Keep only code inside genotoscope and move all other information in f…

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damianosmel · Jan 29, 2022 · 9294162 · 9294162
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diff --git a/genotoscope/LICENSE → LICENSE b/genotoscope/LICENSE → LICENSE
diff --git a/genotoscope/README.md → README.md b/genotoscope/README.md → README.md
diff --git a/.../clinvar_mar_2021/clinvar_20210323.vcf.gz → .../clinvar_mar_2021/clinvar_20210323.vcf.gz b/.../clinvar_mar_2021/clinvar_20210323.vcf.gz → .../clinvar_mar_2021/clinvar_20210323.vcf.gz
diff --git a/...nvar_mar_2021/clinvar_20210323.vcf.gz.tbi → ...nvar_mar_2021/clinvar_20210323.vcf.gz.tbi b/...nvar_mar_2021/clinvar_20210323.vcf.gz.tbi → ...nvar_mar_2021/clinvar_20210323.vcf.gz.tbi
diff --git a/...ope_data/ClinVar/clinvar_review_stars.tsv → ...ope_data/ClinVar/clinvar_review_stars.tsv b/...ope_data/ClinVar/clinvar_review_stars.tsv → ...ope_data/ClinVar/clinvar_review_stars.tsv
diff --git a/...itical_regions_pathogenic_probability.bed → ...itical_regions_pathogenic_probability.bed b/...itical_regions_pathogenic_probability.bed → ...itical_regions_pathogenic_probability.bed
diff --git a/...ions_pathogenic_probability_no_benign.bed → ...ions_pathogenic_probability_no_benign.bed b/...ions_pathogenic_probability_no_benign.bed → ...ions_pathogenic_probability_no_benign.bed
diff --git a/...nomAD_v2.1/clinical_significant_exons.bed → ...nomAD_v2.1/clinical_significant_exons.bed b/...nomAD_v2.1/clinical_significant_exons.bed → ...nomAD_v2.1/clinical_significant_exons.bed
diff --git a/...ring_loss/pheno_relevant_exons_sorted.bed → ...ring_loss/pheno_relevant_exons_sorted.bed b/...ring_loss/pheno_relevant_exons_sorted.bed → ...ring_loss/pheno_relevant_exons_sorted.bed
diff --git a/...beds/hearing_loss/pm1_regions_hl_hg19.bed → ...beds/hearing_loss/pm1_regions_hl_hg19.bed b/...beds/hearing_loss/pm1_regions_hl_hg19.bed → ...beds/hearing_loss/pm1_regions_hl_hg19.bed
diff --git a/...ene_inheritance_patterns_clingen_mhh.xlsx → ...ene_inheritance_patterns_clingen_mhh.xlsx b/...ene_inheritance_patterns_clingen_mhh.xlsx → ...ene_inheritance_patterns_clingen_mhh.xlsx
diff --git a/...toscope_data/hgnc_complete_set_strand.txt → ...toscope_data/hgnc_complete_set_strand.txt b/...toscope_data/hgnc_complete_set_strand.txt → ...toscope_data/hgnc_complete_set_strand.txt
diff --git a/...scope/genotoscope_data/hl_variants.vcf.gz → genotoscope_data/hl_variants.vcf.gz b/...scope/genotoscope_data/hl_variants.vcf.gz → genotoscope_data/hl_variants.vcf.gz
diff --git a/...e/genotoscope_data/hl_variants.vcf.gz.tbi → genotoscope_data/hl_variants.vcf.gz.tbi b/...e/genotoscope_data/hl_variants.vcf.gz.tbi → genotoscope_data/hl_variants.vcf.gz.tbi
diff --git a/...pe_data/misc/hl_relevant_transcripts.xlsx → ...pe_data/misc/hl_relevant_transcripts.xlsx b/...pe_data/misc/hl_relevant_transcripts.xlsx → ...pe_data/misc/hl_relevant_transcripts.xlsx
diff --git a/...cope_data/thresholds_inheritance_mode.csv → ...cope_data/thresholds_inheritance_mode.csv b/...cope_data/thresholds_inheritance_mode.csv → ...cope_data/thresholds_inheritance_mode.csv
diff --git a/...P000005640_9606_domain_hg19_15columns.bed → ...P000005640_9606_domain_hg19_15columns.bed b/...P000005640_9606_domain_hg19_15columns.bed → ...P000005640_9606_domain_hg19_15columns.bed
diff --git a/...P000005640_9606_repeat_hg19_16columns.bed → ...P000005640_9606_repeat_hg19_16columns.bed b/...P000005640_9606_repeat_hg19_16columns.bed → ...P000005640_9606_repeat_hg19_16columns.bed
diff --git a/genotoscope/genotoscope_env_requirements.txt → genotoscope_env_requirements.txt b/genotoscope/genotoscope_env_requirements.txt → genotoscope_env_requirements.txt
diff --git a/genotoscope/genotoscope_local.yaml_ → genotoscope_local.yaml_ b/genotoscope/genotoscope_local.yaml_ → genotoscope_local.yaml_
diff --git a/...dataset/brca2_missense/brca2_missense.vcf → ...dataset/brca2_missense/brca2_missense.vcf b/...dataset/brca2_missense/brca2_missense.vcf → ...dataset/brca2_missense/brca2_missense.vcf
diff --git a/...brca2_missense/brca2_missense_annot.GSvar → ...brca2_missense/brca2_missense_annot.GSvar b/...brca2_missense/brca2_missense_annot.GSvar → ...brca2_missense/brca2_missense_annot.GSvar
diff --git a/...t/brca2_missense/brca2_missense_annot.vcf → ...t/brca2_missense/brca2_missense_annot.vcf b/...t/brca2_missense/brca2_missense_annot.vcf → ...t/brca2_missense/brca2_missense_annot.vcf
diff --git a/...se/brca2_missense_annot_genotoscope.GSvar → ...se/brca2_missense_annot_genotoscope.GSvar b/...se/brca2_missense_annot_genotoscope.GSvar → ...se/brca2_missense_annot_genotoscope.GSvar
diff --git a/...pe/toy_dataset/diaph1/diaph1_deletion.vcf → toy_dataset/diaph1/diaph1_deletion.vcf b/...pe/toy_dataset/diaph1/diaph1_deletion.vcf → toy_dataset/diaph1/diaph1_deletion.vcf
diff --git a/...ataset/diaph1/diaph1_deletion_annot.GSvar → ...ataset/diaph1/diaph1_deletion_annot.GSvar b/...ataset/diaph1/diaph1_deletion_annot.GSvar → ...ataset/diaph1/diaph1_deletion_annot.GSvar
diff --git a/..._dataset/diaph1/diaph1_deletion_annot.vcf → toy_dataset/diaph1/diaph1_deletion_annot.vcf b/..._dataset/diaph1/diaph1_deletion_annot.vcf → toy_dataset/diaph1/diaph1_deletion_annot.vcf
diff --git a/...1/diaph1_deletion_annot_genotoscope.GSvar → ...1/diaph1_deletion_annot_genotoscope.GSvar b/...1/diaph1_deletion_annot_genotoscope.GSvar → ...1/diaph1_deletion_annot_genotoscope.GSvar
diff --git a/...cope/toy_dataset/myo6/myo6_frameshift.vcf → toy_dataset/myo6/myo6_frameshift.vcf b/...cope/toy_dataset/myo6/myo6_frameshift.vcf → toy_dataset/myo6/myo6_frameshift.vcf
diff --git a/..._dataset/myo6/myo6_frameshift_annot.GSvar → toy_dataset/myo6/myo6_frameshift_annot.GSvar b/..._dataset/myo6/myo6_frameshift_annot.GSvar → toy_dataset/myo6/myo6_frameshift_annot.GSvar
diff --git a/...oy_dataset/myo6/myo6_frameshift_annot.vcf → toy_dataset/myo6/myo6_frameshift_annot.vcf b/...oy_dataset/myo6/myo6_frameshift_annot.vcf → toy_dataset/myo6/myo6_frameshift_annot.vcf
diff --git a/...6/myo6_frameshift_annot_genotoscope.GSvar → ...6/myo6_frameshift_annot_genotoscope.GSvar b/...6/myo6_frameshift_annot_genotoscope.GSvar → ...6/myo6_frameshift_annot_genotoscope.GSvar
diff --git a/genotoscope/website_settings_server.ini_ → website_settings_server.ini_ b/genotoscope/website_settings_server.ini_ → website_settings_server.ini_