MANIFEST.in
README.md
requirements.txt
setup.cfg
setup.py
docs/Makefile
docs/source/conf.py
docs/source/file_formats.rst
docs/source/general.rst
docs/source/index.rst
docs/source/installation.rst
docs/source/spladder_cohort.rst
docs/source/spladder_modes.rst
docs/source/img/splice_events.png
spladder/__init__.py
spladder/count.py
spladder/editgraph.py
spladder/hdf5.py
spladder/helpers.py
spladder/helpers_viz.py
spladder/init.py
spladder/merge.py
spladder/reads.py
spladder/settings.py
spladder/spladder.py
spladder/spladder_build.py
spladder/spladder_prep.py
spladder/spladder_test.py
spladder/spladder_viz.py
spladder/utils.py
spladder.egg-info/PKG-INFO
spladder.egg-info/SOURCES.txt
spladder.egg-info/dependency_links.txt
spladder.egg-info/entry_points.txt
spladder.egg-info/not-zip-safe
spladder.egg-info/requires.txt
spladder.egg-info/top_level.txt
spladder/alt_splice/__init__.py
spladder/alt_splice/analyze.py
spladder/alt_splice/collect.py
spladder/alt_splice/detect.py
spladder/alt_splice/events.py
spladder/alt_splice/quantify.py
spladder/alt_splice/verify.py
spladder/alt_splice/write.py
spladder/classes/__init__.py
spladder/classes/counts.py
spladder/classes/datatrack.py
spladder/classes/event.py
spladder/classes/gene.py
spladder/classes/region.py
spladder/classes/segmentgraph.py
spladder/classes/splicegraph.py
spladder/core/__init__.py
spladder/core/gen_graphs.py
spladder/core/spladdercore.py
spladder/testing/__init__.py
spladder/testing/likelihood.py
spladder/viz/__init__.py
spladder/viz/axes.py
spladder/viz/coverage.py
spladder/viz/diagnose.py
spladder/viz/genelets.py
spladder/viz/graph.py
spladder/viz/highlight.py
tests/__init__.py
tests/test_end_to_end.py
tests/templates/annotation_pos.gtf
tests/testcase_basic/data/annotation_neg.gtf
tests/testcase_basic/data/annotation_neg.gtf.pickle
tests/testcase_basic/data/annotation_pos.gtf
tests/testcase_basic/data/annotation_pos.gtf.pickle
tests/testcase_basic/data/expr_ts.txt
tests/testcase_basic/data/genome_neg.fa
tests/testcase_basic/data/genome_pos.fa
tests/testcase_basic/data/testcase_basic_1.fq
tests/testcase_basic/data/testcase_basic_2.fq
tests/testcase_basic/data/testcase_basic_3.fq
tests/testcase_basic/data/testcase_basic_4.fq
tests/testcase_basic/data/testcase_basic_5.fq
tests/testcase_basic/data/align/neg_1.bam
tests/testcase_basic/data/align/neg_1.bam.bai
tests/testcase_basic/data/align/neg_1.conf_3.filt.hdf5
tests/testcase_basic/data/align/neg_1.hdf5
tests/testcase_basic/data/align/neg_2.bam
tests/testcase_basic/data/align/neg_2.bam.bai
tests/testcase_basic/data/align/neg_3.bam
tests/testcase_basic/data/align/neg_3.bam.bai
tests/testcase_basic/data/align/neg_4.bam
tests/testcase_basic/data/align/neg_4.bam.bai
tests/testcase_basic/data/align/neg_5.bam
tests/testcase_basic/data/align/neg_5.bam.bai
tests/testcase_basic/data/align/pos_1.bam
tests/testcase_basic/data/align/pos_1.bam.bai
tests/testcase_basic/data/align/pos_1.conf_3.filt.hdf5
tests/testcase_basic/data/align/pos_1.hdf5
tests/testcase_basic/data/align/pos_2.bam
tests/testcase_basic/data/align/pos_2.bam.bai
tests/testcase_basic/data/align/pos_3.bam
tests/testcase_basic/data/align/pos_3.bam.bai
tests/testcase_basic/data/align/pos_4.bam
tests/testcase_basic/data/align/pos_4.bam.bai
tests/testcase_basic/data/align/pos_5.bam
tests/testcase_basic/data/align/pos_5.bam.bai
tests/testcase_basic/data/align/neg_1/Aligned.sortedByCoord.out.bam
tests/testcase_basic/data/align/neg_2/Aligned.sortedByCoord.out.bam
tests/testcase_basic/data/align/neg_3/Aligned.sortedByCoord.out.bam
tests/testcase_basic/data/align/neg_4/Aligned.sortedByCoord.out.bam
tests/testcase_basic/data/align/neg_5/Aligned.sortedByCoord.out.bam
tests/testcase_basic/data/align/pos_1/Aligned.sortedByCoord.out.bam
tests/testcase_basic/data/align/pos_2/Aligned.sortedByCoord.out.bam
tests/testcase_basic/data/align/pos_3/Aligned.sortedByCoord.out.bam
tests/testcase_basic/data/align/pos_4/Aligned.sortedByCoord.out.bam
tests/testcase_basic/data/align/pos_5/Aligned.sortedByCoord.out.bam
tests/testcase_basic/results_merged_neg/merge_graphs_alt_3prime_C3.confirmed.pickle
tests/testcase_basic/results_merged_neg/merge_graphs_alt_3prime_C3.counts.hdf5
tests/testcase_basic/results_merged_neg/merge_graphs_alt_3prime_C3.pickle
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.bed
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.confirmed.bed
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.confirmed.gff3
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.confirmed.pickle
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.confirmed.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.counts.hdf5
tests/testcase_basic/results_merged_neg/merge_graphs_alt_5prime_C3.gff3
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tests/testcase_basic/results_merged_neg/merge_graphs_exon_skip_C3.confirmed.pickle
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tests/testcase_basic/results_merged_neg/merge_graphs_exon_skip_C3.pickle
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.bed
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.confirmed.bed
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.confirmed.gff3
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.confirmed.pickle
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.confirmed.struc.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.confirmed.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.counts.hdf5
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.gff3
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.pickle
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.struc.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_intron_retention_C3.txt.gz
tests/testcase_basic/results_merged_neg/merge_graphs_mult_exon_skip_C3.confirmed.pickle
tests/testcase_basic/results_merged_neg/merge_graphs_mult_exon_skip_C3.counts.hdf5
tests/testcase_basic/results_merged_neg/merge_graphs_mult_exon_skip_C3.pickle
tests/testcase_basic/results_merged_neg/merge_graphs_mutex_exons_C3.confirmed.pickle
tests/testcase_basic/results_merged_neg/merge_graphs_mutex_exons_C3.counts.hdf5
tests/testcase_basic/results_merged_neg/merge_graphs_mutex_exons_C3.pickle
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.merge_graphs.count.hdf5
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.merge_graphs.count.hdf5.quick_edge_idx
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_edges
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_segs
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.merge_graphs.gene_exp.hdf5
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.merge_graphs.pickle
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.neg_1.pickle
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.neg_2.pickle
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.neg_3.pickle
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.neg_4.pickle
tests/testcase_basic/results_merged_neg/spladder/genes_graph_conf3.neg_5.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_alt_3prime_C3.confirmed.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_alt_3prime_C3.counts.hdf5
tests/testcase_basic/results_merged_pos/merge_graphs_alt_3prime_C3.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.bed
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.confirmed.bed
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.confirmed.gff3
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.confirmed.icgc.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.confirmed.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.confirmed.struc.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.confirmed.tcga.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.confirmed.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.counts.hdf5
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.gff3
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.struc.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_alt_5prime_C3.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_exon_skip_C3.confirmed.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_exon_skip_C3.counts.hdf5
tests/testcase_basic/results_merged_pos/merge_graphs_exon_skip_C3.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.bed
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.confirmed.bed
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.confirmed.gff3
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.confirmed.icgc.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.confirmed.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.confirmed.struc.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.confirmed.tcga.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.confirmed.txt.gz
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.counts.hdf5
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.gff3
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_intron_retention_C3.struc.txt.gz
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tests/testcase_basic/results_merged_pos/merge_graphs_mult_exon_skip_C3.confirmed.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_mult_exon_skip_C3.counts.hdf5
tests/testcase_basic/results_merged_pos/merge_graphs_mult_exon_skip_C3.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_mutex_exons_C3.confirmed.pickle
tests/testcase_basic/results_merged_pos/merge_graphs_mutex_exons_C3.counts.hdf5
tests/testcase_basic/results_merged_pos/merge_graphs_mutex_exons_C3.pickle
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.merge_graphs.count.hdf5
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.merge_graphs.count.hdf5.quick_edge_idx
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_edges
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.merge_graphs.count.hdf5.quick_ids_segs
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.merge_graphs.gene_exp.hdf5
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.merge_graphs.pickle
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.pos_1.pickle
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.pos_2.pickle
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.pos_3.pickle
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.pos_4.pickle
tests/testcase_basic/results_merged_pos/spladder/genes_graph_conf3.pos_5.pickle
tests/testcase_basic/results_single_neg/neg_1_alt_3prime_C3.confirmed.pickle
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tests/testcase_basic/results_single_neg/neg_1_alt_5prime_C3.confirmed.gff3
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tests/testcase_basic/results_single_neg/neg_1_exon_skip_C3.confirmed.pickle
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tests/testcase_basic/results_single_neg/spladder/genes_graph_conf3.neg_1.pickle
tests/testcase_basic/results_single_pos/pos_1_alt_3prime_C3.confirmed.pickle
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tests/testcase_events/.gitignore
tests/testcase_events/data/genome.fa
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tests/testcase_events/data/testcase_events.gtf
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tests/testcase_events/data/align/testcase_events_1_sample10.bam.bai
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tests/testcase_events/data/align/testcase_events_1_sample13.cram
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tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample14.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample15.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample16.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample17.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample18.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample19.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample2.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample20.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample3.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample4.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample5.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample6.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample7.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample8.pickle
tests/testcase_events/results_merged_cram/spladder/genes_graph_conf3.testcase_events_1_sample9.pickle
tests/testcase_events/results_merged_cram/testing/test_results_C3_exon_skip.gene_unique.tsv
tests/testcase_events/results_merged_cram/testing/test_results_C3_exon_skip.tsv
tests/testcase_events/results_merged_cram/testing/test_results_extended_C3_exon_skip.tsv
tests/testcase_events/results_merged_cram/testing/test_setup_C3_exon_skip.pickle
tests/testcase_events/results_merged_cram/testing/plots/count_distribution.exon_skip.log10.pdf
tests/testcase_events/results_merged_cram/testing/plots/count_distribution.exon_skip.pdf
tests/testcase_events/results_merged_cram/testing/plots/dispersion_adjusted_exon_skip.pdf
tests/testcase_events/results_merged_cram/testing/plots/dispersion_fitted_exon_skip.pdf
tests/testcase_events/results_merged_cram/testing/plots/dispersion_raw_exon_skip.pdf
tests/testcase_events/results_merged_cram/testing/plots/ma_plot_exon_skip.pdf
tests/testcase_events/results_merged_cram/testing/plots/qq_plot_exon_skip.adj.log10.pdf
tests/testcase_events/results_merged_cram/testing/plots/qq_plot_exon_skip.adj.pdf
tests/testcase_events/results_merged_cram/testing/plots/qq_plot_exon_skip.log10.pdf
tests/testcase_events/results_merged_cram/testing/plots/qq_plot_exon_skip.pdf