From 3240f42ff77afbedb25cc675a4ed787154ebb8bc Mon Sep 17 00:00:00 2001
From: Judy Yao <xiaozheng.yao@nih.gov>
Date: Thu, 10 Aug 2023 10:51:33 -0400
Subject: [PATCH] fix the column of ldtrait

---
 client/LDlink.js | 14 +++++++-------
 client/news.html |  2 +-
 server/LDlink.py |  6 +++---
 3 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/client/LDlink.js b/client/LDlink.js
index 3a939270..493c5828 100644
--- a/client/LDlink.js
+++ b/client/LDlink.js
@@ -1740,7 +1740,7 @@ function createTraitDetailsTable() {
 				render: function (data, type, row) {
 					return ldtrait_parse_float(data);
 				},
-				targets: [8],
+				targets: [9],
 			},
 			{
 				render: function (data, type, row) {
@@ -1751,7 +1751,7 @@ function createTraitDetailsTable() {
 						return data;
 					}
 				},
-				targets: [7],
+				targets: [8],
 			},
 			{
 				render: function (data, type, row) {
@@ -1782,7 +1782,7 @@ function createTraitDetailsTable() {
 						return data;
 					}
 				},
-				targets: [10],
+				targets: [11],
 			},
 			{
 				render: function (data, type, row) {
@@ -1792,23 +1792,23 @@ function createTraitDetailsTable() {
 					var pops = row[6][2];
 					return ldtrait_ldpair_results_link(snp1, snp2, pops, data);
 				},
-				targets: [4, 5],
+				targets: [5, 6],
 			},
 			{
 				bVisible: false,
-				targets: 6,
+				targets: 7,
 			},
 			{
 				render: function (data, type, row) {
 					// Provide link to gwas catalog
 					return ldtrait_gwas_catalog_link(data, type, row);
 				},
-				targets: 11,
+				targets: 12,
 			},
 			{
 				className: 'dt-head-left',
 				className: 'dt-body-left',
-				targets: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],
+				targets: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12],
 			},
 		],
 	});
diff --git a/client/news.html b/client/news.html
index c1331598..658160df 100644
--- a/client/news.html
+++ b/client/news.html
@@ -1,4 +1,4 @@
-<p><b>LDlink 5.6.5 Release (8/6/2023)</b></p>
+<p><b>LDlink 5.6.5 Release (8/11/2023)</b></p>
 <ul>
     <li>Added more citations for LDtrait and LDexpress</li>
     <li>Added PUBMEDID(PMID) for LDtrait outputs</li>
diff --git a/server/LDlink.py b/server/LDlink.py
index 2ef33d84..62ae6185 100644
--- a/server/LDlink.py
+++ b/server/LDlink.py
@@ -1410,7 +1410,7 @@ def ldtrait():
                         for snp in thinned_snps:
                             for matched_gwas in details[snp]["aaData"]:
                                 f.write(snp + "\t")
-                                f.write("\t".join([str(element) for i, element in enumerate(matched_gwas) if i not in {6, 11}]) + "\n")
+                                f.write("\t".join([str(element) for i, element in enumerate(matched_gwas) if i not in {7, 12}]) + "\n")
                         if "warning" in json_dict:
                             trait["warning"] = json_dict["warning"]
                             f.write("Warning(s):\n")
@@ -1463,11 +1463,11 @@ def ldtrait():
                 return sendTraceback(json_dict["error"])
             else:
                 with open(tmp_dir + 'trait_variants_annotated' + reference + '.txt', 'w') as f:
-                    f.write("Query\tPMID\tGWAS Trait\tRS Number\tPosition (" + genome_build_vars[genome_build]['title'] + ")\tAlleles\tR2\tD'\tRisk Allele\tEffect Size (95% CI)\tBeta or OR\tP-value\n")
+                    f.write("Query\tGWAS Trait\tPMID\tRS Number\tPosition (" + genome_build_vars[genome_build]['title'] + ")\tAlleles\tR2\tD'\tRisk Allele\tEffect Size (95% CI)\tBeta or OR\tP-value\n")
                     for snp in thinned_snps:
                         for matched_gwas in details[snp]["aaData"]:
                             f.write(snp + "\t")
-                            f.write("\t".join([str(element) for i, element in enumerate(matched_gwas) if i not in {6, 11}]) + "\n")
+                            f.write("\t".join([str(element) for i, element in enumerate(matched_gwas) if i not in {7, 12}]) + "\n")
                     if "warning" in json_dict:
                         # trait["warning"] = json_dict["warning"]
                         f.write("Warning(s):\n")