Merge pull request #28 from CBIIT/LDlink_3.2.1

L dlink 3.2.1

Author: kvnjng

LDlink/LDlink.js

@@ -931,7 +931,7 @@ function ldproxy_haploreg_link(data, type, row) {
 
     // Create RegulomeDB links
 
-    var server = 'http://www.broadinstitute.org/mammals/haploreg/detail_v4.1.php';
+    var server = 'http://pubs.broadinstitute.org/mammals/haploreg/detail_v4.1.php';
 
     var rs_number = row[0];
     var params = {

LDlink/LDpair.py

@@ -123,10 +123,9 @@ def get_coords(rs):
         if "warning" in output:
             output["warning"] = output["warning"] + \
                 ". Genomic position for query variant1 (" + snp1 + \
-                ") does not match RS number at 1000G position (chr"+geno[0]+":"+geno[1]+")"
+                ") does not match RS number at 1000G position (chr"+geno1[0]+":"+geno1[1]+")"
         else:
-            output[
-                "warning"] = "Genomic position for query variant1 (" + snp1 + ") does not match RS number at 1000G position (chr"+geno[0]+":"+geno[1]+")"
+            output["warning"] = "Genomic position for query variant1 (" + snp1 + ") does not match RS number at 1000G position (chr"+geno1[0]+":"+geno1[1]+")"
         snp1 = geno1[2]
 
     if "," in geno1[3] or "," in geno1[4]:
@@ -171,10 +170,9 @@ def get_coords(rs):
         if "warning" in output:
             output["warning"] = output["warning"] + \
                 ". Genomic position for query variant2 (" + snp2 + \
-                ") does not match RS number at 1000G position (chr"+geno[0]+":"+geno[1]+")"
+                ") does not match RS number at 1000G position (chr"+geno2[0]+":"+geno2[1]+")"
         else:
-            output[
-                "warning"] = "Genomic position for query variant2 (" + snp2 + ") does not match RS number at 1000G position (chr"+geno[0]+":"+geno[1]+")"
+            output["warning"] = "Genomic position for query variant2 (" + snp2 + ") does not match RS number at 1000G position (chr"+geno2[0]+":"+geno2[1]+")"
         snp2 = geno2[2]
 
     if "," in geno2[3] or "," in geno2[4]: