From 407959755f16107982ec8e02d630f61e617ba90a Mon Sep 17 00:00:00 2001
From: Likhitha Surapaneni
 <10923198+likhitha-surapaneni@users.noreply.github.com>
Date: Thu, 18 Sep 2025 10:26:08 +0100
Subject: [PATCH 1/3] Support CADD for turkey

---
 plugin_config.txt | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/plugin_config.txt b/plugin_config.txt
index ade6a0ae..9c40aa76 100644
--- a/plugin_config.txt
+++ b/plugin_config.txt
@@ -634,7 +634,11 @@ my $VEP_PLUGIN_CONFIG = {
       "species" => [
         "homo_sapiens",
         "sus_scrofa",
+<<<<<<< HEAD
         "gallus_gallus_GCA_000002315.5"
+=======
+        "meleagris_gallopavo"
+>>>>>>> f622549 (Support CADD for turkey)
       ],
       "form" => [
         {
@@ -656,6 +660,7 @@ my $VEP_PLUGIN_CONFIG = {
         #"indels=/path/to/CADD_GRCh38_1.6_InDels.tsv.gz",
         #"snv_pig=/path/to/ALL_pCADD-PHRED-scores.tsv.gz",
         #"snv_chicken_rjf=/path/to/chCADD_updated.tsv.gz"
+        #"snv_turkey=/path/to/CADD_ALL.tsv.gz",
         #"sv=/path/to/CADD_prescored_variants.tsv.gz"
       ]
     },

From 31c23a497fae3330a0608f951f2ab50c8c0e2668 Mon Sep 17 00:00:00 2001
From: Likhitha Surapaneni
 <10923198+likhitha-surapaneni@users.noreply.github.com>
Date: Thu, 25 Sep 2025 14:11:43 +0100
Subject: [PATCH 2/3] Resolved conflicts

---
 plugin_config.txt | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/plugin_config.txt b/plugin_config.txt
index 9c40aa76..1a7b6d41 100644
--- a/plugin_config.txt
+++ b/plugin_config.txt
@@ -634,11 +634,8 @@ my $VEP_PLUGIN_CONFIG = {
       "species" => [
         "homo_sapiens",
         "sus_scrofa",
-<<<<<<< HEAD
-        "gallus_gallus_GCA_000002315.5"
-=======
+        "gallus_gallus_GCA_000002315.5",
         "meleagris_gallopavo"
->>>>>>> f622549 (Support CADD for turkey)
       ],
       "form" => [
         {
@@ -659,7 +656,7 @@ my $VEP_PLUGIN_CONFIG = {
         #"snv=/path/to/CADD_whole_genome_SNVs.tsv.gz",
         #"indels=/path/to/CADD_GRCh38_1.6_InDels.tsv.gz",
         #"snv_pig=/path/to/ALL_pCADD-PHRED-scores.tsv.gz",
-        #"snv_chicken_rjf=/path/to/chCADD_updated.tsv.gz"
+        #"snv_chicken_rjf=/path/to/chCADD_updated.tsv.gz",
         #"snv_turkey=/path/to/CADD_ALL.tsv.gz",
         #"sv=/path/to/CADD_prescored_variants.tsv.gz"
       ]

From bceb8852220c4f98044a94e161ba56cdf9f6815b Mon Sep 17 00:00:00 2001
From: Likhitha Surapaneni
 <10923198+likhitha-surapaneni@users.noreply.github.com>
Date: Wed, 8 Oct 2025 11:26:13 +0100
Subject: [PATCH 3/3] Filename change

---
 plugin_config.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugin_config.txt b/plugin_config.txt
index 1a7b6d41..c189feb2 100644
--- a/plugin_config.txt
+++ b/plugin_config.txt
@@ -657,7 +657,7 @@ my $VEP_PLUGIN_CONFIG = {
         #"indels=/path/to/CADD_GRCh38_1.6_InDels.tsv.gz",
         #"snv_pig=/path/to/ALL_pCADD-PHRED-scores.tsv.gz",
         #"snv_chicken_rjf=/path/to/chCADD_updated.tsv.gz",
-        #"snv_turkey=/path/to/CADD_ALL.tsv.gz",
+        #"snv_turkey=/path/to/tCADD.tsv.gz",
         #"sv=/path/to/CADD_prescored_variants.tsv.gz"
       ]
     },