config: added IGV and viz required files

pandora-config.example.toml

@@ -47,6 +47,16 @@ refseq_gff = "/home/t_steimle/ref/hs1/chm13v2.0_RefSeq_Liftoff_v5.1_sorted.gff3.
 # dbSNP vcf.gz file (should be indexed)
 db_snp = "/home/t_steimle/ref/hs1/chm13v2.0_dbSNPv155.vcf.gz"
 
+# BED with genes on the 4th column should be sorted
+genes_bed = "/home/t_steimle/ref/hs1/chm13v2.0_RefSeq_Liftoff_v5.1_Genes.bed"
+
+# Cytobands BED file
+cytobands_bed = "/home/t_steimle/ref/hs1/chm13v2.0_cytobands_allchrs.bed"
+
+# Chromosome alias file
+# ex: https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/GCA_009914755.4.chromAlias.txt
+chromosomes_alias = "/home/t_steimle/ref/hs1/GCA_009914755.4.chromAlias.txt"
+
 # Template for mask BED file (low-quality / filtered regions).
 # {result_dir} -> global result directory
 # {id}         -> case identifier
@@ -54,8 +64,7 @@ mask_bed = "{result_dir}/{id}/diag/mask.bed"
 
 # Panels of interest: [ [name, bed_path], ... ]
 panels = [
-  ["Cytoband", "/home/t_steimle/ref/hs1/chm13v2.0_cytobands_allchrs.bed"],
-	["PanelCM", "/home/t_steimle/ref/hs1/panel_cm_hs1.bed"],
+	["CM", "/home/t_steimle/ref/hs1/panel_cm_hs1.bed"],
 ]
 
 repeats_bed = "/home/t_steimle/ref/hs1/all_repeats_chm13_final.bed"

src/config.rs

@@ -66,6 +66,15 @@ pub struct Config {
     ///  dbSNP vcf.gz file (should be indexed)
     pub db_snp: String,
 
+    /// BED with genes on the 4th column
+    pub genes_bed: String,
+
+    /// Cytobands BED file
+    pub cytobands_bed: String,
+
+    /// Chromosome alias file
+    pub chromosomes_alias: String,
+
     /// BED template used to mask low-quality or filtered regions.
     ///
     /// Placeholders: