From 3ba9dd123bff80e7c4a89c5b4d140daa9edae90e Mon Sep 17 00:00:00 2001
From: suzanahmad <suzan.ahmad@sickkids.ca>
Date: Sun, 14 Apr 2024 17:32:38 -0400
Subject: [PATCH] Add LinSight_Score to cre repo

---
 cre.gemini2txt.vcf2db.sh | 3 ++-
 cre.vcf2db.R             | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/cre.gemini2txt.vcf2db.sh b/cre.gemini2txt.vcf2db.sh
index 19e2fcf..5bac97e 100755
--- a/cre.gemini2txt.vcf2db.sh
+++ b/cre.gemini2txt.vcf2db.sh
@@ -50,7 +50,8 @@ then
             enh_cellline_tissue as ENH_cellline_tissue,
             tf_binding_sites as TF_binding_sites,
             c4r_wgs_counts as C4R_WGS_counts,
-            c4r_wgs_samples as C4R_WGS_samples"
+            c4r_wgs_samples as C4R_WGS_samples,
+            LinSight_Score"
 else
     noncoding_anno="00 as noncoding"
 fi
diff --git a/cre.vcf2db.R b/cre.vcf2db.R
index ab5c658..dbbb5d3 100644
--- a/cre.vcf2db.R
+++ b/cre.vcf2db.R
@@ -429,7 +429,7 @@ select_and_write2 <- function(variants, samples, prefix, type)
 {
     print(colnames(variants))
     if (type == 'wgs' || type == 'denovo'){
-        noncoding_cols <- c("DNaseI_hypersensitive_site", "CTCF_binding_site", "ENH_cellline_tissue", "TF_binding_sites")
+        noncoding_cols <- c("DNaseI_hypersensitive_site", "CTCF_binding_site", "ENH_cellline_tissue", "TF_binding_sites", "LinSight_Score")
         wgs_counts <- c("C4R_WGS_counts", "C4R_WGS_samples")
         variants$C4R_WGS_counts[variants$C4R_WGS_counts == "None"] <- 0 
         variants$C4R_WGS_counts <- as.integer(variants$C4R_WGS_counts)