results_merged │ ├── merge_graphs_alt_3prime_C3.bed │ ├── merge_graphs_alt_3prime_C3.confirmed.bed │ ├── merge_graphs_alt_3prime_C3.confirmed.gff3 │ ├── merge_graphs_alt_3prime_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_alt_3prime_C3.confirmed.pickle │ ├── merge_graphs_alt_3prime_C3.confirmed.struc.txt.gz │ ├── merge_graphs_alt_3prime_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_alt_3prime_C3.confirmed.txt.gz │ ├── merge_graphs_alt_3prime_C3.counts.hdf5 │ ├── merge_graphs_alt_3prime_C3.gff3 │ ├── merge_graphs_alt_3prime_C3.pickle │ ├── merge_graphs_alt_3prime_C3.struc.txt.gz │ ├── merge_graphs_alt_3prime_C3.txt.gz │ ├── merge_graphs_alt_5prime_C3.bed │ ├── merge_graphs_alt_5prime_C3.confirmed.bed │ ├── merge_graphs_alt_5prime_C3.confirmed.gff3 │ ├── merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_alt_5prime_C3.confirmed.pickle │ ├── merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz │ ├── merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_alt_5prime_C3.confirmed.txt.gz │ ├── merge_graphs_alt_5prime_C3.counts.hdf5 │ ├── merge_graphs_alt_5prime_C3.gff3 │ ├── merge_graphs_alt_5prime_C3.pickle │ ├── merge_graphs_alt_5prime_C3.struc.txt.gz │ ├── merge_graphs_alt_5prime_C3.txt.gz │ ├── merge_graphs_exon_skip_C3.bed │ ├── merge_graphs_exon_skip_C3.confirmed.bed │ ├── merge_graphs_exon_skip_C3.confirmed.gff3 │ ├── merge_graphs_exon_skip_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_exon_skip_C3.confirmed.pickle │ ├── merge_graphs_exon_skip_C3.confirmed.struc.txt.gz │ ├── merge_graphs_exon_skip_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_exon_skip_C3.confirmed.txt.gz │ ├── merge_graphs_exon_skip_C3.counts.hdf5 │ ├── merge_graphs_exon_skip_C3.gff3 │ ├── merge_graphs_exon_skip_C3.pickle │ ├── merge_graphs_exon_skip_C3.struc.txt.gz │ ├── merge_graphs_exon_skip_C3.txt.gz │ ├── merge_graphs_intron_retention_C3.bed │ ├── merge_graphs_intron_retention_C3.confirmed.bed │ ├── merge_graphs_intron_retention_C3.confirmed.gff3 │ ├── merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_intron_retention_C3.confirmed.pickle │ ├── merge_graphs_intron_retention_C3.confirmed.struc.txt.gz │ ├── merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_intron_retention_C3.confirmed.txt.gz │ ├── merge_graphs_intron_retention_C3.counts.hdf5 │ ├── merge_graphs_intron_retention_C3.gff3 │ ├── merge_graphs_intron_retention_C3.pickle │ ├── merge_graphs_intron_retention_C3.struc.txt.gz │ ├── merge_graphs_intron_retention_C3.txt.gz │ ├── merge_graphs_mult_exon_skip_C3.confirmed.pickle │ ├── merge_graphs_mult_exon_skip_C3.counts.hdf5 │ ├── merge_graphs_mult_exon_skip_C3.pickle │ ├── merge_graphs_mutex_exons_C3.bed │ ├── merge_graphs_mutex_exons_C3.confirmed.bed │ ├── merge_graphs_mutex_exons_C3.confirmed.gff3 │ ├── merge_graphs_mutex_exons_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_mutex_exons_C3.confirmed.pickle │ ├── merge_graphs_mutex_exons_C3.confirmed.struc.txt.gz │ ├── merge_graphs_mutex_exons_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_mutex_exons_C3.confirmed.txt.gz │ ├── merge_graphs_mutex_exons_C3.counts.hdf5 │ ├── merge_graphs_mutex_exons_C3.gff3 │ ├── merge_graphs_mutex_exons_C3.pickle │ ├── merge_graphs_mutex_exons_C3.struc.txt.gz │ ├── merge_graphs_mutex_exons_C3.txt.gz │ ├── spladder │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5 │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_edge_idx │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_edges │ │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_segs │ │ ├── genes_graph_conf3.merge_graphs.gene_exp.hdf5 │ │ ├── genes_graph_conf3.merge_graphs.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample1.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample10.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample11.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample12.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample13.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample14.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample15.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample16.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample17.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample18.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample19.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample2.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample20.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample3.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample4.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample5.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample6.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample7.pickle │ │ ├── genes_graph_conf3.testcase_events_1_sample8.pickle │ │ └── genes_graph_conf3.testcase_events_1_sample9.pickle │ └── testing │ │ ├── plots │ │ ├── count_distribution.exon_skip.log10.pdf │ │ ├── count_distribution.exon_skip.pdf │ │ ├── dispersion_adjusted_exon_skip.pdf │ │ ├── dispersion_fitted_exon_skip.pdf │ │ ├── dispersion_raw_exon_skip.pdf │ │ ├── ma_plot_exon_skip.pdf │ │ ├── qq_plot_exon_skip.adj.log10.pdf │ │ ├── qq_plot_exon_skip.adj.pdf │ │ ├── qq_plot_exon_skip.log10.pdf │ │ └── qq_plot_exon_skip.pdf │ │ ├── test_results_C3_exon_skip.gene_unique.tsv │ │ ├── test_results_C3_exon_skip.tsv │ │ ├── test_results_extended_C3_exon_skip.tsv │ │ └── test_setup_C3_exon_skip.pickle │ └── results_merged_cram │ ├── merge_graphs_alt_3prime_C3.bed │ ├── merge_graphs_alt_3prime_C3.confirmed.bed │ ├── merge_graphs_alt_3prime_C3.confirmed.gff3 │ ├── merge_graphs_alt_3prime_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_alt_3prime_C3.confirmed.pickle │ ├── merge_graphs_alt_3prime_C3.confirmed.struc.txt.gz │ ├── merge_graphs_alt_3prime_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_alt_3prime_C3.confirmed.txt.gz │ ├── merge_graphs_alt_3prime_C3.counts.hdf5 │ ├── merge_graphs_alt_3prime_C3.gff3 │ ├── merge_graphs_alt_3prime_C3.pickle │ ├── merge_graphs_alt_3prime_C3.struc.txt.gz │ ├── merge_graphs_alt_3prime_C3.txt.gz │ ├── merge_graphs_alt_5prime_C3.bed │ ├── merge_graphs_alt_5prime_C3.confirmed.bed │ ├── merge_graphs_alt_5prime_C3.confirmed.gff3 │ ├── merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_alt_5prime_C3.confirmed.pickle │ ├── merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz │ ├── merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_alt_5prime_C3.confirmed.txt.gz │ ├── merge_graphs_alt_5prime_C3.counts.hdf5 │ ├── merge_graphs_alt_5prime_C3.gff3 │ ├── merge_graphs_alt_5prime_C3.pickle │ ├── merge_graphs_alt_5prime_C3.struc.txt.gz │ ├── merge_graphs_alt_5prime_C3.txt.gz │ ├── merge_graphs_exon_skip_C3.bed │ ├── merge_graphs_exon_skip_C3.confirmed.bed │ ├── merge_graphs_exon_skip_C3.confirmed.gff3 │ ├── merge_graphs_exon_skip_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_exon_skip_C3.confirmed.pickle │ ├── merge_graphs_exon_skip_C3.confirmed.struc.txt.gz │ ├── merge_graphs_exon_skip_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_exon_skip_C3.confirmed.txt.gz │ ├── merge_graphs_exon_skip_C3.counts.hdf5 │ ├── merge_graphs_exon_skip_C3.gff3 │ ├── merge_graphs_exon_skip_C3.pickle │ ├── merge_graphs_exon_skip_C3.struc.txt.gz │ ├── merge_graphs_exon_skip_C3.txt.gz │ ├── merge_graphs_intron_retention_C3.bed │ ├── merge_graphs_intron_retention_C3.confirmed.bed │ ├── merge_graphs_intron_retention_C3.confirmed.gff3 │ ├── merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_intron_retention_C3.confirmed.pickle │ ├── merge_graphs_intron_retention_C3.confirmed.struc.txt.gz │ ├── merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_intron_retention_C3.confirmed.txt.gz │ ├── merge_graphs_intron_retention_C3.counts.hdf5 │ ├── merge_graphs_intron_retention_C3.gff3 │ ├── merge_graphs_intron_retention_C3.pickle │ ├── merge_graphs_intron_retention_C3.struc.txt.gz │ ├── merge_graphs_intron_retention_C3.txt.gz │ ├── merge_graphs_mult_exon_skip_C3.confirmed.pickle │ ├── merge_graphs_mult_exon_skip_C3.counts.hdf5 │ ├── merge_graphs_mult_exon_skip_C3.pickle │ ├── merge_graphs_mutex_exons_C3.bed │ ├── merge_graphs_mutex_exons_C3.confirmed.bed │ ├── merge_graphs_mutex_exons_C3.confirmed.gff3 │ ├── merge_graphs_mutex_exons_C3.confirmed.icgc.txt.gz │ ├── merge_graphs_mutex_exons_C3.confirmed.pickle │ ├── merge_graphs_mutex_exons_C3.confirmed.struc.txt.gz │ ├── merge_graphs_mutex_exons_C3.confirmed.tcga.txt.gz │ ├── merge_graphs_mutex_exons_C3.confirmed.txt.gz │ ├── merge_graphs_mutex_exons_C3.counts.hdf5 │ ├── merge_graphs_mutex_exons_C3.gff3 │ ├── merge_graphs_mutex_exons_C3.pickle │ ├── merge_graphs_mutex_exons_C3.struc.txt.gz │ ├── merge_graphs_mutex_exons_C3.txt.gz │ ├── spladder │ ├── genes_graph_conf3.merge_graphs.count.hdf5 │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_edge_idx │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_edges │ ├── genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_segs │ ├── genes_graph_conf3.merge_graphs.gene_exp.hdf5 │ ├── genes_graph_conf3.merge_graphs.pickle │ ├── genes_graph_conf3.testcase_events_1_sample1.pickle │ ├── genes_graph_conf3.testcase_events_1_sample10.pickle │ ├── genes_graph_conf3.testcase_events_1_sample11.pickle │ ├── genes_graph_conf3.testcase_events_1_sample12.pickle │ ├── genes_graph_conf3.testcase_events_1_sample13.pickle │ ├── genes_graph_conf3.testcase_events_1_sample14.pickle │ ├── genes_graph_conf3.testcase_events_1_sample15.pickle │ ├── genes_graph_conf3.testcase_events_1_sample16.pickle │ ├── genes_graph_conf3.testcase_events_1_sample17.pickle │ ├── genes_graph_conf3.testcase_events_1_sample18.pickle │ ├── genes_graph_conf3.testcase_events_1_sample19.pickle │ ├── genes_graph_conf3.testcase_events_1_sample2.pickle │ ├── genes_graph_conf3.testcase_events_1_sample20.pickle │ ├── genes_graph_conf3.testcase_events_1_sample3.pickle │ ├── genes_graph_conf3.testcase_events_1_sample4.pickle │ ├── genes_graph_conf3.testcase_events_1_sample5.pickle │ ├── genes_graph_conf3.testcase_events_1_sample6.pickle │ ├── genes_graph_conf3.testcase_events_1_sample7.pickle │ ├── genes_graph_conf3.testcase_events_1_sample8.pickle │ └── genes_graph_conf3.testcase_events_1_sample9.pickle │ └── testing │ ├── plots │ ├── count_distribution.exon_skip.log10.pdf │ ├── count_distribution.exon_skip.pdf │ ├── dispersion_adjusted_exon_skip.pdf │ ├── dispersion_fitted_exon_skip.pdf │ ├── dispersion_raw_exon_skip.pdf │ ├── ma_plot_exon_skip.pdf │ ├── qq_plot_exon_skip.adj.log10.pdf │ ├── qq_plot_exon_skip.adj.pdf │ ├── qq_plot_exon_skip.log10.pdf │ └── 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