--- a/remove_files.txt	Fri Nov 05 13:41:03 2021 +0000
+++ b/remove_files.txt	Tue Jan 25 11:28:29 2022 +0000
@@ -1,171 +1,160 @@
-results/aa_histogram.txt
-results/aa_histogram_absent.txt
-results/aa_histogram_absent_IGA.txt
-results/aa_histogram_absent_IGG.txt
-results/aa_histogram_absent_IGM.txt
-results/aa_histogram_count.txt
-results/aa_histogram_count_IGA.txt
-results/aa_histogram_count_IGG.txt
-results/aa_histogram_count_IGM.txt
-results/aa_histogram_IGA.txt
-results/aa_histogram_IGG.txt
-results/aa_histogram_IGM.txt
-results/after_unique_filter.txt
-results/all_mean_n.txt
-results/all_mean_value.txt
-results/all_median_n.txt
-results/all_median_value.txt
-results/all_sum_n.txt
-results/all_sum_value.txt
-results/before_filters.txt
-results/before_unique_filter.txt
-results/data_sum.txt
-results/filtering_steps.txt
-results/hotspot_analysis_mean.txt
-results/hotspot_analysis_median.txt
-results/hotspot_analysis_sum.txt
-results/identified_genes.txt
-results/IGA1_mean_n.txt
-results/IGA1_mean_value.txt
-results/IGA1_median_n.txt
-results/IGA1_median_value.txt
-results/IGA1_sum_n.txt
-results/IGA1_sum_value.txt
-results/IGA2_mean_n.txt
-results/IGA2_mean_value.txt
-results/IGA2_median_n.txt
-results/IGA2_median_value.txt
-results/IGA2_sum_n.txt
-results/IGA2_sum_value.txt
-results/IGA_mean_n.txt
-results/IGA_mean_value.txt
-results/IGA_median_n.txt
-results/IGA_median_value.txt
-results/IGA_sum_n.txt
-results/IGA_sum_value.txt
-results/IGE_mean_n.txt
-results/IGE_mean_value.txt
-results/IGE_median_n.txt
-results/IGE_median_value.txt
-results/IGE_sum_n.txt
-results/IGE_sum_value.txt
-results/IGG1_mean_n.txt
-results/IGG1_mean_value.txt
-results/IGG1_median_n.txt
-results/IGG1_median_value.txt
-results/IGG1_sum_n.txt
-results/IGG1_sum_value.txt
-results/IGG2_mean_n.txt
-results/IGG2_mean_value.txt
-results/IGG2_median_n.txt
-results/IGG2_median_value.txt
-results/IGG2_sum_n.txt
-results/IGG2_sum_value.txt
-results/IGG3_mean_n.txt
-results/IGG3_mean_value.txt
-results/IGG3_median_n.txt
-results/IGG3_median_value.txt
-results/IGG3_sum_n.txt
-results/IGG3_sum_value.txt
-results/IGG4_mean_n.txt
-results/IGG4_mean_value.txt
-results/IGG4_median_n.txt
-results/IGG4_median_value.txt
-results/IGG4_sum_n.txt
-results/IGG4_sum_value.txt
-results/IGG_mean_n.txt
-results/IGG_mean_value.txt
-results/IGG_median_n.txt
-results/IGG_median_value.txt
-results/IGG_sum_n.txt
-results/IGG_sum_value.txt
-results/IGM_mean_n.txt
-results/IGM_mean_value.txt
-results/IGM_median_n.txt
-results/IGM_median_value.txt
-results/IGM_sum_n.txt
-results/IGM_sum_value.txt
-results/matched_all_mean.txt
-results/matched_all_median.txt
-results/matched_IGA1_mean.txt
-results/matched_IGA1_median.txt
-results/matched_IGA2_mean.txt
-results/matched_IGA2_median.txt
-results/matched_IGA_mean.txt
-results/matched_IGA_median.txt
-results/matched_IGE_mean.txt
-results/matched_IGE_median.txt
-results/matched_IGG1_mean.txt
-results/matched_IGG1_median.txt
-results/matched_IGG2_mean.txt
-results/matched_IGG2_median.txt
-results/matched_IGG3_mean.txt
-results/matched_IGG3_median.txt
-results/matched_IGG4_mean.txt
-results/matched_IGG4_median.txt
-results/matched_IGG_mean.txt
-results/matched_IGG_median.txt
-results/matched_IGM_mean.txt
-results/matched_IGM_median.txt
-results/matched_unmatched_mean.txt
-results/matched_unmatched_median.txt
-results/matched_unmatched_sum.txt
-results/mutationdict.txt
-results/mutation_in_motifs.txt
-results/mutations_mean.txt
-results/mutations_median.txt
-results/mutations_sum.txt
-results/RGYW.txt
-results/shm_overview_tandem_row.txt
-results/tandem_frequency.txt
-results/transitions_all_mean.txt
-results/transitions_all_median.txt
-results/transitions_IGA1_mean.txt
-results/transitions_IGA1_median.txt
-results/transitions_IGA2_mean.txt
-results/transitions_IGA2_median.txt
-results/transitions_IGA_mean.txt
-results/transitions_IGA_median.txt
-results/transitions_IGE_mean.txt
-results/transitions_IGE_median.txt
-results/transitions_IGG1_mean.txt
-results/transitions_IGG1_median.txt
-results/transitions_IGG2_mean.txt
-results/transitions_IGG2_median.txt
-results/transitions_IGG3_mean.txt
-results/transitions_IGG3_median.txt
-results/transitions_IGG4_mean.txt
-results/transitions_IGG4_median.txt
-results/transitions_IGG_mean.txt
-results/transitions_IGG_median.txt
-results/transitions_IGM_mean.txt
-results/transitions_IGM_median.txt
-results/transitions_unmatched_mean.txt
-results/transitions_unmatched_median.txt
-results/transitions_unmatched_sum.txt
-results/unmatched_mean_n.txt
-results/unmatched_mean_value.txt
-results/unmatched_median_n.txt
-results/unmatched_median_value.txt
-results/unmatched_sum_n.txt
-results/unmatched_sum_value.txt
-results/change_o/change-o-db.txt
-results/change_o/change-o-db-defined_first_clones.txt
-results/change_o/change-o-db-defined_first_clones-IGA.txt
-results/change_o/change-o-db-defined_first_clones-IGG.txt
-results/change_o/change-o-db-defined_first_clones-IGM.txt
-results/change_o/change-o-db-IGA.txt
-results/change_o/change-o-db-IGG.txt
-results/change_o/change-o-db-IGM.txt
-results/change_o/input.tab
-aa.txt
-aa_change_stats.txt
-gapped_aa.txt
-gapped_nt.txt
-hotspots.txt
-junction.txt
-mutationanalysis.txt
-mutationstats.txt
-sequences.txt
-summary.txt
-Rplots.pdf
+aa_histogram.txt
+aa_histogram_absent.txt
+aa_histogram_absent_IGA.txt
+aa_histogram_absent_IGG.txt
+aa_histogram_absent_IGM.txt
+aa_histogram_count.txt
+aa_histogram_count_IGA.txt
+aa_histogram_count_IGG.txt
+aa_histogram_count_IGM.txt
+aa_histogram_IGA.txt
+aa_histogram_IGG.txt
+aa_histogram_IGM.txt
+after_unique_filter.txt
+all_mean_n.txt
+all_mean_value.txt
+all_median_n.txt
+all_median_value.txt
+all_sum_n.txt
+all_sum_value.txt
+before_filters.txt
+before_unique_filter.txt
+data_sum.txt
+filtering_steps.txt
+hotspot_analysis_mean.txt
+hotspot_analysis_median.txt
+hotspot_analysis_sum.txt
+identified_genes.txt
+IGA1_mean_n.txt
+IGA1_mean_value.txt
+IGA1_median_n.txt
+IGA1_median_value.txt
+IGA1_sum_n.txt
+IGA1_sum_value.txt
+IGA2_mean_n.txt
+IGA2_mean_value.txt
+IGA2_median_n.txt
+IGA2_median_value.txt
+IGA2_sum_n.txt
+IGA2_sum_value.txt
+IGA_mean_n.txt
+IGA_mean_value.txt
+IGA_median_n.txt
+IGA_median_value.txt
+IGA_sum_n.txt
+IGA_sum_value.txt
+IGE_mean_n.txt
+IGE_mean_value.txt
+IGE_median_n.txt
+IGE_median_value.txt
+IGE_sum_n.txt
+IGE_sum_value.txt
+IGG1_mean_n.txt
+IGG1_mean_value.txt
+IGG1_median_n.txt
+IGG1_median_value.txt
+IGG1_sum_n.txt
+IGG1_sum_value.txt
+IGG2_mean_n.txt
+IGG2_mean_value.txt
+IGG2_median_n.txt
+IGG2_median_value.txt
+IGG2_sum_n.txt
+IGG2_sum_value.txt
+IGG3_mean_n.txt
+IGG3_mean_value.txt
+IGG3_median_n.txt
+IGG3_median_value.txt
+IGG3_sum_n.txt
+IGG3_sum_value.txt
+IGG4_mean_n.txt
+IGG4_mean_value.txt
+IGG4_median_n.txt
+IGG4_median_value.txt
+IGG4_sum_n.txt
+IGG4_sum_value.txt
+IGG_mean_n.txt
+IGG_mean_value.txt
+IGG_median_n.txt
+IGG_median_value.txt
+IGG_sum_n.txt
+IGG_sum_value.txt
+IGM_mean_n.txt
+IGM_mean_value.txt
+IGM_median_n.txt
+IGM_median_value.txt
+IGM_sum_n.txt
+IGM_sum_value.txt
+matched_all_mean.txt
+matched_all_median.txt
+matched_IGA1_mean.txt
+matched_IGA1_median.txt
+matched_IGA2_mean.txt
+matched_IGA2_median.txt
+matched_IGA_mean.txt
+matched_IGA_median.txt
+matched_IGE_mean.txt
+matched_IGE_median.txt
+matched_IGG1_mean.txt
+matched_IGG1_median.txt
+matched_IGG2_mean.txt
+matched_IGG2_median.txt
+matched_IGG3_mean.txt
+matched_IGG3_median.txt
+matched_IGG4_mean.txt
+matched_IGG4_median.txt
+matched_IGG_mean.txt
+matched_IGG_median.txt
+matched_IGM_mean.txt
+matched_IGM_median.txt
+matched_unmatched_mean.txt
+matched_unmatched_median.txt
+matched_unmatched_sum.txt
+mutationdict.txt
+mutation_in_motifs.txt
+mutations_mean.txt
+mutations_median.txt
+mutations_sum.txt
+RGYW.txt
+shm_overview_tandem_row.txt
+tandem_frequency.txt
+transitions_all_mean.txt
+transitions_all_median.txt
+transitions_IGA1_mean.txt
+transitions_IGA1_median.txt
+transitions_IGA2_mean.txt
+transitions_IGA2_median.txt
+transitions_IGA_mean.txt
+transitions_IGA_median.txt
+transitions_IGE_mean.txt
+transitions_IGE_median.txt
+transitions_IGG1_mean.txt
+transitions_IGG1_median.txt
+transitions_IGG2_mean.txt
+transitions_IGG2_median.txt
+transitions_IGG3_mean.txt
+transitions_IGG3_median.txt
+transitions_IGG4_mean.txt
+transitions_IGG4_median.txt
+transitions_IGG_mean.txt
+transitions_IGG_median.txt
+transitions_IGM_mean.txt
+transitions_IGM_median.txt
+transitions_unmatched_mean.txt
+transitions_unmatched_median.txt
+transitions_unmatched_sum.txt
+unmatched_mean_n.txt
+unmatched_mean_value.txt
+unmatched_median_n.txt
+unmatched_median_value.txt
+unmatched_sum_n.txt
+unmatched_sum_value.txt
+change_o/change-o-db.txt
+change_o/change-o-db-defined_first_clones.txt
+change_o/change-o-db-defined_first_clones-IGA.txt
+change_o/change-o-db-defined_first_clones-IGG.txt
+change_o/change-o-db-defined_first_clones-IGM.txt
+change_o/change-o-db-IGA.txt
+change_o/change-o-db-IGG.txt
+change_o/change-o-db-IGM.txt
+change_o/input.tab