Merge pull request cBioPortal#4123 from alisman/profileDetect

Fix detection of rna_seq molecular profile Former-commit-id: a9e3964571cd3db2c167b3824de6f6d8332ba32d
thehyve · Jan 13, 2022 · 55d82ac · 55d82ac
2 parents 2d7cafe + 51a1f80
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diff --git a/...ference/adds_mutation_count_vs_diagnosis_age_chart_element_chrome_1600x1000.png b/...ference/adds_mutation_count_vs_diagnosis_age_chart_element_chrome_1600x1000.png
diff --git a/...hots/reference/applies_log-scale_in_waterfall_plot_element_chrome_1600x1000.png b/...hots/reference/applies_log-scale_in_waterfall_plot_element_chrome_1600x1000.png
diff --git a/...l/screenshots/reference/ascn_columns_are_displayed_element_chrome_1600x1000.png b/...l/screenshots/reference/ascn_columns_are_displayed_element_chrome_1600x1000.png
diff --git a/...screenshots/reference/ascn_columns_are_unavailable_element_chrome_1600x1000.png b/...screenshots/reference/ascn_columns_are_unavailable_element_chrome_1600x1000.png
diff --git a/.../breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png b/.../breadcrumbs_are_editable_for_mutation_count_chart_element_chrome_1600x1000.png
diff --git a/.../local/screenshots/reference/displays_ascn_columns_element_chrome_1600x1000.png b/.../local/screenshots/reference/displays_ascn_columns_element_chrome_1600x1000.png
diff --git a/...display_ascn_columns_for_studies_with_no_ascn_data_element_chrome_1600x1000.png b/...display_ascn_columns_for_studies_with_no_ascn_data_element_chrome_1600x1000.png
diff --git a/...does_not_show_ascn_columns_study_with_no_ascn_data_element_chrome_1600x1000.png b/...does_not_show_ascn_columns_study_with_no_ascn_data_element_chrome_1600x1000.png
diff --git a/...on_genes_for_go_atp_dependent_chromatin_remodeling_element_chrome_1600x1000.png b/...on_genes_for_go_atp_dependent_chromatin_remodeling_element_chrome_1600x1000.png
diff --git a/...lters_mutation_tracks_based_on_gene_filter_setting_element_chrome_1600x1000.png b/...lters_mutation_tracks_based_on_gene_filter_setting_element_chrome_1600x1000.png
diff --git a/...ene_filter_setting_when_switching_to__all_samples__element_chrome_1600x1000.png b/...ene_filter_setting_when_switching_to__all_samples__element_chrome_1600x1000.png
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diff --git a/...ric_assay_chart_should_be_added_in_the_summary_tab_element_chrome_1600x1000.png b/...ric_assay_chart_should_be_added_in_the_summary_tab_element_chrome_1600x1000.png
diff --git a/...assay_pie_chart_should_be_added_in_the_summary_tab_element_chrome_1600x1000.png b/...assay_pie_chart_should_be_added_in_the_summary_tab_element_chrome_1600x1000.png
diff --git a/...group_comparison_alteration_enrichments_two_groups_element_chrome_1600x1000.png b/...group_comparison_alteration_enrichments_two_groups_element_chrome_1600x1000.png
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diff --git a/...ration_enrichments_tab_gene_box_user-defined_genes_element_chrome_1600x1000.png b/...ration_enrichments_tab_gene_box_user-defined_genes_element_chrome_1600x1000.png
diff --git a/...rison_page_alteration_enrichments_tab_patient_mode_element_chrome_1600x1000.png b/...rison_page_alteration_enrichments_tab_patient_mode_element_chrome_1600x1000.png
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diff --git a/...stylings_when_selecting_none_in_gene_selection_box_element_chrome_1600x1000.png b/...stylings_when_selecting_none_in_gene_selection_box_element_chrome_1600x1000.png
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diff --git a/...comparison_tab_alteration_enrichments_patient_mode_element_chrome_1600x1000.png b/...comparison_tab_alteration_enrichments_patient_mode_element_chrome_1600x1000.png
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diff --git a/...ference/results_view_mutation_table_for_ascn_study_element_chrome_1600x1000.png b/...ference/results_view_mutation_table_for_ascn_study_element_chrome_1600x1000.png
diff --git a/...e/results_view_mutation_table_for_mixed_ascn_study_element_chrome_1600x1000.png b/...e/results_view_mutation_table_for_mixed_ascn_study_element_chrome_1600x1000.png
diff --git a/...nce/results_view_mutation_table_for_non-ascn_study_element_chrome_1600x1000.png b/...nce/results_view_mutation_table_for_non-ascn_study_element_chrome_1600x1000.png
diff --git a/...terfall_plot_data_when_`sort_order`_button_pressed_element_chrome_1600x1000.png b/...terfall_plot_data_when_`sort_order`_button_pressed_element_chrome_1600x1000.png
diff --git a/...eference/rotates_waterfall_plot_when_swapping_axes_element_chrome_1600x1000.png b/...eference/rotates_waterfall_plot_when_swapping_axes_element_chrome_1600x1000.png
diff --git a/...shots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png b/...shots/reference/show_binary_vs_mutation_count_plot_element_chrome_1600x1000.png
diff --git a/...creenshots/reference/show_binary_vs_os_status_plot_element_chrome_1600x1000.png b/...creenshots/reference/show_binary_vs_os_status_plot_element_chrome_1600x1000.png
diff --git a/...ots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png b/...ots/reference/show_category_vs_mutation_count_plot_element_chrome_1600x1000.png
diff --git a/...eenshots/reference/show_category_vs_os_status_plot_element_chrome_1600x1000.png b/...eenshots/reference/show_category_vs_os_status_plot_element_chrome_1600x1000.png
diff --git a/...ient_who_has_significant_v2_significant_signatures_element_chrome_1600x1000.png b/...ient_who_has_significant_v2_significant_signatures_element_chrome_1600x1000.png
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diff --git a/...nd_and_indicates_sub-threshold_data_points_in_plot_element_chrome_1600x1000.png b/...nd_and_indicates_sub-threshold_data_points_in_plot_element_chrome_1600x1000.png
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diff --git a/...earch_indicator_when_sample_search_term_is_entered_element_chrome_1600x1000.png b/...earch_indicator_when_sample_search_term_is_entered_element_chrome_1600x1000.png
diff --git a/..._where_some_samples_have_ascn_data_and_some_do_not_element_chrome_1600x1000.png b/..._where_some_samples_have_ascn_data_and_some_do_not_element_chrome_1600x1000.png
diff --git a/...erence/shows_ascn_columns_for_study_with_ascn_data_element_chrome_1600x1000.png b/...erence/shows_ascn_columns_for_study_with_ascn_data_element_chrome_1600x1000.png
diff --git a/...eference/shows_binary_and_multiple_category_tracks_element_chrome_1600x1000.png b/...eference/shows_binary_and_multiple_category_tracks_element_chrome_1600x1000.png
diff --git a/..._cna_types_in_clinical_attribute_vs_treatment_plot_element_chrome_1600x1000.png b/..._cna_types_in_clinical_attribute_vs_treatment_plot_element_chrome_1600x1000.png
diff --git a/..._cna_types_in_clinical_attribute_vs_treatment_plot_element_chrome_1600x1000.png b/..._cna_types_in_clinical_attribute_vs_treatment_plot_element_chrome_1600x1000.png
diff --git a/...panel_icons_behind_mutation_and_cna_genomic_tracks_element_chrome_1600x1000.png b/...panel_icons_behind_mutation_and_cna_genomic_tracks_element_chrome_1600x1000.png
diff --git a/...cal/screenshots/reference/shows_gsva_heatmap_track_element_chrome_1600x1000.png b/...cal/screenshots/reference/shows_gsva_heatmap_track_element_chrome_1600x1000.png
diff --git a/..._gsva_profile_data_on_horizontal_and_vertical_axes_element_chrome_1600x1000.png b/..._gsva_profile_data_on_horizontal_and_vertical_axes_element_chrome_1600x1000.png
diff --git a/...enshots/reference/shows_gsva_scores_in_scatterplot_element_chrome_1600x1000.png b/...enshots/reference/shows_gsva_scores_in_scatterplot_element_chrome_1600x1000.png
diff --git a/...eference/shows_mutation_and_copy_number_by_default_element_chrome_1600x1000.png b/...eference/shows_mutation_and_copy_number_by_default_element_chrome_1600x1000.png
diff --git a/...tion_types_in_clinical_attribute_vs_treatment_plot_element_chrome_1600x1000.png b/...tion_types_in_clinical_attribute_vs_treatment_plot_element_chrome_1600x1000.png
diff --git a/...nly_cna_types_when_mutation_checkbox_is_deselected_element_chrome_1600x1000.png b/...nly_cna_types_when_mutation_checkbox_is_deselected_element_chrome_1600x1000.png
diff --git a/...nly_mutation_types_when_copy_number_is_de-selected_element_chrome_1600x1000.png b/...nly_mutation_types_when_copy_number_is_de-selected_element_chrome_1600x1000.png
diff --git a/...hows_treatment_profile_heatmap_track_for_treatment_element_chrome_1600x1000.png b/...hows_treatment_profile_heatmap_track_for_treatment_element_chrome_1600x1000.png
diff --git a/...ference/shows_volcano_plot_for_gene_sets_selection_element_chrome_1600x1000.png b/...ference/shows_volcano_plot_for_gene_sets_selection_element_chrome_1600x1000.png
diff --git a/...all_plot_when_`ordered_samples`_option_is_selected_element_chrome_1600x1000.png b/...all_plot_when_`ordered_samples`_option_is_selected_element_chrome_1600x1000.png
diff --git a/...creenshots/reference/swaps_axis_from_dropdown_menu_element_chrome_1600x1000.png b/...creenshots/reference/swaps_axis_from_dropdown_menu_element_chrome_1600x1000.png
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diff --git a/...ts/reference/turns_on_log_scale_from_dropdown_menu_element_chrome_1600x1000.png b/...ts/reference/turns_on_log_scale_from_dropdown_menu_element_chrome_1600x1000.png
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diff --git a/...igure_legend_and_sub-threshold_data_points_in_plot_element_chrome_1600x1000.png b/...igure_legend_and_sub-threshold_data_points_in_plot_element_chrome_1600x1000.png
diff --git a/end-to-end-test/local/studies/lgg_ucsf_2014_test_generic_assay/data_mutations_extended.txt b/end-to-end-test/local/studies/lgg_ucsf_2014_test_generic_assay/data_mutations_extended.txt
diff --git a/...local/studies/lgg_ucsf_2014_test_generic_assay/data_mutations_extended.txt.REMOVED.git-id b/...local/studies/lgg_ucsf_2014_test_generic_assay/data_mutations_extended.txt.REMOVED.git-id
diff --git a/end-to-end-test/local/studies/lgg_ucsf_2014_test_generic_assay/data_mutations_mskcc.txt b/end-to-end-test/local/studies/lgg_ucsf_2014_test_generic_assay/data_mutations_mskcc.txt
diff --git a/...st/local/studies/lgg_ucsf_2014_test_generic_assay/data_mutations_mskcc.txt.REMOVED.git-id b/...st/local/studies/lgg_ucsf_2014_test_generic_assay/data_mutations_mskcc.txt.REMOVED.git-id
diff --git a/...e_filterattributeid_is_not_available_for_the_study_element_chrome_1600x1000.png b/...e_filterattributeid_is_not_available_for_the_study_element_chrome_1600x1000.png
diff --git a/...reference/a_new_chart_should_be_added_and_filtered_element_chrome_1600x1000.png b/...reference/a_new_chart_should_be_added_and_filtered_element_chrome_1600x1000.png
diff --git a/...eference/acc_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png b/...eference/acc_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png
diff --git a/...ference/blca_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png b/...ference/blca_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png
diff --git a/...with_kras_nras_braf_and_methylation_heatmap_tracks_element_chrome_1600x1000.png b/...with_kras_nras_braf_and_methylation_heatmap_tracks_element_chrome_1600x1000.png
diff --git a/...reference/can_filter_a_study_by_patient_treatments_element_chrome_1600x1000.png b/...reference/can_filter_a_study_by_patient_treatments_element_chrome_1600x1000.png
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diff --git a/...coadread_tcga_pub_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png b/...coadread_tcga_pub_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png
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diff --git a/...ad_tcga_pub_log_scale_x_and_y_with_regression_line_element_chrome_1600x1000.png b/...ad_tcga_pub_log_scale_x_and_y_with_regression_line_element_chrome_1600x1000.png
diff --git a/...oadread_tcga_pub_switch_profiles_+_regression_line_element_chrome_1600x1000.png b/...oadread_tcga_pub_switch_profiles_+_regression_line_element_chrome_1600x1000.png
diff --git a/...coexpression_tab_coadread_tcga_pub_switch_profiles_element_chrome_1600x1000.png b/...coexpression_tab_coadread_tcga_pub_switch_profiles_element_chrome_1600x1000.png
diff --git a/...nce/coexpression_tab_coadread_tcga_pub_switch_tabs_element_chrome_1600x1000.png b/...nce/coexpression_tab_coadread_tcga_pub_switch_tabs_element_chrome_1600x1000.png
diff --git a/...pression_tab_coadread_tcga_pub_with_a_lot_of_genes_element_chrome_1600x1000.png b/...pression_tab_coadread_tcga_pub_with_a_lot_of_genes_element_chrome_1600x1000.png
diff --git a/..._tab_coadread_tcga_pub_with_user_defined_case_list_element_chrome_1600x1000.png b/..._tab_coadread_tcga_pub_with_user_defined_case_list_element_chrome_1600x1000.png
diff --git a/...est/remote/screenshots/reference/data_download_tab_element_chrome_1600x1000.png b/...est/remote/screenshots/reference/data_download_tab_element_chrome_1600x1000.png
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diff --git a/...sclc_tcga_broad_2016_for_query_egfr:_mut=t790m_amp_element_chrome_1600x1000.png b/...sclc_tcga_broad_2016_for_query_egfr:_mut=t790m_amp_element_chrome_1600x1000.png
diff --git a/...d_2016_with_cdkn2a_mdm2_and_merged_track_mdm4_tp53_element_chrome_1600x1000.png b/...d_2016_with_cdkn2a_mdm2_and_merged_track_mdm4_tp53_element_chrome_1600x1000.png
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diff --git a/...nce/enrichments_tab_coadread_tcga_pub_mrna_profile_element_chrome_1600x1000.png b/...nce/enrichments_tab_coadread_tcga_pub_mrna_profile_element_chrome_1600x1000.png
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diff --git a/...eference/excluding_unprofiled_samples_survival_tab_element_chrome_1600x1000.png b/...eference/excluding_unprofiled_samples_survival_tab_element_chrome_1600x1000.png
diff --git a/...eenshots/reference/expression_tab_with_complex_oql_element_chrome_1600x1000.png b/...eenshots/reference/expression_tab_with_complex_oql_element_chrome_1600x1000.png
diff --git a/...remote/screenshots/reference/filter_study_from_url_element_chrome_1600x1000.png b/...remote/screenshots/reference/filter_study_from_url_element_chrome_1600x1000.png
diff --git a/...eference/filter_study_from_url_using_simple_filter_element_chrome_1600x1000.png b/...eference/filter_study_from_url_using_simple_filter_element_chrome_1600x1000.png
diff --git a/...hots/reference/fusion_filter_filter_study_from_url_element_chrome_1600x1000.png b/...hots/reference/fusion_filter_filter_study_from_url_element_chrome_1600x1000.png
diff --git a/...ric_assay_chart_should_be_added_in_the_summary_tab_element_chrome_1600x1000.png b/...ric_assay_chart_should_be_added_in_the_summary_tab_element_chrome_1600x1000.png
diff --git a/...emote/screenshots/reference/group_by_detailed_type_element_chrome_1600x1000.png b/...emote/screenshots/reference/group_by_detailed_type_element_chrome_1600x1000.png
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diff --git a/...rison_page_clinical_tab_bar_chart_chi_squared_test_element_chrome_1600x1000.png b/...rison_page_clinical_tab_bar_chart_chi_squared_test_element_chrome_1600x1000.png
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diff --git a/...chart_exclude_overlapping_samples_chi_squared_test_element_chrome_1600x1000.png b/...chart_exclude_overlapping_samples_chi_squared_test_element_chrome_1600x1000.png
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diff --git a/...stacked_bar_chart_horizontal_bars_chi_squared_test_element_chrome_1600x1000.png b/...stacked_bar_chart_horizontal_bars_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...tab_stacked_bar_chart_swaped_axes_chi_squared_test_element_chrome_1600x1000.png b/...tab_stacked_bar_chart_swaped_axes_chi_squared_test_element_chrome_1600x1000.png
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diff --git a/...p_comparison_page_cna_enrichments_tab_patient_mode_element_chrome_1600x1000.png b/...p_comparison_page_cna_enrichments_tab_patient_mode_element_chrome_1600x1000.png
diff --git a/...comparison_page_cna_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...comparison_page_cna_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...oup_comparison_page_cna_enrichments_tab_two_groups_element_chrome_1600x1000.png b/...oup_comparison_page_cna_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...ce/group_comparison_page_delete_group_from_session_element_chrome_1600x1000.png b/...ce/group_comparison_page_delete_group_from_session_element_chrome_1600x1000.png
diff --git a/...on_page_methylation_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...on_page_methylation_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...arison_page_methylation_enrichments_tab_two_groups_element_chrome_1600x1000.png b/...arison_page_methylation_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...rison_page_microbiome_signature_tab_several_groups_element_chrome_1600x1000.png b/...rison_page_microbiome_signature_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...omparison_page_microbiome_signature_tab_two_groups_element_chrome_1600x1000.png b/...omparison_page_microbiome_signature_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...omparison_page_mrna_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...omparison_page_mrna_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...up_comparison_page_mrna_enrichments_tab_two_groups_element_chrome_1600x1000.png b/...up_comparison_page_mrna_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...s_tab_20_genes_with_highest_frequency_in_any_group_element_chrome_1600x1000.png b/...s_tab_20_genes_with_highest_frequency_in_any_group_element_chrome_1600x1000.png
diff --git a/...enrichments_tab_gene_box_highest_average_frequency_element_chrome_1600x1000.png b/...enrichments_tab_gene_box_highest_average_frequency_element_chrome_1600x1000.png
diff --git a/..._enrichments_tab_gene_box_most_significant_pvalues_element_chrome_1600x1000.png b/..._enrichments_tab_gene_box_most_significant_pvalues_element_chrome_1600x1000.png
diff --git a/...tation_enrichments_tab_gene_box_user-defined_genes_element_chrome_1600x1000.png b/...tation_enrichments_tab_gene_box_user-defined_genes_element_chrome_1600x1000.png
diff --git a/...parison_page_mutation_enrichments_tab_patient_mode_element_chrome_1600x1000.png b/...parison_page_mutation_enrichments_tab_patient_mode_element_chrome_1600x1000.png
diff --git a/...rison_page_mutation_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...rison_page_mutation_enrichments_tab_several_groups_element_chrome_1600x1000.png
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diff --git a/...omparison_page_overlap_tab_3_disjoint_venn_diagram_element_chrome_1600x1000.png b/...omparison_page_overlap_tab_3_disjoint_venn_diagram_element_chrome_1600x1000.png
diff --git a/...arison_page_overlap_tab_disjoint_venn_diagram_view_element_chrome_1600x1000.png b/...arison_page_overlap_tab_disjoint_venn_diagram_view_element_chrome_1600x1000.png
diff --git a/...joint_venn_diagram_view_with_a_group_selected_view_element_chrome_1600x1000.png b/...joint_venn_diagram_view_with_a_group_selected_view_element_chrome_1600x1000.png
diff --git a/...rison_page_overlap_tab_upset_deselect_active_group_element_chrome_1600x1000.png b/...rison_page_overlap_tab_upset_deselect_active_group_element_chrome_1600x1000.png
diff --git a/..._comparison_page_overlap_tab_upset_groups_selected_element_chrome_1600x1000.png b/..._comparison_page_overlap_tab_upset_groups_selected_element_chrome_1600x1000.png
diff --git a/.../group_comparison_page_overlap_tab_upset_plot_view_element_chrome_1600x1000.png b/.../group_comparison_page_overlap_tab_upset_plot_view_element_chrome_1600x1000.png
diff --git a/...iagram_view_with_overlap_and_session_selected_view_element_chrome_1600x1000.png b/...iagram_view_with_overlap_and_session_selected_view_element_chrome_1600x1000.png
diff --git a/...nn_diagram_view_with_overlap_deselect_active_group_element_chrome_1600x1000.png b/...nn_diagram_view_with_overlap_deselect_active_group_element_chrome_1600x1000.png
diff --git a/...on_page_overlap_tab_venn_diagram_with_overlap_view_element_chrome_1600x1000.png b/...on_page_overlap_tab_venn_diagram_with_overlap_view_element_chrome_1600x1000.png
diff --git a/...arison_page_protein_enrichments_tab_several_groups_element_chrome_1600x1000.png b/...arison_page_protein_enrichments_tab_several_groups_element_chrome_1600x1000.png
diff --git a/...comparison_page_protein_enrichments_tab_two_groups_element_chrome_1600x1000.png b/...comparison_page_protein_enrichments_tab_two_groups_element_chrome_1600x1000.png
diff --git a/...ison_page_survival_tab_exclude_overlapping_samples_element_chrome_1600x1000.png b/...ison_page_survival_tab_exclude_overlapping_samples_element_chrome_1600x1000.png
diff --git a/...ison_page_survival_tab_include_overlapping_samples_element_chrome_1600x1000.png b/...ison_page_survival_tab_include_overlapping_samples_element_chrome_1600x1000.png
diff --git a/...s/reference/handles_change_to_absolute_value_yaxis_element_chrome_1600x1000.png b/...s/reference/handles_change_to_absolute_value_yaxis_element_chrome_1600x1000.png
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diff --git a/...reference/handles_change_to_sample_total_threshold_element_chrome_1600x1000.png b/...reference/handles_change_to_sample_total_threshold_element_chrome_1600x1000.png
diff --git a/...eenshots/reference/handles_change_to_sort_of_xaxis_element_chrome_1600x1000.png b/...eenshots/reference/handles_change_to_sort_of_xaxis_element_chrome_1600x1000.png
diff --git a/...-_it_should_show_orange_promoter_mutations_in_tert_element_chrome_1600x1000.png b/...-_it_should_show_orange_promoter_mutations_in_tert_element_chrome_1600x1000.png
diff --git a/...-end-test/remote/screenshots/reference/igv_tab_tab_element_chrome_1600x1000.png b/...-end-test/remote/screenshots/reference/igv_tab_tab_element_chrome_1600x1000.png
diff --git a/...remote/screenshots/reference/loads_a_virtual_study_element_chrome_1600x1000.png b/...remote/screenshots/reference/loads_a_virtual_study_element_chrome_1600x1000.png
diff --git a/...ence/loads_multiple_studies_with_treatments_tables_element_chrome_1600x1000.png b/...ence/loads_multiple_studies_with_treatments_tables_element_chrome_1600x1000.png
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diff --git a/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png b/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png
diff --git a/...pact_2017_with_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png b/...pact_2017_with_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png
diff --git a/...h_sos1_with_cna_profile_-_sos1_should_be_sequenced_element_chrome_1600x1000.png b/...h_sos1_with_cna_profile_-_sos1_should_be_sequenced_element_chrome_1600x1000.png
diff --git a/...s1_with_cna_profile_-_sos1_should_not_be_sequenced_element_chrome_1600x1000.png b/...s1_with_cna_profile_-_sos1_should_not_be_sequenced_element_chrome_1600x1000.png
diff --git a/.../reference/multi-study_copy-number_enrichments_tab_element_chrome_1600x1000.png b/.../reference/multi-study_copy-number_enrichments_tab_element_chrome_1600x1000.png
diff --git a/...ots/reference/multi-study_mutation_enrichments_tab_element_chrome_1600x1000.png b/...ots/reference/multi-study_mutation_enrichments_tab_element_chrome_1600x1000.png
diff --git a/...reenshots/reference/multiple_tracks_with_same_gene_element_chrome_1600x1000.png b/...reenshots/reference/multiple_tracks_with_same_gene_element_chrome_1600x1000.png
diff --git a/...reenshots/reference/no_session_cancer_type_summary_element_chrome_1600x1000.png b/...reenshots/reference/no_session_cancer_type_summary_element_chrome_1600x1000.png
diff --git a/.../screenshots/reference/no_session_coexpression_tab_element_chrome_1600x1000.png b/.../screenshots/reference/no_session_coexpression_tab_element_chrome_1600x1000.png
diff --git a/...comparison_tab_alteration_enrichments_patient_mode_element_chrome_1600x1000.png b/...comparison_tab_alteration_enrichments_patient_mode_element_chrome_1600x1000.png
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diff --git a/...shots/reference/no_session_comparison_tab_clinical_element_chrome_1600x1000.png b/...shots/reference/no_session_comparison_tab_clinical_element_chrome_1600x1000.png
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diff --git a/...mote/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png b/...mote/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png
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diff --git a/...ference/oncoprint_loads_and_expands_a_merged_track_element_chrome_1600x1000.png b/...ference/oncoprint_loads_and_expands_a_merged_track_element_chrome_1600x1000.png
diff --git a/...e/oncoprint_should_cluster_heatmap_group_correctly_element_chrome_1600x1000.png b/...e/oncoprint_should_cluster_heatmap_group_correctly_element_chrome_1600x1000.png
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diff --git a/...int_should_return_to_non-clustered_state_correctly_element_chrome_1600x1000.png b/...int_should_return_to_non-clustered_state_correctly_element_chrome_1600x1000.png
diff --git a/...hould_sort_patients_correctly_in_coadread_tcga_pub_element_chrome_1600x1000.png b/...hould_sort_patients_correctly_in_coadread_tcga_pub_element_chrome_1600x1000.png
diff --git a/...int_should_sort_patients_correctly_in_gbm_tcga_pub_element_chrome_1600x1000.png b/...int_should_sort_patients_correctly_in_gbm_tcga_pub_element_chrome_1600x1000.png
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diff --git a/...s/reference/oncoprinter_clinical_only_example_data_element_chrome_1600x1000.png b/...s/reference/oncoprinter_clinical_only_example_data_element_chrome_1600x1000.png
diff --git a/...ence/oncoprinter_example_data,_annotated_by_oncokb_element_chrome_1600x1000.png b/...ence/oncoprinter_example_data,_annotated_by_oncokb_element_chrome_1600x1000.png
diff --git a/...oprinter_example_data,_dont_color_by_driver_vs_vus_element_chrome_1600x1000.png b/...oprinter_example_data,_dont_color_by_driver_vs_vus_element_chrome_1600x1000.png
diff --git a/...oprinter_example_data,_dont_color_by_mutation_type_element_chrome_1600x1000.png b/...oprinter_example_data,_dont_color_by_mutation_type_element_chrome_1600x1000.png
diff --git a/...shots/reference/oncoprinter_example_data,_hide_vus_element_chrome_1600x1000.png b/...shots/reference/oncoprinter_example_data,_hide_vus_element_chrome_1600x1000.png
diff --git a/...ta,_start_by_set_gene_order,_then_set_sample_order_element_chrome_1600x1000.png b/...ta,_start_by_set_gene_order,_then_set_sample_order_element_chrome_1600x1000.png
diff --git a/...ta,_start_by_set_sample_order,_then_set_gene_order_element_chrome_1600x1000.png b/...ta,_start_by_set_sample_order,_then_set_gene_order_element_chrome_1600x1000.png
diff --git a/...ple_data,_then_set_gene_order,_including_all_genes_element_chrome_1600x1000.png b/...ple_data,_then_set_gene_order,_including_all_genes_element_chrome_1600x1000.png
diff --git a/...data,_then_set_gene_order,_not_including_all_genes_element_chrome_1600x1000.png b/...data,_then_set_gene_order,_not_including_all_genes_element_chrome_1600x1000.png
diff --git a/...data,_then_set_sample_order,_including_all_samples_element_chrome_1600x1000.png b/...data,_then_set_sample_order,_including_all_samples_element_chrome_1600x1000.png
diff --git a/...,_then_set_sample_order,_not_including_all_samples_element_chrome_1600x1000.png b/...,_then_set_sample_order,_not_including_all_samples_element_chrome_1600x1000.png
diff --git a/...ote/screenshots/reference/oncoprinter_example_data_element_chrome_1600x1000.png b/...ote/screenshots/reference/oncoprinter_example_data_element_chrome_1600x1000.png
diff --git a/...ts/reference/oncoprinter_genetic_only_example_data_element_chrome_1600x1000.png b/...ts/reference/oncoprinter_genetic_only_example_data_element_chrome_1600x1000.png
diff --git a/...ts/reference/oncoprinter_heatmap_only_example_data_element_chrome_1600x1000.png b/...ts/reference/oncoprinter_heatmap_only_example_data_element_chrome_1600x1000.png
diff --git a/...hots/reference/ov_tcga_pub_with_germline_mutations_element_chrome_1600x1000.png b/...hots/reference/ov_tcga_pub_with_germline_mutations_element_chrome_1600x1000.png
diff --git a/...iew_-_gene_is_cancer_gene_but_has_not_been_curated_element_chrome_1600x1000.png b/...iew_-_gene_is_cancer_gene_but_has_not_been_curated_element_chrome_1600x1000.png
diff --git a/..._with_levels_-_mutation_effect_tab_shows_correctly_element_chrome_1600x1000.png b/..._with_levels_-_mutation_effect_tab_shows_correctly_element_chrome_1600x1000.png
diff --git a/...w_-_with_levels_-_oncogenicity_tab_shows_correctly_element_chrome_1600x1000.png b/...w_-_with_levels_-_oncogenicity_tab_shows_correctly_element_chrome_1600x1000.png
diff --git a/...thout_levels_-_mutation_effect_tab_shows_correctly_element_chrome_1600x1000.png b/...thout_levels_-_mutation_effect_tab_shows_correctly_element_chrome_1600x1000.png
diff --git a/..._without_levels_-_oncogenicity_tab_shows_correctly_element_chrome_1600x1000.png b/..._without_levels_-_oncogenicity_tab_shows_correctly_element_chrome_1600x1000.png
diff --git a/...reenshots/reference/patient_view_lgg_ucsf_2014_p04_element_chrome_1600x1000.png b/...reenshots/reference/patient_view_lgg_ucsf_2014_p04_element_chrome_1600x1000.png
diff --git a/...iew_pathways_tab_msk_impact_2017_p-0000377-t03-im3_element_chrome_1600x1000.png b/...iew_pathways_tab_msk_impact_2017_p-0000377-t03-im3_element_chrome_1600x1000.png
diff --git a/...atient_view_pathways_tab_msk_impact_2017_p-0000377_element_chrome_1600x1000.png b/...atient_view_pathways_tab_msk_impact_2017_p-0000377_element_chrome_1600x1000.png
diff --git a/...with_0_mutations_msk_impact_2017_p-0000053-t01-im3_element_chrome_1600x1000.png b/...with_0_mutations_msk_impact_2017_p-0000053-t01-im3_element_chrome_1600x1000.png
diff --git a/...ference/plots_tab_box_plot_color_by_mutation_count_element_chrome_1600x1000.png b/...ference/plots_tab_box_plot_color_by_mutation_count_element_chrome_1600x1000.png
diff --git a/...ots_tab_box_plot_color_by_mutation_count_log_scale_element_chrome_1600x1000.png b/...ots_tab_box_plot_color_by_mutation_count_log_scale_element_chrome_1600x1000.png
diff --git a/...s/reference/plots_tab_box_plot_color_by_tumor_type_element_chrome_1600x1000.png b/...s/reference/plots_tab_box_plot_color_by_tumor_type_element_chrome_1600x1000.png
diff --git a/..._box_plot_color_by_tumor_type_highlight_categories_element_chrome_1600x1000.png b/..._box_plot_color_by_tumor_type_highlight_categories_element_chrome_1600x1000.png
diff --git a/...s/reference/plots_tab_clinical_vs_clinical_boxplot_element_chrome_1600x1000.png b/...s/reference/plots_tab_clinical_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...b_clinical_vs_clinical_horizontal_grouped_bar_plot_element_chrome_1600x1000.png b/...b_clinical_vs_clinical_horizontal_grouped_bar_plot_element_chrome_1600x1000.png
diff --git a/...vs_clinical_horizontal_percentage_stacked_bar_plot_element_chrome_1600x1000.png b/...vs_clinical_horizontal_percentage_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/...b_clinical_vs_clinical_horizontal_stacked_bar_plot_element_chrome_1600x1000.png b/...b_clinical_vs_clinical_horizontal_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/...b_clinical_vs_clinical_percentage_stacked_bar_plot_element_chrome_1600x1000.png b/...b_clinical_vs_clinical_percentage_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/...ce/plots_tab_clinical_vs_clinical_stacked_bar_plot_element_chrome_1600x1000.png b/...ce/plots_tab_clinical_vs_clinical_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/...eference/plots_tab_clinical_vs_clinical_table_plot_element_chrome_1600x1000.png b/...eference/plots_tab_clinical_vs_clinical_table_plot_element_chrome_1600x1000.png
diff --git a/.../reference/plots_tab_clinical_vs_molecular_boxplot_element_chrome_1600x1000.png b/.../reference/plots_tab_clinical_vs_molecular_boxplot_element_chrome_1600x1000.png
diff --git a/...eenshots/reference/plots_tab_clinical_vs_molecular_element_chrome_1600x1000.png b/...eenshots/reference/plots_tab_clinical_vs_molecular_element_chrome_1600x1000.png
diff --git a/...e/screenshots/reference/plots_tab_copy_number_view_element_chrome_1600x1000.png b/...e/screenshots/reference/plots_tab_copy_number_view_element_chrome_1600x1000.png
diff --git a/...vs_clinical_horizontal_percentage_stacked_bar_plot_element_chrome_1600x1000.png b/...vs_clinical_horizontal_percentage_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/...opy_number_vs_clinical_horizontal_stacked_bar_plot_element_chrome_1600x1000.png b/...opy_number_vs_clinical_horizontal_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/...opy_number_vs_clinical_percentage_stacked_bar_plot_element_chrome_1600x1000.png b/...opy_number_vs_clinical_percentage_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/...plots_tab_copy_number_vs_clinical_stacked_bar_plot_element_chrome_1600x1000.png b/...plots_tab_copy_number_vs_clinical_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/...rence/plots_tab_copy_number_vs_clinical_table_plot_element_chrome_1600x1000.png b/...rence/plots_tab_copy_number_vs_clinical_table_plot_element_chrome_1600x1000.png
diff --git a/...mote/screenshots/reference/plots_tab_log_scale_off_element_chrome_1600x1000.png b/...mote/screenshots/reference/plots_tab_log_scale_off_element_chrome_1600x1000.png
diff --git a/...molecular_vs_clinical_boxplot,_mutation_search_off_element_chrome_1600x1000.png b/...molecular_vs_clinical_boxplot,_mutation_search_off_element_chrome_1600x1000.png
diff --git a/...ar_vs_molecular_different_genes_different_profiles_element_chrome_1600x1000.png b/...ar_vs_molecular_different_genes_different_profiles_element_chrome_1600x1000.png
diff --git a/...e/plots_tab_molecular_vs_molecular_different_genes_element_chrome_1600x1000.png b/...e/plots_tab_molecular_vs_molecular_different_genes_element_chrome_1600x1000.png
diff --git a/..._tab_molecular_vs_molecular_same_gene_changed_gene_element_chrome_1600x1000.png b/..._tab_molecular_vs_molecular_same_gene_changed_gene_element_chrome_1600x1000.png
diff --git a/...ference/plots_tab_molecular_vs_molecular_same_gene_element_chrome_1600x1000.png b/...ference/plots_tab_molecular_vs_molecular_same_gene_element_chrome_1600x1000.png
diff --git a/...ence/plots_tab_molecular_vs_molecular_swapped_axes_element_chrome_1600x1000.png b/...ence/plots_tab_molecular_vs_molecular_swapped_axes_element_chrome_1600x1000.png
diff --git a/..._tab_multiple_studies_with_data_availability_alert_element_chrome_1600x1000.png b/..._tab_multiple_studies_with_data_availability_alert_element_chrome_1600x1000.png
diff --git a/...rence/plots_tab_mutation_type_and_copy_number_view_element_chrome_1600x1000.png b/...rence/plots_tab_mutation_type_and_copy_number_view_element_chrome_1600x1000.png
diff --git a/...screenshots/reference/plots_tab_mutation_type_view_element_chrome_1600x1000.png b/...screenshots/reference/plots_tab_mutation_type_view_element_chrome_1600x1000.png
diff --git a/...lots_tab_mutations_driver_mode_vs_clinical_boxplot_element_chrome_1600x1000.png b/...lots_tab_mutations_driver_mode_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...erence/plots_tab_mutations_profile_with_duplicates_element_chrome_1600x1000.png b/...erence/plots_tab_mutations_profile_with_duplicates_element_chrome_1600x1000.png
diff --git a/.../reference/plots_tab_mutations_vs_clinical_boxplot_element_chrome_1600x1000.png b/.../reference/plots_tab_mutations_vs_clinical_boxplot_element_chrome_1600x1000.png
diff --git a/...vs_clinical_horizontal_percentage_stacked_bar_plot_element_chrome_1600x1000.png b/...vs_clinical_horizontal_percentage_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/..._mutations_vs_clinical_horizontal_stacked_bar_plot_element_chrome_1600x1000.png b/..._mutations_vs_clinical_horizontal_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/..._mutations_vs_clinical_percentage_stacked_bar_plot_element_chrome_1600x1000.png b/..._mutations_vs_clinical_percentage_stacked_bar_plot_element_chrome_1600x1000.png
diff --git a/...e/plots_tab_mutations_vs_clinical_stacked_bar_plot_element_chrome_1600x1000.png b/...e/plots_tab_mutations_vs_clinical_stacked_bar_plot_element_chrome_1600x1000.png